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commit/galaxy-central: dan: Fix for DynamicOptions AdditionalValueFilter when columns have not been assigned and to give value preference over name.
by commits-noreply＠bitbucket.org 03 Dec '14

03 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c85032480141/ Changeset: c85032480141 User: dan Date: 2014-12-03 21:52:56+00:00 Summary: Fix for DynamicOptions AdditionalValueFilter when columns have not been assigned and to give value preference over name. Affected #: 1 file diff -r 37cf9cd764fa3a306e5a74ec05ddfe4046060ae7 -r c85032480141d4280903fc11382e38e9176f39b0 lib/galaxy/tools/parameters/dynamic_options.py --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -301,8 +301,11 @@ add_value = [] for i in range( self.dynamic_option.largest_index + 1 ): add_value.append( "" ) - add_value[self.dynamic_option.columns['value']] = self.value - add_value[self.dynamic_option.columns['name']] = self.name + value_col = self.dynamic_option.columns.get( 'value', 0 ) + name_col = self.dynamic_option.columns.get( 'name', value_col ) + # Set name first, then value, in case they are the same column + add_value[ name_col ] = self.name + add_value[ value_col ] = self.value if self.index is not None: rval.insert( self.index, add_value ) else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Small tweak to DataCollectionToolParameter interface for uniformity with DataToolParameter.
by commits-noreply＠bitbucket.org 03 Dec '14

03 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/37cf9cd764fa/ Changeset: 37cf9cd764fa User: jmchilton Date: 2014-12-03 21:34:00+00:00 Summary: Small tweak to DataCollectionToolParameter interface for uniformity with DataToolParameter. Affected #: 1 file diff -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 -r 37cf9cd764fa3a306e5a74ec05ddfe4046060ae7 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2222,6 +2222,10 @@ raise ValueError( "History does not include a dataset collection of the correct type or containing the correct types of datasets" ) if value in [None, "None"]: return None + # would really like to not need to handle lists in here but + # doing it for uniformity with DataToolParameters for now. + if isinstance( value, list ): + value = value[ 0 ] if isinstance( value, str ) and value.find( "," ) > 0: value = [ int( value_part ) for value_part in value.split( "," ) ] elif isinstance( value, trans.app.model.HistoryDatasetCollectionAssociation ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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[galaxyproject/usegalaxy-playbook] bf3e33: Install Guru's rhmm tool on Test.
by GitHub 03 Dec '14

03 Dec '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bf3e33ebe79612a317eace809ba1a71c32390f76 https://github.com/galaxyproject/usegalaxy-playbook/commit/bf3e33ebe79612a3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-12-03 (Wed, 03 Dec 2014) Changed paths: M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml Log Message: ----------- Install Guru's rhmm tool on Test.

1 0

[galaxyproject/usegalaxy-playbook] a4d7d2: Update Test
by GitHub 03 Dec '14

03 Dec '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a4d7d206a9fba51bb975863201bc8ffda81d0d5a https://github.com/galaxyproject/usegalaxy-playbook/commit/a4d7d206a9fba51b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-12-03 (Wed, 03 Dec 2014) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M stage/group_vars/all.yml Log Message: ----------- Update Test Commit: 5755dc1564f69a276a9a3b57f4d1ee840e17097e https://github.com/galaxyproject/usegalaxy-playbook/commit/5755dc1564f69a27… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-12-03 (Wed, 03 Dec 2014) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/ecd10db580aa...…

1 0

commit/galaxy-central: dannon: Merged in martenson/galaxy-central-marten/stable (pull request #585)
by commits-noreply＠bitbucket.org 03 Dec '14

03 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0e663285c743/ Changeset: 0e663285c743 Branch: stable User: dannon Date: 2014-12-03 19:15:51+00:00 Summary: Merged in martenson/galaxy-central-marten/stable (pull request #585) [STABLE] propagate the commit of 795336f22d8b94b86256b1d4738ee1bf24e18b57 that is already in next-stable to the stable Affected #: 18 files diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/admin/forms/create_form.mako --- a/templates/admin/forms/create_form.mako +++ b/templates/admin/forms/create_form.mako @@ -9,7 +9,7 @@ <div class="toolFormTitle">Create a new form definition</div> %for label, input in inputs: <div class="form-row"> - <label>${label}</label> + <label>${label | h}</label> ${input.get_html()} <div style="clear: both"></div></div> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/admin/forms/edit_form_definition.mako --- a/templates/admin/forms/edit_form_definition.mako +++ b/templates/admin/forms/edit_form_definition.mako @@ -96,14 +96,14 @@ <form id="edit_form_definition" name="edit_form_definition" action="${h.url_for( controller='forms', action='edit_form_definition', id=trans.security.encode_id( form_definition.current.id ) )}" method="post" ><div class="toolForm"> - <div class="toolFormTitle">Edit form definition "${form_definition.name}" (${form_definition.type})</div> + <div class="toolFormTitle">Edit form definition "${form_definition.name | h}" (${form_definition.type | h})</div> %if response_redirect: <input type="hidden" name="response_redirect" value="${response_redirect}" size="40" /> %endif %for label, input in form_details: <div class="form-row"> %if label != 'Type': - <label>${label}</label> + <label>${label | h}</label> %endif <div style="float: left; width: 250px; margin-right: 10px;"> ${input.get_html()} diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/admin/request_type/common.mako --- a/templates/admin/request_type/common.mako +++ b/templates/admin/request_type/common.mako @@ -2,7 +2,7 @@ <div class="repeat-group-item"><div class="form-row"><label>${1+element_count}. State name:</label> - <input type="text" name="state_name_${element_count}" value="${state_name}" size="40"/> + <input type="text" name="state_name_${element_count}" value="${state_name | h}" size="40"/> ## Do not show remove button for the first state %if element_count > 0: <input type="submit" name="remove_state_button" value="Remove state ${1+element_count}"/> @@ -10,7 +10,7 @@ </div><div class="form-row"><label>Description:</label> - <input type="text" name="state_desc_${element_count}" value="${state_desc}" size="40"/> + <input type="text" name="state_desc_${element_count}" value="${state_desc | h}" size="40"/><div class="toolParamHelp" style="clear: both;"> optional </div> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/admin/request_type/create_request_type.mako --- a/templates/admin/request_type/create_request_type.mako +++ b/templates/admin/request_type/create_request_type.mako @@ -23,7 +23,7 @@ <div class="toolFormTitle">Create a new request type</div> %for rt_info in rt_info_widgets: <div class="form-row"> - <label>${rt_info['label']}</label> + <label>${rt_info['label'] | h}</label><div style="float: left; width: 250px; margin-right: 10px;"> ${rt_info['widget'].get_html()} </div> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/admin/request_type/edit_request_type.mako --- a/templates/admin/request_type/edit_request_type.mako +++ b/templates/admin/request_type/edit_request_type.mako @@ -32,26 +32,26 @@ <form name="edit_request_type" action="${h.url_for( controller='request_type', action='edit_request_type', id=trans.security.encode_id( request_type.id ) )}" method="post" ><div class="toolForm"> - <div class="toolFormTitle">"Edit ${request_type.name}" request type</div> + <div class="toolFormTitle">"Edit ${request_type.name | h}" request type</div><div class="form-row"><label>Name:</label> - <input type="text" name="name" value="${request_type.name}" size="40"/> + <input type="text" name="name" value="${request_type.name | }" size="40"/><div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - <input type="text" name="desc" value="${request_type.desc}" size="40"/> + <input type="text" name="desc" value="${request_type.desc | h}" size="40"/><div style="clear: both"></div></div><div class="form-row"><label>Sequencing request form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name | h}</a> ## Hidden field needed by the __save_request_type() method <input type="hidden" name="request_form_id" value="${trans.security.encode_id( request_type.request_form_id )}" size="40"/></div><div class="form-row"><label>Sample form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name | h}</a> ## Hidden field needed by the __save_request_type() method <input type="hidden" name="sample_form_id" value="${trans.security.encode_id( request_type.sample_form_id )}" size="40"/></div> @@ -63,11 +63,11 @@ <div class="repeat-group-item"><div class="form-row"><label>${1+element_count}. State name:</label> - <input type="text" name="state_name_${trans.security.encode_id( state.id )}" value="${state.name}" size="40"/> + <input type="text" name="state_name_${trans.security.encode_id( state.id )}" value="${state.name | h}" size="40"/></div><div class="form-row"><label>Description:</label> - <input type="text" name="state_desc_${trans.security.encode_id( state.id )}" value="${state.desc}" size="40"/> + <input type="text" name="state_desc_${trans.security.encode_id( state.id )}" value="${state.desc | h}" size="40"/><div class="toolParamHelp" style="clear: both;"> optional </div> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/admin/request_type/request_type_permissions.mako --- a/templates/admin/request_type/request_type_permissions.mako +++ b/templates/admin/request_type/request_type_permissions.mako @@ -48,7 +48,7 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Manage access permissions on request type "${request_type.name}"</div> + <div class="toolFormTitle">Manage access permissions on request type "${request_type.name | h}"</div><div class="toolFormBody"><form name="request_type_permissions" id="request_type_permissions" action="${h.url_for( controller='request_type', action='request_type_permissions', id=trans.security.encode_id( request_type.id ) )}" method="post"><div class="form-row"> @@ -65,13 +65,13 @@ in_roles.add( a.role ) out_roles = filter( lambda x: x not in in_roles, all_roles ) %> - ${action.description}<br/><br/> + ${action.description | h}<br/><br/><div style="width: 100%; white-space: nowrap;"><div style="float: left; width: 50%;"> Roles associated:<br/><select name="${action_key}_in" id="${action_key}_in_select" class="in_select" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple> %for role in in_roles: - <option value="${role.id}">${role.name}</option> + <option value="${role.id}">${role.name | h}</option> %endfor </select><br/><div style="width: 98%; text-align: right"><input type="submit" id="${action_key}_remove_button" class="role_remove_button" value=">>"/></div> @@ -80,7 +80,7 @@ Roles not associated:<br/><select name="${action_key}_out" id="${action_key}_out_select" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple> %for role in out_roles: - <option value="${role.id}">${role.name}</option> + <option value="${role.id}">${role.name | h}</option> %endfor </select><br/><input type="submit" id="${action_key}_add_button" class="role_add_button" value="<<"/> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/admin/request_type/view_request_type.mako --- a/templates/admin/request_type/view_request_type.mako +++ b/templates/admin/request_type/view_request_type.mako @@ -30,24 +30,24 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">"${request_type.name}" request type</div> + <div class="toolFormTitle">"${request_type.name | h}" request type</div><div class="form-row"><label>Name:</label> - ${request_type.name} + ${request_type.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - ${request_type.desc} + ${request_type.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>Sequencing request form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name | h}</a></div><div class="form-row"><label>Sample form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name | h}</a></div></div><p/> @@ -55,8 +55,8 @@ <div class="toolFormTitle">Sample states defined for this request type</div> %for state in request_type.states: <div class="form-row"> - <label>${state.name}</label> - ${state.desc} + <label>${state.name | h}</label> + ${state.desc | h} </div><div style="clear: both"></div> %endfor @@ -67,8 +67,8 @@ %if request_type.external_services: %for index, external_service in enumerate( request_type.external_services ): <div class="form-row"> - <label><a href="${h.url_for( controller='external_service', action='view_external_service', id=trans.security.encode_id( external_service.id ) )}">${external_service.name}</a></label> - ${external_service.get_external_service_type( trans ).name} + <label><a href="${h.url_for( controller='external_service', action='view_external_service', id=trans.security.encode_id( external_service.id ) )}">${external_service.name | h}</a></label> + ${external_service.get_external_service_type( trans ).name | h} </div> %endfor %else: diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/admin/requests/reject.mako --- a/templates/admin/requests/reject.mako +++ b/templates/admin/requests/reject.mako @@ -15,7 +15,7 @@ </ul><div class="toolForm"> - <div class="toolFormTitle">Reject sequencing request "${request.name}"</div> + <div class="toolFormTitle">Reject sequencing request "${request.name | h}"</div><form name="event" action="${h.url_for( controller='requests_admin', action='reject_request', id=trans.security.encode_id( request.id ) )}" method="post" ><div class="form-row"> Rejecting this request will move the request state to <b>Rejected</b>. diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/admin/requests/rename_datasets.mako --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -3,7 +3,7 @@ <% from galaxy.webapps.galaxy.controllers.requests_admin import build_rename_datasets_for_sample_select_field %> -<h3>Rename datasets for Sample "${sample.name}"</h3> +<h3>Rename datasets for Sample "${sample.name | h}"</h3><ul class="manage-table-actions"><li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Browse datasets</a></li> @@ -35,7 +35,7 @@ ${rename_datasets_for_sample_select_field.get_html()} </td><td> - <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id ) }" value="${sample_dataset.name}" size="100"/> + <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id ) }" value="${sample_dataset.name | h}" size="100"/></td><td>${sample_dataset.file_path}</td></tr> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/admin/requests/view_sample_dataset.mako --- a/templates/admin/requests/view_sample_dataset.mako +++ b/templates/admin/requests/view_sample_dataset.mako @@ -21,19 +21,19 @@ </ul><div class="toolForm"> - <div class="toolFormTitle">"${sample.name}" Dataset</div> + <div class="toolFormTitle">"${sample.name | h}" Dataset</div><div class="toolFormBody"><div class="form-row"><label>Name:</label><div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.name} + ${sample_dataset.name | h} </div><div style="clear: both"></div></div><div class="form-row"><label>External service:</label><div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.external_service.name} (${sample_dataset.external_service.get_external_service_type( trans ).name}) + ${sample_dataset.external_service.name | h} (${sample_dataset.external_service.get_external_service_type( trans ).name | h}) </div><div style="clear: both"></div></div> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/webapps/galaxy/requests/common/common.mako --- a/templates/webapps/galaxy/requests/common/common.mako +++ b/templates/webapps/galaxy/requests/common/common.mako @@ -257,18 +257,18 @@ <td valign="top"><input type="checkbox" name=select_sample_${sample.id} id="sample_checkbox" value="true" ${checked_str}/><input type="hidden" name=select_sample_${sample.id} id="sample_checkbox" value="true"/></td> %endif <td valign="top"> - <input type="text" name="sample_${sample_widget_index}_name" value="${sample_widget['name']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_name" value="${sample_widget['name'] | h}" size="10"/><div class="toolParamHelp" style="clear: both;"> - <i>${' (required)' }</i> + <i>(required)</i></div></td> %if display_bar_code: <td valign="top"> %if is_admin and is_submitted: - <input type="text" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code'] | h}" size="10"/> %else: - ${sample_widget['bar_code']} - <input type="hidden" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}"/> + ${sample_widget['bar_code'] | h} + <input type="hidden" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code'] | h}"/> %endif </td> %endif @@ -416,7 +416,7 @@ transferred_dataset_files = [] %><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="sample-${sample.id}-popup"> - <a class="view-info" href="${h.url_for( controller='requests_common', action='view_sample', cntrller=cntrller, id=trans.security.encode_id( sample.id ) )}">${sample.name}</a> + <a class="view-info" href="${h.url_for( controller='requests_common', action='view_sample', cntrller=cntrller, id=trans.security.encode_id( sample.id ) )}">${sample.name | h}</a></div><div popupmenu="sample-${sample.id}-popup"> %if can_select_datasets: @@ -439,11 +439,11 @@ %endif </div> %else: - ${sample_widget_name} + ${sample_widget_name | h} %endif </td> %if display_bar_code: - <td>${sample_widget_bar_code}</td> + <td>${sample_widget_bar_code | h}</td> %endif %if is_unsubmitted: <td>Unsubmitted</td> @@ -451,12 +451,12 @@ <td><a id="sampleState-${sample.id}" href="${h.url_for( controller='requests_common', action='view_sample_history', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${render_sample_state( sample )}</a></td> %endif %if sample_widget_library and library_cntrller is not None: - <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( sample_widget_library.id ) )}">${sample_widget_library.name}</a></td> + <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( sample_widget_library.id ) )}">${sample_widget_library.name | h}</a></td> %else: <td></td> %endif %if sample_widget_folder: - <td>${sample_widget_folder.name}</td> + <td>${sample_widget_folder.name | h}</td> %else: <td></td> %endif @@ -464,11 +464,11 @@ %if trans.user == sample_widget_history.user: <td><a target='_parent' href="${h.url_for( controller='history', action='list', operation="Switch", id=trans.security.encode_id(sample_widget_history.id), use_panels=False )}"> - ${sample_widget_history.name} + ${sample_widget_history.name | h} </a></td> %else: - <td>${sample_widget_history.name}</td> + <td>${sample_widget_history.name | h}</td> %endif %else: <td></td> @@ -477,11 +477,11 @@ %if trans.user == sample_widget_workflow.stored_workflow.user: <td><a target='_parent' href="${h.url_for( controller='workflow', action='editor', id=trans.security.encode_id(sample_widget_workflow.stored_workflow.id) )}"> - ${sample_widget_workflow.name} + ${sample_widget_workflow.name | h} </a></td> %else: - <td>${sample_widget_workflow.name}</td> + <td>${sample_widget_workflow.name | h}</td> %endif %else: <td></td> @@ -519,7 +519,7 @@ <%def name="render_sample_form( index, sample_name, sample_values, fields_dict, display_only )"><tr> - <td>${sample_name}</td> + <td>${sample_name | h}</td> %for field_index, field in fields_dict.items(): <% field_type = field[ 'type' ] @@ -532,17 +532,17 @@ %if field_type == 'WorkflowField': %if str( field_value ) != 'none': <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int( field_value ) ) %> - <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">${workflow.name}</a> + <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">${workflow.name | h}</a> %endif %else: - ${field_value} + ${field_value | h} %endif %else: <i>None</i> %endif %else: %if field_type == 'TextField': - <input type="text" name="sample_${index}_field_${field_index}" value="${field_value}" size="7"/> + <input type="text" name="sample_${index}_field_${field_index}" value="${field_value | h}" size="7"/> %elif field_type == 'SelectField': <select name="sample_${index}_field_${field_index}" last_selected_value="2"> %for option_index, option in enumerate(field[ 'selectlist' ]): @@ -695,7 +695,7 @@ %if is_admin: <span class="expandLink dataset-${dataset}-click"><span class="rowIcon"></span><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="dataset-${dataset.id}-popup"> - <a class="dataset-${encoded_id}-click" href="${h.url_for( controller='requests_admin', action='manage_datasets', operation='view', id=trans.security.encode_id( dataset.id ) )}">${dataset.name}</a> + <a class="dataset-${encoded_id}-click" href="${h.url_for( controller='requests_admin', action='manage_datasets', operation='view', id=trans.security.encode_id( dataset.id ) )}">${dataset.name | h}</a></div></span><div popupmenu="dataset-${dataset.id}-popup"> @@ -704,12 +704,12 @@ %endif </div> %else: - ${dataset.name} + ${dataset.name | h} %endif </td><td>${dataset.size}</td> - <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">${dataset.sample.library.name}</a></td> - <td>${dataset.sample.folder.name}</td> + <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">${dataset.sample.library.name | h}</a></td> + <td>${dataset.sample.folder.name | h}</td><td id="datasetTransferStatus-${encoded_id}">${dataset.status}</td></tr> %endfor @@ -723,7 +723,7 @@ <%def name="render_samples_messages( request, is_admin=False, is_submitted=False, message=None, status=None)"> %if request.is_rejected: <div class='errormessage'> - ${request.last_comment} + ${request.last_comment | h} </div><br/> %endif %if is_admin and is_submitted and request.samples_without_library_destinations: diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/webapps/galaxy/requests/common/create_request.mako --- a/templates/webapps/galaxy/requests/common/create_request.mako +++ b/templates/webapps/galaxy/requests/common/create_request.mako @@ -23,7 +23,7 @@ <div class="toolForm"><div class="toolFormTitle">Create a new sequencing request</div> %if len( request_type_select_field.options ) < 1: - There are no request types available for ${trans.user.email} to create sequencing requests. + There are no request types available for ${trans.user.email | h} to create sequencing requests. %else: <div class="toolFormBody"><form name="create_request" id="create_request" action="${h.url_for( controller='requests_common', action='create_request', cntrller=cntrller )}" method="post" > diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/webapps/galaxy/requests/common/edit_basic_request_info.mako --- a/templates/webapps/galaxy/requests/common/edit_basic_request_info.mako +++ b/templates/webapps/galaxy/requests/common/edit_basic_request_info.mako @@ -31,7 +31,7 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Edit sequencing request "${request.name}"</div> + <div class="toolFormTitle">Edit sequencing request "${request.name | h}"</div><div class="toolFormBody"><form name="edit_basic_request_info" id="edit_basic_request_info" action="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}" method="post" > %for i, field in enumerate( widgets ): @@ -70,11 +70,11 @@ %><div class="form-row"><label>Send to:</label> - <input type="checkbox" name="email_address" value="true" ${email_address}>${request.user.email} (sequencing request owner)<input type="hidden" name="email_address" value="true"> + <input type="checkbox" name="email_address" value="true" ${email_address}>${request.user.email | h} (sequencing request owner)<input type="hidden" name="email_address" value="true"></div><div class="form-row"><label>Additional email addresses:</label> - <textarea name="additional_email_addresses" rows="3" cols="40">${emails}</textarea> + <textarea name="additional_email_addresses" rows="3" cols="40">${emails | h}</textarea><div class="toolParamHelp" style="clear: both;"> Enter one email address per line </div> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/webapps/galaxy/requests/common/find_samples.mako --- a/templates/webapps/galaxy/requests/common/find_samples.mako +++ b/templates/webapps/galaxy/requests/common/find_samples.mako @@ -72,7 +72,7 @@ %if samples: %for sample in samples: <div class="form-row"> - Sample: <b>${sample.name}</b> | Barcode: ${sample.bar_code}<br/> + Sample: <b>${sample.name | h}</b> | Barcode: ${sample.bar_code | h}<br/> %if sample.request.is_new or not sample.state: State: Unsubmitted<br/> %else: @@ -85,10 +85,10 @@ %> Datasets: <a href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, external_service_id=trans.security.encode_id( external_service.id ), sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a><br/> %if is_admin: - <i>User: ${sample.request.user.email}</i> + <i>User: ${sample.request.user.email | h}</i> %endif <div class="toolParamHelp" style="clear: both;"> - <a href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Sequencing request: ${sample.request.name} | Type: ${sample.request.type.name} | State: ${sample.request.state}</a> + <a href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Sequencing request: ${sample.request.name | h} | Type: ${sample.request.type.name} | State: ${sample.request.state}</a></div></div><br/> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/webapps/galaxy/requests/common/view_request.mako --- a/templates/webapps/galaxy/requests/common/view_request.mako +++ b/templates/webapps/galaxy/requests/common/view_request.mako @@ -58,7 +58,7 @@ ${render_samples_messages(request, is_admin, is_submitted, message, status)} <div class="toolForm"> - <div class="toolFormTitle">Sequencing request "${request.name}"</div> + <div class="toolFormTitle">Sequencing request "${request.name | h}"</div><div class="toolFormBody"><div class="form-row"><label>Current state:</label> @@ -67,12 +67,12 @@ </div><div class="form-row"><label>Description:</label> - ${request.desc} + ${request.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>User:</label> - ${request.user.email} + ${request.user.email | h} <div style="clear: both"></div></div><div class="form-row"> @@ -94,7 +94,7 @@ %><div class="form-row"><label>${field_label}:</label> - ${field_value} + ${field_value | h} </div><div style="clear: both"></div> %endfor @@ -116,7 +116,7 @@ else: emails = '' %> - ${emails} + ${emails | h} <div style="clear: both"></div></div><div class="form-row"> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/webapps/galaxy/requests/common/view_request_history.mako --- a/templates/webapps/galaxy/requests/common/view_request_history.mako +++ b/templates/webapps/galaxy/requests/common/view_request_history.mako @@ -36,7 +36,7 @@ ${render_msg( message, status )} %endif -<h3>History of sequencing request "${request.name}"</h3> +<h3>History of sequencing request "${request.name | h}"</h3><div class="toolForm"><table class="grid"> @@ -52,7 +52,7 @@ <tr><td><b>${event.state}</b></td><td>${time_ago( event.update_time )}</td> - <td>${event.comment}</td> + <td>${event.comment | h}</td></tr> %endfor </tbody> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/webapps/galaxy/requests/common/view_sample.mako --- a/templates/webapps/galaxy/requests/common/view_sample.mako +++ b/templates/webapps/galaxy/requests/common/view_sample.mako @@ -6,7 +6,7 @@ %if external_service: <p><div class="toolForm"> - <div class="toolFormTitle">Available External Service Actions for ${sample.name} at ${external_service.name}</div> + <div class="toolFormTitle">Available External Service Actions for ${sample.name | h} at ${external_service.name | h}</div><div class="toolFormBody"><div class="toolMenu"> %for item in external_service.actions: @@ -25,7 +25,7 @@ <div class="form-row"><div class="toolSectionList"><div class="toolSectionTitle"> - <span>${external_service_group.label}</span> + <span>${external_service_group.label | h}</span></div><div class="toolSectionBody"><div class="toolSectionBg"> @@ -54,7 +54,7 @@ target = 'galaxy_main' %><div class="toolTitle"> - <a href="${external_service_action.get_action_access_link( trans )}" target="${target}">${external_service_action.label}</a> + <a href="${external_service_action.get_action_access_link( trans )}" target="${target}">${external_service_action.label | h}</a></div></%def> @@ -75,38 +75,38 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Sample "${sample.name}"</div> + <div class="toolFormTitle">Sample "${sample.name | h}"</div><div class="toolFormBody"><div class="form-row"><label>Name:</label> - ${sample.name} + ${sample.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - ${sample.desc} + ${sample.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>Barcode:</label> - ${sample.bar_code} + ${sample.bar_code | h} <div style="clear: both"></div></div> %if sample.library: <div class="form-row"><label>Library:</label> - ${sample.library.name} + ${sample.library.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Folder:</label> - ${sample.folder.name} + ${sample.folder.name | h} <div style="clear: both"></div></div> %endif <div class="form-row"><label>Request:</label> - ${sample.request.name} + ${sample.request.name | h} <div style="clear: both"></div></div></div> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/webapps/galaxy/requests/common/view_sample_history.mako --- a/templates/webapps/galaxy/requests/common/view_sample_history.mako +++ b/templates/webapps/galaxy/requests/common/view_sample_history.mako @@ -12,7 +12,7 @@ ${render_msg( message, status )} %endif -<h3>History of sample "${sample.name}"</h3> +<h3>History of sample "${sample.name | h}"</h3><div class="toolForm"><table class="grid"> @@ -27,10 +27,10 @@ <tbody> %for event in sample.events: <tr> - <td><b>${event.state.name}</b></td> - <td>${event.state.desc}</td> + <td><b>${event.state.name | h}</b></td> + <td>${event.state.desc | h}</td><td>${time_ago( event.update_time )}</td> - <td>${event.comment}</td> + <td>${event.comment | h}</td></tr> %endfor </tbody> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 03 Dec '14

03 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5f61882fd1c1/ Changeset: 5f61882fd1c1 Branch: stable User: martenson Date: 2014-12-03 18:29:03+00:00 Summary: propagate the commit of 795336f22d8b94b86256b1d4738ee1bf24e18b57 that is already in next-stable to the stable original commit msg: none of the requests & forms controllers used escaping so I escaped the variables exclusively in the templates Affected #: 18 files diff -r 546ff6ef27b4b83e26ae228c292fd981173ac550 -r 5f61882fd1c18b0f32f8c9fd40260f37257186de templates/admin/forms/create_form.mako --- a/templates/admin/forms/create_form.mako +++ b/templates/admin/forms/create_form.mako @@ -9,7 +9,7 @@ <div class="toolFormTitle">Create a new form definition</div> %for label, input in inputs: <div class="form-row"> - <label>${label}</label> + <label>${label | h}</label> ${input.get_html()} <div style="clear: both"></div></div> diff -r 546ff6ef27b4b83e26ae228c292fd981173ac550 -r 5f61882fd1c18b0f32f8c9fd40260f37257186de templates/admin/forms/edit_form_definition.mako --- a/templates/admin/forms/edit_form_definition.mako +++ b/templates/admin/forms/edit_form_definition.mako @@ -96,14 +96,14 @@ <form id="edit_form_definition" name="edit_form_definition" action="${h.url_for( controller='forms', action='edit_form_definition', id=trans.security.encode_id( form_definition.current.id ) )}" method="post" ><div class="toolForm"> - <div class="toolFormTitle">Edit form definition "${form_definition.name}" (${form_definition.type})</div> + <div class="toolFormTitle">Edit form definition "${form_definition.name | h}" (${form_definition.type | h})</div> %if response_redirect: <input type="hidden" name="response_redirect" value="${response_redirect}" size="40" /> %endif %for label, input in form_details: <div class="form-row"> %if label != 'Type': - <label>${label}</label> + <label>${label | h}</label> %endif <div style="float: left; width: 250px; margin-right: 10px;"> ${input.get_html()} diff -r 546ff6ef27b4b83e26ae228c292fd981173ac550 -r 5f61882fd1c18b0f32f8c9fd40260f37257186de templates/admin/request_type/common.mako --- a/templates/admin/request_type/common.mako +++ b/templates/admin/request_type/common.mako @@ -2,7 +2,7 @@ <div class="repeat-group-item"><div class="form-row"><label>${1+element_count}. State name:</label> - <input type="text" name="state_name_${element_count}" value="${state_name}" size="40"/> + <input type="text" name="state_name_${element_count}" value="${state_name | h}" size="40"/> ## Do not show remove button for the first state %if element_count > 0: <input type="submit" name="remove_state_button" value="Remove state ${1+element_count}"/> @@ -10,7 +10,7 @@ </div><div class="form-row"><label>Description:</label> - <input type="text" name="state_desc_${element_count}" value="${state_desc}" size="40"/> + <input type="text" name="state_desc_${element_count}" value="${state_desc | h}" size="40"/><div class="toolParamHelp" style="clear: both;"> optional </div> diff -r 546ff6ef27b4b83e26ae228c292fd981173ac550 -r 5f61882fd1c18b0f32f8c9fd40260f37257186de templates/admin/request_type/create_request_type.mako --- a/templates/admin/request_type/create_request_type.mako +++ b/templates/admin/request_type/create_request_type.mako @@ -23,7 +23,7 @@ <div class="toolFormTitle">Create a new request type</div> %for rt_info in rt_info_widgets: <div class="form-row"> - <label>${rt_info['label']}</label> + <label>${rt_info['label'] | h}</label><div style="float: left; width: 250px; margin-right: 10px;"> ${rt_info['widget'].get_html()} </div> diff -r 546ff6ef27b4b83e26ae228c292fd981173ac550 -r 5f61882fd1c18b0f32f8c9fd40260f37257186de templates/admin/request_type/edit_request_type.mako --- a/templates/admin/request_type/edit_request_type.mako +++ b/templates/admin/request_type/edit_request_type.mako @@ -32,26 +32,26 @@ <form name="edit_request_type" action="${h.url_for( controller='request_type', action='edit_request_type', id=trans.security.encode_id( request_type.id ) )}" method="post" ><div class="toolForm"> - <div class="toolFormTitle">"Edit ${request_type.name}" request type</div> + <div class="toolFormTitle">"Edit ${request_type.name | h}" request type</div><div class="form-row"><label>Name:</label> - <input type="text" name="name" value="${request_type.name}" size="40"/> + <input type="text" name="name" value="${request_type.name | }" size="40"/><div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - <input type="text" name="desc" value="${request_type.desc}" size="40"/> + <input type="text" name="desc" value="${request_type.desc | h}" size="40"/><div style="clear: both"></div></div><div class="form-row"><label>Sequencing request form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name | h}</a> ## Hidden field needed by the __save_request_type() method <input type="hidden" name="request_form_id" value="${trans.security.encode_id( request_type.request_form_id )}" size="40"/></div><div class="form-row"><label>Sample form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name | h}</a> ## Hidden field needed by the __save_request_type() method <input type="hidden" name="sample_form_id" value="${trans.security.encode_id( request_type.sample_form_id )}" size="40"/></div> @@ -63,11 +63,11 @@ <div class="repeat-group-item"><div class="form-row"><label>${1+element_count}. State name:</label> - <input type="text" name="state_name_${trans.security.encode_id( state.id )}" value="${state.name}" size="40"/> + <input type="text" name="state_name_${trans.security.encode_id( state.id )}" value="${state.name | h}" size="40"/></div><div class="form-row"><label>Description:</label> - <input type="text" name="state_desc_${trans.security.encode_id( state.id )}" value="${state.desc}" size="40"/> + <input type="text" name="state_desc_${trans.security.encode_id( state.id )}" value="${state.desc | h}" size="40"/><div class="toolParamHelp" style="clear: both;"> optional </div> diff -r 546ff6ef27b4b83e26ae228c292fd981173ac550 -r 5f61882fd1c18b0f32f8c9fd40260f37257186de templates/admin/request_type/request_type_permissions.mako --- a/templates/admin/request_type/request_type_permissions.mako +++ b/templates/admin/request_type/request_type_permissions.mako @@ -48,7 +48,7 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Manage access permissions on request type "${request_type.name}"</div> + <div class="toolFormTitle">Manage access permissions on request type "${request_type.name | h}"</div><div class="toolFormBody"><form name="request_type_permissions" id="request_type_permissions" action="${h.url_for( controller='request_type', action='request_type_permissions', id=trans.security.encode_id( request_type.id ) )}" method="post"><div class="form-row"> @@ -65,13 +65,13 @@ in_roles.add( a.role ) out_roles = filter( lambda x: x not in in_roles, all_roles ) %> - ${action.description}<br/><br/> + ${action.description | h}<br/><br/><div style="width: 100%; white-space: nowrap;"><div style="float: left; width: 50%;"> Roles associated:<br/><select name="${action_key}_in" id="${action_key}_in_select" class="in_select" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple> %for role in in_roles: - <option value="${role.id}">${role.name}</option> + <option value="${role.id}">${role.name | h}</option> %endfor </select><br/><div style="width: 98%; text-align: right"><input type="submit" id="${action_key}_remove_button" class="role_remove_button" value=">>"/></div> @@ -80,7 +80,7 @@ Roles not associated:<br/><select name="${action_key}_out" id="${action_key}_out_select" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple> %for role in out_roles: - <option value="${role.id}">${role.name}</option> + <option value="${role.id}">${role.name | h}</option> %endfor </select><br/><input type="submit" id="${action_key}_add_button" class="role_add_button" value="<<"/> diff -r 546ff6ef27b4b83e26ae228c292fd981173ac550 -r 5f61882fd1c18b0f32f8c9fd40260f37257186de templates/admin/request_type/view_request_type.mako --- a/templates/admin/request_type/view_request_type.mako +++ b/templates/admin/request_type/view_request_type.mako @@ -30,24 +30,24 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">"${request_type.name}" request type</div> + <div class="toolFormTitle">"${request_type.name | h}" request type</div><div class="form-row"><label>Name:</label> - ${request_type.name} + ${request_type.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - ${request_type.desc} + ${request_type.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>Sequencing request form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name | h}</a></div><div class="form-row"><label>Sample form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name | h}</a></div></div><p/> @@ -55,8 +55,8 @@ <div class="toolFormTitle">Sample states defined for this request type</div> %for state in request_type.states: <div class="form-row"> - <label>${state.name}</label> - ${state.desc} + <label>${state.name | h}</label> + ${state.desc | h} </div><div style="clear: both"></div> %endfor @@ -67,8 +67,8 @@ %if request_type.external_services: %for index, external_service in enumerate( request_type.external_services ): <div class="form-row"> - <label><a href="${h.url_for( controller='external_service', action='view_external_service', id=trans.security.encode_id( external_service.id ) )}">${external_service.name}</a></label> - ${external_service.get_external_service_type( trans ).name} + <label><a href="${h.url_for( controller='external_service', action='view_external_service', id=trans.security.encode_id( external_service.id ) )}">${external_service.name | h}</a></label> + ${external_service.get_external_service_type( trans ).name | h} </div> %endfor %else: diff -r 546ff6ef27b4b83e26ae228c292fd981173ac550 -r 5f61882fd1c18b0f32f8c9fd40260f37257186de templates/admin/requests/reject.mako --- a/templates/admin/requests/reject.mako +++ b/templates/admin/requests/reject.mako @@ -15,7 +15,7 @@ </ul><div class="toolForm"> - <div class="toolFormTitle">Reject sequencing request "${request.name}"</div> + <div class="toolFormTitle">Reject sequencing request "${request.name | h}"</div><form name="event" action="${h.url_for( controller='requests_admin', action='reject_request', id=trans.security.encode_id( request.id ) )}" method="post" ><div class="form-row"> Rejecting this request will move the request state to <b>Rejected</b>. diff -r 546ff6ef27b4b83e26ae228c292fd981173ac550 -r 5f61882fd1c18b0f32f8c9fd40260f37257186de templates/admin/requests/rename_datasets.mako --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -3,7 +3,7 @@ <% from galaxy.webapps.galaxy.controllers.requests_admin import build_rename_datasets_for_sample_select_field %> -<h3>Rename datasets for Sample "${sample.name}"</h3> +<h3>Rename datasets for Sample "${sample.name | h}"</h3><ul class="manage-table-actions"><li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Browse datasets</a></li> @@ -35,7 +35,7 @@ ${rename_datasets_for_sample_select_field.get_html()} </td><td> - <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id ) }" value="${sample_dataset.name}" size="100"/> + <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id ) }" value="${sample_dataset.name | h}" size="100"/></td><td>${sample_dataset.file_path}</td></tr> diff -r 546ff6ef27b4b83e26ae228c292fd981173ac550 -r 5f61882fd1c18b0f32f8c9fd40260f37257186de templates/admin/requests/view_sample_dataset.mako --- a/templates/admin/requests/view_sample_dataset.mako +++ b/templates/admin/requests/view_sample_dataset.mako @@ -21,19 +21,19 @@ </ul><div class="toolForm"> - <div class="toolFormTitle">"${sample.name}" Dataset</div> + <div class="toolFormTitle">"${sample.name | h}" Dataset</div><div class="toolFormBody"><div class="form-row"><label>Name:</label><div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.name} + ${sample_dataset.name | h} </div><div style="clear: both"></div></div><div class="form-row"><label>External service:</label><div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.external_service.name} (${sample_dataset.external_service.get_external_service_type( trans ).name}) + ${sample_dataset.external_service.name | h} (${sample_dataset.external_service.get_external_service_type( trans ).name | h}) </div><div style="clear: both"></div></div> diff -r 546ff6ef27b4b83e26ae228c292fd981173ac550 -r 5f61882fd1c18b0f32f8c9fd40260f37257186de templates/webapps/galaxy/requests/common/common.mako --- a/templates/webapps/galaxy/requests/common/common.mako +++ b/templates/webapps/galaxy/requests/common/common.mako @@ -257,18 +257,18 @@ <td valign="top"><input type="checkbox" name=select_sample_${sample.id} id="sample_checkbox" value="true" ${checked_str}/><input type="hidden" name=select_sample_${sample.id} id="sample_checkbox" value="true"/></td> %endif <td valign="top"> - <input type="text" name="sample_${sample_widget_index}_name" value="${sample_widget['name']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_name" value="${sample_widget['name'] | h}" size="10"/><div class="toolParamHelp" style="clear: both;"> - <i>${' (required)' }</i> + <i>(required)</i></div></td> %if display_bar_code: <td valign="top"> %if is_admin and is_submitted: - <input type="text" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code'] | h}" size="10"/> %else: - ${sample_widget['bar_code']} - <input type="hidden" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}"/> + ${sample_widget['bar_code'] | h} + <input type="hidden" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code'] | h}"/> %endif </td> %endif @@ -416,7 +416,7 @@ transferred_dataset_files = [] %><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="sample-${sample.id}-popup"> - <a class="view-info" href="${h.url_for( controller='requests_common', action='view_sample', cntrller=cntrller, id=trans.security.encode_id( sample.id ) )}">${sample.name}</a> + <a class="view-info" href="${h.url_for( controller='requests_common', action='view_sample', cntrller=cntrller, id=trans.security.encode_id( sample.id ) )}">${sample.name | h}</a></div><div popupmenu="sample-${sample.id}-popup"> %if can_select_datasets: @@ -439,11 +439,11 @@ %endif </div> %else: - ${sample_widget_name} + ${sample_widget_name | h} %endif </td> %if display_bar_code: - <td>${sample_widget_bar_code}</td> + <td>${sample_widget_bar_code | h}</td> %endif %if is_unsubmitted: <td>Unsubmitted</td> @@ -451,12 +451,12 @@ <td><a id="sampleState-${sample.id}" href="${h.url_for( controller='requests_common', action='view_sample_history', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${render_sample_state( sample )}</a></td> %endif %if sample_widget_library and library_cntrller is not None: - <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( sample_widget_library.id ) )}">${sample_widget_library.name}</a></td> + <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( sample_widget_library.id ) )}">${sample_widget_library.name | h}</a></td> %else: <td></td> %endif %if sample_widget_folder: - <td>${sample_widget_folder.name}</td> + <td>${sample_widget_folder.name | h}</td> %else: <td></td> %endif @@ -464,11 +464,11 @@ %if trans.user == sample_widget_history.user: <td><a target='_parent' href="${h.url_for( controller='history', action='list', operation="Switch", id=trans.security.encode_id(sample_widget_history.id), use_panels=False )}"> - ${sample_widget_history.name} + ${sample_widget_history.name | h} </a></td> %else: - <td>${sample_widget_history.name}</td> + <td>${sample_widget_history.name | h}</td> %endif %else: <td></td> @@ -477,11 +477,11 @@ %if trans.user == sample_widget_workflow.stored_workflow.user: <td><a target='_parent' href="${h.url_for( controller='workflow', action='editor', id=trans.security.encode_id(sample_widget_workflow.stored_workflow.id) )}"> - ${sample_widget_workflow.name} + ${sample_widget_workflow.name | h} </a></td> %else: - <td>${sample_widget_workflow.name}</td> + <td>${sample_widget_workflow.name | h}</td> %endif %else: <td></td> @@ -519,7 +519,7 @@ <%def name="render_sample_form( index, sample_name, sample_values, fields_dict, display_only )"><tr> - <td>${sample_name}</td> + <td>${sample_name | h}</td> %for field_index, field in fields_dict.items(): <% field_type = field[ 'type' ] @@ -532,17 +532,17 @@ %if field_type == 'WorkflowField': %if str( field_value ) != 'none': <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int( field_value ) ) %> - <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">${workflow.name}</a> + <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">${workflow.name | h}</a> %endif %else: - ${field_value} + ${field_value | h} %endif %else: <i>None</i> %endif %else: %if field_type == 'TextField': - <input type="text" name="sample_${index}_field_${field_index}" value="${field_value}" size="7"/> + <input type="text" name="sample_${index}_field_${field_index}" value="${field_value | h}" size="7"/> %elif field_type == 'SelectField': <select name="sample_${index}_field_${field_index}" last_selected_value="2"> %for option_index, option in enumerate(field[ 'selectlist' ]): @@ -695,7 +695,7 @@ %if is_admin: <span class="expandLink dataset-${dataset}-click"><span class="rowIcon"></span><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="dataset-${dataset.id}-popup"> - <a class="dataset-${encoded_id}-click" href="${h.url_for( controller='requests_admin', action='manage_datasets', operation='view', id=trans.security.encode_id( dataset.id ) )}">${dataset.name}</a> + <a class="dataset-${encoded_id}-click" href="${h.url_for( controller='requests_admin', action='manage_datasets', operation='view', id=trans.security.encode_id( dataset.id ) )}">${dataset.name | h}</a></div></span><div popupmenu="dataset-${dataset.id}-popup"> @@ -704,12 +704,12 @@ %endif </div> %else: - ${dataset.name} + ${dataset.name | h} %endif </td><td>${dataset.size}</td> - <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">${dataset.sample.library.name}</a></td> - <td>${dataset.sample.folder.name}</td> + <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">${dataset.sample.library.name | h}</a></td> + <td>${dataset.sample.folder.name | h}</td><td id="datasetTransferStatus-${encoded_id}">${dataset.status}</td></tr> %endfor @@ -723,7 +723,7 @@ <%def name="render_samples_messages( request, is_admin=False, is_submitted=False, message=None, status=None)"> %if request.is_rejected: <div class='errormessage'> - ${request.last_comment} + ${request.last_comment | h} </div><br/> %endif %if is_admin and is_submitted and request.samples_without_library_destinations: diff -r 546ff6ef27b4b83e26ae228c292fd981173ac550 -r 5f61882fd1c18b0f32f8c9fd40260f37257186de templates/webapps/galaxy/requests/common/create_request.mako --- a/templates/webapps/galaxy/requests/common/create_request.mako +++ b/templates/webapps/galaxy/requests/common/create_request.mako @@ -23,7 +23,7 @@ <div class="toolForm"><div class="toolFormTitle">Create a new sequencing request</div> %if len( request_type_select_field.options ) < 1: - There are no request types available for ${trans.user.email} to create sequencing requests. + There are no request types available for ${trans.user.email | h} to create sequencing requests. %else: <div class="toolFormBody"><form name="create_request" id="create_request" action="${h.url_for( controller='requests_common', action='create_request', cntrller=cntrller )}" method="post" > diff -r 546ff6ef27b4b83e26ae228c292fd981173ac550 -r 5f61882fd1c18b0f32f8c9fd40260f37257186de templates/webapps/galaxy/requests/common/edit_basic_request_info.mako --- a/templates/webapps/galaxy/requests/common/edit_basic_request_info.mako +++ b/templates/webapps/galaxy/requests/common/edit_basic_request_info.mako @@ -31,7 +31,7 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Edit sequencing request "${request.name}"</div> + <div class="toolFormTitle">Edit sequencing request "${request.name | h}"</div><div class="toolFormBody"><form name="edit_basic_request_info" id="edit_basic_request_info" action="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}" method="post" > %for i, field in enumerate( widgets ): @@ -70,11 +70,11 @@ %><div class="form-row"><label>Send to:</label> - <input type="checkbox" name="email_address" value="true" ${email_address}>${request.user.email} (sequencing request owner)<input type="hidden" name="email_address" value="true"> + <input type="checkbox" name="email_address" value="true" ${email_address}>${request.user.email | h} (sequencing request owner)<input type="hidden" name="email_address" value="true"></div><div class="form-row"><label>Additional email addresses:</label> - <textarea name="additional_email_addresses" rows="3" cols="40">${emails}</textarea> + <textarea name="additional_email_addresses" rows="3" cols="40">${emails | h}</textarea><div class="toolParamHelp" style="clear: both;"> Enter one email address per line </div> diff -r 546ff6ef27b4b83e26ae228c292fd981173ac550 -r 5f61882fd1c18b0f32f8c9fd40260f37257186de templates/webapps/galaxy/requests/common/find_samples.mako --- a/templates/webapps/galaxy/requests/common/find_samples.mako +++ b/templates/webapps/galaxy/requests/common/find_samples.mako @@ -72,7 +72,7 @@ %if samples: %for sample in samples: <div class="form-row"> - Sample: <b>${sample.name}</b> | Barcode: ${sample.bar_code}<br/> + Sample: <b>${sample.name | h}</b> | Barcode: ${sample.bar_code | h}<br/> %if sample.request.is_new or not sample.state: State: Unsubmitted<br/> %else: @@ -85,10 +85,10 @@ %> Datasets: <a href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, external_service_id=trans.security.encode_id( external_service.id ), sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a><br/> %if is_admin: - <i>User: ${sample.request.user.email}</i> + <i>User: ${sample.request.user.email | h}</i> %endif <div class="toolParamHelp" style="clear: both;"> - <a href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Sequencing request: ${sample.request.name} | Type: ${sample.request.type.name} | State: ${sample.request.state}</a> + <a href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Sequencing request: ${sample.request.name | h} | Type: ${sample.request.type.name} | State: ${sample.request.state}</a></div></div><br/> diff -r 546ff6ef27b4b83e26ae228c292fd981173ac550 -r 5f61882fd1c18b0f32f8c9fd40260f37257186de templates/webapps/galaxy/requests/common/view_request.mako --- a/templates/webapps/galaxy/requests/common/view_request.mako +++ b/templates/webapps/galaxy/requests/common/view_request.mako @@ -58,7 +58,7 @@ ${render_samples_messages(request, is_admin, is_submitted, message, status)} <div class="toolForm"> - <div class="toolFormTitle">Sequencing request "${request.name}"</div> + <div class="toolFormTitle">Sequencing request "${request.name | h}"</div><div class="toolFormBody"><div class="form-row"><label>Current state:</label> @@ -67,12 +67,12 @@ </div><div class="form-row"><label>Description:</label> - ${request.desc} + ${request.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>User:</label> - ${request.user.email} + ${request.user.email | h} <div style="clear: both"></div></div><div class="form-row"> @@ -94,7 +94,7 @@ %><div class="form-row"><label>${field_label}:</label> - ${field_value} + ${field_value | h} </div><div style="clear: both"></div> %endfor @@ -116,7 +116,7 @@ else: emails = '' %> - ${emails} + ${emails | h} <div style="clear: both"></div></div><div class="form-row"> diff -r 546ff6ef27b4b83e26ae228c292fd981173ac550 -r 5f61882fd1c18b0f32f8c9fd40260f37257186de templates/webapps/galaxy/requests/common/view_request_history.mako --- a/templates/webapps/galaxy/requests/common/view_request_history.mako +++ b/templates/webapps/galaxy/requests/common/view_request_history.mako @@ -36,7 +36,7 @@ ${render_msg( message, status )} %endif -<h3>History of sequencing request "${request.name}"</h3> +<h3>History of sequencing request "${request.name | h}"</h3><div class="toolForm"><table class="grid"> @@ -52,7 +52,7 @@ <tr><td><b>${event.state}</b></td><td>${time_ago( event.update_time )}</td> - <td>${event.comment}</td> + <td>${event.comment | h}</td></tr> %endfor </tbody> diff -r 546ff6ef27b4b83e26ae228c292fd981173ac550 -r 5f61882fd1c18b0f32f8c9fd40260f37257186de templates/webapps/galaxy/requests/common/view_sample.mako --- a/templates/webapps/galaxy/requests/common/view_sample.mako +++ b/templates/webapps/galaxy/requests/common/view_sample.mako @@ -6,7 +6,7 @@ %if external_service: <p><div class="toolForm"> - <div class="toolFormTitle">Available External Service Actions for ${sample.name} at ${external_service.name}</div> + <div class="toolFormTitle">Available External Service Actions for ${sample.name | h} at ${external_service.name | h}</div><div class="toolFormBody"><div class="toolMenu"> %for item in external_service.actions: @@ -25,7 +25,7 @@ <div class="form-row"><div class="toolSectionList"><div class="toolSectionTitle"> - <span>${external_service_group.label}</span> + <span>${external_service_group.label | h}</span></div><div class="toolSectionBody"><div class="toolSectionBg"> @@ -54,7 +54,7 @@ target = 'galaxy_main' %><div class="toolTitle"> - <a href="${external_service_action.get_action_access_link( trans )}" target="${target}">${external_service_action.label}</a> + <a href="${external_service_action.get_action_access_link( trans )}" target="${target}">${external_service_action.label | h}</a></div></%def> @@ -75,38 +75,38 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Sample "${sample.name}"</div> + <div class="toolFormTitle">Sample "${sample.name | h}"</div><div class="toolFormBody"><div class="form-row"><label>Name:</label> - ${sample.name} + ${sample.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - ${sample.desc} + ${sample.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>Barcode:</label> - ${sample.bar_code} + ${sample.bar_code | h} <div style="clear: both"></div></div> %if sample.library: <div class="form-row"><label>Library:</label> - ${sample.library.name} + ${sample.library.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Folder:</label> - ${sample.folder.name} + ${sample.folder.name | h} <div style="clear: both"></div></div> %endif <div class="form-row"><label>Request:</label> - ${sample.request.name} + ${sample.request.name | h} <div style="clear: both"></div></div></div> diff -r 546ff6ef27b4b83e26ae228c292fd981173ac550 -r 5f61882fd1c18b0f32f8c9fd40260f37257186de templates/webapps/galaxy/requests/common/view_sample_history.mako --- a/templates/webapps/galaxy/requests/common/view_sample_history.mako +++ b/templates/webapps/galaxy/requests/common/view_sample_history.mako @@ -12,7 +12,7 @@ ${render_msg( message, status )} %endif -<h3>History of sample "${sample.name}"</h3> +<h3>History of sample "${sample.name | h}"</h3><div class="toolForm"><table class="grid"> @@ -27,10 +27,10 @@ <tbody> %for event in sample.events: <tr> - <td><b>${event.state.name}</b></td> - <td>${event.state.desc}</td> + <td><b>${event.state.name | h}</b></td> + <td>${event.state.desc | h}</td><td>${time_ago( event.update_time )}</td> - <td>${event.comment}</td> + <td>${event.comment | h}</td></tr> %endfor </tbody> https://bitbucket.org/galaxy/galaxy-central/commits/0e663285c743/ Changeset: 0e663285c743 Branch: stable User: dannon Date: 2014-12-03 19:15:51+00:00 Summary: Merged in martenson/galaxy-central-marten/stable (pull request #585) [STABLE] propagate the commit of 795336f22d8b94b86256b1d4738ee1bf24e18b57 that is already in next-stable to the stable Affected #: 18 files diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/admin/forms/create_form.mako --- a/templates/admin/forms/create_form.mako +++ b/templates/admin/forms/create_form.mako @@ -9,7 +9,7 @@ <div class="toolFormTitle">Create a new form definition</div> %for label, input in inputs: <div class="form-row"> - <label>${label}</label> + <label>${label | h}</label> ${input.get_html()} <div style="clear: both"></div></div> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/admin/forms/edit_form_definition.mako --- a/templates/admin/forms/edit_form_definition.mako +++ b/templates/admin/forms/edit_form_definition.mako @@ -96,14 +96,14 @@ <form id="edit_form_definition" name="edit_form_definition" action="${h.url_for( controller='forms', action='edit_form_definition', id=trans.security.encode_id( form_definition.current.id ) )}" method="post" ><div class="toolForm"> - <div class="toolFormTitle">Edit form definition "${form_definition.name}" (${form_definition.type})</div> + <div class="toolFormTitle">Edit form definition "${form_definition.name | h}" (${form_definition.type | h})</div> %if response_redirect: <input type="hidden" name="response_redirect" value="${response_redirect}" size="40" /> %endif %for label, input in form_details: <div class="form-row"> %if label != 'Type': - <label>${label}</label> + <label>${label | h}</label> %endif <div style="float: left; width: 250px; margin-right: 10px;"> ${input.get_html()} diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/admin/request_type/common.mako --- a/templates/admin/request_type/common.mako +++ b/templates/admin/request_type/common.mako @@ -2,7 +2,7 @@ <div class="repeat-group-item"><div class="form-row"><label>${1+element_count}. State name:</label> - <input type="text" name="state_name_${element_count}" value="${state_name}" size="40"/> + <input type="text" name="state_name_${element_count}" value="${state_name | h}" size="40"/> ## Do not show remove button for the first state %if element_count > 0: <input type="submit" name="remove_state_button" value="Remove state ${1+element_count}"/> @@ -10,7 +10,7 @@ </div><div class="form-row"><label>Description:</label> - <input type="text" name="state_desc_${element_count}" value="${state_desc}" size="40"/> + <input type="text" name="state_desc_${element_count}" value="${state_desc | h}" size="40"/><div class="toolParamHelp" style="clear: both;"> optional </div> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/admin/request_type/create_request_type.mako --- a/templates/admin/request_type/create_request_type.mako +++ b/templates/admin/request_type/create_request_type.mako @@ -23,7 +23,7 @@ <div class="toolFormTitle">Create a new request type</div> %for rt_info in rt_info_widgets: <div class="form-row"> - <label>${rt_info['label']}</label> + <label>${rt_info['label'] | h}</label><div style="float: left; width: 250px; margin-right: 10px;"> ${rt_info['widget'].get_html()} </div> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/admin/request_type/edit_request_type.mako --- a/templates/admin/request_type/edit_request_type.mako +++ b/templates/admin/request_type/edit_request_type.mako @@ -32,26 +32,26 @@ <form name="edit_request_type" action="${h.url_for( controller='request_type', action='edit_request_type', id=trans.security.encode_id( request_type.id ) )}" method="post" ><div class="toolForm"> - <div class="toolFormTitle">"Edit ${request_type.name}" request type</div> + <div class="toolFormTitle">"Edit ${request_type.name | h}" request type</div><div class="form-row"><label>Name:</label> - <input type="text" name="name" value="${request_type.name}" size="40"/> + <input type="text" name="name" value="${request_type.name | }" size="40"/><div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - <input type="text" name="desc" value="${request_type.desc}" size="40"/> + <input type="text" name="desc" value="${request_type.desc | h}" size="40"/><div style="clear: both"></div></div><div class="form-row"><label>Sequencing request form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name | h}</a> ## Hidden field needed by the __save_request_type() method <input type="hidden" name="request_form_id" value="${trans.security.encode_id( request_type.request_form_id )}" size="40"/></div><div class="form-row"><label>Sample form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name | h}</a> ## Hidden field needed by the __save_request_type() method <input type="hidden" name="sample_form_id" value="${trans.security.encode_id( request_type.sample_form_id )}" size="40"/></div> @@ -63,11 +63,11 @@ <div class="repeat-group-item"><div class="form-row"><label>${1+element_count}. State name:</label> - <input type="text" name="state_name_${trans.security.encode_id( state.id )}" value="${state.name}" size="40"/> + <input type="text" name="state_name_${trans.security.encode_id( state.id )}" value="${state.name | h}" size="40"/></div><div class="form-row"><label>Description:</label> - <input type="text" name="state_desc_${trans.security.encode_id( state.id )}" value="${state.desc}" size="40"/> + <input type="text" name="state_desc_${trans.security.encode_id( state.id )}" value="${state.desc | h}" size="40"/><div class="toolParamHelp" style="clear: both;"> optional </div> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/admin/request_type/request_type_permissions.mako --- a/templates/admin/request_type/request_type_permissions.mako +++ b/templates/admin/request_type/request_type_permissions.mako @@ -48,7 +48,7 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Manage access permissions on request type "${request_type.name}"</div> + <div class="toolFormTitle">Manage access permissions on request type "${request_type.name | h}"</div><div class="toolFormBody"><form name="request_type_permissions" id="request_type_permissions" action="${h.url_for( controller='request_type', action='request_type_permissions', id=trans.security.encode_id( request_type.id ) )}" method="post"><div class="form-row"> @@ -65,13 +65,13 @@ in_roles.add( a.role ) out_roles = filter( lambda x: x not in in_roles, all_roles ) %> - ${action.description}<br/><br/> + ${action.description | h}<br/><br/><div style="width: 100%; white-space: nowrap;"><div style="float: left; width: 50%;"> Roles associated:<br/><select name="${action_key}_in" id="${action_key}_in_select" class="in_select" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple> %for role in in_roles: - <option value="${role.id}">${role.name}</option> + <option value="${role.id}">${role.name | h}</option> %endfor </select><br/><div style="width: 98%; text-align: right"><input type="submit" id="${action_key}_remove_button" class="role_remove_button" value=">>"/></div> @@ -80,7 +80,7 @@ Roles not associated:<br/><select name="${action_key}_out" id="${action_key}_out_select" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple> %for role in out_roles: - <option value="${role.id}">${role.name}</option> + <option value="${role.id}">${role.name | h}</option> %endfor </select><br/><input type="submit" id="${action_key}_add_button" class="role_add_button" value="<<"/> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/admin/request_type/view_request_type.mako --- a/templates/admin/request_type/view_request_type.mako +++ b/templates/admin/request_type/view_request_type.mako @@ -30,24 +30,24 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">"${request_type.name}" request type</div> + <div class="toolFormTitle">"${request_type.name | h}" request type</div><div class="form-row"><label>Name:</label> - ${request_type.name} + ${request_type.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - ${request_type.desc} + ${request_type.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>Sequencing request form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name | h}</a></div><div class="form-row"><label>Sample form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name | h}</a></div></div><p/> @@ -55,8 +55,8 @@ <div class="toolFormTitle">Sample states defined for this request type</div> %for state in request_type.states: <div class="form-row"> - <label>${state.name}</label> - ${state.desc} + <label>${state.name | h}</label> + ${state.desc | h} </div><div style="clear: both"></div> %endfor @@ -67,8 +67,8 @@ %if request_type.external_services: %for index, external_service in enumerate( request_type.external_services ): <div class="form-row"> - <label><a href="${h.url_for( controller='external_service', action='view_external_service', id=trans.security.encode_id( external_service.id ) )}">${external_service.name}</a></label> - ${external_service.get_external_service_type( trans ).name} + <label><a href="${h.url_for( controller='external_service', action='view_external_service', id=trans.security.encode_id( external_service.id ) )}">${external_service.name | h}</a></label> + ${external_service.get_external_service_type( trans ).name | h} </div> %endfor %else: diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/admin/requests/reject.mako --- a/templates/admin/requests/reject.mako +++ b/templates/admin/requests/reject.mako @@ -15,7 +15,7 @@ </ul><div class="toolForm"> - <div class="toolFormTitle">Reject sequencing request "${request.name}"</div> + <div class="toolFormTitle">Reject sequencing request "${request.name | h}"</div><form name="event" action="${h.url_for( controller='requests_admin', action='reject_request', id=trans.security.encode_id( request.id ) )}" method="post" ><div class="form-row"> Rejecting this request will move the request state to <b>Rejected</b>. diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/admin/requests/rename_datasets.mako --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -3,7 +3,7 @@ <% from galaxy.webapps.galaxy.controllers.requests_admin import build_rename_datasets_for_sample_select_field %> -<h3>Rename datasets for Sample "${sample.name}"</h3> +<h3>Rename datasets for Sample "${sample.name | h}"</h3><ul class="manage-table-actions"><li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Browse datasets</a></li> @@ -35,7 +35,7 @@ ${rename_datasets_for_sample_select_field.get_html()} </td><td> - <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id ) }" value="${sample_dataset.name}" size="100"/> + <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id ) }" value="${sample_dataset.name | h}" size="100"/></td><td>${sample_dataset.file_path}</td></tr> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/admin/requests/view_sample_dataset.mako --- a/templates/admin/requests/view_sample_dataset.mako +++ b/templates/admin/requests/view_sample_dataset.mako @@ -21,19 +21,19 @@ </ul><div class="toolForm"> - <div class="toolFormTitle">"${sample.name}" Dataset</div> + <div class="toolFormTitle">"${sample.name | h}" Dataset</div><div class="toolFormBody"><div class="form-row"><label>Name:</label><div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.name} + ${sample_dataset.name | h} </div><div style="clear: both"></div></div><div class="form-row"><label>External service:</label><div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.external_service.name} (${sample_dataset.external_service.get_external_service_type( trans ).name}) + ${sample_dataset.external_service.name | h} (${sample_dataset.external_service.get_external_service_type( trans ).name | h}) </div><div style="clear: both"></div></div> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/webapps/galaxy/requests/common/common.mako --- a/templates/webapps/galaxy/requests/common/common.mako +++ b/templates/webapps/galaxy/requests/common/common.mako @@ -257,18 +257,18 @@ <td valign="top"><input type="checkbox" name=select_sample_${sample.id} id="sample_checkbox" value="true" ${checked_str}/><input type="hidden" name=select_sample_${sample.id} id="sample_checkbox" value="true"/></td> %endif <td valign="top"> - <input type="text" name="sample_${sample_widget_index}_name" value="${sample_widget['name']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_name" value="${sample_widget['name'] | h}" size="10"/><div class="toolParamHelp" style="clear: both;"> - <i>${' (required)' }</i> + <i>(required)</i></div></td> %if display_bar_code: <td valign="top"> %if is_admin and is_submitted: - <input type="text" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code'] | h}" size="10"/> %else: - ${sample_widget['bar_code']} - <input type="hidden" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}"/> + ${sample_widget['bar_code'] | h} + <input type="hidden" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code'] | h}"/> %endif </td> %endif @@ -416,7 +416,7 @@ transferred_dataset_files = [] %><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="sample-${sample.id}-popup"> - <a class="view-info" href="${h.url_for( controller='requests_common', action='view_sample', cntrller=cntrller, id=trans.security.encode_id( sample.id ) )}">${sample.name}</a> + <a class="view-info" href="${h.url_for( controller='requests_common', action='view_sample', cntrller=cntrller, id=trans.security.encode_id( sample.id ) )}">${sample.name | h}</a></div><div popupmenu="sample-${sample.id}-popup"> %if can_select_datasets: @@ -439,11 +439,11 @@ %endif </div> %else: - ${sample_widget_name} + ${sample_widget_name | h} %endif </td> %if display_bar_code: - <td>${sample_widget_bar_code}</td> + <td>${sample_widget_bar_code | h}</td> %endif %if is_unsubmitted: <td>Unsubmitted</td> @@ -451,12 +451,12 @@ <td><a id="sampleState-${sample.id}" href="${h.url_for( controller='requests_common', action='view_sample_history', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${render_sample_state( sample )}</a></td> %endif %if sample_widget_library and library_cntrller is not None: - <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( sample_widget_library.id ) )}">${sample_widget_library.name}</a></td> + <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( sample_widget_library.id ) )}">${sample_widget_library.name | h}</a></td> %else: <td></td> %endif %if sample_widget_folder: - <td>${sample_widget_folder.name}</td> + <td>${sample_widget_folder.name | h}</td> %else: <td></td> %endif @@ -464,11 +464,11 @@ %if trans.user == sample_widget_history.user: <td><a target='_parent' href="${h.url_for( controller='history', action='list', operation="Switch", id=trans.security.encode_id(sample_widget_history.id), use_panels=False )}"> - ${sample_widget_history.name} + ${sample_widget_history.name | h} </a></td> %else: - <td>${sample_widget_history.name}</td> + <td>${sample_widget_history.name | h}</td> %endif %else: <td></td> @@ -477,11 +477,11 @@ %if trans.user == sample_widget_workflow.stored_workflow.user: <td><a target='_parent' href="${h.url_for( controller='workflow', action='editor', id=trans.security.encode_id(sample_widget_workflow.stored_workflow.id) )}"> - ${sample_widget_workflow.name} + ${sample_widget_workflow.name | h} </a></td> %else: - <td>${sample_widget_workflow.name}</td> + <td>${sample_widget_workflow.name | h}</td> %endif %else: <td></td> @@ -519,7 +519,7 @@ <%def name="render_sample_form( index, sample_name, sample_values, fields_dict, display_only )"><tr> - <td>${sample_name}</td> + <td>${sample_name | h}</td> %for field_index, field in fields_dict.items(): <% field_type = field[ 'type' ] @@ -532,17 +532,17 @@ %if field_type == 'WorkflowField': %if str( field_value ) != 'none': <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int( field_value ) ) %> - <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">${workflow.name}</a> + <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">${workflow.name | h}</a> %endif %else: - ${field_value} + ${field_value | h} %endif %else: <i>None</i> %endif %else: %if field_type == 'TextField': - <input type="text" name="sample_${index}_field_${field_index}" value="${field_value}" size="7"/> + <input type="text" name="sample_${index}_field_${field_index}" value="${field_value | h}" size="7"/> %elif field_type == 'SelectField': <select name="sample_${index}_field_${field_index}" last_selected_value="2"> %for option_index, option in enumerate(field[ 'selectlist' ]): @@ -695,7 +695,7 @@ %if is_admin: <span class="expandLink dataset-${dataset}-click"><span class="rowIcon"></span><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="dataset-${dataset.id}-popup"> - <a class="dataset-${encoded_id}-click" href="${h.url_for( controller='requests_admin', action='manage_datasets', operation='view', id=trans.security.encode_id( dataset.id ) )}">${dataset.name}</a> + <a class="dataset-${encoded_id}-click" href="${h.url_for( controller='requests_admin', action='manage_datasets', operation='view', id=trans.security.encode_id( dataset.id ) )}">${dataset.name | h}</a></div></span><div popupmenu="dataset-${dataset.id}-popup"> @@ -704,12 +704,12 @@ %endif </div> %else: - ${dataset.name} + ${dataset.name | h} %endif </td><td>${dataset.size}</td> - <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">${dataset.sample.library.name}</a></td> - <td>${dataset.sample.folder.name}</td> + <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">${dataset.sample.library.name | h}</a></td> + <td>${dataset.sample.folder.name | h}</td><td id="datasetTransferStatus-${encoded_id}">${dataset.status}</td></tr> %endfor @@ -723,7 +723,7 @@ <%def name="render_samples_messages( request, is_admin=False, is_submitted=False, message=None, status=None)"> %if request.is_rejected: <div class='errormessage'> - ${request.last_comment} + ${request.last_comment | h} </div><br/> %endif %if is_admin and is_submitted and request.samples_without_library_destinations: diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/webapps/galaxy/requests/common/create_request.mako --- a/templates/webapps/galaxy/requests/common/create_request.mako +++ b/templates/webapps/galaxy/requests/common/create_request.mako @@ -23,7 +23,7 @@ <div class="toolForm"><div class="toolFormTitle">Create a new sequencing request</div> %if len( request_type_select_field.options ) < 1: - There are no request types available for ${trans.user.email} to create sequencing requests. + There are no request types available for ${trans.user.email | h} to create sequencing requests. %else: <div class="toolFormBody"><form name="create_request" id="create_request" action="${h.url_for( controller='requests_common', action='create_request', cntrller=cntrller )}" method="post" > diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/webapps/galaxy/requests/common/edit_basic_request_info.mako --- a/templates/webapps/galaxy/requests/common/edit_basic_request_info.mako +++ b/templates/webapps/galaxy/requests/common/edit_basic_request_info.mako @@ -31,7 +31,7 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Edit sequencing request "${request.name}"</div> + <div class="toolFormTitle">Edit sequencing request "${request.name | h}"</div><div class="toolFormBody"><form name="edit_basic_request_info" id="edit_basic_request_info" action="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}" method="post" > %for i, field in enumerate( widgets ): @@ -70,11 +70,11 @@ %><div class="form-row"><label>Send to:</label> - <input type="checkbox" name="email_address" value="true" ${email_address}>${request.user.email} (sequencing request owner)<input type="hidden" name="email_address" value="true"> + <input type="checkbox" name="email_address" value="true" ${email_address}>${request.user.email | h} (sequencing request owner)<input type="hidden" name="email_address" value="true"></div><div class="form-row"><label>Additional email addresses:</label> - <textarea name="additional_email_addresses" rows="3" cols="40">${emails}</textarea> + <textarea name="additional_email_addresses" rows="3" cols="40">${emails | h}</textarea><div class="toolParamHelp" style="clear: both;"> Enter one email address per line </div> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/webapps/galaxy/requests/common/find_samples.mako --- a/templates/webapps/galaxy/requests/common/find_samples.mako +++ b/templates/webapps/galaxy/requests/common/find_samples.mako @@ -72,7 +72,7 @@ %if samples: %for sample in samples: <div class="form-row"> - Sample: <b>${sample.name}</b> | Barcode: ${sample.bar_code}<br/> + Sample: <b>${sample.name | h}</b> | Barcode: ${sample.bar_code | h}<br/> %if sample.request.is_new or not sample.state: State: Unsubmitted<br/> %else: @@ -85,10 +85,10 @@ %> Datasets: <a href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, external_service_id=trans.security.encode_id( external_service.id ), sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a><br/> %if is_admin: - <i>User: ${sample.request.user.email}</i> + <i>User: ${sample.request.user.email | h}</i> %endif <div class="toolParamHelp" style="clear: both;"> - <a href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Sequencing request: ${sample.request.name} | Type: ${sample.request.type.name} | State: ${sample.request.state}</a> + <a href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Sequencing request: ${sample.request.name | h} | Type: ${sample.request.type.name} | State: ${sample.request.state}</a></div></div><br/> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/webapps/galaxy/requests/common/view_request.mako --- a/templates/webapps/galaxy/requests/common/view_request.mako +++ b/templates/webapps/galaxy/requests/common/view_request.mako @@ -58,7 +58,7 @@ ${render_samples_messages(request, is_admin, is_submitted, message, status)} <div class="toolForm"> - <div class="toolFormTitle">Sequencing request "${request.name}"</div> + <div class="toolFormTitle">Sequencing request "${request.name | h}"</div><div class="toolFormBody"><div class="form-row"><label>Current state:</label> @@ -67,12 +67,12 @@ </div><div class="form-row"><label>Description:</label> - ${request.desc} + ${request.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>User:</label> - ${request.user.email} + ${request.user.email | h} <div style="clear: both"></div></div><div class="form-row"> @@ -94,7 +94,7 @@ %><div class="form-row"><label>${field_label}:</label> - ${field_value} + ${field_value | h} </div><div style="clear: both"></div> %endfor @@ -116,7 +116,7 @@ else: emails = '' %> - ${emails} + ${emails | h} <div style="clear: both"></div></div><div class="form-row"> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/webapps/galaxy/requests/common/view_request_history.mako --- a/templates/webapps/galaxy/requests/common/view_request_history.mako +++ b/templates/webapps/galaxy/requests/common/view_request_history.mako @@ -36,7 +36,7 @@ ${render_msg( message, status )} %endif -<h3>History of sequencing request "${request.name}"</h3> +<h3>History of sequencing request "${request.name | h}"</h3><div class="toolForm"><table class="grid"> @@ -52,7 +52,7 @@ <tr><td><b>${event.state}</b></td><td>${time_ago( event.update_time )}</td> - <td>${event.comment}</td> + <td>${event.comment | h}</td></tr> %endfor </tbody> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/webapps/galaxy/requests/common/view_sample.mako --- a/templates/webapps/galaxy/requests/common/view_sample.mako +++ b/templates/webapps/galaxy/requests/common/view_sample.mako @@ -6,7 +6,7 @@ %if external_service: <p><div class="toolForm"> - <div class="toolFormTitle">Available External Service Actions for ${sample.name} at ${external_service.name}</div> + <div class="toolFormTitle">Available External Service Actions for ${sample.name | h} at ${external_service.name | h}</div><div class="toolFormBody"><div class="toolMenu"> %for item in external_service.actions: @@ -25,7 +25,7 @@ <div class="form-row"><div class="toolSectionList"><div class="toolSectionTitle"> - <span>${external_service_group.label}</span> + <span>${external_service_group.label | h}</span></div><div class="toolSectionBody"><div class="toolSectionBg"> @@ -54,7 +54,7 @@ target = 'galaxy_main' %><div class="toolTitle"> - <a href="${external_service_action.get_action_access_link( trans )}" target="${target}">${external_service_action.label}</a> + <a href="${external_service_action.get_action_access_link( trans )}" target="${target}">${external_service_action.label | h}</a></div></%def> @@ -75,38 +75,38 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Sample "${sample.name}"</div> + <div class="toolFormTitle">Sample "${sample.name | h}"</div><div class="toolFormBody"><div class="form-row"><label>Name:</label> - ${sample.name} + ${sample.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - ${sample.desc} + ${sample.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>Barcode:</label> - ${sample.bar_code} + ${sample.bar_code | h} <div style="clear: both"></div></div> %if sample.library: <div class="form-row"><label>Library:</label> - ${sample.library.name} + ${sample.library.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Folder:</label> - ${sample.folder.name} + ${sample.folder.name | h} <div style="clear: both"></div></div> %endif <div class="form-row"><label>Request:</label> - ${sample.request.name} + ${sample.request.name | h} <div style="clear: both"></div></div></div> diff -r 7ba05957588aff263132db3d7c0fad6a94b3a466 -r 0e663285c74326737d4ff3c637d4c8aba8847755 templates/webapps/galaxy/requests/common/view_sample_history.mako --- a/templates/webapps/galaxy/requests/common/view_sample_history.mako +++ b/templates/webapps/galaxy/requests/common/view_sample_history.mako @@ -12,7 +12,7 @@ ${render_msg( message, status )} %endif -<h3>History of sample "${sample.name}"</h3> +<h3>History of sample "${sample.name | h}"</h3><div class="toolForm"><table class="grid"> @@ -27,10 +27,10 @@ <tbody> %for event in sample.events: <tr> - <td><b>${event.state.name}</b></td> - <td>${event.state.desc}</td> + <td><b>${event.state.name | h}</b></td> + <td>${event.state.desc | h}</td><td>${time_ago( event.update_time )}</td> - <td>${event.comment}</td> + <td>${event.comment | h}</td></tr> %endfor </tbody> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Update tag latest_2014.10.06 for changeset 546ff6ef27b4
by commits-noreply＠bitbucket.org 03 Dec '14

03 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7ba05957588a/ Changeset: 7ba05957588a Branch: stable User: natefoo Date: 2014-12-03 19:00:28+00:00 Summary: Update tag latest_2014.10.06 for changeset 546ff6ef27b4 Affected #: 1 file diff -r 546ff6ef27b4b83e26ae228c292fd981173ac550 -r 7ba05957588aff263132db3d7c0fad6a94b3a466 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -acb2548443ae42d39ef200d035ccc0481d6b930c latest_2014.10.06 +546ff6ef27b4b83e26ae228c292fd981173ac550 latest_2014.10.06 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 03 Dec '14

03 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4b6b1d2d7407/ Changeset: 4b6b1d2d7407 Branch: next-stable User: natefoo Date: 2014-12-03 18:30:44+00:00 Summary: Merge stable changes to next-stable. Affected #: 9 files diff -r 3808622909a6bb561c46d2ff5a5675f1da589c8b -r 4b6b1d2d740732a982c922b264d2027ed2c90370 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -28,7 +28,7 @@ from galaxy.web.base.controller import CreatesApiKeysMixin from galaxy.web.form_builder import CheckboxField from galaxy.web.form_builder import build_select_field -from galaxy.web.framework.helpers import time_ago, grids +from galaxy.web.framework.helpers import time_ago, grids, escape from datetime import datetime, timedelta from galaxy.util import hash_util, biostar @@ -164,7 +164,7 @@ user_openid.provider = openid_provider if trans.user: if user_openid.user and user_openid.user.id != trans.user.id: - message = "The OpenID <strong>%s</strong> is already associated with another Galaxy account, <strong>%s</strong>. Please disassociate it from that account before attempting to associate it with a new account." % ( display_identifier, user_openid.user.email ) + message = "The OpenID <strong>%s</strong> is already associated with another Galaxy account, <strong>%s</strong>. Please disassociate it from that account before attempting to associate it with a new account." % ( escape( display_identifier ), escape( user_openid.user.email ) ) if not trans.user.active and trans.app.config.user_activation_on: # Account activation is ON and the user is INACTIVE. if ( trans.app.config.activation_grace_period != 0 ): # grace period is ON if self.is_outside_grace_period( trans, trans.user.create_time ): # User is outside the grace period. Login is disabled and he will have the activation email resent. @@ -179,23 +179,23 @@ user_openid.session = trans.galaxy_session if not openid_provider_obj.never_associate_with_user: if not auto_associate and ( user_openid.user and user_openid.user.id == trans.user.id ): - message = "The OpenID <strong>%s</strong> is already associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) + message = "The OpenID <strong>%s</strong> is already associated with your Galaxy account, <strong>%s</strong>." % ( escape( display_identifier ), escape( trans.user.email ) ) status = "warning" else: - message = "The OpenID <strong>%s</strong> has been associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) + message = "The OpenID <strong>%s</strong> has been associated with your Galaxy account, <strong>%s</strong>." % ( escape( display_identifier ), escape( trans.user.email ) ) status = "done" user_openid.user = trans.user trans.sa_session.add( user_openid ) trans.sa_session.flush() trans.log_event( "User associated OpenID: %s" % display_identifier ) else: - message = "The OpenID <strong>%s</strong> cannot be used to log into your Galaxy account, but any post authentication actions have been performed." % ( openid_provider_obj.name ) + message = "The OpenID <strong>%s</strong> cannot be used to log into your Galaxy account, but any post authentication actions have been performed." % escape( openid_provider_obj.name ) status = "info" openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) if redirect: - message = '%s<br>Click <a href="%s"><strong>here</strong></a> to return to the page you were previously viewing.' % ( message, redirect ) + message = '%s<br>Click <a href="%s"><strong>here</strong></a> to return to the page you were previously viewing.' % ( message, escape( self.__get_redirect_url( redirect ) ) ) if redirect and status != "error": - return trans.response.send_redirect( redirect ) + return trans.response.send_redirect( self.__get_redirect_url( redirect ) ) return trans.response.send_redirect( url_for( controller='user', action='openid_manage', use_panels=True, @@ -208,6 +208,7 @@ openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) if not redirect: redirect = url_for( '/' ) + redirect = self.__get_redirect_url( redirect ) return trans.response.send_redirect( redirect ) trans.sa_session.add( user_openid ) trans.sa_session.flush() @@ -448,18 +449,9 @@ @web.expose def login( self, trans, refresh_frames=[], **kwd ): - """Handle Galaxy login""" - redirect = kwd.get( 'redirect', trans.request.referer ).strip() - root_url = url_for( '/', qualified=True ) - # Always start with redirect_url being empty. - redirect_url = '' - # Compare urls, to prevent a redirect from pointing (directly) - # outside of galaxy or to enter a logout/login loop. - if not util.compare_urls( root_url, redirect, compare_path=False ) or util.compare_urls( url_for( controller='user', action='logout', qualified=True ), redirect ): - redirect = root_url - if kwd.get( 'noredirect', False ): - # The referrer is explicitly asking not to redirect. - redirect = '' + '''Handle Galaxy Log in''' + redirect = self.__get_redirect_url( kwd.get( 'redirect', trans.request.referer ).strip() ) + redirect_url = '' # always start with redirect_url being empty use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) @@ -910,7 +902,7 @@ username = util.restore_text( params.get( 'username', '' ) ) if not username: username = user.username - message = util.restore_text( params.get( 'message', '' ) ) + message = escape( util.restore_text( params.get( 'message', '' ) ) ) status = params.get( 'status', 'done' ) if trans.webapp.name == 'galaxy': user_type_form_definition = self.__get_user_type_form_definition( trans, user=user, **kwd ) @@ -1119,8 +1111,8 @@ """Reset the user's password. Send an email with the new password.""" if trans.app.config.smtp_server is None: return trans.show_error_message( "Mail is not configured for this Galaxy instance. Please contact your local Galaxy administrator." ) - message = util.sanitize_text( util.restore_text( kwd.get( 'message', '' ) ) ) - status = 'done' + message = util.sanitize_text(util.restore_text( kwd.get( 'message', '' ) )) + status = kwd.get( 'status', 'done' ) if kwd.get( 'reset_password_button', False ): reset_user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first() user = trans.get_user() @@ -1146,7 +1138,7 @@ trans.sa_session.add( reset_user ) trans.sa_session.flush() trans.log_event( "User reset password: %s" % email ) - message = "Password has been reset and emailed to: %s. <a href='%s'>Click here</a> to return to the login form." % ( email, web.url_for( controller='user', action='login', noredirect='true' ) ) + message = "Password has been reset and emailed to: %s. <a href='%s'>Click here</a> to return to the login form." % ( escape( email ), web.url_for( controller='user', action='login', noredirect='true' ) ) except Exception, e: message = 'Failed to reset password: %s' % str( e ) status = 'error' @@ -1370,17 +1362,20 @@ # User not logged in, history group must be only public return trans.show_error_message( "You must be logged in to change your default permitted actions." ) + @web.require_login( "to add addresses" ) @web.expose def new_address( self, trans, cntrller, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) is_admin = cntrller == 'admin' and trans.user_is_admin() - user_id = params.get( 'user_id', False ) - if not user_id: - # User must be logged in to create a new address - return trans.show_error_message( "You must be logged in to create a new address." ) - user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + user_id = params.get( 'id', False ) + if is_admin: + if not user_id: + return trans.show_error_message( "You must specify a user to add a new address to." ) + user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + else: + user = trans.user short_desc = util.restore_text( params.get( 'short_desc', '' ) ) name = util.restore_text( params.get( 'name', '' ) ) institution = util.restore_text( params.get( 'institution', '' ) ) @@ -1431,10 +1426,10 @@ phone=phone ) trans.sa_session.add( user_address ) trans.sa_session.flush() - message = 'Address (%s) has been added' % user_address.desc + message = 'Address (%s) has been added' % escape( user_address.desc ) new_kwd = dict( message=message, status=status ) if is_admin: - new_kwd[ 'user_id' ] = trans.security.encode_id( user.id ) + new_kwd[ 'id' ] = trans.security.encode_id( user.id ) return trans.response.send_redirect( web.url_for( controller='user', action='manage_user_info', cntrller=cntrller, @@ -1452,24 +1447,29 @@ postal_code=postal_code, country=country, phone=phone, - message=message, + message=escape(message), status=status ) + @web.require_login( "to edit addresses" ) @web.expose def edit_address( self, trans, cntrller, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) is_admin = cntrller == 'admin' and trans.user_is_admin() - user_id = params.get( 'user_id', False ) - if not user_id: - # User must be logged in to create a new address - return trans.show_error_message( "You must be logged in to create a new address." ) - user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + user_id = params.get( 'id', False ) + if is_admin: + if not user_id: + return trans.show_error_message( "You must specify a user to add a new address to." ) + user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + else: + user = trans.user address_id = params.get( 'address_id', None ) if not address_id: - return trans.show_error_message( "No address id received for editing." ) + return trans.show_error_message( "Invalid address id." ) address_obj = trans.sa_session.query( trans.app.model.UserAddress ).get( trans.security.decode_id( address_id ) ) + if address_obj.user_id != user.id: + return trans.show_error_message( "Invalid address id." ) if params.get( 'edit_address_button', False ): short_desc = util.restore_text( params.get( 'short_desc', '' ) ) name = util.restore_text( params.get( 'name', '' ) ) @@ -1517,10 +1517,10 @@ address_obj.phone = phone trans.sa_session.add( address_obj ) trans.sa_session.flush() - message = 'Address (%s) has been updated.' % address_obj.desc + message = 'Address (%s) has been updated.' % escape( address_obj.desc ) new_kwd = dict( message=message, status=status ) if is_admin: - new_kwd[ 'user_id' ] = trans.security.encode_id( user.id ) + new_kwd[ 'id' ] = trans.security.encode_id( user.id ) return trans.response.send_redirect( web.url_for( controller='user', action='manage_user_info', cntrller=cntrller, @@ -1530,45 +1530,44 @@ cntrller=cntrller, user=user, address_obj=address_obj, - message=message, + message=escape( message ), status=status ) + @web.require_login( "to delete addresses" ) @web.expose - def delete_address( self, trans, cntrller, address_id=None, user_id=None ): + def delete_address( self, trans, cntrller, address_id=None, **kwd ): + return self.__delete_undelete_address( trans, cntrller, 'delete', address_id=address_id, **kwd ) + + @web.require_login( "to undelete addresses" ) + @web.expose + def undelete_address( self, trans, cntrller, address_id=None, **kwd ): + return self.__delete_undelete_address( trans, cntrller, 'undelete', address_id=address_id, **kwd ) + + def __delete_undelete_address( self, trans, cntrller, op, address_id=None, **kwd ): + is_admin = cntrller == 'admin' and trans.user_is_admin() + user_id = kwd.get( 'id', False ) + if is_admin: + if not user_id: + return trans.show_error_message( "You must specify a user to %s an address from." % op ) + user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + else: + user = trans.user try: user_address = trans.sa_session.query( trans.app.model.UserAddress ).get( trans.security.decode_id( address_id ) ) except: - message = 'Invalid address is (%s)' % address_id - status = 'error' + return trans.show_error_message( "Invalid address id." ) if user_address: - user_address.deleted = True + if user_address.user_id != user.id: + return trans.show_error_message( "Invalid address id." ) + user_address.deleted = True if op == 'delete' else False trans.sa_session.add( user_address ) trans.sa_session.flush() - message = 'Address (%s) deleted' % user_address.desc + message = 'Address (%s) %sd' % ( escape( user_address.desc ), op ) status = 'done' return trans.response.send_redirect( web.url_for( controller='user', action='manage_user_info', cntrller=cntrller, - user_id=user_id, - message=message, - status=status ) ) - - @web.expose - def undelete_address( self, trans, cntrller, address_id=None, user_id=None ): - try: - user_address = trans.sa_session.query( trans.app.model.UserAddress ).get( trans.security.decode_id( address_id ) ) - except: - message = 'Invalid address is (%s)' % address_id - status = 'error' - if user_address: - user_address.deleted = False - trans.sa_session.flush() - message = 'Address (%s) undeleted' % user_address.desc - status = 'done' - return trans.response.send_redirect( web.url_for( controller='user', - action='manage_user_info', - cntrller=cntrller, - user_id=user_id, + id=trans.security.encode_id( user.id ), message=message, status=status ) ) @@ -1728,7 +1727,7 @@ @web.require_login() def api_keys( self, trans, cntrller, **kwd ): params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) + message = escape( util.restore_text( params.get( 'message', '' ) ) ) status = params.get( 'status', 'done' ) if params.get( 'new_api_key_button', False ): self.create_api_key( trans, trans.user ) @@ -1740,6 +1739,18 @@ message=message, status=status ) + def __get_redirect_url( self, redirect ): + root_url = url_for( '/', qualified=True ) + redirect_url = '' # always start with redirect_url being empty + # compare urls, to prevent a redirect from pointing (directly) outside of galaxy + # or to enter a logout/login loop + if not util.compare_urls( root_url, redirect, compare_path=False ) or util.compare_urls( url_for( controller='user', action='logout', qualified=True ), redirect ): + log.warning('Redirect URL is outside of Galaxy, will redirect to Galaxy root instead: %s', redirect) + redirect = root_url + elif util.compare_urls( url_for( controller='user', action='logout', qualified=True ), redirect ): + redirect = root_url + return redirect + # ===== Methods for building SelectFields ================================ def __build_user_type_fd_id_select_field( self, trans, selected_value ): # Get all the user information forms diff -r 3808622909a6bb561c46d2ff5a5675f1da589c8b -r 4b6b1d2d740732a982c922b264d2027ed2c90370 lib/galaxy/webapps/galaxy/controllers/userskeys.py --- a/lib/galaxy/webapps/galaxy/controllers/userskeys.py +++ b/lib/galaxy/webapps/galaxy/controllers/userskeys.py @@ -3,12 +3,11 @@ """ import logging -import pprint from galaxy import web from galaxy import util, model from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin -from galaxy.web.framework.helpers import time_ago, grids +from galaxy.web.framework.helpers import time_ago, grids, escape from inspect import getmembers @@ -21,65 +20,46 @@ <p/> """ -class UserOpenIDGrid( grids.Grid ): - use_panels = False - title = "OpenIDs linked to your account" - model_class = model.UserOpenID - template = '/user/openid_manage.mako' - default_filter = { "openid" : "All" } - default_sort_key = "-create_time" - columns = [ - grids.TextColumn( "OpenID URL", key="openid", link=( lambda x: dict( action='openid_auth', login_button="Login", openid_url=x.openid if not x.provider else '', openid_provider=x.provider, auto_associate=True ) ) ), - grids.GridColumn( "Created", key="create_time", format=time_ago ), - ] - operations = [ - grids.GridOperation( "Delete", async_compatible=True ), - ] - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( self.model_class ).filter( self.model_class.user_id == trans.user.id ) +# FIXME: This controller is using unencoded IDs, but I am not going to address +# this now since it is admin-side and should be reimplemented in the API +# anyway. + class User( BaseUIController, UsesFormDefinitionsMixin ): - user_openid_grid = UserOpenIDGrid() - installed_len_files = None - - @web.expose @web.require_login() @web.require_admin def index( self, trans, cntrller, **kwd ): return trans.fill_template( 'webapps/galaxy/user/list_users.mako', action='all_users', cntrller=cntrller ) - - @web.expose @web.require_login() @web.require_admin def admin_api_keys( self, trans, cntrller, uid, **kwd ): params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) + message = escape( util.restore_text( params.get( 'message', '' ) ) ) status = params.get( 'status', 'done' ) uid = params.get('uid', uid) - pprint.pprint(uid) if params.get( 'new_api_key_button', False ): new_key = trans.app.model.APIKeys() new_key.user_id = uid new_key.key = trans.app.security.get_new_guid() trans.sa_session.add( new_key ) trans.sa_session.flush() - message = "Generated a new web API key" + message = "A new web API key has been generated for (%s)" % escape( new_key.user.email ) status = "done" - return trans.fill_template( 'webapps/galaxy/user/ok_admin_api_keys.mako', - cntrller=cntrller, - message=message, - status=status ) - - + return trans.response.send_redirect( web.url_for( controller='userskeys', + action='all_users', + cntrller=cntrller, + message=message, + status=status ) ) + @web.expose @web.require_login() @web.require_admin def all_users( self, trans, cntrller="userskeys", **kwd ): params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) + message = escape( util.restore_text( params.get( 'message', '' ) ) ) status = params.get( 'status', 'done' ) users = [] for user in trans.sa_session.query( trans.app.model.User ) \ diff -r 3808622909a6bb561c46d2ff5a5675f1da589c8b -r 4b6b1d2d740732a982c922b264d2027ed2c90370 templates/user/edit_address.mako --- a/templates/user/edit_address.mako +++ b/templates/user/edit_address.mako @@ -10,17 +10,17 @@ <ul class="manage-table-actions"><li> - <a class="action-button" href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, user_id=trans.security.encode_id( user.id) )}">Manage user information</a> + <a class="action-button" href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, id=trans.security.encode_id( user.id) )}">Manage user information</a></li></ul><div class="toolForm"><div class="toolFormTitle">Edit address</div><div class="toolFormBody"> - <form name="login_info" id="login_info" action="${h.url_for( controller='user', action='edit_address', cntrller=cntrller, address_id=trans.security.encode_id( address_obj.id ), user_id=trans.security.encode_id( user.id ) )}" method="post" > + <form name="login_info" id="login_info" action="${h.url_for( controller='user', action='edit_address', cntrller=cntrller, address_id=trans.security.encode_id( address_obj.id ), id=trans.security.encode_id( user.id ) )}" method="post" ><div class="form-row"><label>Short Description:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="short_desc" value="${address_obj.desc}" size="40"> + <input type="text" name="short_desc" value="${address_obj.desc | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -28,7 +28,7 @@ <div class="form-row"><label>Name:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${address_obj.name}" size="40"> + <input type="text" name="name" value="${address_obj.name | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -36,7 +36,7 @@ <div class="form-row"><label>Institution:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="institution" value="${address_obj.institution}" size="40"> + <input type="text" name="institution" value="${address_obj.institution | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -44,7 +44,7 @@ <div class="form-row"><label>Address:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="address" value="${address_obj.address}" size="40"> + <input type="text" name="address" value="${address_obj.address | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -52,7 +52,7 @@ <div class="form-row"><label>City:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="city" value="${address_obj.city}" size="40"> + <input type="text" name="city" value="${address_obj.city | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -60,7 +60,7 @@ <div class="form-row"><label>State/Province/Region:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="state" value="${address_obj.state}" size="40"> + <input type="text" name="state" value="${address_obj.state | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -68,7 +68,7 @@ <div class="form-row"><label>Postal Code:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="postal_code" value="${address_obj.postal_code}" size="40"> + <input type="text" name="postal_code" value="${address_obj.postal_code | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -76,7 +76,7 @@ <div class="form-row"><label>Country:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="country" value="${address_obj.country}" size="40"> + <input type="text" name="country" value="${address_obj.country | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -84,7 +84,7 @@ <div class="form-row"><label>Phone:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="phone" value="${address_obj.phone}" size="40"> + <input type="text" name="phone" value="${address_obj.phone | h}" size="40"></div><div style="clear: both"></div></div> diff -r 3808622909a6bb561c46d2ff5a5675f1da589c8b -r 4b6b1d2d740732a982c922b264d2027ed2c90370 templates/user/index.mako --- a/templates/user/index.mako +++ b/templates/user/index.mako @@ -1,9 +1,4 @@ <%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif %if trans.user: <h2>${_('User preferences')}</h2> diff -r 3808622909a6bb561c46d2ff5a5675f1da589c8b -r 4b6b1d2d740732a982c922b264d2027ed2c90370 templates/user/info.mako --- a/templates/user/info.mako +++ b/templates/user/info.mako @@ -90,7 +90,7 @@ <div class="toolFormTitle">Login Information</div><div class="form-row"><label>Email address:</label> - <input type="text" id ="email_input" name="email" value="${email}" size="40"/> + <input type="text" id ="email_input" name="email" value="${email | h}" size="40"/><div class="toolParamHelp" style="clear: both;"> If you change your email address you will receive an activation link in the new mailbox and you have to activate your account by visiting it. </div> @@ -99,13 +99,13 @@ <label>Public name:</label> %if t.webapp.name == 'tool_shed': %if user.active_repositories: - <input type="hidden" name="username" value="${username}"/> - ${username} + <input type="hidden" name="username" value="${username | h}"/> + ${username | h} <div class="toolParamHelp" style="clear: both;"> You cannot change your public name after you have created a repository in this tool shed. </div> %else: - <input type="text" name="username" size="40" value="${username}"/> + <input type="text" name="username" size="40" value="${username | h}"/><div class="toolParamHelp" style="clear: both;"> Your public name provides a means of identifying you publicly within this tool shed. Public names must be at least four characters in length and contain only lower-case letters, numbers, @@ -114,7 +114,7 @@ </div> %endif %else: - <input type="text" id="name_input" name="username" size="40" value="${username}"/> + <input type="text" id="name_input" name="username" size="40" value="${username | h}"/><div class="toolParamHelp" style="clear: both;"> Your public name is an optional identifier that will be used to generate addresses for information you share publicly. Public names must be at least four characters in length and contain only lower-case diff -r 3808622909a6bb561c46d2ff5a5675f1da589c8b -r 4b6b1d2d740732a982c922b264d2027ed2c90370 templates/user/new_address.mako --- a/templates/user/new_address.mako +++ b/templates/user/new_address.mako @@ -10,18 +10,18 @@ <ul class="manage-table-actions"><li> - <a class="action-button" href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, user_id=trans.security.encode_id( user.id) )}"> + <a class="action-button" href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, id=trans.security.encode_id( user.id) )}"><span>Manage User Information</span></a></li></ul><div class="toolForm"><div class="toolFormTitle">Add new address</div><div class="toolFormBody"> - <form name="login_info" id="login_info" action="${h.url_for( controller='user', action='new_address', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" > + <form name="login_info" id="login_info" action="${h.url_for( controller='user', action='new_address', cntrller=cntrller, id=trans.security.encode_id( user.id ) )}" method="post" ><div class="form-row"><label>Short Description:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="short_desc" value="${short_desc}" size="40"> + <input type="text" name="short_desc" value="${short_desc | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -29,7 +29,7 @@ <div class="form-row"><label>Name:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${name}" size="40"> + <input type="text" name="name" value="${name | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -37,7 +37,7 @@ <div class="form-row"><label>Institution:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="institution" value="${institution}" size="40"> + <input type="text" name="institution" value="${institution | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -45,7 +45,7 @@ <div class="form-row"><label>Address:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="address" value="${address}" size="40"> + <input type="text" name="address" value="${address | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -53,7 +53,7 @@ <div class="form-row"><label>City:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="city" value="${city}" size="40"> + <input type="text" name="city" value="${city | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -61,7 +61,7 @@ <div class="form-row"><label>State/Province/Region:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="state" value="${state}" size="40"> + <input type="text" name="state" value="${state | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -69,7 +69,7 @@ <div class="form-row"><label>Postal Code:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="postal_code" value="${postal_code}" size="40"> + <input type="text" name="postal_code" value="${postal_code | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -77,7 +77,7 @@ <div class="form-row"><label>Country:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="country" value="${country}" size="40"> + <input type="text" name="country" value="${country | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -85,7 +85,7 @@ <div class="form-row"><label>Phone:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="phone" value="${phone}" size="40"> + <input type="text" name="phone" value="${phone | h}" size="40"></div><div style="clear: both"></div></div> diff -r 3808622909a6bb561c46d2ff5a5675f1da589c8b -r 4b6b1d2d740732a982c922b264d2027ed2c90370 templates/webapps/galaxy/user/list_users.mako --- a/templates/webapps/galaxy/user/list_users.mako +++ b/templates/webapps/galaxy/user/list_users.mako @@ -1,4 +1,5 @@ <%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> %if message: ${render_msg( message, status )} diff -r 3808622909a6bb561c46d2ff5a5675f1da589c8b -r 4b6b1d2d740732a982c922b264d2027ed2c90370 templates/webapps/galaxy/user/manage_info.mako --- a/templates/webapps/galaxy/user/manage_info.mako +++ b/templates/webapps/galaxy/user/manage_info.mako @@ -42,7 +42,7 @@ <p/><div class="toolForm"> - <form name="user_addresses" id="user_addresses" action="${h.url_for( controller='user', action='new_address', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" > + <form name="user_addresses" id="user_addresses" action="${h.url_for( controller='user', action='new_address', cntrller=cntrller, id=trans.security.encode_id( user.id ) )}" method="post" ><div class="toolFormTitle">User Addresses</div><div class="toolFormBody"> %if user.addresses: @@ -53,9 +53,9 @@ <span>|</span> %endif %if show_filter == filter: - <span class="filter"><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, show_filter=filter, user_id=trans.security.encode_id( user.id ) )}"><b>${filter}</b></a></span> + <span class="filter"><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, show_filter=filter, id=trans.security.encode_id( user.id ) )}"><b>${filter}</b></a></span> %else: - <span class="filter"><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, show_filter=filter, user_id=trans.security.encode_id( user.id ) )}">${filter}</a></span> + <span class="filter"><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, show_filter=filter, id=trans.security.encode_id( user.id ) )}">${filter}</a></span> %endif %endfor </div> @@ -73,10 +73,10 @@ <ul class="manage-table-actions"><li> %if not address.deleted: - <a class="action-button" href="${h.url_for( controller='user', action='edit_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Edit</a> - <a class="action-button" href="${h.url_for( controller='user', action='delete_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Delete</a> + <a class="action-button" href="${h.url_for( controller='user', action='edit_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), id=trans.security.encode_id( user.id ) )}">Edit</a> + <a class="action-button" href="${h.url_for( controller='user', action='delete_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), id=trans.security.encode_id( user.id ) )}">Delete</a> %else: - <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Undelete</a> + <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), id=trans.security.encode_id( user.id ) )}">Undelete</a> %endif </li></ul> diff -r 3808622909a6bb561c46d2ff5a5675f1da589c8b -r 4b6b1d2d740732a982c922b264d2027ed2c90370 templates/webapps/galaxy/user/ok_admin_api_keys.mako --- a/templates/webapps/galaxy/user/ok_admin_api_keys.mako +++ /dev/null @@ -1,28 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<br/><br/> -<ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='userskeys', action='all_users', cntrller=cntrller )}">List users API keys</a> - </li> -</ul> - -%if message: - ${render_msg( message, status )} -%endif - - <div> - <div style="clear: both;"> - SUCCESS. A new API key has been generated. - </div> - - - <div style="clear: both;"> - An API key will allow you to access Galaxy via its web - API (documentation forthcoming). Please note that - <strong>this key acts as an alternate means to access - your account, and should be treated with the same care - as your login password</strong>. - </div> - </div> https://bitbucket.org/galaxy/galaxy-central/commits/25d6c1903ece/ Changeset: 25d6c1903ece User: natefoo Date: 2014-12-03 18:41:00+00:00 Summary: Merge next-stable to default. Affected #: 28 files diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -28,7 +28,7 @@ from galaxy.web.base.controller import CreatesApiKeysMixin from galaxy.web.form_builder import CheckboxField from galaxy.web.form_builder import build_select_field -from galaxy.web.framework.helpers import time_ago, grids +from galaxy.web.framework.helpers import time_ago, grids, escape from datetime import datetime, timedelta from galaxy.util import hash_util, biostar @@ -164,7 +164,7 @@ user_openid.provider = openid_provider if trans.user: if user_openid.user and user_openid.user.id != trans.user.id: - message = "The OpenID <strong>%s</strong> is already associated with another Galaxy account, <strong>%s</strong>. Please disassociate it from that account before attempting to associate it with a new account." % ( display_identifier, user_openid.user.email ) + message = "The OpenID <strong>%s</strong> is already associated with another Galaxy account, <strong>%s</strong>. Please disassociate it from that account before attempting to associate it with a new account." % ( escape( display_identifier ), escape( user_openid.user.email ) ) if not trans.user.active and trans.app.config.user_activation_on: # Account activation is ON and the user is INACTIVE. if ( trans.app.config.activation_grace_period != 0 ): # grace period is ON if self.is_outside_grace_period( trans, trans.user.create_time ): # User is outside the grace period. Login is disabled and he will have the activation email resent. @@ -179,23 +179,23 @@ user_openid.session = trans.galaxy_session if not openid_provider_obj.never_associate_with_user: if not auto_associate and ( user_openid.user and user_openid.user.id == trans.user.id ): - message = "The OpenID <strong>%s</strong> is already associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) + message = "The OpenID <strong>%s</strong> is already associated with your Galaxy account, <strong>%s</strong>." % ( escape( display_identifier ), escape( trans.user.email ) ) status = "warning" else: - message = "The OpenID <strong>%s</strong> has been associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) + message = "The OpenID <strong>%s</strong> has been associated with your Galaxy account, <strong>%s</strong>." % ( escape( display_identifier ), escape( trans.user.email ) ) status = "done" user_openid.user = trans.user trans.sa_session.add( user_openid ) trans.sa_session.flush() trans.log_event( "User associated OpenID: %s" % display_identifier ) else: - message = "The OpenID <strong>%s</strong> cannot be used to log into your Galaxy account, but any post authentication actions have been performed." % ( openid_provider_obj.name ) + message = "The OpenID <strong>%s</strong> cannot be used to log into your Galaxy account, but any post authentication actions have been performed." % escape( openid_provider_obj.name ) status = "info" openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) if redirect: - message = '%s<br>Click <a href="%s"><strong>here</strong></a> to return to the page you were previously viewing.' % ( message, redirect ) + message = '%s<br>Click <a href="%s"><strong>here</strong></a> to return to the page you were previously viewing.' % ( message, escape( self.__get_redirect_url( redirect ) ) ) if redirect and status != "error": - return trans.response.send_redirect( redirect ) + return trans.response.send_redirect( self.__get_redirect_url( redirect ) ) return trans.response.send_redirect( url_for( controller='user', action='openid_manage', use_panels=True, @@ -208,6 +208,7 @@ openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) if not redirect: redirect = url_for( '/' ) + redirect = self.__get_redirect_url( redirect ) return trans.response.send_redirect( redirect ) trans.sa_session.add( user_openid ) trans.sa_session.flush() @@ -448,18 +449,9 @@ @web.expose def login( self, trans, refresh_frames=[], **kwd ): - """Handle Galaxy login""" - redirect = kwd.get( 'redirect', trans.request.referer ).strip() - root_url = url_for( '/', qualified=True ) - # Always start with redirect_url being empty. - redirect_url = '' - # Compare urls, to prevent a redirect from pointing (directly) - # outside of galaxy or to enter a logout/login loop. - if not util.compare_urls( root_url, redirect, compare_path=False ) or util.compare_urls( url_for( controller='user', action='logout', qualified=True ), redirect ): - redirect = root_url - if kwd.get( 'noredirect', False ): - # The referrer is explicitly asking not to redirect. - redirect = '' + '''Handle Galaxy Log in''' + redirect = self.__get_redirect_url( kwd.get( 'redirect', trans.request.referer ).strip() ) + redirect_url = '' # always start with redirect_url being empty use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) @@ -910,7 +902,7 @@ username = util.restore_text( params.get( 'username', '' ) ) if not username: username = user.username - message = util.restore_text( params.get( 'message', '' ) ) + message = escape( util.restore_text( params.get( 'message', '' ) ) ) status = params.get( 'status', 'done' ) if trans.webapp.name == 'galaxy': user_type_form_definition = self.__get_user_type_form_definition( trans, user=user, **kwd ) @@ -1146,7 +1138,7 @@ trans.sa_session.add( reset_user ) trans.sa_session.flush() trans.log_event( "User reset password: %s" % email ) - message = "Password has been reset and emailed to: %s. <a href='%s'>Click here</a> to return to the login form." % ( email, web.url_for( controller='user', action='login', noredirect='true' ) ) + message = "Password has been reset and emailed to: %s. <a href='%s'>Click here</a> to return to the login form." % ( escape( email ), web.url_for( controller='user', action='login', noredirect='true' ) ) except Exception, e: status = 'error' message = 'Failed to reset password: %s' % str( e ) @@ -1371,17 +1363,20 @@ # User not logged in, history group must be only public return trans.show_error_message( "You must be logged in to change your default permitted actions." ) + @web.require_login( "to add addresses" ) @web.expose def new_address( self, trans, cntrller, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) is_admin = cntrller == 'admin' and trans.user_is_admin() - user_id = params.get( 'user_id', False ) - if not user_id: - # User must be logged in to create a new address - return trans.show_error_message( "You must be logged in to create a new address." ) - user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + user_id = params.get( 'id', False ) + if is_admin: + if not user_id: + return trans.show_error_message( "You must specify a user to add a new address to." ) + user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + else: + user = trans.user short_desc = util.restore_text( params.get( 'short_desc', '' ) ) name = util.restore_text( params.get( 'name', '' ) ) institution = util.restore_text( params.get( 'institution', '' ) ) @@ -1432,10 +1427,10 @@ phone=phone ) trans.sa_session.add( user_address ) trans.sa_session.flush() - message = 'Address (%s) has been added' % user_address.desc + message = 'Address (%s) has been added' % escape( user_address.desc ) new_kwd = dict( message=message, status=status ) if is_admin: - new_kwd[ 'user_id' ] = trans.security.encode_id( user.id ) + new_kwd[ 'id' ] = trans.security.encode_id( user.id ) return trans.response.send_redirect( web.url_for( controller='user', action='manage_user_info', cntrller=cntrller, @@ -1453,24 +1448,29 @@ postal_code=postal_code, country=country, phone=phone, - message=message, + message=escape(message), status=status ) + @web.require_login( "to edit addresses" ) @web.expose def edit_address( self, trans, cntrller, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) is_admin = cntrller == 'admin' and trans.user_is_admin() - user_id = params.get( 'user_id', False ) - if not user_id: - # User must be logged in to create a new address - return trans.show_error_message( "You must be logged in to create a new address." ) - user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + user_id = params.get( 'id', False ) + if is_admin: + if not user_id: + return trans.show_error_message( "You must specify a user to add a new address to." ) + user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + else: + user = trans.user address_id = params.get( 'address_id', None ) if not address_id: - return trans.show_error_message( "No address id received for editing." ) + return trans.show_error_message( "Invalid address id." ) address_obj = trans.sa_session.query( trans.app.model.UserAddress ).get( trans.security.decode_id( address_id ) ) + if address_obj.user_id != user.id: + return trans.show_error_message( "Invalid address id." ) if params.get( 'edit_address_button', False ): short_desc = util.restore_text( params.get( 'short_desc', '' ) ) name = util.restore_text( params.get( 'name', '' ) ) @@ -1518,10 +1518,10 @@ address_obj.phone = phone trans.sa_session.add( address_obj ) trans.sa_session.flush() - message = 'Address (%s) has been updated.' % address_obj.desc + message = 'Address (%s) has been updated.' % escape( address_obj.desc ) new_kwd = dict( message=message, status=status ) if is_admin: - new_kwd[ 'user_id' ] = trans.security.encode_id( user.id ) + new_kwd[ 'id' ] = trans.security.encode_id( user.id ) return trans.response.send_redirect( web.url_for( controller='user', action='manage_user_info', cntrller=cntrller, @@ -1531,45 +1531,44 @@ cntrller=cntrller, user=user, address_obj=address_obj, - message=message, + message=escape( message ), status=status ) + @web.require_login( "to delete addresses" ) @web.expose - def delete_address( self, trans, cntrller, address_id=None, user_id=None ): + def delete_address( self, trans, cntrller, address_id=None, **kwd ): + return self.__delete_undelete_address( trans, cntrller, 'delete', address_id=address_id, **kwd ) + + @web.require_login( "to undelete addresses" ) + @web.expose + def undelete_address( self, trans, cntrller, address_id=None, **kwd ): + return self.__delete_undelete_address( trans, cntrller, 'undelete', address_id=address_id, **kwd ) + + def __delete_undelete_address( self, trans, cntrller, op, address_id=None, **kwd ): + is_admin = cntrller == 'admin' and trans.user_is_admin() + user_id = kwd.get( 'id', False ) + if is_admin: + if not user_id: + return trans.show_error_message( "You must specify a user to %s an address from." % op ) + user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + else: + user = trans.user try: user_address = trans.sa_session.query( trans.app.model.UserAddress ).get( trans.security.decode_id( address_id ) ) except: - message = 'Invalid address is (%s)' % address_id - status = 'error' + return trans.show_error_message( "Invalid address id." ) if user_address: - user_address.deleted = True + if user_address.user_id != user.id: + return trans.show_error_message( "Invalid address id." ) + user_address.deleted = True if op == 'delete' else False trans.sa_session.add( user_address ) trans.sa_session.flush() - message = 'Address (%s) deleted' % user_address.desc + message = 'Address (%s) %sd' % ( escape( user_address.desc ), op ) status = 'done' return trans.response.send_redirect( web.url_for( controller='user', action='manage_user_info', cntrller=cntrller, - user_id=user_id, - message=message, - status=status ) ) - - @web.expose - def undelete_address( self, trans, cntrller, address_id=None, user_id=None ): - try: - user_address = trans.sa_session.query( trans.app.model.UserAddress ).get( trans.security.decode_id( address_id ) ) - except: - message = 'Invalid address is (%s)' % address_id - status = 'error' - if user_address: - user_address.deleted = False - trans.sa_session.flush() - message = 'Address (%s) undeleted' % user_address.desc - status = 'done' - return trans.response.send_redirect( web.url_for( controller='user', - action='manage_user_info', - cntrller=cntrller, - user_id=user_id, + id=trans.security.encode_id( user.id ), message=message, status=status ) ) @@ -1729,7 +1728,7 @@ @web.require_login() def api_keys( self, trans, cntrller, **kwd ): params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) + message = escape( util.restore_text( params.get( 'message', '' ) ) ) status = params.get( 'status', 'done' ) if params.get( 'new_api_key_button', False ): self.create_api_key( trans, trans.user ) @@ -1741,6 +1740,18 @@ message=message, status=status ) + def __get_redirect_url( self, redirect ): + root_url = url_for( '/', qualified=True ) + redirect_url = '' # always start with redirect_url being empty + # compare urls, to prevent a redirect from pointing (directly) outside of galaxy + # or to enter a logout/login loop + if not util.compare_urls( root_url, redirect, compare_path=False ) or util.compare_urls( url_for( controller='user', action='logout', qualified=True ), redirect ): + log.warning('Redirect URL is outside of Galaxy, will redirect to Galaxy root instead: %s', redirect) + redirect = root_url + elif util.compare_urls( url_for( controller='user', action='logout', qualified=True ), redirect ): + redirect = root_url + return redirect + # ===== Methods for building SelectFields ================================ def __build_user_type_fd_id_select_field( self, trans, selected_value ): # Get all the user information forms diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 lib/galaxy/webapps/galaxy/controllers/userskeys.py --- a/lib/galaxy/webapps/galaxy/controllers/userskeys.py +++ b/lib/galaxy/webapps/galaxy/controllers/userskeys.py @@ -3,12 +3,11 @@ """ import logging -import pprint from galaxy import web from galaxy import util, model from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin -from galaxy.web.framework.helpers import time_ago, grids +from galaxy.web.framework.helpers import time_ago, grids, escape from inspect import getmembers @@ -21,65 +20,46 @@ <p/> """ -class UserOpenIDGrid( grids.Grid ): - use_panels = False - title = "OpenIDs linked to your account" - model_class = model.UserOpenID - template = '/user/openid_manage.mako' - default_filter = { "openid" : "All" } - default_sort_key = "-create_time" - columns = [ - grids.TextColumn( "OpenID URL", key="openid", link=( lambda x: dict( action='openid_auth', login_button="Login", openid_url=x.openid if not x.provider else '', openid_provider=x.provider, auto_associate=True ) ) ), - grids.GridColumn( "Created", key="create_time", format=time_ago ), - ] - operations = [ - grids.GridOperation( "Delete", async_compatible=True ), - ] - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( self.model_class ).filter( self.model_class.user_id == trans.user.id ) +# FIXME: This controller is using unencoded IDs, but I am not going to address +# this now since it is admin-side and should be reimplemented in the API +# anyway. + class User( BaseUIController, UsesFormDefinitionsMixin ): - user_openid_grid = UserOpenIDGrid() - installed_len_files = None - - @web.expose @web.require_login() @web.require_admin def index( self, trans, cntrller, **kwd ): return trans.fill_template( 'webapps/galaxy/user/list_users.mako', action='all_users', cntrller=cntrller ) - - @web.expose @web.require_login() @web.require_admin def admin_api_keys( self, trans, cntrller, uid, **kwd ): params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) + message = escape( util.restore_text( params.get( 'message', '' ) ) ) status = params.get( 'status', 'done' ) uid = params.get('uid', uid) - pprint.pprint(uid) if params.get( 'new_api_key_button', False ): new_key = trans.app.model.APIKeys() new_key.user_id = uid new_key.key = trans.app.security.get_new_guid() trans.sa_session.add( new_key ) trans.sa_session.flush() - message = "Generated a new web API key" + message = "A new web API key has been generated for (%s)" % escape( new_key.user.email ) status = "done" - return trans.fill_template( 'webapps/galaxy/user/ok_admin_api_keys.mako', - cntrller=cntrller, - message=message, - status=status ) - - + return trans.response.send_redirect( web.url_for( controller='userskeys', + action='all_users', + cntrller=cntrller, + message=message, + status=status ) ) + @web.expose @web.require_login() @web.require_admin def all_users( self, trans, cntrller="userskeys", **kwd ): params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) + message = escape( util.restore_text( params.get( 'message', '' ) ) ) status = params.get( 'status', 'done' ) users = [] for user in trans.sa_session.query( trans.app.model.User ) \ diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 lib/tool_shed/util/basic_util.py --- a/lib/tool_shed/util/basic_util.py +++ b/lib/tool_shed/util/basic_util.py @@ -4,7 +4,7 @@ import sys from string import Template -from galaxy.util import unicodify +from galaxy.util import unicodify, nice_size from galaxy import eggs @@ -13,10 +13,10 @@ log = logging.getLogger( __name__ ) -CHUNK_SIZE = 2**20 # 1Mb +CHUNK_SIZE = 2**20 # 1Mb INSTALLATION_LOG = 'INSTALLATION.log' # Set no activity timeout to 20 minutes. -NO_OUTPUT_TIMEOUT = 1200.0 +NO_OUTPUT_TIMEOUT = 3600.0 MAXDIFFSIZE = 8000 MAX_DISPLAY_SIZE = 32768 @@ -48,6 +48,7 @@ RUN install-repository "--url ${tool_shed_url} -o ${repository_owner} --name ${repository_name}" ''' + def evaluate_template( text, install_environment ): """ Substitute variables defined in XML blocks from dependencies file. The value of the received @@ -57,6 +58,7 @@ """ return Template( text ).safe_substitute( get_env_var_values( install_environment ) ) + def get_env_var_values( install_environment ): """ Return a dictionary of values, some of which enable substitution of reserved words for the values. @@ -73,6 +75,7 @@ env_var_dict[ '__is64bit__' ] = sys.maxsize > 2**32 return env_var_dict + def get_file_type_str( changeset_revision, file_type ): if file_type == 'zip': file_type_str = '%s.zip' % changeset_revision @@ -84,6 +87,7 @@ file_type_str = '' return file_type_str + def move_file( current_dir, source, destination, rename_to=None ): source_path = os.path.abspath( os.path.join( current_dir, source ) ) source_file = os.path.basename( source_path ) @@ -98,6 +102,7 @@ os.makedirs( destination_directory ) shutil.move( source_path, destination_path ) + def remove_dir( dir ): """Attempt to remove a directory from disk.""" if dir: @@ -107,18 +112,21 @@ except: pass + def size_string( raw_text, size=MAX_DISPLAY_SIZE ): """Return a subset of a string (up to MAX_DISPLAY_SIZE) translated to a safe string for display in a browser.""" if raw_text and len( raw_text ) >= size: - large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( size ) + large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % nice_size( size ) raw_text = '%s%s' % ( raw_text[ 0:size ], large_str ) return raw_text or '' + def stringify( list ): if list: return ','.join( list ) return '' + def strip_path( fpath ): """Attempt to strip the path from a file name.""" if not fpath: @@ -129,6 +137,7 @@ file_name = fpath return file_name + def to_html_string( text ): """Translates the characters in text to an html string""" if text: diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/admin/forms/create_form.mako --- a/templates/admin/forms/create_form.mako +++ b/templates/admin/forms/create_form.mako @@ -9,7 +9,7 @@ <div class="toolFormTitle">Create a new form definition</div> %for label, input in inputs: <div class="form-row"> - <label>${label}</label> + <label>${label | h}</label> ${input.get_html()} <div style="clear: both"></div></div> diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/admin/forms/edit_form_definition.mako --- a/templates/admin/forms/edit_form_definition.mako +++ b/templates/admin/forms/edit_form_definition.mako @@ -96,14 +96,14 @@ <form id="edit_form_definition" name="edit_form_definition" action="${h.url_for( controller='forms', action='edit_form_definition', id=trans.security.encode_id( form_definition.current.id ) )}" method="post" ><div class="toolForm"> - <div class="toolFormTitle">Edit form definition "${form_definition.name}" (${form_definition.type})</div> + <div class="toolFormTitle">Edit form definition "${form_definition.name | h}" (${form_definition.type | h})</div> %if response_redirect: <input type="hidden" name="response_redirect" value="${response_redirect}" size="40" /> %endif %for label, input in form_details: <div class="form-row"> %if label != 'Type': - <label>${label}</label> + <label>${label | h}</label> %endif <div style="float: left; width: 250px; margin-right: 10px;"> ${input.get_html()} diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/admin/request_type/common.mako --- a/templates/admin/request_type/common.mako +++ b/templates/admin/request_type/common.mako @@ -2,7 +2,7 @@ <div class="repeat-group-item"><div class="form-row"><label>${1+element_count}. State name:</label> - <input type="text" name="state_name_${element_count}" value="${state_name}" size="40"/> + <input type="text" name="state_name_${element_count}" value="${state_name | h}" size="40"/> ## Do not show remove button for the first state %if element_count > 0: <input type="submit" name="remove_state_button" value="Remove state ${1+element_count}"/> @@ -10,7 +10,7 @@ </div><div class="form-row"><label>Description:</label> - <input type="text" name="state_desc_${element_count}" value="${state_desc}" size="40"/> + <input type="text" name="state_desc_${element_count}" value="${state_desc | h}" size="40"/><div class="toolParamHelp" style="clear: both;"> optional </div> diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/admin/request_type/create_request_type.mako --- a/templates/admin/request_type/create_request_type.mako +++ b/templates/admin/request_type/create_request_type.mako @@ -23,7 +23,7 @@ <div class="toolFormTitle">Create a new request type</div> %for rt_info in rt_info_widgets: <div class="form-row"> - <label>${rt_info['label']}</label> + <label>${rt_info['label'] | h}</label><div style="float: left; width: 250px; margin-right: 10px;"> ${rt_info['widget'].get_html()} </div> diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/admin/request_type/edit_request_type.mako --- a/templates/admin/request_type/edit_request_type.mako +++ b/templates/admin/request_type/edit_request_type.mako @@ -32,26 +32,26 @@ <form name="edit_request_type" action="${h.url_for( controller='request_type', action='edit_request_type', id=trans.security.encode_id( request_type.id ) )}" method="post" ><div class="toolForm"> - <div class="toolFormTitle">"Edit ${request_type.name}" request type</div> + <div class="toolFormTitle">"Edit ${request_type.name | h}" request type</div><div class="form-row"><label>Name:</label> - <input type="text" name="name" value="${request_type.name}" size="40"/> + <input type="text" name="name" value="${request_type.name | }" size="40"/><div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - <input type="text" name="desc" value="${request_type.desc}" size="40"/> + <input type="text" name="desc" value="${request_type.desc | h}" size="40"/><div style="clear: both"></div></div><div class="form-row"><label>Sequencing request form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name | h}</a> ## Hidden field needed by the __save_request_type() method <input type="hidden" name="request_form_id" value="${trans.security.encode_id( request_type.request_form_id )}" size="40"/></div><div class="form-row"><label>Sample form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name | h}</a> ## Hidden field needed by the __save_request_type() method <input type="hidden" name="sample_form_id" value="${trans.security.encode_id( request_type.sample_form_id )}" size="40"/></div> @@ -63,11 +63,11 @@ <div class="repeat-group-item"><div class="form-row"><label>${1+element_count}. State name:</label> - <input type="text" name="state_name_${trans.security.encode_id( state.id )}" value="${state.name}" size="40"/> + <input type="text" name="state_name_${trans.security.encode_id( state.id )}" value="${state.name | h}" size="40"/></div><div class="form-row"><label>Description:</label> - <input type="text" name="state_desc_${trans.security.encode_id( state.id )}" value="${state.desc}" size="40"/> + <input type="text" name="state_desc_${trans.security.encode_id( state.id )}" value="${state.desc | h}" size="40"/><div class="toolParamHelp" style="clear: both;"> optional </div> diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/admin/request_type/request_type_permissions.mako --- a/templates/admin/request_type/request_type_permissions.mako +++ b/templates/admin/request_type/request_type_permissions.mako @@ -48,7 +48,7 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Manage access permissions on request type "${request_type.name}"</div> + <div class="toolFormTitle">Manage access permissions on request type "${request_type.name | h}"</div><div class="toolFormBody"><form name="request_type_permissions" id="request_type_permissions" action="${h.url_for( controller='request_type', action='request_type_permissions', id=trans.security.encode_id( request_type.id ) )}" method="post"><div class="form-row"> @@ -65,13 +65,13 @@ in_roles.add( a.role ) out_roles = filter( lambda x: x not in in_roles, all_roles ) %> - ${action.description}<br/><br/> + ${action.description | h}<br/><br/><div style="width: 100%; white-space: nowrap;"><div style="float: left; width: 50%;"> Roles associated:<br/><select name="${action_key}_in" id="${action_key}_in_select" class="in_select" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple> %for role in in_roles: - <option value="${role.id}">${role.name}</option> + <option value="${role.id}">${role.name | h}</option> %endfor </select><br/><div style="width: 98%; text-align: right"><input type="submit" id="${action_key}_remove_button" class="role_remove_button" value=">>"/></div> @@ -80,7 +80,7 @@ Roles not associated:<br/><select name="${action_key}_out" id="${action_key}_out_select" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple> %for role in out_roles: - <option value="${role.id}">${role.name}</option> + <option value="${role.id}">${role.name | h}</option> %endfor </select><br/><input type="submit" id="${action_key}_add_button" class="role_add_button" value="<<"/> diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/admin/request_type/view_request_type.mako --- a/templates/admin/request_type/view_request_type.mako +++ b/templates/admin/request_type/view_request_type.mako @@ -30,24 +30,24 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">"${request_type.name}" request type</div> + <div class="toolFormTitle">"${request_type.name | h}" request type</div><div class="form-row"><label>Name:</label> - ${request_type.name} + ${request_type.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - ${request_type.desc} + ${request_type.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>Sequencing request form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name | h}</a></div><div class="form-row"><label>Sample form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name | h}</a></div></div><p/> @@ -55,8 +55,8 @@ <div class="toolFormTitle">Sample states defined for this request type</div> %for state in request_type.states: <div class="form-row"> - <label>${state.name}</label> - ${state.desc} + <label>${state.name | h}</label> + ${state.desc | h} </div><div style="clear: both"></div> %endfor @@ -67,8 +67,8 @@ %if request_type.external_services: %for index, external_service in enumerate( request_type.external_services ): <div class="form-row"> - <label><a href="${h.url_for( controller='external_service', action='view_external_service', id=trans.security.encode_id( external_service.id ) )}">${external_service.name}</a></label> - ${external_service.get_external_service_type( trans ).name} + <label><a href="${h.url_for( controller='external_service', action='view_external_service', id=trans.security.encode_id( external_service.id ) )}">${external_service.name | h}</a></label> + ${external_service.get_external_service_type( trans ).name | h} </div> %endfor %else: diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/admin/requests/reject.mako --- a/templates/admin/requests/reject.mako +++ b/templates/admin/requests/reject.mako @@ -15,7 +15,7 @@ </ul><div class="toolForm"> - <div class="toolFormTitle">Reject sequencing request "${request.name}"</div> + <div class="toolFormTitle">Reject sequencing request "${request.name | h}"</div><form name="event" action="${h.url_for( controller='requests_admin', action='reject_request', id=trans.security.encode_id( request.id ) )}" method="post" ><div class="form-row"> Rejecting this request will move the request state to <b>Rejected</b>. diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/admin/requests/rename_datasets.mako --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -3,7 +3,7 @@ <% from galaxy.webapps.galaxy.controllers.requests_admin import build_rename_datasets_for_sample_select_field %> -<h3>Rename datasets for Sample "${sample.name}"</h3> +<h3>Rename datasets for Sample "${sample.name | h}"</h3><ul class="manage-table-actions"><li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Browse datasets</a></li> @@ -35,7 +35,7 @@ ${rename_datasets_for_sample_select_field.get_html()} </td><td> - <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id ) }" value="${sample_dataset.name}" size="100"/> + <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id ) }" value="${sample_dataset.name | h}" size="100"/></td><td>${sample_dataset.file_path}</td></tr> diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/admin/requests/view_sample_dataset.mako --- a/templates/admin/requests/view_sample_dataset.mako +++ b/templates/admin/requests/view_sample_dataset.mako @@ -21,19 +21,19 @@ </ul><div class="toolForm"> - <div class="toolFormTitle">"${sample.name}" Dataset</div> + <div class="toolFormTitle">"${sample.name | h}" Dataset</div><div class="toolFormBody"><div class="form-row"><label>Name:</label><div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.name} + ${sample_dataset.name | h} </div><div style="clear: both"></div></div><div class="form-row"><label>External service:</label><div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.external_service.name} (${sample_dataset.external_service.get_external_service_type( trans ).name}) + ${sample_dataset.external_service.name | h} (${sample_dataset.external_service.get_external_service_type( trans ).name | h}) </div><div style="clear: both"></div></div> diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/user/edit_address.mako --- a/templates/user/edit_address.mako +++ b/templates/user/edit_address.mako @@ -10,17 +10,17 @@ <ul class="manage-table-actions"><li> - <a class="action-button" href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, user_id=trans.security.encode_id( user.id) )}">Manage user information</a> + <a class="action-button" href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, id=trans.security.encode_id( user.id) )}">Manage user information</a></li></ul><div class="toolForm"><div class="toolFormTitle">Edit address</div><div class="toolFormBody"> - <form name="login_info" id="login_info" action="${h.url_for( controller='user', action='edit_address', cntrller=cntrller, address_id=trans.security.encode_id( address_obj.id ), user_id=trans.security.encode_id( user.id ) )}" method="post" > + <form name="login_info" id="login_info" action="${h.url_for( controller='user', action='edit_address', cntrller=cntrller, address_id=trans.security.encode_id( address_obj.id ), id=trans.security.encode_id( user.id ) )}" method="post" ><div class="form-row"><label>Short Description:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="short_desc" value="${address_obj.desc}" size="40"> + <input type="text" name="short_desc" value="${address_obj.desc | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -28,7 +28,7 @@ <div class="form-row"><label>Name:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${address_obj.name}" size="40"> + <input type="text" name="name" value="${address_obj.name | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -36,7 +36,7 @@ <div class="form-row"><label>Institution:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="institution" value="${address_obj.institution}" size="40"> + <input type="text" name="institution" value="${address_obj.institution | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -44,7 +44,7 @@ <div class="form-row"><label>Address:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="address" value="${address_obj.address}" size="40"> + <input type="text" name="address" value="${address_obj.address | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -52,7 +52,7 @@ <div class="form-row"><label>City:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="city" value="${address_obj.city}" size="40"> + <input type="text" name="city" value="${address_obj.city | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -60,7 +60,7 @@ <div class="form-row"><label>State/Province/Region:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="state" value="${address_obj.state}" size="40"> + <input type="text" name="state" value="${address_obj.state | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -68,7 +68,7 @@ <div class="form-row"><label>Postal Code:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="postal_code" value="${address_obj.postal_code}" size="40"> + <input type="text" name="postal_code" value="${address_obj.postal_code | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -76,7 +76,7 @@ <div class="form-row"><label>Country:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="country" value="${address_obj.country}" size="40"> + <input type="text" name="country" value="${address_obj.country | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -84,7 +84,7 @@ <div class="form-row"><label>Phone:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="phone" value="${address_obj.phone}" size="40"> + <input type="text" name="phone" value="${address_obj.phone | h}" size="40"></div><div style="clear: both"></div></div> diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/user/index.mako --- a/templates/user/index.mako +++ b/templates/user/index.mako @@ -1,9 +1,4 @@ <%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif %if trans.user: <h2>${_('User preferences')}</h2> diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/user/info.mako --- a/templates/user/info.mako +++ b/templates/user/info.mako @@ -90,7 +90,7 @@ <div class="toolFormTitle">Login Information</div><div class="form-row"><label>Email address:</label> - <input type="text" id ="email_input" name="email" value="${email}" size="40"/> + <input type="text" id ="email_input" name="email" value="${email | h}" size="40"/><div class="toolParamHelp" style="clear: both;"> If you change your email address you will receive an activation link in the new mailbox and you have to activate your account by visiting it. </div> @@ -99,13 +99,13 @@ <label>Public name:</label> %if t.webapp.name == 'tool_shed': %if user.active_repositories: - <input type="hidden" name="username" value="${username}"/> - ${username} + <input type="hidden" name="username" value="${username | h}"/> + ${username | h} <div class="toolParamHelp" style="clear: both;"> You cannot change your public name after you have created a repository in this tool shed. </div> %else: - <input type="text" name="username" size="40" value="${username}"/> + <input type="text" name="username" size="40" value="${username | h}"/><div class="toolParamHelp" style="clear: both;"> Your public name provides a means of identifying you publicly within this tool shed. Public names must be at least four characters in length and contain only lower-case letters, numbers, @@ -114,7 +114,7 @@ </div> %endif %else: - <input type="text" id="name_input" name="username" size="40" value="${username}"/> + <input type="text" id="name_input" name="username" size="40" value="${username | h}"/><div class="toolParamHelp" style="clear: both;"> Your public name is an optional identifier that will be used to generate addresses for information you share publicly. Public names must be at least four characters in length and contain only lower-case diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/user/new_address.mako --- a/templates/user/new_address.mako +++ b/templates/user/new_address.mako @@ -10,18 +10,18 @@ <ul class="manage-table-actions"><li> - <a class="action-button" href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, user_id=trans.security.encode_id( user.id) )}"> + <a class="action-button" href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, id=trans.security.encode_id( user.id) )}"><span>Manage User Information</span></a></li></ul><div class="toolForm"><div class="toolFormTitle">Add new address</div><div class="toolFormBody"> - <form name="login_info" id="login_info" action="${h.url_for( controller='user', action='new_address', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" > + <form name="login_info" id="login_info" action="${h.url_for( controller='user', action='new_address', cntrller=cntrller, id=trans.security.encode_id( user.id ) )}" method="post" ><div class="form-row"><label>Short Description:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="short_desc" value="${short_desc}" size="40"> + <input type="text" name="short_desc" value="${short_desc | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -29,7 +29,7 @@ <div class="form-row"><label>Name:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${name}" size="40"> + <input type="text" name="name" value="${name | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -37,7 +37,7 @@ <div class="form-row"><label>Institution:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="institution" value="${institution}" size="40"> + <input type="text" name="institution" value="${institution | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -45,7 +45,7 @@ <div class="form-row"><label>Address:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="address" value="${address}" size="40"> + <input type="text" name="address" value="${address | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -53,7 +53,7 @@ <div class="form-row"><label>City:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="city" value="${city}" size="40"> + <input type="text" name="city" value="${city | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -61,7 +61,7 @@ <div class="form-row"><label>State/Province/Region:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="state" value="${state}" size="40"> + <input type="text" name="state" value="${state | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -69,7 +69,7 @@ <div class="form-row"><label>Postal Code:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="postal_code" value="${postal_code}" size="40"> + <input type="text" name="postal_code" value="${postal_code | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -77,7 +77,7 @@ <div class="form-row"><label>Country:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="country" value="${country}" size="40"> + <input type="text" name="country" value="${country | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -85,7 +85,7 @@ <div class="form-row"><label>Phone:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="phone" value="${phone}" size="40"> + <input type="text" name="phone" value="${phone | h}" size="40"></div><div style="clear: both"></div></div> diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/webapps/galaxy/requests/common/common.mako --- a/templates/webapps/galaxy/requests/common/common.mako +++ b/templates/webapps/galaxy/requests/common/common.mako @@ -257,18 +257,18 @@ <td valign="top"><input type="checkbox" name=select_sample_${sample.id} id="sample_checkbox" value="true" ${checked_str}/><input type="hidden" name=select_sample_${sample.id} id="sample_checkbox" value="true"/></td> %endif <td valign="top"> - <input type="text" name="sample_${sample_widget_index}_name" value="${sample_widget['name']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_name" value="${sample_widget['name'] | h}" size="10"/><div class="toolParamHelp" style="clear: both;"> - <i>${' (required)' }</i> + <i>(required)</i></div></td> %if display_bar_code: <td valign="top"> %if is_admin and is_submitted: - <input type="text" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code'] | h}" size="10"/> %else: - ${sample_widget['bar_code']} - <input type="hidden" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}"/> + ${sample_widget['bar_code'] | h} + <input type="hidden" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code'] | h}"/> %endif </td> %endif @@ -416,7 +416,7 @@ transferred_dataset_files = [] %><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="sample-${sample.id}-popup"> - <a class="view-info" href="${h.url_for( controller='requests_common', action='view_sample', cntrller=cntrller, id=trans.security.encode_id( sample.id ) )}">${sample.name}</a> + <a class="view-info" href="${h.url_for( controller='requests_common', action='view_sample', cntrller=cntrller, id=trans.security.encode_id( sample.id ) )}">${sample.name | h}</a></div><div popupmenu="sample-${sample.id}-popup"> %if can_select_datasets: @@ -439,11 +439,11 @@ %endif </div> %else: - ${sample_widget_name} + ${sample_widget_name | h} %endif </td> %if display_bar_code: - <td>${sample_widget_bar_code}</td> + <td>${sample_widget_bar_code | h}</td> %endif %if is_unsubmitted: <td>Unsubmitted</td> @@ -451,12 +451,12 @@ <td><a id="sampleState-${sample.id}" href="${h.url_for( controller='requests_common', action='view_sample_history', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${render_sample_state( sample )}</a></td> %endif %if sample_widget_library and library_cntrller is not None: - <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( sample_widget_library.id ) )}">${sample_widget_library.name}</a></td> + <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( sample_widget_library.id ) )}">${sample_widget_library.name | h}</a></td> %else: <td></td> %endif %if sample_widget_folder: - <td>${sample_widget_folder.name}</td> + <td>${sample_widget_folder.name | h}</td> %else: <td></td> %endif @@ -464,11 +464,11 @@ %if trans.user == sample_widget_history.user: <td><a target='_parent' href="${h.url_for( controller='history', action='list', operation="Switch", id=trans.security.encode_id(sample_widget_history.id), use_panels=False )}"> - ${sample_widget_history.name} + ${sample_widget_history.name | h} </a></td> %else: - <td>${sample_widget_history.name}</td> + <td>${sample_widget_history.name | h}</td> %endif %else: <td></td> @@ -477,11 +477,11 @@ %if trans.user == sample_widget_workflow.stored_workflow.user: <td><a target='_parent' href="${h.url_for( controller='workflow', action='editor', id=trans.security.encode_id(sample_widget_workflow.stored_workflow.id) )}"> - ${sample_widget_workflow.name} + ${sample_widget_workflow.name | h} </a></td> %else: - <td>${sample_widget_workflow.name}</td> + <td>${sample_widget_workflow.name | h}</td> %endif %else: <td></td> @@ -519,7 +519,7 @@ <%def name="render_sample_form( index, sample_name, sample_values, fields_dict, display_only )"><tr> - <td>${sample_name}</td> + <td>${sample_name | h}</td> %for field_index, field in fields_dict.items(): <% field_type = field[ 'type' ] @@ -532,17 +532,17 @@ %if field_type == 'WorkflowField': %if str( field_value ) != 'none': <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int( field_value ) ) %> - <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">${workflow.name}</a> + <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">${workflow.name | h}</a> %endif %else: - ${field_value} + ${field_value | h} %endif %else: <i>None</i> %endif %else: %if field_type == 'TextField': - <input type="text" name="sample_${index}_field_${field_index}" value="${field_value}" size="7"/> + <input type="text" name="sample_${index}_field_${field_index}" value="${field_value | h}" size="7"/> %elif field_type == 'SelectField': <select name="sample_${index}_field_${field_index}" last_selected_value="2"> %for option_index, option in enumerate(field[ 'selectlist' ]): @@ -695,7 +695,7 @@ %if is_admin: <span class="expandLink dataset-${dataset}-click"><span class="rowIcon"></span><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="dataset-${dataset.id}-popup"> - <a class="dataset-${encoded_id}-click" href="${h.url_for( controller='requests_admin', action='manage_datasets', operation='view', id=trans.security.encode_id( dataset.id ) )}">${dataset.name}</a> + <a class="dataset-${encoded_id}-click" href="${h.url_for( controller='requests_admin', action='manage_datasets', operation='view', id=trans.security.encode_id( dataset.id ) )}">${dataset.name | h}</a></div></span><div popupmenu="dataset-${dataset.id}-popup"> @@ -704,12 +704,12 @@ %endif </div> %else: - ${dataset.name} + ${dataset.name | h} %endif </td><td>${dataset.size}</td> - <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">${dataset.sample.library.name}</a></td> - <td>${dataset.sample.folder.name}</td> + <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">${dataset.sample.library.name | h}</a></td> + <td>${dataset.sample.folder.name | h}</td><td id="datasetTransferStatus-${encoded_id}">${dataset.status}</td></tr> %endfor @@ -723,7 +723,7 @@ <%def name="render_samples_messages( request, is_admin=False, is_submitted=False, message=None, status=None)"> %if request.is_rejected: <div class='errormessage'> - ${request.last_comment} + ${request.last_comment | h} </div><br/> %endif %if is_admin and is_submitted and request.samples_without_library_destinations: diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/webapps/galaxy/requests/common/create_request.mako --- a/templates/webapps/galaxy/requests/common/create_request.mako +++ b/templates/webapps/galaxy/requests/common/create_request.mako @@ -23,7 +23,7 @@ <div class="toolForm"><div class="toolFormTitle">Create a new sequencing request</div> %if len( request_type_select_field.options ) < 1: - There are no request types available for ${trans.user.email} to create sequencing requests. + There are no request types available for ${trans.user.email | h} to create sequencing requests. %else: <div class="toolFormBody"><form name="create_request" id="create_request" action="${h.url_for( controller='requests_common', action='create_request', cntrller=cntrller )}" method="post" > diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/webapps/galaxy/requests/common/edit_basic_request_info.mako --- a/templates/webapps/galaxy/requests/common/edit_basic_request_info.mako +++ b/templates/webapps/galaxy/requests/common/edit_basic_request_info.mako @@ -31,7 +31,7 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Edit sequencing request "${request.name}"</div> + <div class="toolFormTitle">Edit sequencing request "${request.name | h}"</div><div class="toolFormBody"><form name="edit_basic_request_info" id="edit_basic_request_info" action="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}" method="post" > %for i, field in enumerate( widgets ): @@ -70,11 +70,11 @@ %><div class="form-row"><label>Send to:</label> - <input type="checkbox" name="email_address" value="true" ${email_address}>${request.user.email} (sequencing request owner)<input type="hidden" name="email_address" value="true"> + <input type="checkbox" name="email_address" value="true" ${email_address}>${request.user.email | h} (sequencing request owner)<input type="hidden" name="email_address" value="true"></div><div class="form-row"><label>Additional email addresses:</label> - <textarea name="additional_email_addresses" rows="3" cols="40">${emails}</textarea> + <textarea name="additional_email_addresses" rows="3" cols="40">${emails | h}</textarea><div class="toolParamHelp" style="clear: both;"> Enter one email address per line </div> diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/webapps/galaxy/requests/common/find_samples.mako --- a/templates/webapps/galaxy/requests/common/find_samples.mako +++ b/templates/webapps/galaxy/requests/common/find_samples.mako @@ -72,7 +72,7 @@ %if samples: %for sample in samples: <div class="form-row"> - Sample: <b>${sample.name}</b> | Barcode: ${sample.bar_code}<br/> + Sample: <b>${sample.name | h}</b> | Barcode: ${sample.bar_code | h}<br/> %if sample.request.is_new or not sample.state: State: Unsubmitted<br/> %else: @@ -85,10 +85,10 @@ %> Datasets: <a href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, external_service_id=trans.security.encode_id( external_service.id ), sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a><br/> %if is_admin: - <i>User: ${sample.request.user.email}</i> + <i>User: ${sample.request.user.email | h}</i> %endif <div class="toolParamHelp" style="clear: both;"> - <a href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Sequencing request: ${sample.request.name} | Type: ${sample.request.type.name} | State: ${sample.request.state}</a> + <a href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Sequencing request: ${sample.request.name | h} | Type: ${sample.request.type.name} | State: ${sample.request.state}</a></div></div><br/> diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/webapps/galaxy/requests/common/view_request.mako --- a/templates/webapps/galaxy/requests/common/view_request.mako +++ b/templates/webapps/galaxy/requests/common/view_request.mako @@ -58,7 +58,7 @@ ${render_samples_messages(request, is_admin, is_submitted, message, status)} <div class="toolForm"> - <div class="toolFormTitle">Sequencing request "${request.name}"</div> + <div class="toolFormTitle">Sequencing request "${request.name | h}"</div><div class="toolFormBody"><div class="form-row"><label>Current state:</label> @@ -67,12 +67,12 @@ </div><div class="form-row"><label>Description:</label> - ${request.desc} + ${request.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>User:</label> - ${request.user.email} + ${request.user.email | h} <div style="clear: both"></div></div><div class="form-row"> @@ -94,7 +94,7 @@ %><div class="form-row"><label>${field_label}:</label> - ${field_value} + ${field_value | h} </div><div style="clear: both"></div> %endfor @@ -116,7 +116,7 @@ else: emails = '' %> - ${emails} + ${emails | h} <div style="clear: both"></div></div><div class="form-row"> diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/webapps/galaxy/requests/common/view_request_history.mako --- a/templates/webapps/galaxy/requests/common/view_request_history.mako +++ b/templates/webapps/galaxy/requests/common/view_request_history.mako @@ -36,7 +36,7 @@ ${render_msg( message, status )} %endif -<h3>History of sequencing request "${request.name}"</h3> +<h3>History of sequencing request "${request.name | h}"</h3><div class="toolForm"><table class="grid"> @@ -52,7 +52,7 @@ <tr><td><b>${event.state}</b></td><td>${time_ago( event.update_time )}</td> - <td>${event.comment}</td> + <td>${event.comment | h}</td></tr> %endfor </tbody> diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/webapps/galaxy/requests/common/view_sample.mako --- a/templates/webapps/galaxy/requests/common/view_sample.mako +++ b/templates/webapps/galaxy/requests/common/view_sample.mako @@ -6,7 +6,7 @@ %if external_service: <p><div class="toolForm"> - <div class="toolFormTitle">Available External Service Actions for ${sample.name} at ${external_service.name}</div> + <div class="toolFormTitle">Available External Service Actions for ${sample.name | h} at ${external_service.name | h}</div><div class="toolFormBody"><div class="toolMenu"> %for item in external_service.actions: @@ -25,7 +25,7 @@ <div class="form-row"><div class="toolSectionList"><div class="toolSectionTitle"> - <span>${external_service_group.label}</span> + <span>${external_service_group.label | h}</span></div><div class="toolSectionBody"><div class="toolSectionBg"> @@ -54,7 +54,7 @@ target = 'galaxy_main' %><div class="toolTitle"> - <a href="${external_service_action.get_action_access_link( trans )}" target="${target}">${external_service_action.label}</a> + <a href="${external_service_action.get_action_access_link( trans )}" target="${target}">${external_service_action.label | h}</a></div></%def> @@ -75,38 +75,38 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Sample "${sample.name}"</div> + <div class="toolFormTitle">Sample "${sample.name | h}"</div><div class="toolFormBody"><div class="form-row"><label>Name:</label> - ${sample.name} + ${sample.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - ${sample.desc} + ${sample.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>Barcode:</label> - ${sample.bar_code} + ${sample.bar_code | h} <div style="clear: both"></div></div> %if sample.library: <div class="form-row"><label>Library:</label> - ${sample.library.name} + ${sample.library.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Folder:</label> - ${sample.folder.name} + ${sample.folder.name | h} <div style="clear: both"></div></div> %endif <div class="form-row"><label>Request:</label> - ${sample.request.name} + ${sample.request.name | h} <div style="clear: both"></div></div></div> diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/webapps/galaxy/requests/common/view_sample_history.mako --- a/templates/webapps/galaxy/requests/common/view_sample_history.mako +++ b/templates/webapps/galaxy/requests/common/view_sample_history.mako @@ -12,7 +12,7 @@ ${render_msg( message, status )} %endif -<h3>History of sample "${sample.name}"</h3> +<h3>History of sample "${sample.name | h}"</h3><div class="toolForm"><table class="grid"> @@ -27,10 +27,10 @@ <tbody> %for event in sample.events: <tr> - <td><b>${event.state.name}</b></td> - <td>${event.state.desc}</td> + <td><b>${event.state.name | h}</b></td> + <td>${event.state.desc | h}</td><td>${time_ago( event.update_time )}</td> - <td>${event.comment}</td> + <td>${event.comment | h}</td></tr> %endfor </tbody> diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/webapps/galaxy/user/list_users.mako --- a/templates/webapps/galaxy/user/list_users.mako +++ b/templates/webapps/galaxy/user/list_users.mako @@ -1,4 +1,5 @@ <%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> %if message: ${render_msg( message, status )} diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/webapps/galaxy/user/manage_info.mako --- a/templates/webapps/galaxy/user/manage_info.mako +++ b/templates/webapps/galaxy/user/manage_info.mako @@ -42,7 +42,7 @@ <p/><div class="toolForm"> - <form name="user_addresses" id="user_addresses" action="${h.url_for( controller='user', action='new_address', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" > + <form name="user_addresses" id="user_addresses" action="${h.url_for( controller='user', action='new_address', cntrller=cntrller, id=trans.security.encode_id( user.id ) )}" method="post" ><div class="toolFormTitle">User Addresses</div><div class="toolFormBody"> %if user.addresses: @@ -53,9 +53,9 @@ <span>|</span> %endif %if show_filter == filter: - <span class="filter"><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, show_filter=filter, user_id=trans.security.encode_id( user.id ) )}"><b>${filter}</b></a></span> + <span class="filter"><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, show_filter=filter, id=trans.security.encode_id( user.id ) )}"><b>${filter}</b></a></span> %else: - <span class="filter"><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, show_filter=filter, user_id=trans.security.encode_id( user.id ) )}">${filter}</a></span> + <span class="filter"><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, show_filter=filter, id=trans.security.encode_id( user.id ) )}">${filter}</a></span> %endif %endfor </div> @@ -73,10 +73,10 @@ <ul class="manage-table-actions"><li> %if not address.deleted: - <a class="action-button" href="${h.url_for( controller='user', action='edit_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Edit</a> - <a class="action-button" href="${h.url_for( controller='user', action='delete_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Delete</a> + <a class="action-button" href="${h.url_for( controller='user', action='edit_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), id=trans.security.encode_id( user.id ) )}">Edit</a> + <a class="action-button" href="${h.url_for( controller='user', action='delete_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), id=trans.security.encode_id( user.id ) )}">Delete</a> %else: - <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Undelete</a> + <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), id=trans.security.encode_id( user.id ) )}">Undelete</a> %endif </li></ul> diff -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 templates/webapps/galaxy/user/ok_admin_api_keys.mako --- a/templates/webapps/galaxy/user/ok_admin_api_keys.mako +++ /dev/null @@ -1,28 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<br/><br/> -<ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='userskeys', action='all_users', cntrller=cntrller )}">List users API keys</a> - </li> -</ul> - -%if message: - ${render_msg( message, status )} -%endif - - <div> - <div style="clear: both;"> - SUCCESS. A new API key has been generated. - </div> - - - <div style="clear: both;"> - An API key will allow you to access Galaxy via its web - API (documentation forthcoming). Please note that - <strong>this key acts as an alternate means to access - your account, and should be treated with the same care - as your login password</strong>. - </div> - </div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 03 Dec '14

03 Dec '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b0d60614d255/ Changeset: b0d60614d255 Branch: stable User: natefoo Date: 2014-12-02 15:42:44+00:00 Summary: Prevent XSS in various user-related templates (OpenID, password reset, manage user, user addresses, admin management of user API keys). Also fix places where the redirect URL used by OpenID methods could point to a site external to Galaxy. Affected #: 7 files diff -r 26aab19109ce7956f29bfc4f5877e6950c0fae56 -r b0d60614d255354f0be66a0ae2434165f5406cb8 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -28,7 +28,7 @@ from galaxy.web.base.controller import CreatesApiKeysMixin from galaxy.web.form_builder import CheckboxField from galaxy.web.form_builder import build_select_field -from galaxy.web.framework.helpers import time_ago, grids +from galaxy.web.framework.helpers import time_ago, grids, escape from datetime import datetime, timedelta from galaxy.util import hash_util, biostar @@ -164,7 +164,7 @@ user_openid.provider = openid_provider if trans.user: if user_openid.user and user_openid.user.id != trans.user.id: - message = "The OpenID <strong>%s</strong> is already associated with another Galaxy account, <strong>%s</strong>. Please disassociate it from that account before attempting to associate it with a new account." % ( display_identifier, user_openid.user.email ) + message = escape( "The OpenID <strong>%s</strong> is already associated with another Galaxy account, <strong>%s</strong>. Please disassociate it from that account before attempting to associate it with a new account." % ( display_identifier, user_openid.user.email ) ) if not trans.user.active and trans.app.config.user_activation_on: # Account activation is ON and the user is INACTIVE. if ( trans.app.config.activation_grace_period != 0 ): # grace period is ON if self.is_outside_grace_period( trans, trans.user.create_time ): # User is outside the grace period. Login is disabled and he will have the activation email resent. @@ -179,23 +179,23 @@ user_openid.session = trans.galaxy_session if not openid_provider_obj.never_associate_with_user: if not auto_associate and ( user_openid.user and user_openid.user.id == trans.user.id ): - message = "The OpenID <strong>%s</strong> is already associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) + message = escape( "The OpenID <strong>%s</strong> is already associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) ) status = "warning" else: - message = "The OpenID <strong>%s</strong> has been associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) + message = escape( "The OpenID <strong>%s</strong> has been associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) ) status = "done" user_openid.user = trans.user trans.sa_session.add( user_openid ) trans.sa_session.flush() trans.log_event( "User associated OpenID: %s" % display_identifier ) else: - message = "The OpenID <strong>%s</strong> cannot be used to log into your Galaxy account, but any post authentication actions have been performed." % ( openid_provider_obj.name ) + message = escape( "The OpenID <strong>%s</strong> cannot be used to log into your Galaxy account, but any post authentication actions have been performed." % ( openid_provider_obj.name ) ) status = "info" openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) if redirect: - message = '%s<br>Click <a href="%s"><strong>here</strong></a> to return to the page you were previously viewing.' % ( message, redirect ) + message = '%s<br>Click <a href="%s"><strong>here</strong></a> to return to the page you were previously viewing.' % ( message, escape( self.__get_redirect_url( redirect ) ) ) if redirect and status != "error": - return trans.response.send_redirect( redirect ) + return trans.response.send_redirect( self.__get_redirect_url( redirect ) ) return trans.response.send_redirect( url_for( controller='user', action='openid_manage', use_panels=True, @@ -208,6 +208,7 @@ openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) if not redirect: redirect = url_for( '/' ) + redirect = self.__get_redirect_url( redirect ) return trans.response.send_redirect( redirect ) trans.sa_session.add( user_openid ) trans.sa_session.flush() @@ -449,13 +450,7 @@ @web.expose def login( self, trans, refresh_frames=[], **kwd ): '''Handle Galaxy Log in''' - redirect = kwd.get( 'redirect', trans.request.referer ).strip() - root_url = url_for( '/', qualified=True ) - redirect_url = '' # always start with redirect_url being empty - # compare urls, to prevent a redirect from pointing (directly) outside of galaxy - # or to enter a logout/login loop - if not util.compare_urls( root_url, redirect, compare_path=False ) or util.compare_urls( url_for( controller='user', action='logout', qualified=True ), redirect ): - redirect = root_url + redirect = self.__get_redirect_url( kwd.get( 'redirect', trans.request.referer ).strip() ) use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) @@ -908,7 +903,7 @@ username = util.restore_text( params.get( 'username', '' ) ) if not username: username = user.username - message = util.restore_text( params.get( 'message', '' ) ) + message = escape( util.restore_text( params.get( 'message', '' ) ) ) status = params.get( 'status', 'done' ) if trans.webapp.name == 'galaxy': user_type_form_definition = self.__get_user_type_form_definition( trans, user=user, **kwd ) @@ -1096,7 +1091,7 @@ if trans.app.config.smtp_server is None: return trans.show_error_message( "Mail is not configured for this Galaxy instance. Please contact your local Galaxy administrator." ) message = util.sanitize_text(util.restore_text( kwd.get( 'message', '' ) )) - status = 'done' + status = kwd.get( 'status', 'done' ) if kwd.get( 'reset_password_button', False ): reset_user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first() user = trans.get_user() @@ -1123,7 +1118,7 @@ trans.sa_session.add( reset_user ) trans.sa_session.flush() trans.log_event( "User reset password: %s" % email ) - message = "Password has been reset and emailed to: %s. <a href='%s'>Click here</a> to return to the login form." % ( email, web.url_for( controller='user', action='login' ) ) + message = "Password has been reset and emailed to: %s. <a href='%s'>Click here</a> to return to the login form." % ( escape( email ), web.url_for( controller='user', action='login' ) ) except Exception, e: message = 'Failed to reset password: %s' % str( e ) status = 'error' @@ -1439,7 +1434,7 @@ @web.expose def edit_address( self, trans, cntrller, **kwd ): params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) + message = escape( util.restore_text( params.get( 'message', '' ) ) ) status = params.get( 'status', 'done' ) is_admin = cntrller == 'admin' and trans.user_is_admin() user_id = params.get( 'user_id', False ) @@ -1709,7 +1704,7 @@ @web.require_login() def api_keys( self, trans, cntrller, **kwd ): params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) + message = escape( util.restore_text( params.get( 'message', '' ) ) ) status = params.get( 'status', 'done' ) if params.get( 'new_api_key_button', False ): self.create_api_key( trans, trans.user ) @@ -1721,6 +1716,18 @@ message=message, status=status ) + def __get_redirect_url( self, redirect ): + root_url = url_for( '/', qualified=True ) + redirect_url = '' # always start with redirect_url being empty + # compare urls, to prevent a redirect from pointing (directly) outside of galaxy + # or to enter a logout/login loop + if not util.compare_urls( root_url, redirect, compare_path=False ) or util.compare_urls( url_for( controller='user', action='logout', qualified=True ), redirect ): + log.warning('Redirect URL is outside of Galaxy, will redirect to Galaxy root instead: %s', redirect) + redirect = root_url + elif util.compare_urls( url_for( controller='user', action='logout', qualified=True ), redirect ): + redirect = root_url + return redirect + # ===== Methods for building SelectFields ================================ def __build_user_type_fd_id_select_field( self, trans, selected_value ): # Get all the user information forms diff -r 26aab19109ce7956f29bfc4f5877e6950c0fae56 -r b0d60614d255354f0be66a0ae2434165f5406cb8 lib/galaxy/webapps/galaxy/controllers/userskeys.py --- a/lib/galaxy/webapps/galaxy/controllers/userskeys.py +++ b/lib/galaxy/webapps/galaxy/controllers/userskeys.py @@ -3,12 +3,11 @@ """ import logging -import pprint from galaxy import web from galaxy import util, model from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin -from galaxy.web.framework.helpers import time_ago, grids +from galaxy.web.framework.helpers import time_ago, grids, escape from inspect import getmembers @@ -21,65 +20,46 @@ <p/> """ -class UserOpenIDGrid( grids.Grid ): - use_panels = False - title = "OpenIDs linked to your account" - model_class = model.UserOpenID - template = '/user/openid_manage.mako' - default_filter = { "openid" : "All" } - default_sort_key = "-create_time" - columns = [ - grids.TextColumn( "OpenID URL", key="openid", link=( lambda x: dict( action='openid_auth', login_button="Login", openid_url=x.openid if not x.provider else '', openid_provider=x.provider, auto_associate=True ) ) ), - grids.GridColumn( "Created", key="create_time", format=time_ago ), - ] - operations = [ - grids.GridOperation( "Delete", async_compatible=True ), - ] - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( self.model_class ).filter( self.model_class.user_id == trans.user.id ) +# FIXME: This controller is using unencoded IDs, but I am not going to address +# this now since it is admin-side and should be reimplemented in the API +# anyway. + class User( BaseUIController, UsesFormDefinitionsMixin ): - user_openid_grid = UserOpenIDGrid() - installed_len_files = None - - @web.expose @web.require_login() @web.require_admin def index( self, trans, cntrller, **kwd ): return trans.fill_template( 'webapps/galaxy/user/list_users.mako', action='all_users', cntrller=cntrller ) - - @web.expose @web.require_login() @web.require_admin def admin_api_keys( self, trans, cntrller, uid, **kwd ): params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) + message = escape( util.restore_text( params.get( 'message', '' ) ) ) status = params.get( 'status', 'done' ) uid = params.get('uid', uid) - pprint.pprint(uid) if params.get( 'new_api_key_button', False ): new_key = trans.app.model.APIKeys() new_key.user_id = uid new_key.key = trans.app.security.get_new_guid() trans.sa_session.add( new_key ) trans.sa_session.flush() - message = "Generated a new web API key" + message = "A new web API key has been generated for (%s)" % escape( new_key.user.email ) status = "done" - return trans.fill_template( 'webapps/galaxy/user/ok_admin_api_keys.mako', - cntrller=cntrller, - message=message, - status=status ) - - + return trans.response.send_redirect( web.url_for( controller='userskeys', + action='all_users', + cntrller=cntrller, + message=message, + status=status ) ) + @web.expose @web.require_login() @web.require_admin def all_users( self, trans, cntrller="userskeys", **kwd ): params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) + message = escape( util.restore_text( params.get( 'message', '' ) ) ) status = params.get( 'status', 'done' ) users = [] for user in trans.sa_session.query( trans.app.model.User ) \ diff -r 26aab19109ce7956f29bfc4f5877e6950c0fae56 -r b0d60614d255354f0be66a0ae2434165f5406cb8 templates/user/edit_address.mako --- a/templates/user/edit_address.mako +++ b/templates/user/edit_address.mako @@ -20,7 +20,7 @@ <div class="form-row"><label>Short Description:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="short_desc" value="${address_obj.desc}" size="40"> + <input type="text" name="short_desc" value="${address_obj.desc | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -28,7 +28,7 @@ <div class="form-row"><label>Name:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${address_obj.name}" size="40"> + <input type="text" name="name" value="${address_obj.name | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -36,7 +36,7 @@ <div class="form-row"><label>Institution:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="institution" value="${address_obj.institution}" size="40"> + <input type="text" name="institution" value="${address_obj.institution | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -44,7 +44,7 @@ <div class="form-row"><label>Address:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="address" value="${address_obj.address}" size="40"> + <input type="text" name="address" value="${address_obj.address | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -52,7 +52,7 @@ <div class="form-row"><label>City:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="city" value="${address_obj.city}" size="40"> + <input type="text" name="city" value="${address_obj.city | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -60,7 +60,7 @@ <div class="form-row"><label>State/Province/Region:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="state" value="${address_obj.state}" size="40"> + <input type="text" name="state" value="${address_obj.state | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -68,7 +68,7 @@ <div class="form-row"><label>Postal Code:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="postal_code" value="${address_obj.postal_code}" size="40"> + <input type="text" name="postal_code" value="${address_obj.postal_code | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -76,7 +76,7 @@ <div class="form-row"><label>Country:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="country" value="${address_obj.country}" size="40"> + <input type="text" name="country" value="${address_obj.country | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -84,7 +84,7 @@ <div class="form-row"><label>Phone:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="phone" value="${address_obj.phone}" size="40"> + <input type="text" name="phone" value="${address_obj.phone | h}" size="40"></div><div style="clear: both"></div></div> diff -r 26aab19109ce7956f29bfc4f5877e6950c0fae56 -r b0d60614d255354f0be66a0ae2434165f5406cb8 templates/user/index.mako --- a/templates/user/index.mako +++ b/templates/user/index.mako @@ -1,9 +1,4 @@ <%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif %if trans.user: <h2>${_('User preferences')}</h2> diff -r 26aab19109ce7956f29bfc4f5877e6950c0fae56 -r b0d60614d255354f0be66a0ae2434165f5406cb8 templates/user/info.mako --- a/templates/user/info.mako +++ b/templates/user/info.mako @@ -16,19 +16,19 @@ <div class="toolFormTitle">Login Information</div><div class="form-row"><label>Email address:</label> - <input type="text" name="email" value="${email}" size="40"/> + <input type="text" name="email" value="${email | h}" size="40"/></div><div class="form-row"><label>Public name:</label> %if t.webapp.name == 'tool_shed': %if user.active_repositories: - <input type="hidden" name="username" value="${username}"/> - ${username} + <input type="hidden" name="username" value="${username | h}"/> + ${username | h} <div class="toolParamHelp" style="clear: both;"> You cannot change your public name after you have created a repository in this tool shed. </div> %else: - <input type="text" name="username" size="40" value="${username}"/> + <input type="text" name="username" size="40" value="${username | h}"/><div class="toolParamHelp" style="clear: both;"> Your public name provides a means of identifying you publicly within this tool shed. Public names must be at least four characters in length and contain only lower-case letters, numbers, @@ -37,7 +37,7 @@ </div> %endif %else: - <input type="text" name="username" size="40" value="${username}"/> + <input type="text" name="username" size="40" value="${username | h}"/><div class="toolParamHelp" style="clear: both;"> Your public name is an optional identifier that will be used to generate addresses for information you share publicly. Public names must be at least four characters in length and contain only lower-case diff -r 26aab19109ce7956f29bfc4f5877e6950c0fae56 -r b0d60614d255354f0be66a0ae2434165f5406cb8 templates/webapps/galaxy/user/list_users.mako --- a/templates/webapps/galaxy/user/list_users.mako +++ b/templates/webapps/galaxy/user/list_users.mako @@ -1,4 +1,5 @@ <%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> %if message: ${render_msg( message, status )} diff -r 26aab19109ce7956f29bfc4f5877e6950c0fae56 -r b0d60614d255354f0be66a0ae2434165f5406cb8 templates/webapps/galaxy/user/ok_admin_api_keys.mako --- a/templates/webapps/galaxy/user/ok_admin_api_keys.mako +++ /dev/null @@ -1,28 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<br/><br/> -<ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='userskeys', action='all_users', cntrller=cntrller )}">List users API keys</a> - </li> -</ul> - -%if message: - ${render_msg( message, status )} -%endif - - <div> - <div style="clear: both;"> - SUCCESS. A new API key has been generated. - </div> - - - <div style="clear: both;"> - An API key will allow you to access Galaxy via its web - API (documentation forthcoming). Please note that - <strong>this key acts as an alternate means to access - your account, and should be treated with the same care - as your login password</strong>. - </div> - </div> https://bitbucket.org/galaxy/galaxy-central/commits/eb0a5dcc9d63/ Changeset: eb0a5dcc9d63 Branch: stable User: natefoo Date: 2014-12-02 17:06:24+00:00 Summary: Fix various bugs and security (XSS and other) issues with user address handling. Affected #: 4 files diff -r b0d60614d255354f0be66a0ae2434165f5406cb8 -r eb0a5dcc9d633fa8122cca5525a6beb1d9940e62 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -451,6 +451,7 @@ def login( self, trans, refresh_frames=[], **kwd ): '''Handle Galaxy Log in''' redirect = self.__get_redirect_url( kwd.get( 'redirect', trans.request.referer ).strip() ) + redirect_url = '' # always start with redirect_url being empty use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) @@ -1346,17 +1347,20 @@ # User not logged in, history group must be only public return trans.show_error_message( "You must be logged in to change your default permitted actions." ) + @web.require_login( "to add addresses" ) @web.expose def new_address( self, trans, cntrller, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) is_admin = cntrller == 'admin' and trans.user_is_admin() - user_id = params.get( 'user_id', False ) - if not user_id: - # User must be logged in to create a new address - return trans.show_error_message( "You must be logged in to create a new address." ) - user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + user_id = params.get( 'id', False ) + if is_admin: + if not user_id: + return trans.show_error_message( "You must specify a user to add a new address to." ) + user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + else: + user = trans.user short_desc = util.restore_text( params.get( 'short_desc', '' ) ) name = util.restore_text( params.get( 'name', '' ) ) institution = util.restore_text( params.get( 'institution', '' ) ) @@ -1407,10 +1411,10 @@ phone=phone ) trans.sa_session.add( user_address ) trans.sa_session.flush() - message = 'Address (%s) has been added' % user_address.desc + message = 'Address (%s) has been added' % escape( user_address.desc ) new_kwd = dict( message=message, status=status ) if is_admin: - new_kwd[ 'user_id' ] = trans.security.encode_id( user.id ) + new_kwd[ 'id' ] = trans.security.encode_id( user.id ) return trans.response.send_redirect( web.url_for( controller='user', action='manage_user_info', cntrller=cntrller, @@ -1428,24 +1432,29 @@ postal_code=postal_code, country=country, phone=phone, - message=message, + message=escape(message), status=status ) + @web.require_login( "to edit addresses" ) @web.expose def edit_address( self, trans, cntrller, **kwd ): params = util.Params( kwd ) - message = escape( util.restore_text( params.get( 'message', '' ) ) ) + message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) is_admin = cntrller == 'admin' and trans.user_is_admin() - user_id = params.get( 'user_id', False ) - if not user_id: - # User must be logged in to create a new address - return trans.show_error_message( "You must be logged in to create a new address." ) - user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + user_id = params.get( 'id', False ) + if is_admin: + if not user_id: + return trans.show_error_message( "You must specify a user to add a new address to." ) + user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + else: + user = trans.user address_id = params.get( 'address_id', None ) if not address_id: - return trans.show_error_message( "No address id received for editing." ) + return trans.show_error_message( "Invalid address id." ) address_obj = trans.sa_session.query( trans.app.model.UserAddress ).get( trans.security.decode_id( address_id ) ) + if address_obj.user_id != user.id: + return trans.show_error_message( "Invalid address id." ) if params.get( 'edit_address_button', False ): short_desc = util.restore_text( params.get( 'short_desc', '' ) ) name = util.restore_text( params.get( 'name', '' ) ) @@ -1493,10 +1502,10 @@ address_obj.phone = phone trans.sa_session.add( address_obj ) trans.sa_session.flush() - message = 'Address (%s) has been updated.' % address_obj.desc + message = 'Address (%s) has been updated.' % escape( address_obj.desc ) new_kwd = dict( message=message, status=status ) if is_admin: - new_kwd[ 'user_id' ] = trans.security.encode_id( user.id ) + new_kwd[ 'id' ] = trans.security.encode_id( user.id ) return trans.response.send_redirect( web.url_for( controller='user', action='manage_user_info', cntrller=cntrller, @@ -1506,45 +1515,44 @@ cntrller=cntrller, user=user, address_obj=address_obj, - message=message, + message=escape( message ), status=status ) + @web.require_login( "to delete addresses" ) @web.expose - def delete_address( self, trans, cntrller, address_id=None, user_id=None ): + def delete_address( self, trans, cntrller, address_id=None, **kwd ): + return self.__delete_undelete_address( trans, cntrller, 'delete', address_id=address_id, **kwd ) + + @web.require_login( "to undelete addresses" ) + @web.expose + def undelete_address( self, trans, cntrller, address_id=None, **kwd ): + return self.__delete_undelete_address( trans, cntrller, 'undelete', address_id=address_id, **kwd ) + + def __delete_undelete_address( self, trans, cntrller, op, address_id=None, **kwd ): + is_admin = cntrller == 'admin' and trans.user_is_admin() + user_id = kwd.get( 'id', False ) + if is_admin: + if not user_id: + return trans.show_error_message( "You must specify a user to %s an address from." % op ) + user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + else: + user = trans.user try: user_address = trans.sa_session.query( trans.app.model.UserAddress ).get( trans.security.decode_id( address_id ) ) except: - message = 'Invalid address is (%s)' % address_id - status = 'error' + return trans.show_error_message( "Invalid address id." ) if user_address: - user_address.deleted = True + if user_address.user_id != user.id: + return trans.show_error_message( "Invalid address id." ) + user_address.deleted = True if op == 'delete' else False trans.sa_session.add( user_address ) trans.sa_session.flush() - message = 'Address (%s) deleted' % user_address.desc + message = 'Address (%s) %sd' % ( escape( user_address.desc ), op ) status = 'done' return trans.response.send_redirect( web.url_for( controller='user', action='manage_user_info', cntrller=cntrller, - user_id=user_id, - message=message, - status=status ) ) - - @web.expose - def undelete_address( self, trans, cntrller, address_id=None, user_id=None ): - try: - user_address = trans.sa_session.query( trans.app.model.UserAddress ).get( trans.security.decode_id( address_id ) ) - except: - message = 'Invalid address is (%s)' % address_id - status = 'error' - if user_address: - user_address.deleted = False - trans.sa_session.flush() - message = 'Address (%s) undeleted' % user_address.desc - status = 'done' - return trans.response.send_redirect( web.url_for( controller='user', - action='manage_user_info', - cntrller=cntrller, - user_id=user_id, + id=trans.security.encode_id( user.id ), message=message, status=status ) ) diff -r b0d60614d255354f0be66a0ae2434165f5406cb8 -r eb0a5dcc9d633fa8122cca5525a6beb1d9940e62 templates/user/edit_address.mako --- a/templates/user/edit_address.mako +++ b/templates/user/edit_address.mako @@ -10,13 +10,13 @@ <ul class="manage-table-actions"><li> - <a class="action-button" href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, user_id=trans.security.encode_id( user.id) )}">Manage user information</a> + <a class="action-button" href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, id=trans.security.encode_id( user.id) )}">Manage user information</a></li></ul><div class="toolForm"><div class="toolFormTitle">Edit address</div><div class="toolFormBody"> - <form name="login_info" id="login_info" action="${h.url_for( controller='user', action='edit_address', cntrller=cntrller, address_id=trans.security.encode_id( address_obj.id ), user_id=trans.security.encode_id( user.id ) )}" method="post" > + <form name="login_info" id="login_info" action="${h.url_for( controller='user', action='edit_address', cntrller=cntrller, address_id=trans.security.encode_id( address_obj.id ), id=trans.security.encode_id( user.id ) )}" method="post" ><div class="form-row"><label>Short Description:</label><div style="float: left; width: 250px; margin-right: 10px;"> diff -r b0d60614d255354f0be66a0ae2434165f5406cb8 -r eb0a5dcc9d633fa8122cca5525a6beb1d9940e62 templates/user/new_address.mako --- a/templates/user/new_address.mako +++ b/templates/user/new_address.mako @@ -10,14 +10,14 @@ <ul class="manage-table-actions"><li> - <a class="action-button" href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, user_id=trans.security.encode_id( user.id) )}"> + <a class="action-button" href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, id=trans.security.encode_id( user.id) )}"><span>Manage User Information</span></a></li></ul><div class="toolForm"><div class="toolFormTitle">Add new address</div><div class="toolFormBody"> - <form name="login_info" id="login_info" action="${h.url_for( controller='user', action='new_address', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" > + <form name="login_info" id="login_info" action="${h.url_for( controller='user', action='new_address', cntrller=cntrller, id=trans.security.encode_id( user.id ) )}" method="post" ><div class="form-row"><label>Short Description:</label><div style="float: left; width: 250px; margin-right: 10px;"> diff -r b0d60614d255354f0be66a0ae2434165f5406cb8 -r eb0a5dcc9d633fa8122cca5525a6beb1d9940e62 templates/webapps/galaxy/user/manage_info.mako --- a/templates/webapps/galaxy/user/manage_info.mako +++ b/templates/webapps/galaxy/user/manage_info.mako @@ -42,7 +42,7 @@ <p/><div class="toolForm"> - <form name="user_addresses" id="user_addresses" action="${h.url_for( controller='user', action='new_address', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" > + <form name="user_addresses" id="user_addresses" action="${h.url_for( controller='user', action='new_address', cntrller=cntrller, id=trans.security.encode_id( user.id ) )}" method="post" ><div class="toolFormTitle">User Addresses</div><div class="toolFormBody"> %if user.addresses: @@ -53,9 +53,9 @@ <span>|</span> %endif %if show_filter == filter: - <span class="filter"><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, show_filter=filter, user_id=trans.security.encode_id( user.id ) )}"><b>${filter}</b></a></span> + <span class="filter"><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, show_filter=filter, id=trans.security.encode_id( user.id ) )}"><b>${filter}</b></a></span> %else: - <span class="filter"><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, show_filter=filter, user_id=trans.security.encode_id( user.id ) )}">${filter}</a></span> + <span class="filter"><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, show_filter=filter, id=trans.security.encode_id( user.id ) )}">${filter}</a></span> %endif %endfor </div> @@ -73,10 +73,10 @@ <ul class="manage-table-actions"><li> %if not address.deleted: - <a class="action-button" href="${h.url_for( controller='user', action='edit_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Edit</a> - <a class="action-button" href="${h.url_for( controller='user', action='delete_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Delete</a> + <a class="action-button" href="${h.url_for( controller='user', action='edit_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), id=trans.security.encode_id( user.id ) )}">Edit</a> + <a class="action-button" href="${h.url_for( controller='user', action='delete_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), id=trans.security.encode_id( user.id ) )}">Delete</a> %else: - <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Undelete</a> + <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), id=trans.security.encode_id( user.id ) )}">Undelete</a> %endif </li></ul> https://bitbucket.org/galaxy/galaxy-central/commits/c4276377c37e/ Changeset: c4276377c37e Branch: stable User: natefoo Date: 2014-12-02 17:17:42+00:00 Summary: Escape input values in new user address form. Affected #: 1 file diff -r eb0a5dcc9d633fa8122cca5525a6beb1d9940e62 -r c4276377c37e6ecd1f7b8de39336bde35d302450 templates/user/new_address.mako --- a/templates/user/new_address.mako +++ b/templates/user/new_address.mako @@ -21,7 +21,7 @@ <div class="form-row"><label>Short Description:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="short_desc" value="${short_desc}" size="40"> + <input type="text" name="short_desc" value="${short_desc | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -29,7 +29,7 @@ <div class="form-row"><label>Name:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${name}" size="40"> + <input type="text" name="name" value="${name | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -37,7 +37,7 @@ <div class="form-row"><label>Institution:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="institution" value="${institution}" size="40"> + <input type="text" name="institution" value="${institution | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -45,7 +45,7 @@ <div class="form-row"><label>Address:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="address" value="${address}" size="40"> + <input type="text" name="address" value="${address | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -53,7 +53,7 @@ <div class="form-row"><label>City:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="city" value="${city}" size="40"> + <input type="text" name="city" value="${city | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -61,7 +61,7 @@ <div class="form-row"><label>State/Province/Region:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="state" value="${state}" size="40"> + <input type="text" name="state" value="${state | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -69,7 +69,7 @@ <div class="form-row"><label>Postal Code:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="postal_code" value="${postal_code}" size="40"> + <input type="text" name="postal_code" value="${postal_code | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -77,7 +77,7 @@ <div class="form-row"><label>Country:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="country" value="${country}" size="40"> + <input type="text" name="country" value="${country | h}" size="40"></div><div class="toolParamHelp" style="clear: both;">Required</div><div style="clear: both"></div> @@ -85,7 +85,7 @@ <div class="form-row"><label>Phone:</label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="phone" value="${phone}" size="40"> + <input type="text" name="phone" value="${phone | h}" size="40"></div><div style="clear: both"></div></div> https://bitbucket.org/galaxy/galaxy-central/commits/546ff6ef27b4/ Changeset: 546ff6ef27b4 Branch: stable User: natefoo Date: 2014-12-02 18:50:32+00:00 Summary: Don't escape full strings containing desired html. Affected #: 1 file diff -r c4276377c37e6ecd1f7b8de39336bde35d302450 -r 546ff6ef27b4b83e26ae228c292fd981173ac550 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -164,7 +164,7 @@ user_openid.provider = openid_provider if trans.user: if user_openid.user and user_openid.user.id != trans.user.id: - message = escape( "The OpenID <strong>%s</strong> is already associated with another Galaxy account, <strong>%s</strong>. Please disassociate it from that account before attempting to associate it with a new account." % ( display_identifier, user_openid.user.email ) ) + message = "The OpenID <strong>%s</strong> is already associated with another Galaxy account, <strong>%s</strong>. Please disassociate it from that account before attempting to associate it with a new account." % ( escape( display_identifier ), escape( user_openid.user.email ) ) if not trans.user.active and trans.app.config.user_activation_on: # Account activation is ON and the user is INACTIVE. if ( trans.app.config.activation_grace_period != 0 ): # grace period is ON if self.is_outside_grace_period( trans, trans.user.create_time ): # User is outside the grace period. Login is disabled and he will have the activation email resent. @@ -179,17 +179,17 @@ user_openid.session = trans.galaxy_session if not openid_provider_obj.never_associate_with_user: if not auto_associate and ( user_openid.user and user_openid.user.id == trans.user.id ): - message = escape( "The OpenID <strong>%s</strong> is already associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) ) + message = "The OpenID <strong>%s</strong> is already associated with your Galaxy account, <strong>%s</strong>." % ( escape( display_identifier ), escape( trans.user.email ) ) status = "warning" else: - message = escape( "The OpenID <strong>%s</strong> has been associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) ) + message = "The OpenID <strong>%s</strong> has been associated with your Galaxy account, <strong>%s</strong>." % ( escape( display_identifier ), escape( trans.user.email ) ) status = "done" user_openid.user = trans.user trans.sa_session.add( user_openid ) trans.sa_session.flush() trans.log_event( "User associated OpenID: %s" % display_identifier ) else: - message = escape( "The OpenID <strong>%s</strong> cannot be used to log into your Galaxy account, but any post authentication actions have been performed." % ( openid_provider_obj.name ) ) + message = "The OpenID <strong>%s</strong> cannot be used to log into your Galaxy account, but any post authentication actions have been performed." % escape( openid_provider_obj.name ) status = "info" openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) if redirect: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Specify the third argument for HdaImplicitMatch.
by commits-noreply＠bitbucket.org 03 Dec '14

03 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f7e9759b27a0/ Changeset: f7e9759b27a0 User: dan Date: 2014-12-03 17:18:38+00:00 Summary: Specify the third argument for HdaImplicitMatch. Affected #: 1 file diff -r 0273de7467e0f42a56ffa018c5fb9a53a6396e76 -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 lib/galaxy/tools/parameters/dataset_matcher.py --- a/lib/galaxy/tools/parameters/dataset_matcher.py +++ b/lib/galaxy/tools/parameters/dataset_matcher.py @@ -53,11 +53,12 @@ return False target_ext, converted_dataset = hda.find_conversion_destination( formats ) if target_ext: + original_hda = hda if converted_dataset: hda = converted_dataset if check_security and not self.__can_access_dataset( hda.dataset ): return False - rval = HdaImplicitMatch( hda, target_ext ) + rval = HdaImplicitMatch( hda, target_ext, original_hda ) else: return False if self.filter( hda ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Specify the third argument for HdaImplicitMatch.
by commits-noreply＠bitbucket.org 03 Dec '14

03 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3808622909a6/ Changeset: 3808622909a6 Branch: next-stable User: dan Date: 2014-12-03 17:17:25+00:00 Summary: Specify the third argument for HdaImplicitMatch. Affected #: 1 file diff -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 -r 3808622909a6bb561c46d2ff5a5675f1da589c8b lib/galaxy/tools/parameters/dataset_matcher.py --- a/lib/galaxy/tools/parameters/dataset_matcher.py +++ b/lib/galaxy/tools/parameters/dataset_matcher.py @@ -53,11 +53,12 @@ return False target_ext, converted_dataset = hda.find_conversion_destination( formats ) if target_ext: + original_hda = hda if converted_dataset: hda = converted_dataset if check_security and not self.__can_access_dataset( hda.dataset ): return False - rval = HdaImplicitMatch( hda, target_ext ) + rval = HdaImplicitMatch( hda, target_ext, original_hda ) else: return False if self.filter( hda ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: martenson: Merged in martenson/galaxy-central-marten/mako_escape_requests (pull request #579)
by commits-noreply＠bitbucket.org 03 Dec '14

03 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/172f91ec31ef/ Changeset: 172f91ec31ef Branch: next-stable User: martenson Date: 2014-12-03 17:01:23+00:00 Summary: Merged in martenson/galaxy-central-marten/mako_escape_requests (pull request #579) [next-stable] escaping of the templates in the 'requests' and 'forms' sections Affected #: 18 files diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/admin/forms/create_form.mako --- a/templates/admin/forms/create_form.mako +++ b/templates/admin/forms/create_form.mako @@ -9,7 +9,7 @@ <div class="toolFormTitle">Create a new form definition</div> %for label, input in inputs: <div class="form-row"> - <label>${label}</label> + <label>${label | h}</label> ${input.get_html()} <div style="clear: both"></div></div> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/admin/forms/edit_form_definition.mako --- a/templates/admin/forms/edit_form_definition.mako +++ b/templates/admin/forms/edit_form_definition.mako @@ -96,14 +96,14 @@ <form id="edit_form_definition" name="edit_form_definition" action="${h.url_for( controller='forms', action='edit_form_definition', id=trans.security.encode_id( form_definition.current.id ) )}" method="post" ><div class="toolForm"> - <div class="toolFormTitle">Edit form definition "${form_definition.name}" (${form_definition.type})</div> + <div class="toolFormTitle">Edit form definition "${form_definition.name | h}" (${form_definition.type | h})</div> %if response_redirect: <input type="hidden" name="response_redirect" value="${response_redirect}" size="40" /> %endif %for label, input in form_details: <div class="form-row"> %if label != 'Type': - <label>${label}</label> + <label>${label | h}</label> %endif <div style="float: left; width: 250px; margin-right: 10px;"> ${input.get_html()} diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/admin/request_type/common.mako --- a/templates/admin/request_type/common.mako +++ b/templates/admin/request_type/common.mako @@ -2,7 +2,7 @@ <div class="repeat-group-item"><div class="form-row"><label>${1+element_count}. State name:</label> - <input type="text" name="state_name_${element_count}" value="${state_name}" size="40"/> + <input type="text" name="state_name_${element_count}" value="${state_name | h}" size="40"/> ## Do not show remove button for the first state %if element_count > 0: <input type="submit" name="remove_state_button" value="Remove state ${1+element_count}"/> @@ -10,7 +10,7 @@ </div><div class="form-row"><label>Description:</label> - <input type="text" name="state_desc_${element_count}" value="${state_desc}" size="40"/> + <input type="text" name="state_desc_${element_count}" value="${state_desc | h}" size="40"/><div class="toolParamHelp" style="clear: both;"> optional </div> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/admin/request_type/create_request_type.mako --- a/templates/admin/request_type/create_request_type.mako +++ b/templates/admin/request_type/create_request_type.mako @@ -23,7 +23,7 @@ <div class="toolFormTitle">Create a new request type</div> %for rt_info in rt_info_widgets: <div class="form-row"> - <label>${rt_info['label']}</label> + <label>${rt_info['label'] | h}</label><div style="float: left; width: 250px; margin-right: 10px;"> ${rt_info['widget'].get_html()} </div> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/admin/request_type/edit_request_type.mako --- a/templates/admin/request_type/edit_request_type.mako +++ b/templates/admin/request_type/edit_request_type.mako @@ -32,26 +32,26 @@ <form name="edit_request_type" action="${h.url_for( controller='request_type', action='edit_request_type', id=trans.security.encode_id( request_type.id ) )}" method="post" ><div class="toolForm"> - <div class="toolFormTitle">"Edit ${request_type.name}" request type</div> + <div class="toolFormTitle">"Edit ${request_type.name | h}" request type</div><div class="form-row"><label>Name:</label> - <input type="text" name="name" value="${request_type.name}" size="40"/> + <input type="text" name="name" value="${request_type.name | }" size="40"/><div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - <input type="text" name="desc" value="${request_type.desc}" size="40"/> + <input type="text" name="desc" value="${request_type.desc | h}" size="40"/><div style="clear: both"></div></div><div class="form-row"><label>Sequencing request form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name | h}</a> ## Hidden field needed by the __save_request_type() method <input type="hidden" name="request_form_id" value="${trans.security.encode_id( request_type.request_form_id )}" size="40"/></div><div class="form-row"><label>Sample form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name | h}</a> ## Hidden field needed by the __save_request_type() method <input type="hidden" name="sample_form_id" value="${trans.security.encode_id( request_type.sample_form_id )}" size="40"/></div> @@ -63,11 +63,11 @@ <div class="repeat-group-item"><div class="form-row"><label>${1+element_count}. State name:</label> - <input type="text" name="state_name_${trans.security.encode_id( state.id )}" value="${state.name}" size="40"/> + <input type="text" name="state_name_${trans.security.encode_id( state.id )}" value="${state.name | h}" size="40"/></div><div class="form-row"><label>Description:</label> - <input type="text" name="state_desc_${trans.security.encode_id( state.id )}" value="${state.desc}" size="40"/> + <input type="text" name="state_desc_${trans.security.encode_id( state.id )}" value="${state.desc | h}" size="40"/><div class="toolParamHelp" style="clear: both;"> optional </div> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/admin/request_type/request_type_permissions.mako --- a/templates/admin/request_type/request_type_permissions.mako +++ b/templates/admin/request_type/request_type_permissions.mako @@ -48,7 +48,7 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Manage access permissions on request type "${request_type.name}"</div> + <div class="toolFormTitle">Manage access permissions on request type "${request_type.name | h}"</div><div class="toolFormBody"><form name="request_type_permissions" id="request_type_permissions" action="${h.url_for( controller='request_type', action='request_type_permissions', id=trans.security.encode_id( request_type.id ) )}" method="post"><div class="form-row"> @@ -65,13 +65,13 @@ in_roles.add( a.role ) out_roles = filter( lambda x: x not in in_roles, all_roles ) %> - ${action.description}<br/><br/> + ${action.description | h}<br/><br/><div style="width: 100%; white-space: nowrap;"><div style="float: left; width: 50%;"> Roles associated:<br/><select name="${action_key}_in" id="${action_key}_in_select" class="in_select" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple> %for role in in_roles: - <option value="${role.id}">${role.name}</option> + <option value="${role.id}">${role.name | h}</option> %endfor </select><br/><div style="width: 98%; text-align: right"><input type="submit" id="${action_key}_remove_button" class="role_remove_button" value=">>"/></div> @@ -80,7 +80,7 @@ Roles not associated:<br/><select name="${action_key}_out" id="${action_key}_out_select" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple> %for role in out_roles: - <option value="${role.id}">${role.name}</option> + <option value="${role.id}">${role.name | h}</option> %endfor </select><br/><input type="submit" id="${action_key}_add_button" class="role_add_button" value="<<"/> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/admin/request_type/view_request_type.mako --- a/templates/admin/request_type/view_request_type.mako +++ b/templates/admin/request_type/view_request_type.mako @@ -30,24 +30,24 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">"${request_type.name}" request type</div> + <div class="toolFormTitle">"${request_type.name | h}" request type</div><div class="form-row"><label>Name:</label> - ${request_type.name} + ${request_type.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - ${request_type.desc} + ${request_type.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>Sequencing request form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name | h}</a></div><div class="form-row"><label>Sample form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name | h}</a></div></div><p/> @@ -55,8 +55,8 @@ <div class="toolFormTitle">Sample states defined for this request type</div> %for state in request_type.states: <div class="form-row"> - <label>${state.name}</label> - ${state.desc} + <label>${state.name | h}</label> + ${state.desc | h} </div><div style="clear: both"></div> %endfor @@ -67,8 +67,8 @@ %if request_type.external_services: %for index, external_service in enumerate( request_type.external_services ): <div class="form-row"> - <label><a href="${h.url_for( controller='external_service', action='view_external_service', id=trans.security.encode_id( external_service.id ) )}">${external_service.name}</a></label> - ${external_service.get_external_service_type( trans ).name} + <label><a href="${h.url_for( controller='external_service', action='view_external_service', id=trans.security.encode_id( external_service.id ) )}">${external_service.name | h}</a></label> + ${external_service.get_external_service_type( trans ).name | h} </div> %endfor %else: diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/admin/requests/reject.mako --- a/templates/admin/requests/reject.mako +++ b/templates/admin/requests/reject.mako @@ -15,7 +15,7 @@ </ul><div class="toolForm"> - <div class="toolFormTitle">Reject sequencing request "${request.name}"</div> + <div class="toolFormTitle">Reject sequencing request "${request.name | h}"</div><form name="event" action="${h.url_for( controller='requests_admin', action='reject_request', id=trans.security.encode_id( request.id ) )}" method="post" ><div class="form-row"> Rejecting this request will move the request state to <b>Rejected</b>. diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/admin/requests/rename_datasets.mako --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -3,7 +3,7 @@ <% from galaxy.webapps.galaxy.controllers.requests_admin import build_rename_datasets_for_sample_select_field %> -<h3>Rename datasets for Sample "${sample.name}"</h3> +<h3>Rename datasets for Sample "${sample.name | h}"</h3><ul class="manage-table-actions"><li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Browse datasets</a></li> @@ -35,7 +35,7 @@ ${rename_datasets_for_sample_select_field.get_html()} </td><td> - <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id ) }" value="${sample_dataset.name}" size="100"/> + <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id ) }" value="${sample_dataset.name | h}" size="100"/></td><td>${sample_dataset.file_path}</td></tr> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/admin/requests/view_sample_dataset.mako --- a/templates/admin/requests/view_sample_dataset.mako +++ b/templates/admin/requests/view_sample_dataset.mako @@ -21,19 +21,19 @@ </ul><div class="toolForm"> - <div class="toolFormTitle">"${sample.name}" Dataset</div> + <div class="toolFormTitle">"${sample.name | h}" Dataset</div><div class="toolFormBody"><div class="form-row"><label>Name:</label><div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.name} + ${sample_dataset.name | h} </div><div style="clear: both"></div></div><div class="form-row"><label>External service:</label><div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.external_service.name} (${sample_dataset.external_service.get_external_service_type( trans ).name}) + ${sample_dataset.external_service.name | h} (${sample_dataset.external_service.get_external_service_type( trans ).name | h}) </div><div style="clear: both"></div></div> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/webapps/galaxy/requests/common/common.mako --- a/templates/webapps/galaxy/requests/common/common.mako +++ b/templates/webapps/galaxy/requests/common/common.mako @@ -257,18 +257,18 @@ <td valign="top"><input type="checkbox" name=select_sample_${sample.id} id="sample_checkbox" value="true" ${checked_str}/><input type="hidden" name=select_sample_${sample.id} id="sample_checkbox" value="true"/></td> %endif <td valign="top"> - <input type="text" name="sample_${sample_widget_index}_name" value="${sample_widget['name']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_name" value="${sample_widget['name'] | h}" size="10"/><div class="toolParamHelp" style="clear: both;"> - <i>${' (required)' }</i> + <i>(required)</i></div></td> %if display_bar_code: <td valign="top"> %if is_admin and is_submitted: - <input type="text" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code'] | h}" size="10"/> %else: - ${sample_widget['bar_code']} - <input type="hidden" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}"/> + ${sample_widget['bar_code'] | h} + <input type="hidden" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code'] | h}"/> %endif </td> %endif @@ -416,7 +416,7 @@ transferred_dataset_files = [] %><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="sample-${sample.id}-popup"> - <a class="view-info" href="${h.url_for( controller='requests_common', action='view_sample', cntrller=cntrller, id=trans.security.encode_id( sample.id ) )}">${sample.name}</a> + <a class="view-info" href="${h.url_for( controller='requests_common', action='view_sample', cntrller=cntrller, id=trans.security.encode_id( sample.id ) )}">${sample.name | h}</a></div><div popupmenu="sample-${sample.id}-popup"> %if can_select_datasets: @@ -439,11 +439,11 @@ %endif </div> %else: - ${sample_widget_name} + ${sample_widget_name | h} %endif </td> %if display_bar_code: - <td>${sample_widget_bar_code}</td> + <td>${sample_widget_bar_code | h}</td> %endif %if is_unsubmitted: <td>Unsubmitted</td> @@ -451,12 +451,12 @@ <td><a id="sampleState-${sample.id}" href="${h.url_for( controller='requests_common', action='view_sample_history', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${render_sample_state( sample )}</a></td> %endif %if sample_widget_library and library_cntrller is not None: - <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( sample_widget_library.id ) )}">${sample_widget_library.name}</a></td> + <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( sample_widget_library.id ) )}">${sample_widget_library.name | h}</a></td> %else: <td></td> %endif %if sample_widget_folder: - <td>${sample_widget_folder.name}</td> + <td>${sample_widget_folder.name | h}</td> %else: <td></td> %endif @@ -464,11 +464,11 @@ %if trans.user == sample_widget_history.user: <td><a target='_parent' href="${h.url_for( controller='history', action='list', operation="Switch", id=trans.security.encode_id(sample_widget_history.id), use_panels=False )}"> - ${sample_widget_history.name} + ${sample_widget_history.name | h} </a></td> %else: - <td>${sample_widget_history.name}</td> + <td>${sample_widget_history.name | h}</td> %endif %else: <td></td> @@ -477,11 +477,11 @@ %if trans.user == sample_widget_workflow.stored_workflow.user: <td><a target='_parent' href="${h.url_for( controller='workflow', action='editor', id=trans.security.encode_id(sample_widget_workflow.stored_workflow.id) )}"> - ${sample_widget_workflow.name} + ${sample_widget_workflow.name | h} </a></td> %else: - <td>${sample_widget_workflow.name}</td> + <td>${sample_widget_workflow.name | h}</td> %endif %else: <td></td> @@ -519,7 +519,7 @@ <%def name="render_sample_form( index, sample_name, sample_values, fields_dict, display_only )"><tr> - <td>${sample_name}</td> + <td>${sample_name | h}</td> %for field_index, field in fields_dict.items(): <% field_type = field[ 'type' ] @@ -532,17 +532,17 @@ %if field_type == 'WorkflowField': %if str( field_value ) != 'none': <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int( field_value ) ) %> - <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">${workflow.name}</a> + <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">${workflow.name | h}</a> %endif %else: - ${field_value} + ${field_value | h} %endif %else: <i>None</i> %endif %else: %if field_type == 'TextField': - <input type="text" name="sample_${index}_field_${field_index}" value="${field_value}" size="7"/> + <input type="text" name="sample_${index}_field_${field_index}" value="${field_value | h}" size="7"/> %elif field_type == 'SelectField': <select name="sample_${index}_field_${field_index}" last_selected_value="2"> %for option_index, option in enumerate(field[ 'selectlist' ]): @@ -695,7 +695,7 @@ %if is_admin: <span class="expandLink dataset-${dataset}-click"><span class="rowIcon"></span><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="dataset-${dataset.id}-popup"> - <a class="dataset-${encoded_id}-click" href="${h.url_for( controller='requests_admin', action='manage_datasets', operation='view', id=trans.security.encode_id( dataset.id ) )}">${dataset.name}</a> + <a class="dataset-${encoded_id}-click" href="${h.url_for( controller='requests_admin', action='manage_datasets', operation='view', id=trans.security.encode_id( dataset.id ) )}">${dataset.name | h}</a></div></span><div popupmenu="dataset-${dataset.id}-popup"> @@ -704,12 +704,12 @@ %endif </div> %else: - ${dataset.name} + ${dataset.name | h} %endif </td><td>${dataset.size}</td> - <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">${dataset.sample.library.name}</a></td> - <td>${dataset.sample.folder.name}</td> + <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">${dataset.sample.library.name | h}</a></td> + <td>${dataset.sample.folder.name | h}</td><td id="datasetTransferStatus-${encoded_id}">${dataset.status}</td></tr> %endfor @@ -723,7 +723,7 @@ <%def name="render_samples_messages( request, is_admin=False, is_submitted=False, message=None, status=None)"> %if request.is_rejected: <div class='errormessage'> - ${request.last_comment} + ${request.last_comment | h} </div><br/> %endif %if is_admin and is_submitted and request.samples_without_library_destinations: diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/webapps/galaxy/requests/common/create_request.mako --- a/templates/webapps/galaxy/requests/common/create_request.mako +++ b/templates/webapps/galaxy/requests/common/create_request.mako @@ -23,7 +23,7 @@ <div class="toolForm"><div class="toolFormTitle">Create a new sequencing request</div> %if len( request_type_select_field.options ) < 1: - There are no request types available for ${trans.user.email} to create sequencing requests. + There are no request types available for ${trans.user.email | h} to create sequencing requests. %else: <div class="toolFormBody"><form name="create_request" id="create_request" action="${h.url_for( controller='requests_common', action='create_request', cntrller=cntrller )}" method="post" > diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/webapps/galaxy/requests/common/edit_basic_request_info.mako --- a/templates/webapps/galaxy/requests/common/edit_basic_request_info.mako +++ b/templates/webapps/galaxy/requests/common/edit_basic_request_info.mako @@ -31,7 +31,7 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Edit sequencing request "${request.name}"</div> + <div class="toolFormTitle">Edit sequencing request "${request.name | h}"</div><div class="toolFormBody"><form name="edit_basic_request_info" id="edit_basic_request_info" action="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}" method="post" > %for i, field in enumerate( widgets ): @@ -70,11 +70,11 @@ %><div class="form-row"><label>Send to:</label> - <input type="checkbox" name="email_address" value="true" ${email_address}>${request.user.email} (sequencing request owner)<input type="hidden" name="email_address" value="true"> + <input type="checkbox" name="email_address" value="true" ${email_address}>${request.user.email | h} (sequencing request owner)<input type="hidden" name="email_address" value="true"></div><div class="form-row"><label>Additional email addresses:</label> - <textarea name="additional_email_addresses" rows="3" cols="40">${emails}</textarea> + <textarea name="additional_email_addresses" rows="3" cols="40">${emails | h}</textarea><div class="toolParamHelp" style="clear: both;"> Enter one email address per line </div> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/webapps/galaxy/requests/common/find_samples.mako --- a/templates/webapps/galaxy/requests/common/find_samples.mako +++ b/templates/webapps/galaxy/requests/common/find_samples.mako @@ -72,7 +72,7 @@ %if samples: %for sample in samples: <div class="form-row"> - Sample: <b>${sample.name}</b> | Barcode: ${sample.bar_code}<br/> + Sample: <b>${sample.name | h}</b> | Barcode: ${sample.bar_code | h}<br/> %if sample.request.is_new or not sample.state: State: Unsubmitted<br/> %else: @@ -85,10 +85,10 @@ %> Datasets: <a href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, external_service_id=trans.security.encode_id( external_service.id ), sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a><br/> %if is_admin: - <i>User: ${sample.request.user.email}</i> + <i>User: ${sample.request.user.email | h}</i> %endif <div class="toolParamHelp" style="clear: both;"> - <a href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Sequencing request: ${sample.request.name} | Type: ${sample.request.type.name} | State: ${sample.request.state}</a> + <a href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Sequencing request: ${sample.request.name | h} | Type: ${sample.request.type.name} | State: ${sample.request.state}</a></div></div><br/> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/webapps/galaxy/requests/common/view_request.mako --- a/templates/webapps/galaxy/requests/common/view_request.mako +++ b/templates/webapps/galaxy/requests/common/view_request.mako @@ -58,7 +58,7 @@ ${render_samples_messages(request, is_admin, is_submitted, message, status)} <div class="toolForm"> - <div class="toolFormTitle">Sequencing request "${request.name}"</div> + <div class="toolFormTitle">Sequencing request "${request.name | h}"</div><div class="toolFormBody"><div class="form-row"><label>Current state:</label> @@ -67,12 +67,12 @@ </div><div class="form-row"><label>Description:</label> - ${request.desc} + ${request.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>User:</label> - ${request.user.email} + ${request.user.email | h} <div style="clear: both"></div></div><div class="form-row"> @@ -94,7 +94,7 @@ %><div class="form-row"><label>${field_label}:</label> - ${field_value} + ${field_value | h} </div><div style="clear: both"></div> %endfor @@ -116,7 +116,7 @@ else: emails = '' %> - ${emails} + ${emails | h} <div style="clear: both"></div></div><div class="form-row"> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/webapps/galaxy/requests/common/view_request_history.mako --- a/templates/webapps/galaxy/requests/common/view_request_history.mako +++ b/templates/webapps/galaxy/requests/common/view_request_history.mako @@ -36,7 +36,7 @@ ${render_msg( message, status )} %endif -<h3>History of sequencing request "${request.name}"</h3> +<h3>History of sequencing request "${request.name | h}"</h3><div class="toolForm"><table class="grid"> @@ -52,7 +52,7 @@ <tr><td><b>${event.state}</b></td><td>${time_ago( event.update_time )}</td> - <td>${event.comment}</td> + <td>${event.comment | h}</td></tr> %endfor </tbody> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/webapps/galaxy/requests/common/view_sample.mako --- a/templates/webapps/galaxy/requests/common/view_sample.mako +++ b/templates/webapps/galaxy/requests/common/view_sample.mako @@ -6,7 +6,7 @@ %if external_service: <p><div class="toolForm"> - <div class="toolFormTitle">Available External Service Actions for ${sample.name} at ${external_service.name}</div> + <div class="toolFormTitle">Available External Service Actions for ${sample.name | h} at ${external_service.name | h}</div><div class="toolFormBody"><div class="toolMenu"> %for item in external_service.actions: @@ -25,7 +25,7 @@ <div class="form-row"><div class="toolSectionList"><div class="toolSectionTitle"> - <span>${external_service_group.label}</span> + <span>${external_service_group.label | h}</span></div><div class="toolSectionBody"><div class="toolSectionBg"> @@ -54,7 +54,7 @@ target = 'galaxy_main' %><div class="toolTitle"> - <a href="${external_service_action.get_action_access_link( trans )}" target="${target}">${external_service_action.label}</a> + <a href="${external_service_action.get_action_access_link( trans )}" target="${target}">${external_service_action.label | h}</a></div></%def> @@ -75,38 +75,38 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Sample "${sample.name}"</div> + <div class="toolFormTitle">Sample "${sample.name | h}"</div><div class="toolFormBody"><div class="form-row"><label>Name:</label> - ${sample.name} + ${sample.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - ${sample.desc} + ${sample.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>Barcode:</label> - ${sample.bar_code} + ${sample.bar_code | h} <div style="clear: both"></div></div> %if sample.library: <div class="form-row"><label>Library:</label> - ${sample.library.name} + ${sample.library.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Folder:</label> - ${sample.folder.name} + ${sample.folder.name | h} <div style="clear: both"></div></div> %endif <div class="form-row"><label>Request:</label> - ${sample.request.name} + ${sample.request.name | h} <div style="clear: both"></div></div></div> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/webapps/galaxy/requests/common/view_sample_history.mako --- a/templates/webapps/galaxy/requests/common/view_sample_history.mako +++ b/templates/webapps/galaxy/requests/common/view_sample_history.mako @@ -12,7 +12,7 @@ ${render_msg( message, status )} %endif -<h3>History of sample "${sample.name}"</h3> +<h3>History of sample "${sample.name | h}"</h3><div class="toolForm"><table class="grid"> @@ -27,10 +27,10 @@ <tbody> %for event in sample.events: <tr> - <td><b>${event.state.name}</b></td> - <td>${event.state.desc}</td> + <td><b>${event.state.name | h}</b></td> + <td>${event.state.desc | h}</td><td>${time_ago( event.update_time )}</td> - <td>${event.comment}</td> + <td>${event.comment | h}</td></tr> %endfor </tbody> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 03 Dec '14

03 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/795336f22d8b/ Changeset: 795336f22d8b Branch: mako_escape_requests User: martenson Date: 2014-12-01 22:38:24+00:00 Summary: none of the requests & forms controllers used escaping so I escaped the variables exclusively in the templates Affected #: 18 files diff -r 1034c973ec1d2ce424f711d750ecc6de582d02aa -r 795336f22d8b94b86256b1d4738ee1bf24e18b57 templates/admin/forms/create_form.mako --- a/templates/admin/forms/create_form.mako +++ b/templates/admin/forms/create_form.mako @@ -9,7 +9,7 @@ <div class="toolFormTitle">Create a new form definition</div> %for label, input in inputs: <div class="form-row"> - <label>${label}</label> + <label>${label | h}</label> ${input.get_html()} <div style="clear: both"></div></div> diff -r 1034c973ec1d2ce424f711d750ecc6de582d02aa -r 795336f22d8b94b86256b1d4738ee1bf24e18b57 templates/admin/forms/edit_form_definition.mako --- a/templates/admin/forms/edit_form_definition.mako +++ b/templates/admin/forms/edit_form_definition.mako @@ -96,14 +96,14 @@ <form id="edit_form_definition" name="edit_form_definition" action="${h.url_for( controller='forms', action='edit_form_definition', id=trans.security.encode_id( form_definition.current.id ) )}" method="post" ><div class="toolForm"> - <div class="toolFormTitle">Edit form definition "${form_definition.name}" (${form_definition.type})</div> + <div class="toolFormTitle">Edit form definition "${form_definition.name | h}" (${form_definition.type | h})</div> %if response_redirect: <input type="hidden" name="response_redirect" value="${response_redirect}" size="40" /> %endif %for label, input in form_details: <div class="form-row"> %if label != 'Type': - <label>${label}</label> + <label>${label | h}</label> %endif <div style="float: left; width: 250px; margin-right: 10px;"> ${input.get_html()} diff -r 1034c973ec1d2ce424f711d750ecc6de582d02aa -r 795336f22d8b94b86256b1d4738ee1bf24e18b57 templates/admin/request_type/common.mako --- a/templates/admin/request_type/common.mako +++ b/templates/admin/request_type/common.mako @@ -2,7 +2,7 @@ <div class="repeat-group-item"><div class="form-row"><label>${1+element_count}. State name:</label> - <input type="text" name="state_name_${element_count}" value="${state_name}" size="40"/> + <input type="text" name="state_name_${element_count}" value="${state_name | h}" size="40"/> ## Do not show remove button for the first state %if element_count > 0: <input type="submit" name="remove_state_button" value="Remove state ${1+element_count}"/> @@ -10,7 +10,7 @@ </div><div class="form-row"><label>Description:</label> - <input type="text" name="state_desc_${element_count}" value="${state_desc}" size="40"/> + <input type="text" name="state_desc_${element_count}" value="${state_desc | h}" size="40"/><div class="toolParamHelp" style="clear: both;"> optional </div> diff -r 1034c973ec1d2ce424f711d750ecc6de582d02aa -r 795336f22d8b94b86256b1d4738ee1bf24e18b57 templates/admin/request_type/create_request_type.mako --- a/templates/admin/request_type/create_request_type.mako +++ b/templates/admin/request_type/create_request_type.mako @@ -23,7 +23,7 @@ <div class="toolFormTitle">Create a new request type</div> %for rt_info in rt_info_widgets: <div class="form-row"> - <label>${rt_info['label']}</label> + <label>${rt_info['label'] | h}</label><div style="float: left; width: 250px; margin-right: 10px;"> ${rt_info['widget'].get_html()} </div> diff -r 1034c973ec1d2ce424f711d750ecc6de582d02aa -r 795336f22d8b94b86256b1d4738ee1bf24e18b57 templates/admin/request_type/edit_request_type.mako --- a/templates/admin/request_type/edit_request_type.mako +++ b/templates/admin/request_type/edit_request_type.mako @@ -32,26 +32,26 @@ <form name="edit_request_type" action="${h.url_for( controller='request_type', action='edit_request_type', id=trans.security.encode_id( request_type.id ) )}" method="post" ><div class="toolForm"> - <div class="toolFormTitle">"Edit ${request_type.name}" request type</div> + <div class="toolFormTitle">"Edit ${request_type.name | h}" request type</div><div class="form-row"><label>Name:</label> - <input type="text" name="name" value="${request_type.name}" size="40"/> + <input type="text" name="name" value="${request_type.name | }" size="40"/><div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - <input type="text" name="desc" value="${request_type.desc}" size="40"/> + <input type="text" name="desc" value="${request_type.desc | h}" size="40"/><div style="clear: both"></div></div><div class="form-row"><label>Sequencing request form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name | h}</a> ## Hidden field needed by the __save_request_type() method <input type="hidden" name="request_form_id" value="${trans.security.encode_id( request_type.request_form_id )}" size="40"/></div><div class="form-row"><label>Sample form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name | h}</a> ## Hidden field needed by the __save_request_type() method <input type="hidden" name="sample_form_id" value="${trans.security.encode_id( request_type.sample_form_id )}" size="40"/></div> @@ -63,11 +63,11 @@ <div class="repeat-group-item"><div class="form-row"><label>${1+element_count}. State name:</label> - <input type="text" name="state_name_${trans.security.encode_id( state.id )}" value="${state.name}" size="40"/> + <input type="text" name="state_name_${trans.security.encode_id( state.id )}" value="${state.name | h}" size="40"/></div><div class="form-row"><label>Description:</label> - <input type="text" name="state_desc_${trans.security.encode_id( state.id )}" value="${state.desc}" size="40"/> + <input type="text" name="state_desc_${trans.security.encode_id( state.id )}" value="${state.desc | h}" size="40"/><div class="toolParamHelp" style="clear: both;"> optional </div> diff -r 1034c973ec1d2ce424f711d750ecc6de582d02aa -r 795336f22d8b94b86256b1d4738ee1bf24e18b57 templates/admin/request_type/request_type_permissions.mako --- a/templates/admin/request_type/request_type_permissions.mako +++ b/templates/admin/request_type/request_type_permissions.mako @@ -48,7 +48,7 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Manage access permissions on request type "${request_type.name}"</div> + <div class="toolFormTitle">Manage access permissions on request type "${request_type.name | h}"</div><div class="toolFormBody"><form name="request_type_permissions" id="request_type_permissions" action="${h.url_for( controller='request_type', action='request_type_permissions', id=trans.security.encode_id( request_type.id ) )}" method="post"><div class="form-row"> @@ -65,13 +65,13 @@ in_roles.add( a.role ) out_roles = filter( lambda x: x not in in_roles, all_roles ) %> - ${action.description}<br/><br/> + ${action.description | h}<br/><br/><div style="width: 100%; white-space: nowrap;"><div style="float: left; width: 50%;"> Roles associated:<br/><select name="${action_key}_in" id="${action_key}_in_select" class="in_select" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple> %for role in in_roles: - <option value="${role.id}">${role.name}</option> + <option value="${role.id}">${role.name | h}</option> %endfor </select><br/><div style="width: 98%; text-align: right"><input type="submit" id="${action_key}_remove_button" class="role_remove_button" value=">>"/></div> @@ -80,7 +80,7 @@ Roles not associated:<br/><select name="${action_key}_out" id="${action_key}_out_select" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple> %for role in out_roles: - <option value="${role.id}">${role.name}</option> + <option value="${role.id}">${role.name | h}</option> %endfor </select><br/><input type="submit" id="${action_key}_add_button" class="role_add_button" value="<<"/> diff -r 1034c973ec1d2ce424f711d750ecc6de582d02aa -r 795336f22d8b94b86256b1d4738ee1bf24e18b57 templates/admin/request_type/view_request_type.mako --- a/templates/admin/request_type/view_request_type.mako +++ b/templates/admin/request_type/view_request_type.mako @@ -30,24 +30,24 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">"${request_type.name}" request type</div> + <div class="toolFormTitle">"${request_type.name | h}" request type</div><div class="form-row"><label>Name:</label> - ${request_type.name} + ${request_type.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - ${request_type.desc} + ${request_type.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>Sequencing request form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name | h}</a></div><div class="form-row"><label>Sample form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name | h}</a></div></div><p/> @@ -55,8 +55,8 @@ <div class="toolFormTitle">Sample states defined for this request type</div> %for state in request_type.states: <div class="form-row"> - <label>${state.name}</label> - ${state.desc} + <label>${state.name | h}</label> + ${state.desc | h} </div><div style="clear: both"></div> %endfor @@ -67,8 +67,8 @@ %if request_type.external_services: %for index, external_service in enumerate( request_type.external_services ): <div class="form-row"> - <label><a href="${h.url_for( controller='external_service', action='view_external_service', id=trans.security.encode_id( external_service.id ) )}">${external_service.name}</a></label> - ${external_service.get_external_service_type( trans ).name} + <label><a href="${h.url_for( controller='external_service', action='view_external_service', id=trans.security.encode_id( external_service.id ) )}">${external_service.name | h}</a></label> + ${external_service.get_external_service_type( trans ).name | h} </div> %endfor %else: diff -r 1034c973ec1d2ce424f711d750ecc6de582d02aa -r 795336f22d8b94b86256b1d4738ee1bf24e18b57 templates/admin/requests/reject.mako --- a/templates/admin/requests/reject.mako +++ b/templates/admin/requests/reject.mako @@ -15,7 +15,7 @@ </ul><div class="toolForm"> - <div class="toolFormTitle">Reject sequencing request "${request.name}"</div> + <div class="toolFormTitle">Reject sequencing request "${request.name | h}"</div><form name="event" action="${h.url_for( controller='requests_admin', action='reject_request', id=trans.security.encode_id( request.id ) )}" method="post" ><div class="form-row"> Rejecting this request will move the request state to <b>Rejected</b>. diff -r 1034c973ec1d2ce424f711d750ecc6de582d02aa -r 795336f22d8b94b86256b1d4738ee1bf24e18b57 templates/admin/requests/rename_datasets.mako --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -3,7 +3,7 @@ <% from galaxy.webapps.galaxy.controllers.requests_admin import build_rename_datasets_for_sample_select_field %> -<h3>Rename datasets for Sample "${sample.name}"</h3> +<h3>Rename datasets for Sample "${sample.name | h}"</h3><ul class="manage-table-actions"><li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Browse datasets</a></li> @@ -35,7 +35,7 @@ ${rename_datasets_for_sample_select_field.get_html()} </td><td> - <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id ) }" value="${sample_dataset.name}" size="100"/> + <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id ) }" value="${sample_dataset.name | h}" size="100"/></td><td>${sample_dataset.file_path}</td></tr> diff -r 1034c973ec1d2ce424f711d750ecc6de582d02aa -r 795336f22d8b94b86256b1d4738ee1bf24e18b57 templates/admin/requests/view_sample_dataset.mako --- a/templates/admin/requests/view_sample_dataset.mako +++ b/templates/admin/requests/view_sample_dataset.mako @@ -21,19 +21,19 @@ </ul><div class="toolForm"> - <div class="toolFormTitle">"${sample.name}" Dataset</div> + <div class="toolFormTitle">"${sample.name | h}" Dataset</div><div class="toolFormBody"><div class="form-row"><label>Name:</label><div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.name} + ${sample_dataset.name | h} </div><div style="clear: both"></div></div><div class="form-row"><label>External service:</label><div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.external_service.name} (${sample_dataset.external_service.get_external_service_type( trans ).name}) + ${sample_dataset.external_service.name | h} (${sample_dataset.external_service.get_external_service_type( trans ).name | h}) </div><div style="clear: both"></div></div> diff -r 1034c973ec1d2ce424f711d750ecc6de582d02aa -r 795336f22d8b94b86256b1d4738ee1bf24e18b57 templates/webapps/galaxy/requests/common/common.mako --- a/templates/webapps/galaxy/requests/common/common.mako +++ b/templates/webapps/galaxy/requests/common/common.mako @@ -257,18 +257,18 @@ <td valign="top"><input type="checkbox" name=select_sample_${sample.id} id="sample_checkbox" value="true" ${checked_str}/><input type="hidden" name=select_sample_${sample.id} id="sample_checkbox" value="true"/></td> %endif <td valign="top"> - <input type="text" name="sample_${sample_widget_index}_name" value="${sample_widget['name']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_name" value="${sample_widget['name'] | h}" size="10"/><div class="toolParamHelp" style="clear: both;"> - <i>${' (required)' }</i> + <i>(required)</i></div></td> %if display_bar_code: <td valign="top"> %if is_admin and is_submitted: - <input type="text" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code'] | h}" size="10"/> %else: - ${sample_widget['bar_code']} - <input type="hidden" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}"/> + ${sample_widget['bar_code'] | h} + <input type="hidden" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code'] | h}"/> %endif </td> %endif @@ -416,7 +416,7 @@ transferred_dataset_files = [] %><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="sample-${sample.id}-popup"> - <a class="view-info" href="${h.url_for( controller='requests_common', action='view_sample', cntrller=cntrller, id=trans.security.encode_id( sample.id ) )}">${sample.name}</a> + <a class="view-info" href="${h.url_for( controller='requests_common', action='view_sample', cntrller=cntrller, id=trans.security.encode_id( sample.id ) )}">${sample.name | h}</a></div><div popupmenu="sample-${sample.id}-popup"> %if can_select_datasets: @@ -439,11 +439,11 @@ %endif </div> %else: - ${sample_widget_name} + ${sample_widget_name | h} %endif </td> %if display_bar_code: - <td>${sample_widget_bar_code}</td> + <td>${sample_widget_bar_code | h}</td> %endif %if is_unsubmitted: <td>Unsubmitted</td> @@ -451,12 +451,12 @@ <td><a id="sampleState-${sample.id}" href="${h.url_for( controller='requests_common', action='view_sample_history', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${render_sample_state( sample )}</a></td> %endif %if sample_widget_library and library_cntrller is not None: - <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( sample_widget_library.id ) )}">${sample_widget_library.name}</a></td> + <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( sample_widget_library.id ) )}">${sample_widget_library.name | h}</a></td> %else: <td></td> %endif %if sample_widget_folder: - <td>${sample_widget_folder.name}</td> + <td>${sample_widget_folder.name | h}</td> %else: <td></td> %endif @@ -464,11 +464,11 @@ %if trans.user == sample_widget_history.user: <td><a target='_parent' href="${h.url_for( controller='history', action='list', operation="Switch", id=trans.security.encode_id(sample_widget_history.id), use_panels=False )}"> - ${sample_widget_history.name} + ${sample_widget_history.name | h} </a></td> %else: - <td>${sample_widget_history.name}</td> + <td>${sample_widget_history.name | h}</td> %endif %else: <td></td> @@ -477,11 +477,11 @@ %if trans.user == sample_widget_workflow.stored_workflow.user: <td><a target='_parent' href="${h.url_for( controller='workflow', action='editor', id=trans.security.encode_id(sample_widget_workflow.stored_workflow.id) )}"> - ${sample_widget_workflow.name} + ${sample_widget_workflow.name | h} </a></td> %else: - <td>${sample_widget_workflow.name}</td> + <td>${sample_widget_workflow.name | h}</td> %endif %else: <td></td> @@ -519,7 +519,7 @@ <%def name="render_sample_form( index, sample_name, sample_values, fields_dict, display_only )"><tr> - <td>${sample_name}</td> + <td>${sample_name | h}</td> %for field_index, field in fields_dict.items(): <% field_type = field[ 'type' ] @@ -532,17 +532,17 @@ %if field_type == 'WorkflowField': %if str( field_value ) != 'none': <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int( field_value ) ) %> - <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">${workflow.name}</a> + <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">${workflow.name | h}</a> %endif %else: - ${field_value} + ${field_value | h} %endif %else: <i>None</i> %endif %else: %if field_type == 'TextField': - <input type="text" name="sample_${index}_field_${field_index}" value="${field_value}" size="7"/> + <input type="text" name="sample_${index}_field_${field_index}" value="${field_value | h}" size="7"/> %elif field_type == 'SelectField': <select name="sample_${index}_field_${field_index}" last_selected_value="2"> %for option_index, option in enumerate(field[ 'selectlist' ]): @@ -695,7 +695,7 @@ %if is_admin: <span class="expandLink dataset-${dataset}-click"><span class="rowIcon"></span><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="dataset-${dataset.id}-popup"> - <a class="dataset-${encoded_id}-click" href="${h.url_for( controller='requests_admin', action='manage_datasets', operation='view', id=trans.security.encode_id( dataset.id ) )}">${dataset.name}</a> + <a class="dataset-${encoded_id}-click" href="${h.url_for( controller='requests_admin', action='manage_datasets', operation='view', id=trans.security.encode_id( dataset.id ) )}">${dataset.name | h}</a></div></span><div popupmenu="dataset-${dataset.id}-popup"> @@ -704,12 +704,12 @@ %endif </div> %else: - ${dataset.name} + ${dataset.name | h} %endif </td><td>${dataset.size}</td> - <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">${dataset.sample.library.name}</a></td> - <td>${dataset.sample.folder.name}</td> + <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">${dataset.sample.library.name | h}</a></td> + <td>${dataset.sample.folder.name | h}</td><td id="datasetTransferStatus-${encoded_id}">${dataset.status}</td></tr> %endfor @@ -723,7 +723,7 @@ <%def name="render_samples_messages( request, is_admin=False, is_submitted=False, message=None, status=None)"> %if request.is_rejected: <div class='errormessage'> - ${request.last_comment} + ${request.last_comment | h} </div><br/> %endif %if is_admin and is_submitted and request.samples_without_library_destinations: diff -r 1034c973ec1d2ce424f711d750ecc6de582d02aa -r 795336f22d8b94b86256b1d4738ee1bf24e18b57 templates/webapps/galaxy/requests/common/create_request.mako --- a/templates/webapps/galaxy/requests/common/create_request.mako +++ b/templates/webapps/galaxy/requests/common/create_request.mako @@ -23,7 +23,7 @@ <div class="toolForm"><div class="toolFormTitle">Create a new sequencing request</div> %if len( request_type_select_field.options ) < 1: - There are no request types available for ${trans.user.email} to create sequencing requests. + There are no request types available for ${trans.user.email | h} to create sequencing requests. %else: <div class="toolFormBody"><form name="create_request" id="create_request" action="${h.url_for( controller='requests_common', action='create_request', cntrller=cntrller )}" method="post" > diff -r 1034c973ec1d2ce424f711d750ecc6de582d02aa -r 795336f22d8b94b86256b1d4738ee1bf24e18b57 templates/webapps/galaxy/requests/common/edit_basic_request_info.mako --- a/templates/webapps/galaxy/requests/common/edit_basic_request_info.mako +++ b/templates/webapps/galaxy/requests/common/edit_basic_request_info.mako @@ -31,7 +31,7 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Edit sequencing request "${request.name}"</div> + <div class="toolFormTitle">Edit sequencing request "${request.name | h}"</div><div class="toolFormBody"><form name="edit_basic_request_info" id="edit_basic_request_info" action="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}" method="post" > %for i, field in enumerate( widgets ): @@ -70,11 +70,11 @@ %><div class="form-row"><label>Send to:</label> - <input type="checkbox" name="email_address" value="true" ${email_address}>${request.user.email} (sequencing request owner)<input type="hidden" name="email_address" value="true"> + <input type="checkbox" name="email_address" value="true" ${email_address}>${request.user.email | h} (sequencing request owner)<input type="hidden" name="email_address" value="true"></div><div class="form-row"><label>Additional email addresses:</label> - <textarea name="additional_email_addresses" rows="3" cols="40">${emails}</textarea> + <textarea name="additional_email_addresses" rows="3" cols="40">${emails | h}</textarea><div class="toolParamHelp" style="clear: both;"> Enter one email address per line </div> diff -r 1034c973ec1d2ce424f711d750ecc6de582d02aa -r 795336f22d8b94b86256b1d4738ee1bf24e18b57 templates/webapps/galaxy/requests/common/find_samples.mako --- a/templates/webapps/galaxy/requests/common/find_samples.mako +++ b/templates/webapps/galaxy/requests/common/find_samples.mako @@ -72,7 +72,7 @@ %if samples: %for sample in samples: <div class="form-row"> - Sample: <b>${sample.name}</b> | Barcode: ${sample.bar_code}<br/> + Sample: <b>${sample.name | h}</b> | Barcode: ${sample.bar_code | h}<br/> %if sample.request.is_new or not sample.state: State: Unsubmitted<br/> %else: @@ -85,10 +85,10 @@ %> Datasets: <a href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, external_service_id=trans.security.encode_id( external_service.id ), sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a><br/> %if is_admin: - <i>User: ${sample.request.user.email}</i> + <i>User: ${sample.request.user.email | h}</i> %endif <div class="toolParamHelp" style="clear: both;"> - <a href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Sequencing request: ${sample.request.name} | Type: ${sample.request.type.name} | State: ${sample.request.state}</a> + <a href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Sequencing request: ${sample.request.name | h} | Type: ${sample.request.type.name} | State: ${sample.request.state}</a></div></div><br/> diff -r 1034c973ec1d2ce424f711d750ecc6de582d02aa -r 795336f22d8b94b86256b1d4738ee1bf24e18b57 templates/webapps/galaxy/requests/common/view_request.mako --- a/templates/webapps/galaxy/requests/common/view_request.mako +++ b/templates/webapps/galaxy/requests/common/view_request.mako @@ -58,7 +58,7 @@ ${render_samples_messages(request, is_admin, is_submitted, message, status)} <div class="toolForm"> - <div class="toolFormTitle">Sequencing request "${request.name}"</div> + <div class="toolFormTitle">Sequencing request "${request.name | h}"</div><div class="toolFormBody"><div class="form-row"><label>Current state:</label> @@ -67,12 +67,12 @@ </div><div class="form-row"><label>Description:</label> - ${request.desc} + ${request.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>User:</label> - ${request.user.email} + ${request.user.email | h} <div style="clear: both"></div></div><div class="form-row"> @@ -94,7 +94,7 @@ %><div class="form-row"><label>${field_label}:</label> - ${field_value} + ${field_value | h} </div><div style="clear: both"></div> %endfor @@ -116,7 +116,7 @@ else: emails = '' %> - ${emails} + ${emails | h} <div style="clear: both"></div></div><div class="form-row"> diff -r 1034c973ec1d2ce424f711d750ecc6de582d02aa -r 795336f22d8b94b86256b1d4738ee1bf24e18b57 templates/webapps/galaxy/requests/common/view_request_history.mako --- a/templates/webapps/galaxy/requests/common/view_request_history.mako +++ b/templates/webapps/galaxy/requests/common/view_request_history.mako @@ -36,7 +36,7 @@ ${render_msg( message, status )} %endif -<h3>History of sequencing request "${request.name}"</h3> +<h3>History of sequencing request "${request.name | h}"</h3><div class="toolForm"><table class="grid"> @@ -52,7 +52,7 @@ <tr><td><b>${event.state}</b></td><td>${time_ago( event.update_time )}</td> - <td>${event.comment}</td> + <td>${event.comment | h}</td></tr> %endfor </tbody> diff -r 1034c973ec1d2ce424f711d750ecc6de582d02aa -r 795336f22d8b94b86256b1d4738ee1bf24e18b57 templates/webapps/galaxy/requests/common/view_sample.mako --- a/templates/webapps/galaxy/requests/common/view_sample.mako +++ b/templates/webapps/galaxy/requests/common/view_sample.mako @@ -6,7 +6,7 @@ %if external_service: <p><div class="toolForm"> - <div class="toolFormTitle">Available External Service Actions for ${sample.name} at ${external_service.name}</div> + <div class="toolFormTitle">Available External Service Actions for ${sample.name | h} at ${external_service.name | h}</div><div class="toolFormBody"><div class="toolMenu"> %for item in external_service.actions: @@ -25,7 +25,7 @@ <div class="form-row"><div class="toolSectionList"><div class="toolSectionTitle"> - <span>${external_service_group.label}</span> + <span>${external_service_group.label | h}</span></div><div class="toolSectionBody"><div class="toolSectionBg"> @@ -54,7 +54,7 @@ target = 'galaxy_main' %><div class="toolTitle"> - <a href="${external_service_action.get_action_access_link( trans )}" target="${target}">${external_service_action.label}</a> + <a href="${external_service_action.get_action_access_link( trans )}" target="${target}">${external_service_action.label | h}</a></div></%def> @@ -75,38 +75,38 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Sample "${sample.name}"</div> + <div class="toolFormTitle">Sample "${sample.name | h}"</div><div class="toolFormBody"><div class="form-row"><label>Name:</label> - ${sample.name} + ${sample.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - ${sample.desc} + ${sample.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>Barcode:</label> - ${sample.bar_code} + ${sample.bar_code | h} <div style="clear: both"></div></div> %if sample.library: <div class="form-row"><label>Library:</label> - ${sample.library.name} + ${sample.library.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Folder:</label> - ${sample.folder.name} + ${sample.folder.name | h} <div style="clear: both"></div></div> %endif <div class="form-row"><label>Request:</label> - ${sample.request.name} + ${sample.request.name | h} <div style="clear: both"></div></div></div> diff -r 1034c973ec1d2ce424f711d750ecc6de582d02aa -r 795336f22d8b94b86256b1d4738ee1bf24e18b57 templates/webapps/galaxy/requests/common/view_sample_history.mako --- a/templates/webapps/galaxy/requests/common/view_sample_history.mako +++ b/templates/webapps/galaxy/requests/common/view_sample_history.mako @@ -12,7 +12,7 @@ ${render_msg( message, status )} %endif -<h3>History of sample "${sample.name}"</h3> +<h3>History of sample "${sample.name | h}"</h3><div class="toolForm"><table class="grid"> @@ -27,10 +27,10 @@ <tbody> %for event in sample.events: <tr> - <td><b>${event.state.name}</b></td> - <td>${event.state.desc}</td> + <td><b>${event.state.name | h}</b></td> + <td>${event.state.desc | h}</td><td>${time_ago( event.update_time )}</td> - <td>${event.comment}</td> + <td>${event.comment | h}</td></tr> %endfor </tbody> https://bitbucket.org/galaxy/galaxy-central/commits/172f91ec31ef/ Changeset: 172f91ec31ef Branch: next-stable User: martenson Date: 2014-12-03 17:01:23+00:00 Summary: Merged in martenson/galaxy-central-marten/mako_escape_requests (pull request #579) [next-stable] escaping of the templates in the 'requests' and 'forms' sections Affected #: 18 files diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/admin/forms/create_form.mako --- a/templates/admin/forms/create_form.mako +++ b/templates/admin/forms/create_form.mako @@ -9,7 +9,7 @@ <div class="toolFormTitle">Create a new form definition</div> %for label, input in inputs: <div class="form-row"> - <label>${label}</label> + <label>${label | h}</label> ${input.get_html()} <div style="clear: both"></div></div> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/admin/forms/edit_form_definition.mako --- a/templates/admin/forms/edit_form_definition.mako +++ b/templates/admin/forms/edit_form_definition.mako @@ -96,14 +96,14 @@ <form id="edit_form_definition" name="edit_form_definition" action="${h.url_for( controller='forms', action='edit_form_definition', id=trans.security.encode_id( form_definition.current.id ) )}" method="post" ><div class="toolForm"> - <div class="toolFormTitle">Edit form definition "${form_definition.name}" (${form_definition.type})</div> + <div class="toolFormTitle">Edit form definition "${form_definition.name | h}" (${form_definition.type | h})</div> %if response_redirect: <input type="hidden" name="response_redirect" value="${response_redirect}" size="40" /> %endif %for label, input in form_details: <div class="form-row"> %if label != 'Type': - <label>${label}</label> + <label>${label | h}</label> %endif <div style="float: left; width: 250px; margin-right: 10px;"> ${input.get_html()} diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/admin/request_type/common.mako --- a/templates/admin/request_type/common.mako +++ b/templates/admin/request_type/common.mako @@ -2,7 +2,7 @@ <div class="repeat-group-item"><div class="form-row"><label>${1+element_count}. State name:</label> - <input type="text" name="state_name_${element_count}" value="${state_name}" size="40"/> + <input type="text" name="state_name_${element_count}" value="${state_name | h}" size="40"/> ## Do not show remove button for the first state %if element_count > 0: <input type="submit" name="remove_state_button" value="Remove state ${1+element_count}"/> @@ -10,7 +10,7 @@ </div><div class="form-row"><label>Description:</label> - <input type="text" name="state_desc_${element_count}" value="${state_desc}" size="40"/> + <input type="text" name="state_desc_${element_count}" value="${state_desc | h}" size="40"/><div class="toolParamHelp" style="clear: both;"> optional </div> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/admin/request_type/create_request_type.mako --- a/templates/admin/request_type/create_request_type.mako +++ b/templates/admin/request_type/create_request_type.mako @@ -23,7 +23,7 @@ <div class="toolFormTitle">Create a new request type</div> %for rt_info in rt_info_widgets: <div class="form-row"> - <label>${rt_info['label']}</label> + <label>${rt_info['label'] | h}</label><div style="float: left; width: 250px; margin-right: 10px;"> ${rt_info['widget'].get_html()} </div> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/admin/request_type/edit_request_type.mako --- a/templates/admin/request_type/edit_request_type.mako +++ b/templates/admin/request_type/edit_request_type.mako @@ -32,26 +32,26 @@ <form name="edit_request_type" action="${h.url_for( controller='request_type', action='edit_request_type', id=trans.security.encode_id( request_type.id ) )}" method="post" ><div class="toolForm"> - <div class="toolFormTitle">"Edit ${request_type.name}" request type</div> + <div class="toolFormTitle">"Edit ${request_type.name | h}" request type</div><div class="form-row"><label>Name:</label> - <input type="text" name="name" value="${request_type.name}" size="40"/> + <input type="text" name="name" value="${request_type.name | }" size="40"/><div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - <input type="text" name="desc" value="${request_type.desc}" size="40"/> + <input type="text" name="desc" value="${request_type.desc | h}" size="40"/><div style="clear: both"></div></div><div class="form-row"><label>Sequencing request form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name | h}</a> ## Hidden field needed by the __save_request_type() method <input type="hidden" name="request_form_id" value="${trans.security.encode_id( request_type.request_form_id )}" size="40"/></div><div class="form-row"><label>Sample form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name | h}</a> ## Hidden field needed by the __save_request_type() method <input type="hidden" name="sample_form_id" value="${trans.security.encode_id( request_type.sample_form_id )}" size="40"/></div> @@ -63,11 +63,11 @@ <div class="repeat-group-item"><div class="form-row"><label>${1+element_count}. State name:</label> - <input type="text" name="state_name_${trans.security.encode_id( state.id )}" value="${state.name}" size="40"/> + <input type="text" name="state_name_${trans.security.encode_id( state.id )}" value="${state.name | h}" size="40"/></div><div class="form-row"><label>Description:</label> - <input type="text" name="state_desc_${trans.security.encode_id( state.id )}" value="${state.desc}" size="40"/> + <input type="text" name="state_desc_${trans.security.encode_id( state.id )}" value="${state.desc | h}" size="40"/><div class="toolParamHelp" style="clear: both;"> optional </div> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/admin/request_type/request_type_permissions.mako --- a/templates/admin/request_type/request_type_permissions.mako +++ b/templates/admin/request_type/request_type_permissions.mako @@ -48,7 +48,7 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Manage access permissions on request type "${request_type.name}"</div> + <div class="toolFormTitle">Manage access permissions on request type "${request_type.name | h}"</div><div class="toolFormBody"><form name="request_type_permissions" id="request_type_permissions" action="${h.url_for( controller='request_type', action='request_type_permissions', id=trans.security.encode_id( request_type.id ) )}" method="post"><div class="form-row"> @@ -65,13 +65,13 @@ in_roles.add( a.role ) out_roles = filter( lambda x: x not in in_roles, all_roles ) %> - ${action.description}<br/><br/> + ${action.description | h}<br/><br/><div style="width: 100%; white-space: nowrap;"><div style="float: left; width: 50%;"> Roles associated:<br/><select name="${action_key}_in" id="${action_key}_in_select" class="in_select" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple> %for role in in_roles: - <option value="${role.id}">${role.name}</option> + <option value="${role.id}">${role.name | h}</option> %endfor </select><br/><div style="width: 98%; text-align: right"><input type="submit" id="${action_key}_remove_button" class="role_remove_button" value=">>"/></div> @@ -80,7 +80,7 @@ Roles not associated:<br/><select name="${action_key}_out" id="${action_key}_out_select" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple> %for role in out_roles: - <option value="${role.id}">${role.name}</option> + <option value="${role.id}">${role.name | h}</option> %endfor </select><br/><input type="submit" id="${action_key}_add_button" class="role_add_button" value="<<"/> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/admin/request_type/view_request_type.mako --- a/templates/admin/request_type/view_request_type.mako +++ b/templates/admin/request_type/view_request_type.mako @@ -30,24 +30,24 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">"${request_type.name}" request type</div> + <div class="toolFormTitle">"${request_type.name | h}" request type</div><div class="form-row"><label>Name:</label> - ${request_type.name} + ${request_type.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - ${request_type.desc} + ${request_type.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>Sequencing request form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.request_form_id ) )}">${request_type.request_form.name | h}</a></div><div class="form-row"><label>Sample form definition:</label> - <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name}</a> + <a href="${h.url_for( controller='request_type', action='view_form_definition', id=trans.security.encode_id( request_type.sample_form_id ) )}">${request_type.sample_form.name | h}</a></div></div><p/> @@ -55,8 +55,8 @@ <div class="toolFormTitle">Sample states defined for this request type</div> %for state in request_type.states: <div class="form-row"> - <label>${state.name}</label> - ${state.desc} + <label>${state.name | h}</label> + ${state.desc | h} </div><div style="clear: both"></div> %endfor @@ -67,8 +67,8 @@ %if request_type.external_services: %for index, external_service in enumerate( request_type.external_services ): <div class="form-row"> - <label><a href="${h.url_for( controller='external_service', action='view_external_service', id=trans.security.encode_id( external_service.id ) )}">${external_service.name}</a></label> - ${external_service.get_external_service_type( trans ).name} + <label><a href="${h.url_for( controller='external_service', action='view_external_service', id=trans.security.encode_id( external_service.id ) )}">${external_service.name | h}</a></label> + ${external_service.get_external_service_type( trans ).name | h} </div> %endfor %else: diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/admin/requests/reject.mako --- a/templates/admin/requests/reject.mako +++ b/templates/admin/requests/reject.mako @@ -15,7 +15,7 @@ </ul><div class="toolForm"> - <div class="toolFormTitle">Reject sequencing request "${request.name}"</div> + <div class="toolFormTitle">Reject sequencing request "${request.name | h}"</div><form name="event" action="${h.url_for( controller='requests_admin', action='reject_request', id=trans.security.encode_id( request.id ) )}" method="post" ><div class="form-row"> Rejecting this request will move the request state to <b>Rejected</b>. diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/admin/requests/rename_datasets.mako --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -3,7 +3,7 @@ <% from galaxy.webapps.galaxy.controllers.requests_admin import build_rename_datasets_for_sample_select_field %> -<h3>Rename datasets for Sample "${sample.name}"</h3> +<h3>Rename datasets for Sample "${sample.name | h}"</h3><ul class="manage-table-actions"><li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Browse datasets</a></li> @@ -35,7 +35,7 @@ ${rename_datasets_for_sample_select_field.get_html()} </td><td> - <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id ) }" value="${sample_dataset.name}" size="100"/> + <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id ) }" value="${sample_dataset.name | h}" size="100"/></td><td>${sample_dataset.file_path}</td></tr> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/admin/requests/view_sample_dataset.mako --- a/templates/admin/requests/view_sample_dataset.mako +++ b/templates/admin/requests/view_sample_dataset.mako @@ -21,19 +21,19 @@ </ul><div class="toolForm"> - <div class="toolFormTitle">"${sample.name}" Dataset</div> + <div class="toolFormTitle">"${sample.name | h}" Dataset</div><div class="toolFormBody"><div class="form-row"><label>Name:</label><div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.name} + ${sample_dataset.name | h} </div><div style="clear: both"></div></div><div class="form-row"><label>External service:</label><div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.external_service.name} (${sample_dataset.external_service.get_external_service_type( trans ).name}) + ${sample_dataset.external_service.name | h} (${sample_dataset.external_service.get_external_service_type( trans ).name | h}) </div><div style="clear: both"></div></div> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/webapps/galaxy/requests/common/common.mako --- a/templates/webapps/galaxy/requests/common/common.mako +++ b/templates/webapps/galaxy/requests/common/common.mako @@ -257,18 +257,18 @@ <td valign="top"><input type="checkbox" name=select_sample_${sample.id} id="sample_checkbox" value="true" ${checked_str}/><input type="hidden" name=select_sample_${sample.id} id="sample_checkbox" value="true"/></td> %endif <td valign="top"> - <input type="text" name="sample_${sample_widget_index}_name" value="${sample_widget['name']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_name" value="${sample_widget['name'] | h}" size="10"/><div class="toolParamHelp" style="clear: both;"> - <i>${' (required)' }</i> + <i>(required)</i></div></td> %if display_bar_code: <td valign="top"> %if is_admin and is_submitted: - <input type="text" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code'] | h}" size="10"/> %else: - ${sample_widget['bar_code']} - <input type="hidden" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}"/> + ${sample_widget['bar_code'] | h} + <input type="hidden" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code'] | h}"/> %endif </td> %endif @@ -416,7 +416,7 @@ transferred_dataset_files = [] %><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="sample-${sample.id}-popup"> - <a class="view-info" href="${h.url_for( controller='requests_common', action='view_sample', cntrller=cntrller, id=trans.security.encode_id( sample.id ) )}">${sample.name}</a> + <a class="view-info" href="${h.url_for( controller='requests_common', action='view_sample', cntrller=cntrller, id=trans.security.encode_id( sample.id ) )}">${sample.name | h}</a></div><div popupmenu="sample-${sample.id}-popup"> %if can_select_datasets: @@ -439,11 +439,11 @@ %endif </div> %else: - ${sample_widget_name} + ${sample_widget_name | h} %endif </td> %if display_bar_code: - <td>${sample_widget_bar_code}</td> + <td>${sample_widget_bar_code | h}</td> %endif %if is_unsubmitted: <td>Unsubmitted</td> @@ -451,12 +451,12 @@ <td><a id="sampleState-${sample.id}" href="${h.url_for( controller='requests_common', action='view_sample_history', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${render_sample_state( sample )}</a></td> %endif %if sample_widget_library and library_cntrller is not None: - <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( sample_widget_library.id ) )}">${sample_widget_library.name}</a></td> + <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( sample_widget_library.id ) )}">${sample_widget_library.name | h}</a></td> %else: <td></td> %endif %if sample_widget_folder: - <td>${sample_widget_folder.name}</td> + <td>${sample_widget_folder.name | h}</td> %else: <td></td> %endif @@ -464,11 +464,11 @@ %if trans.user == sample_widget_history.user: <td><a target='_parent' href="${h.url_for( controller='history', action='list', operation="Switch", id=trans.security.encode_id(sample_widget_history.id), use_panels=False )}"> - ${sample_widget_history.name} + ${sample_widget_history.name | h} </a></td> %else: - <td>${sample_widget_history.name}</td> + <td>${sample_widget_history.name | h}</td> %endif %else: <td></td> @@ -477,11 +477,11 @@ %if trans.user == sample_widget_workflow.stored_workflow.user: <td><a target='_parent' href="${h.url_for( controller='workflow', action='editor', id=trans.security.encode_id(sample_widget_workflow.stored_workflow.id) )}"> - ${sample_widget_workflow.name} + ${sample_widget_workflow.name | h} </a></td> %else: - <td>${sample_widget_workflow.name}</td> + <td>${sample_widget_workflow.name | h}</td> %endif %else: <td></td> @@ -519,7 +519,7 @@ <%def name="render_sample_form( index, sample_name, sample_values, fields_dict, display_only )"><tr> - <td>${sample_name}</td> + <td>${sample_name | h}</td> %for field_index, field in fields_dict.items(): <% field_type = field[ 'type' ] @@ -532,17 +532,17 @@ %if field_type == 'WorkflowField': %if str( field_value ) != 'none': <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int( field_value ) ) %> - <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">${workflow.name}</a> + <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">${workflow.name | h}</a> %endif %else: - ${field_value} + ${field_value | h} %endif %else: <i>None</i> %endif %else: %if field_type == 'TextField': - <input type="text" name="sample_${index}_field_${field_index}" value="${field_value}" size="7"/> + <input type="text" name="sample_${index}_field_${field_index}" value="${field_value | h}" size="7"/> %elif field_type == 'SelectField': <select name="sample_${index}_field_${field_index}" last_selected_value="2"> %for option_index, option in enumerate(field[ 'selectlist' ]): @@ -695,7 +695,7 @@ %if is_admin: <span class="expandLink dataset-${dataset}-click"><span class="rowIcon"></span><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="dataset-${dataset.id}-popup"> - <a class="dataset-${encoded_id}-click" href="${h.url_for( controller='requests_admin', action='manage_datasets', operation='view', id=trans.security.encode_id( dataset.id ) )}">${dataset.name}</a> + <a class="dataset-${encoded_id}-click" href="${h.url_for( controller='requests_admin', action='manage_datasets', operation='view', id=trans.security.encode_id( dataset.id ) )}">${dataset.name | h}</a></div></span><div popupmenu="dataset-${dataset.id}-popup"> @@ -704,12 +704,12 @@ %endif </div> %else: - ${dataset.name} + ${dataset.name | h} %endif </td><td>${dataset.size}</td> - <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">${dataset.sample.library.name}</a></td> - <td>${dataset.sample.folder.name}</td> + <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">${dataset.sample.library.name | h}</a></td> + <td>${dataset.sample.folder.name | h}</td><td id="datasetTransferStatus-${encoded_id}">${dataset.status}</td></tr> %endfor @@ -723,7 +723,7 @@ <%def name="render_samples_messages( request, is_admin=False, is_submitted=False, message=None, status=None)"> %if request.is_rejected: <div class='errormessage'> - ${request.last_comment} + ${request.last_comment | h} </div><br/> %endif %if is_admin and is_submitted and request.samples_without_library_destinations: diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/webapps/galaxy/requests/common/create_request.mako --- a/templates/webapps/galaxy/requests/common/create_request.mako +++ b/templates/webapps/galaxy/requests/common/create_request.mako @@ -23,7 +23,7 @@ <div class="toolForm"><div class="toolFormTitle">Create a new sequencing request</div> %if len( request_type_select_field.options ) < 1: - There are no request types available for ${trans.user.email} to create sequencing requests. + There are no request types available for ${trans.user.email | h} to create sequencing requests. %else: <div class="toolFormBody"><form name="create_request" id="create_request" action="${h.url_for( controller='requests_common', action='create_request', cntrller=cntrller )}" method="post" > diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/webapps/galaxy/requests/common/edit_basic_request_info.mako --- a/templates/webapps/galaxy/requests/common/edit_basic_request_info.mako +++ b/templates/webapps/galaxy/requests/common/edit_basic_request_info.mako @@ -31,7 +31,7 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Edit sequencing request "${request.name}"</div> + <div class="toolFormTitle">Edit sequencing request "${request.name | h}"</div><div class="toolFormBody"><form name="edit_basic_request_info" id="edit_basic_request_info" action="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}" method="post" > %for i, field in enumerate( widgets ): @@ -70,11 +70,11 @@ %><div class="form-row"><label>Send to:</label> - <input type="checkbox" name="email_address" value="true" ${email_address}>${request.user.email} (sequencing request owner)<input type="hidden" name="email_address" value="true"> + <input type="checkbox" name="email_address" value="true" ${email_address}>${request.user.email | h} (sequencing request owner)<input type="hidden" name="email_address" value="true"></div><div class="form-row"><label>Additional email addresses:</label> - <textarea name="additional_email_addresses" rows="3" cols="40">${emails}</textarea> + <textarea name="additional_email_addresses" rows="3" cols="40">${emails | h}</textarea><div class="toolParamHelp" style="clear: both;"> Enter one email address per line </div> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/webapps/galaxy/requests/common/find_samples.mako --- a/templates/webapps/galaxy/requests/common/find_samples.mako +++ b/templates/webapps/galaxy/requests/common/find_samples.mako @@ -72,7 +72,7 @@ %if samples: %for sample in samples: <div class="form-row"> - Sample: <b>${sample.name}</b> | Barcode: ${sample.bar_code}<br/> + Sample: <b>${sample.name | h}</b> | Barcode: ${sample.bar_code | h}<br/> %if sample.request.is_new or not sample.state: State: Unsubmitted<br/> %else: @@ -85,10 +85,10 @@ %> Datasets: <a href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, external_service_id=trans.security.encode_id( external_service.id ), sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a><br/> %if is_admin: - <i>User: ${sample.request.user.email}</i> + <i>User: ${sample.request.user.email | h}</i> %endif <div class="toolParamHelp" style="clear: both;"> - <a href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Sequencing request: ${sample.request.name} | Type: ${sample.request.type.name} | State: ${sample.request.state}</a> + <a href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Sequencing request: ${sample.request.name | h} | Type: ${sample.request.type.name} | State: ${sample.request.state}</a></div></div><br/> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/webapps/galaxy/requests/common/view_request.mako --- a/templates/webapps/galaxy/requests/common/view_request.mako +++ b/templates/webapps/galaxy/requests/common/view_request.mako @@ -58,7 +58,7 @@ ${render_samples_messages(request, is_admin, is_submitted, message, status)} <div class="toolForm"> - <div class="toolFormTitle">Sequencing request "${request.name}"</div> + <div class="toolFormTitle">Sequencing request "${request.name | h}"</div><div class="toolFormBody"><div class="form-row"><label>Current state:</label> @@ -67,12 +67,12 @@ </div><div class="form-row"><label>Description:</label> - ${request.desc} + ${request.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>User:</label> - ${request.user.email} + ${request.user.email | h} <div style="clear: both"></div></div><div class="form-row"> @@ -94,7 +94,7 @@ %><div class="form-row"><label>${field_label}:</label> - ${field_value} + ${field_value | h} </div><div style="clear: both"></div> %endfor @@ -116,7 +116,7 @@ else: emails = '' %> - ${emails} + ${emails | h} <div style="clear: both"></div></div><div class="form-row"> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/webapps/galaxy/requests/common/view_request_history.mako --- a/templates/webapps/galaxy/requests/common/view_request_history.mako +++ b/templates/webapps/galaxy/requests/common/view_request_history.mako @@ -36,7 +36,7 @@ ${render_msg( message, status )} %endif -<h3>History of sequencing request "${request.name}"</h3> +<h3>History of sequencing request "${request.name | h}"</h3><div class="toolForm"><table class="grid"> @@ -52,7 +52,7 @@ <tr><td><b>${event.state}</b></td><td>${time_ago( event.update_time )}</td> - <td>${event.comment}</td> + <td>${event.comment | h}</td></tr> %endfor </tbody> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/webapps/galaxy/requests/common/view_sample.mako --- a/templates/webapps/galaxy/requests/common/view_sample.mako +++ b/templates/webapps/galaxy/requests/common/view_sample.mako @@ -6,7 +6,7 @@ %if external_service: <p><div class="toolForm"> - <div class="toolFormTitle">Available External Service Actions for ${sample.name} at ${external_service.name}</div> + <div class="toolFormTitle">Available External Service Actions for ${sample.name | h} at ${external_service.name | h}</div><div class="toolFormBody"><div class="toolMenu"> %for item in external_service.actions: @@ -25,7 +25,7 @@ <div class="form-row"><div class="toolSectionList"><div class="toolSectionTitle"> - <span>${external_service_group.label}</span> + <span>${external_service_group.label | h}</span></div><div class="toolSectionBody"><div class="toolSectionBg"> @@ -54,7 +54,7 @@ target = 'galaxy_main' %><div class="toolTitle"> - <a href="${external_service_action.get_action_access_link( trans )}" target="${target}">${external_service_action.label}</a> + <a href="${external_service_action.get_action_access_link( trans )}" target="${target}">${external_service_action.label | h}</a></div></%def> @@ -75,38 +75,38 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Sample "${sample.name}"</div> + <div class="toolFormTitle">Sample "${sample.name | h}"</div><div class="toolFormBody"><div class="form-row"><label>Name:</label> - ${sample.name} + ${sample.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Description:</label> - ${sample.desc} + ${sample.desc | h} <div style="clear: both"></div></div><div class="form-row"><label>Barcode:</label> - ${sample.bar_code} + ${sample.bar_code | h} <div style="clear: both"></div></div> %if sample.library: <div class="form-row"><label>Library:</label> - ${sample.library.name} + ${sample.library.name | h} <div style="clear: both"></div></div><div class="form-row"><label>Folder:</label> - ${sample.folder.name} + ${sample.folder.name | h} <div style="clear: both"></div></div> %endif <div class="form-row"><label>Request:</label> - ${sample.request.name} + ${sample.request.name | h} <div style="clear: both"></div></div></div> diff -r 13d43b327511d46e836398fa09330722acccd419 -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 templates/webapps/galaxy/requests/common/view_sample_history.mako --- a/templates/webapps/galaxy/requests/common/view_sample_history.mako +++ b/templates/webapps/galaxy/requests/common/view_sample_history.mako @@ -12,7 +12,7 @@ ${render_msg( message, status )} %endif -<h3>History of sample "${sample.name}"</h3> +<h3>History of sample "${sample.name | h}"</h3><div class="toolForm"><table class="grid"> @@ -27,10 +27,10 @@ <tbody> %for event in sample.events: <tr> - <td><b>${event.state.name}</b></td> - <td>${event.state.desc}</td> + <td><b>${event.state.name | h}</b></td> + <td>${event.state.desc | h}</td><td>${time_ago( event.update_time )}</td> - <td>${event.comment}</td> + <td>${event.comment | h}</td></tr> %endfor </tbody> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 03 Dec '14

03 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0273de7467e0/ Changeset: 0273de7467e0 User: dan Date: 2014-12-03 16:35:35+00:00 Summary: DatasetMatcher should check to see if hda is of the correct format before attempting to filter on e.g. metadata attributes (that may not exist for a non-expected format). Affected #: 1 file diff -r 87ef26ad1876d0d6162eb4b6e7c93c8d69fbc4d6 -r 0273de7467e0f42a56ffa018c5fb9a53a6396e76 lib/galaxy/tools/parameters/dataset_matcher.py --- a/lib/galaxy/tools/parameters/dataset_matcher.py +++ b/lib/galaxy/tools/parameters/dataset_matcher.py @@ -39,27 +39,30 @@ return state_valid and ( not check_security or self.__can_access_dataset( dataset ) ) def valid_hda_match( self, hda, check_implicit_conversions=True, check_security=False ): - """ Return False of this parameter can not be matched to a the supplied + """ Return False of this parameter can not be matched to the supplied HDA, otherwise return a description of the match (either a HdaDirectMatch describing a direct match or a HdaImplicitMatch describing an implicit conversion.) """ + rval = False + formats = self.param.formats + if hda.datatype.matches_any( formats ): + rval = HdaDirectMatch( hda ) + else: + if not check_implicit_conversions: + return False + target_ext, converted_dataset = hda.find_conversion_destination( formats ) + if target_ext: + if converted_dataset: + hda = converted_dataset + if check_security and not self.__can_access_dataset( hda.dataset ): + return False + rval = HdaImplicitMatch( hda, target_ext ) + else: + return False if self.filter( hda ): return False - formats = self.param.formats - if hda.datatype.matches_any( formats ): - return HdaDirectMatch( hda ) - if not check_implicit_conversions: - return False - target_ext, converted_dataset = hda.find_conversion_destination( formats ) - if target_ext: - original_hda = hda - if converted_dataset: - hda = converted_dataset - if check_security and not self.__can_access_dataset( hda.dataset ): - return False - return HdaImplicitMatch( hda, target_ext, original_hda ) - return False + return rval def hda_match( self, hda, check_implicit_conversions=True, ensure_visible=True ): """ If HDA is accessible, return information about whether it could https://bitbucket.org/galaxy/galaxy-central/commits/13d43b327511/ Changeset: 13d43b327511 Branch: next-stable User: dan Date: 2014-12-03 16:35:35+00:00 Summary: DatasetMatcher should check to see if hda is of the correct format before attempting to filter on e.g. metadata attributes (that may not exist for a non-expected format). Affected #: 1 file diff -r f05ed31c16741b5c1a4a43c73697f7ca9a6919d8 -r 13d43b327511d46e836398fa09330722acccd419 lib/galaxy/tools/parameters/dataset_matcher.py --- a/lib/galaxy/tools/parameters/dataset_matcher.py +++ b/lib/galaxy/tools/parameters/dataset_matcher.py @@ -39,27 +39,30 @@ return state_valid and ( not check_security or self.__can_access_dataset( dataset ) ) def valid_hda_match( self, hda, check_implicit_conversions=True, check_security=False ): - """ Return False of this parameter can not be matched to a the supplied + """ Return False of this parameter can not be matched to the supplied HDA, otherwise return a description of the match (either a HdaDirectMatch describing a direct match or a HdaImplicitMatch describing an implicit conversion.) """ + rval = False + formats = self.param.formats + if hda.datatype.matches_any( formats ): + rval = HdaDirectMatch( hda ) + else: + if not check_implicit_conversions: + return False + target_ext, converted_dataset = hda.find_conversion_destination( formats ) + if target_ext: + if converted_dataset: + hda = converted_dataset + if check_security and not self.__can_access_dataset( hda.dataset ): + return False + rval = HdaImplicitMatch( hda, target_ext ) + else: + return False if self.filter( hda ): return False - formats = self.param.formats - if hda.datatype.matches_any( formats ): - return HdaDirectMatch( hda ) - if not check_implicit_conversions: - return False - target_ext, converted_dataset = hda.find_conversion_destination( formats ) - if target_ext: - original_hda = hda - if converted_dataset: - hda = converted_dataset - if check_security and not self.__can_access_dataset( hda.dataset ): - return False - return HdaImplicitMatch( hda, target_ext, original_hda ) - return False + return rval def hda_match( self, hda, check_implicit_conversions=True, ensure_visible=True ): """ If HDA is accessible, return information about whether it could Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 03 Dec '14

03 Dec '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b2df443a12d6/ Changeset: b2df443a12d6 Branch: next-stable User: dannon Date: 2014-12-03 14:21:54+00:00 Summary: Bump NO_OUTPUT_TIMEOUT to 60m; Bjoern said it's causing issues w/ some tools for being too short. Affected #: 1 file diff -r eb9d9ab34d23456d58f291b782b42724a83f711e -r b2df443a12d6a721da2a58b56491fbed08ebc4d9 lib/tool_shed/util/basic_util.py --- a/lib/tool_shed/util/basic_util.py +++ b/lib/tool_shed/util/basic_util.py @@ -16,7 +16,7 @@ CHUNK_SIZE = 2**20 # 1Mb INSTALLATION_LOG = 'INSTALLATION.log' # Set no activity timeout to 20 minutes. -NO_OUTPUT_TIMEOUT = 1200.0 +NO_OUTPUT_TIMEOUT = 3600.0 MAXDIFFSIZE = 8000 MAX_DISPLAY_SIZE = 32768 https://bitbucket.org/galaxy/galaxy-central/commits/81d5a494d274/ Changeset: 81d5a494d274 Branch: next-stable User: dannon Date: 2014-12-03 14:23:14+00:00 Summary: Pep8 tool_shed/util/basic_util Affected #: 1 file diff -r b2df443a12d6a721da2a58b56491fbed08ebc4d9 -r 81d5a494d274918192fe92bd3ac9217bcb22ef2c lib/tool_shed/util/basic_util.py --- a/lib/tool_shed/util/basic_util.py +++ b/lib/tool_shed/util/basic_util.py @@ -13,7 +13,7 @@ log = logging.getLogger( __name__ ) -CHUNK_SIZE = 2**20 # 1Mb +CHUNK_SIZE = 2**20 # 1Mb INSTALLATION_LOG = 'INSTALLATION.log' # Set no activity timeout to 20 minutes. NO_OUTPUT_TIMEOUT = 3600.0 @@ -47,6 +47,7 @@ RUN service postgresql start && service apache2 start && ./run.sh --daemon && sleep 120 && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:8080 --url ${tool_shed_url} -o ${repository_owner} --name ${repository_name} --tool-deps --repository-deps --panel-section-name 'Docker' ''' + def evaluate_template( text, install_environment ): """ Substitute variables defined in XML blocks from dependencies file. The value of the received @@ -56,6 +57,7 @@ """ return Template( text ).safe_substitute( get_env_var_values( install_environment ) ) + def get_env_var_values( install_environment ): """ Return a dictionary of values, some of which enable substitution of reserved words for the values. @@ -72,6 +74,7 @@ env_var_dict[ '__is64bit__' ] = sys.maxsize > 2**32 return env_var_dict + def get_file_type_str( changeset_revision, file_type ): if file_type == 'zip': file_type_str = '%s.zip' % changeset_revision @@ -83,6 +86,7 @@ file_type_str = '' return file_type_str + def move_file( current_dir, source, destination, rename_to=None ): source_path = os.path.abspath( os.path.join( current_dir, source ) ) source_file = os.path.basename( source_path ) @@ -97,6 +101,7 @@ os.makedirs( destination_directory ) shutil.move( source_path, destination_path ) + def remove_dir( dir ): """Attempt to remove a directory from disk.""" if dir: @@ -106,6 +111,7 @@ except: pass + def size_string( raw_text, size=MAX_DISPLAY_SIZE ): """Return a subset of a string (up to MAX_DISPLAY_SIZE) translated to a safe string for display in a browser.""" if raw_text and len( raw_text ) >= size: @@ -113,11 +119,13 @@ raw_text = '%s%s' % ( raw_text[ 0:size ], large_str ) return raw_text or '' + def stringify( list ): if list: return ','.join( list ) return '' + def strip_path( fpath ): """Attempt to strip the path from a file name.""" if not fpath: @@ -128,6 +136,7 @@ file_name = fpath return file_name + def to_html_string( text ): """Translates the characters in text to an html string""" if text: https://bitbucket.org/galaxy/galaxy-central/commits/f05ed31c1674/ Changeset: f05ed31c1674 Branch: next-stable User: dannon Date: 2014-12-03 14:24:44+00:00 Summary: Fix size_string; this would have thrown an exception on being called due to an unimported 'util'. Affected #: 1 file diff -r 81d5a494d274918192fe92bd3ac9217bcb22ef2c -r f05ed31c16741b5c1a4a43c73697f7ca9a6919d8 lib/tool_shed/util/basic_util.py --- a/lib/tool_shed/util/basic_util.py +++ b/lib/tool_shed/util/basic_util.py @@ -4,7 +4,7 @@ import sys from string import Template -from galaxy.util import unicodify +from galaxy.util import unicodify, nice_size from galaxy import eggs @@ -115,7 +115,7 @@ def size_string( raw_text, size=MAX_DISPLAY_SIZE ): """Return a subset of a string (up to MAX_DISPLAY_SIZE) translated to a safe string for display in a browser.""" if raw_text and len( raw_text ) >= size: - large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( size ) + large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % nice_size( size ) raw_text = '%s%s' % ( raw_text[ 0:size ], large_str ) return raw_text or '' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Improvements to test/api/test_workflow_extraction.py.
by commits-noreply＠bitbucket.org 03 Dec '14

03 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/87ef26ad1876/ Changeset: 87ef26ad1876 User: jmchilton Date: 2014-12-03 03:17:25+00:00 Summary: Improvements to test/api/test_workflow_extraction.py. Fill out the dataset collection parameter test and add a new test for a workflow that includes subcollection mapping. Move toward orchestrating jobs in this file via a high-level YAML description of steps and test data as well as some higher-level methods for testing various stuff about extracted workflows (step counts, input types, tools used, connected-ness, etc...). Allow ordering jobs index API by create_time instead of update_time. Affected #: 4 files diff -r a734cbf4bd368198e2c813b5ea61e807f9a1af33 -r 87ef26ad1876d0d6162eb4b6e7c93c8d69fbc4d6 lib/galaxy/webapps/galaxy/api/jobs.py --- a/lib/galaxy/webapps/galaxy/api/jobs.py +++ b/lib/galaxy/webapps/galaxy/api/jobs.py @@ -73,9 +73,11 @@ raise exceptions.ObjectAttributeInvalidException() out = [] - for job in query.order_by( - trans.app.model.Job.update_time.desc() - ).all(): + if kwd.get( 'order_by' ) == 'create_time': + order_by = trans.app.model.Job.create_time.desc() + else: + order_by = trans.app.model.Job.update_time.desc() + for job in query.order_by( order_by ).all(): out.append( self.encode_all_ids( trans, job.to_dict( 'collection' ), True ) ) return out diff -r a734cbf4bd368198e2c813b5ea61e807f9a1af33 -r 87ef26ad1876d0d6162eb4b6e7c93c8d69fbc4d6 test/api/helpers.py --- a/test/api/helpers.py +++ b/test/api/helpers.py @@ -76,7 +76,10 @@ return run_response.json()["outputs"][0] def wait_for_history( self, history_id, assert_ok=False, timeout=DEFAULT_HISTORY_TIMEOUT ): - wait_on_state( lambda: self.galaxy_interactor.get( "histories/%s" % history_id ), assert_ok=assert_ok, timeout=timeout ) + return wait_on_state( lambda: self.galaxy_interactor.get( "histories/%s" % history_id ), assert_ok=assert_ok, timeout=timeout ) + + def wait_for_job( self, job_id, assert_ok=False, timeout=DEFAULT_HISTORY_TIMEOUT ): + return wait_on_state( lambda: self.galaxy_interactor.get( "jobs/%s" % job_id ), assert_ok=assert_ok, timeout=timeout ) def new_history( self, **kwds ): name = kwds.get( "name", "API Test History" ) @@ -296,6 +299,12 @@ ) return self.__create( payload ) + def create_list_of_pairs_in_history( self, history_id, **kwds ): + pair1 = self.create_pair_in_history( history_id, **kwds ).json()["id"] + #pair2 = self.create_pair_in_history( history_id, **kwds ).json()["id"] + #pair3 = self.create_pair_in_history( history_id, **kwds ).json()["id"] + return self.create_list_from_pairs( history_id, [ pair1 ] ) + def create_pair_in_history( self, history_id, **kwds ): payload = self.create_pair_payload( history_id, @@ -375,13 +384,13 @@ response = state_func() assert response.status_code == 200, "Failed to fetch state update while waiting." state = response.json()[ "state" ] - if state not in [ "running", "queued", "new" ]: + if state not in [ "running", "queued", "new", "ready" ]: if assert_ok: assert state == "ok", "Final state - %s - not okay." % state return state else: return None - wait_on( get_state, desc="state", timeout=timeout) + return wait_on( get_state, desc="state", timeout=timeout) def wait_on( function, desc, timeout=5 ): diff -r a734cbf4bd368198e2c813b5ea61e807f9a1af33 -r 87ef26ad1876d0d6162eb4b6e7c93c8d69fbc4d6 test/api/test_workflow_extraction.py --- a/test/api/test_workflow_extraction.py +++ b/test/api/test_workflow_extraction.py @@ -1,8 +1,12 @@ +from collections import namedtuple +import functools from json import dumps, loads import operator from .helpers import skip_without_tool +from .helpers import wait_on_state from .test_workflows import BaseWorkflowsApiTestCase +import yaml class WorkflowExtractionApiTestCase( BaseWorkflowsApiTestCase ): @@ -110,27 +114,147 @@ @skip_without_tool( "collection_paired_test" ) def test_extract_workflows_with_dataset_collections( self ): - hdca = self.dataset_collection_populator.create_pair_in_history( self.history_id ).json() - hdca_id = hdca[ "id" ] - inputs = { - "f1": dict( src="hdca", id=hdca_id ) - } - run_output = self.dataset_populator.run_tool( - tool_id="collection_paired_test", - inputs=inputs, - history_id=self.history_id, - ) - job_id = run_output[ "jobs" ][ 0 ][ "id" ] - self.dataset_populator.wait_for_history( self.history_id, assert_ok=True ) + jobs_summary = self._run_jobs(""" +steps: + - label: text_input1 + type: input_collection + - tool_id: collection_paired_test + state: + f1: + $link: text_input1 +test_data: + text_input1: + type: paired +""") + job_id = self._job_id_for_tool( jobs_summary.jobs, "collection_paired_test" ) downloaded_workflow = self._extract_and_download_workflow( - dataset_collection_ids=[ hdca[ "hid" ] ], + dataset_collection_ids=[ jobs_summary.inputs["text_input1"]["hid"] ], job_ids=[ job_id ], ) - collection_steps = self._get_steps_of_type( downloaded_workflow, "data_collection_input", expected_len=1 ) - collection_step = collection_steps[ 0 ] + self.__check_workflow( + downloaded_workflow, + step_count=2, + verify_connected=True, + data_input_count=0, + data_collection_input_count=1, + tool_ids=["collection_paired_test"] + ) + + collection_step = self._get_steps_of_type( downloaded_workflow, "data_collection_input", expected_len=1 )[ 0 ] collection_step_state = loads( collection_step[ "tool_state" ] ) self.assertEquals( collection_step_state[ "collection_type" ], u"paired" ) + def test_subcollection_mapping( self ): + jobs_summary = self._run_jobs(""" +steps: + - label: text_input1 + type: input_collection + - label: noop + tool_id: cat1 + state: + input1: + $link: text_input1 + - tool_id: cat_collection + state: + input1: + $link: noop#out_file1 +test_data: + text_input1: + type: "list:paired" + """) + job1_id = self._job_id_for_tool( jobs_summary.jobs, "cat1" ) + job2_id = self._job_id_for_tool( jobs_summary.jobs, "cat_collection" ) + downloaded_workflow = self._extract_and_download_workflow( + dataset_collection_ids=[ jobs_summary.inputs["text_input1"]["hid"] ], + job_ids=[ job1_id, job2_id ], + ) + print jobs_summary.inputs["text_input1"] + self.__check_workflow( + downloaded_workflow, + step_count=3, + verify_connected=True, + data_input_count=0, + data_collection_input_count=1, + tool_ids=["cat_collection", "cat1"], + ) + + collection_step = self._get_steps_of_type( downloaded_workflow, "data_collection_input", expected_len=1 )[ 0 ] + collection_step_state = loads( collection_step[ "tool_state" ] ) + self.assertEquals( collection_step_state[ "collection_type" ], u"list:paired" ) + + def _run_jobs( self, jobs_yaml ): + history_id = self.history_id + workflow_id = self._upload_yaml_workflow( + jobs_yaml + ) + jobs_descriptions = yaml.load( jobs_yaml ) + test_data = jobs_descriptions["test_data"] + + label_map = {} + inputs = {} + for key, value in test_data.items(): + if isinstance( value, dict ): + elements_data = value.get( "elements", [] ) + elements = [] + for element_data in elements_data: + identifier = element_data[ "identifier" ] + content = element_data["content"] + elements.append( ( identifier, content ) ) + collection_type = value["type"] + if collection_type == "list:paired": + hdca = self.dataset_collection_populator.create_list_of_pairs_in_history( history_id ).json() + elif collection_type == "list": + hdca = self.dataset_collection_populator.create_list_in_history( history_id, contents=elements ).json() + else: + hdca = self.dataset_collection_populator.create_pair_in_history( history_id, contents=elements ).json() + label_map[key] = self._ds_entry( hdca ) + inputs[key] = hdca + else: + hda = self.dataset_populator.new_dataset( history_id, content=value ) + label_map[key] = self._ds_entry( hda ) + inputs[key] = hda + workflow_request = dict( + history="hist_id=%s" % history_id, + workflow_id=workflow_id, + ) + workflow_request[ "inputs" ] = dumps( label_map ) + workflow_request[ "inputs_by" ] = 'name' + self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + url = "workflows/%s/usage" % ( workflow_id ) + invocation_response = self._post( url, data=workflow_request ) + self._assert_status_code_is( invocation_response, 200 ) + invocation = invocation_response.json() + invocation_id = invocation[ "id" ] + # Wait for workflow to become fully scheduled and then for all jobs + # complete. + self.wait_for_invocation( workflow_id, invocation_id ) + self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + jobs = self._history_jobs( history_id ) + return RunJobsSummary( + history_id=history_id, + workflow_id=workflow_id, + inputs=inputs, + jobs=jobs, + ) + + def wait_for_invocation( self, workflow_id, invocation_id ): + url = "workflows/%s/usage/%s" % ( workflow_id, invocation_id ) + return wait_on_state( lambda: self._get( url ) ) + + def _history_jobs( self, history_id ): + return self._get("jobs", { "history_id": history_id, "order_by": "create_time" } ).json() + + def _job_id_for_tool( self, jobs, tool_id ): + return self._job_for_tool( jobs, tool_id )[ "id" ] + + def _job_for_tool( self, jobs, tool_id ): + tool_jobs = filter( lambda j: j["tool_id"] == tool_id, jobs ) + if not tool_jobs: + assert False, "Failed to find job for tool %s" % tool_id + # if len( tool_jobs ) > 1: + # assert False, "Found multiple jobs for tool %s" % tool_id + return tool_jobs[ -1 ] + def __run_random_lines_mapped_over_pair( self, history_id ): hdca = self.dataset_collection_populator.create_pair_in_history( history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"] ).json() hdca_id = hdca[ "id" ] @@ -266,3 +390,45 @@ job_id = run_output1[ "jobs" ][ 0 ][ "id" ] self.dataset_populator.wait_for_history( history_id, assert_ok=True, timeout=20 ) return implicit_hdca, job_id + + def __check_workflow( + self, + workflow, + step_count=None, + verify_connected=False, + data_input_count=None, + data_collection_input_count=None, + tool_ids=None, + ): + steps = workflow[ 'steps' ] + + if step_count is not None: + assert len( steps ) == step_count + if verify_connected: + self.__assert_connected( workflow, steps ) + if tool_ids is not None: + tool_steps = self._get_steps_of_type( workflow, "tool" ) + found_steps = set(map(operator.itemgetter("tool_id"), tool_steps)) + expected_steps = set(tool_ids) + assert found_steps == expected_steps + if data_input_count is not None: + self._get_steps_of_type( workflow, "data_input", expected_len=data_input_count ) + if data_collection_input_count is not None: + self._get_steps_of_type( workflow, "data_collection_input", expected_len=data_collection_input_count ) + + def __assert_connected( self, workflow, steps ): + disconnected_inputs = [] + + for key, value in steps.items(): + if value[ 'type' ] == "tool": + input_connections = value[ "input_connections" ] + if not input_connections: + disconnected_inputs.append( value ) + + if disconnected_inputs: + template = "%d step(s_ disconnected in extracted workflow - disconnectect steps are %s - workflow is %s" + message = template % ( len( disconnected_inputs ), disconnected_inputs, workflow ) + raise AssertionError( message ) + + +RunJobsSummary = namedtuple('RunJobsSummary', ['history_id', 'workflow_id', 'inputs', 'jobs']) diff -r a734cbf4bd368198e2c813b5ea61e807f9a1af33 -r 87ef26ad1876d0d6162eb4b6e7c93c8d69fbc4d6 test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -95,6 +95,12 @@ workflow_inputs = workflow_show_resposne.json()[ "inputs" ] return workflow_inputs + def _invocation_details( self, workflow_id, invocation_id ): + invocation_details_response = self._get( "workflows/%s/usage/%s" % ( workflow_id, invocation_id ) ) + self._assert_status_code_is( invocation_details_response, 200 ) + invocation_details = invocation_details_response.json() + return invocation_details + # Workflow API TODO: # - Allow history_id as param to workflow run action. (hist_id) @@ -530,12 +536,6 @@ self._assert_status_code_is( step_response, 200 ) self._assert_has_keys( step_response.json(), "id", "order_index" ) - def _invocation_details( self, workflow_id, invocation_id ): - invocation_details_response = self._get( "workflows/%s/usage/%s" % ( workflow_id, invocation_id ) ) - self._assert_status_code_is( invocation_details_response, 200 ) - invocation_details = invocation_details_response.json() - return invocation_details - def _invocation_step_details( self, workflow_id, invocation_id, step_id ): invocation_step_response = self._get( "workflows/%s/usage/%s/steps/%s" % ( workflow_id, invocation_id, step_id ) ) self._assert_status_code_is( invocation_step_response, 200 ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Merge next-stable to default
by commits-noreply＠bitbucket.org 02 Dec '14

02 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a734cbf4bd36/ Changeset: a734cbf4bd36 User: jgoecks Date: 2014-12-02 18:31:09+00:00 Summary: Merge next-stable to default Affected #: 3 files diff -r 447e69511115f2e2d5a13d8bbe2282cf0c94c5db -r a734cbf4bd368198e2c813b5ea61e807f9a1af33 client/galaxy/scripts/viz/trackster/slotting.js --- a/client/galaxy/scripts/viz/trackster/slotting.js +++ b/client/galaxy/scripts/viz/trackster/slotting.js @@ -138,7 +138,6 @@ // Feature is slotted; if feature now has larger start/end coordinates, // update drawing coordinates. if (feature[1] < slotted_info.feature[1] || slotted_info.feature[2] < feature[2]) { - console.log(feature[3], slotted_info.slot, this._find_slot(this._get_draw_coords(feature))); // Feature has changed (e.g. a single read now has its pair), so recalculate its // drawing coordinates. var old_draw_coords = this._get_draw_coords(slotted_info.feature), diff -r 447e69511115f2e2d5a13d8bbe2282cf0c94c5db -r a734cbf4bd368198e2c813b5ea61e807f9a1af33 static/scripts/packed/viz/trackster/slotting.js --- a/static/scripts/packed/viz/trackster/slotting.js +++ b/static/scripts/packed/viz/trackster/slotting.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(c){var f=c.extend;var d=2,b=5;var a=function(h,g){this.slot=h;this.feature=g};var e=function(j,i,g,h){this.slots={};this.start_end_dct={};this.w_scale=j;this.mode=i;this.include_label=(i==="Pack");this.max_rows=g;this.measureText=h};f(e.prototype,{_get_draw_coords:function(j){var h=Math.floor(j[1]*this.w_scale),i=Math.ceil(j[2]*this.w_scale),g=j[3],k;if(g!==undefined&&this.include_label){var l=this.measureText(g).width+(d+b);if(h-l>=0){h-=l;k="left"}else{i+=l;k="right"}}return[h,i]},_find_slot:function(j){var o=j[0],n=j[1];for(var l=0;l<=this.max_rows;l++){var p=false,m=this.start_end_dct[l];if(m!==undefined){for(var g=0,h=m.length;g<h;g++){var i=m[g];if(n>i[0]&&o<i[1]){p=true;break}}}if(!p){return l}}return -1},slot_features:function(h){var q=this.start_end_dct,v=[],m=0,x,l;for(var o=0,t=h.length;o<t;o++){x=h[o];l=x[0];var g=this.slots[l];if(g){if(x[1]<g.feature[1]||g.feature[2]<x[2]){console.log(x[3],g.slot,this._find_slot(this._get_draw_coords(x)));var s=this._get_draw_coords(g.feature),p=this._get_draw_coords(x),j=this.start_end_dct[g.slot];for(var n=0;n<j.length;n++){var w=j[n];if(w[0]===s[0]&&w[1]===s[1]){j[n]=p}}}m=Math.max(m,this.slots[l].slot)}else{v.push(o)}}for(var o=0,t=v.length;o<t;o++){x=h[v[o]];l=x[0];var r=this._get_draw_coords(x);var u=this._find_slot(r);if(u>=0){if(q[u]===undefined){q[u]=[]}q[u].push(r);this.slots[l]=new a(u,x);m=Math.max(m,u)}}return m+1}});return{FeatureSlotter:e}}); \ No newline at end of file +define(["libs/underscore"],function(c){var f=c.extend;var d=2,b=5;var a=function(h,g){this.slot=h;this.feature=g};var e=function(j,i,g,h){this.slots={};this.start_end_dct={};this.w_scale=j;this.mode=i;this.include_label=(i==="Pack");this.max_rows=g;this.measureText=h};f(e.prototype,{_get_draw_coords:function(j){var h=Math.floor(j[1]*this.w_scale),i=Math.ceil(j[2]*this.w_scale),g=j[3],k;if(g!==undefined&&this.include_label){var l=this.measureText(g).width+(d+b);if(h-l>=0){h-=l;k="left"}else{i+=l;k="right"}}return[h,i]},_find_slot:function(j){var o=j[0],n=j[1];for(var l=0;l<=this.max_rows;l++){var p=false,m=this.start_end_dct[l];if(m!==undefined){for(var g=0,h=m.length;g<h;g++){var i=m[g];if(n>i[0]&&o<i[1]){p=true;break}}}if(!p){return l}}return -1},slot_features:function(h){var q=this.start_end_dct,v=[],m=0,x,l;for(var o=0,t=h.length;o<t;o++){x=h[o];l=x[0];var g=this.slots[l];if(g){if(x[1]<g.feature[1]||g.feature[2]<x[2]){var s=this._get_draw_coords(g.feature),p=this._get_draw_coords(x),j=this.start_end_dct[g.slot];for(var n=0;n<j.length;n++){var w=j[n];if(w[0]===s[0]&&w[1]===s[1]){j[n]=p}}}m=Math.max(m,this.slots[l].slot)}else{v.push(o)}}for(var o=0,t=v.length;o<t;o++){x=h[v[o]];l=x[0];var r=this._get_draw_coords(x);var u=this._find_slot(r);if(u>=0){if(q[u]===undefined){q[u]=[]}q[u].push(r);this.slots[l]=new a(u,x);m=Math.max(m,u)}}return m+1}});return{FeatureSlotter:e}}); \ No newline at end of file diff -r 447e69511115f2e2d5a13d8bbe2282cf0c94c5db -r a734cbf4bd368198e2c813b5ea61e807f9a1af33 static/scripts/viz/trackster/slotting.js --- a/static/scripts/viz/trackster/slotting.js +++ b/static/scripts/viz/trackster/slotting.js @@ -138,7 +138,6 @@ // Feature is slotted; if feature now has larger start/end coordinates, // update drawing coordinates. if (feature[1] < slotted_info.feature[1] || slotted_info.feature[2] < feature[2]) { - console.log(feature[3], slotted_info.slot, this._find_slot(this._get_draw_coords(feature))); // Feature has changed (e.g. a single read now has its pair), so recalculate its // drawing coordinates. var old_draw_coords = this._get_draw_coords(slotted_info.feature), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Remove debugging statement.
by commits-noreply＠bitbucket.org 02 Dec '14

02 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eb9d9ab34d23/ Changeset: eb9d9ab34d23 Branch: next-stable User: jgoecks Date: 2014-12-02 18:30:19+00:00 Summary: Remove debugging statement. Affected #: 3 files diff -r 1a2ef4a380ff35ca7f97ca2c50bab474400c6275 -r eb9d9ab34d23456d58f291b782b42724a83f711e client/galaxy/scripts/viz/trackster/slotting.js --- a/client/galaxy/scripts/viz/trackster/slotting.js +++ b/client/galaxy/scripts/viz/trackster/slotting.js @@ -138,7 +138,6 @@ // Feature is slotted; if feature now has larger start/end coordinates, // update drawing coordinates. if (feature[1] < slotted_info.feature[1] || slotted_info.feature[2] < feature[2]) { - console.log(feature[3], slotted_info.slot, this._find_slot(this._get_draw_coords(feature))); // Feature has changed (e.g. a single read now has its pair), so recalculate its // drawing coordinates. var old_draw_coords = this._get_draw_coords(slotted_info.feature), diff -r 1a2ef4a380ff35ca7f97ca2c50bab474400c6275 -r eb9d9ab34d23456d58f291b782b42724a83f711e static/scripts/packed/viz/trackster/slotting.js --- a/static/scripts/packed/viz/trackster/slotting.js +++ b/static/scripts/packed/viz/trackster/slotting.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(c){var f=c.extend;var d=2,b=5;var a=function(h,g){this.slot=h;this.feature=g};var e=function(j,i,g,h){this.slots={};this.start_end_dct={};this.w_scale=j;this.mode=i;this.include_label=(i==="Pack");this.max_rows=g;this.measureText=h};f(e.prototype,{_get_draw_coords:function(j){var h=Math.floor(j[1]*this.w_scale),i=Math.ceil(j[2]*this.w_scale),g=j[3],k;if(g!==undefined&&this.include_label){var l=this.measureText(g).width+(d+b);if(h-l>=0){h-=l;k="left"}else{i+=l;k="right"}}return[h,i]},_find_slot:function(j){var o=j[0],n=j[1];for(var l=0;l<=this.max_rows;l++){var p=false,m=this.start_end_dct[l];if(m!==undefined){for(var g=0,h=m.length;g<h;g++){var i=m[g];if(n>i[0]&&o<i[1]){p=true;break}}}if(!p){return l}}return -1},slot_features:function(h){var q=this.start_end_dct,v=[],m=0,x,l;for(var o=0,t=h.length;o<t;o++){x=h[o];l=x[0];var g=this.slots[l];if(g){if(x[1]<g.feature[1]||g.feature[2]<x[2]){console.log(x[3],g.slot,this._find_slot(this._get_draw_coords(x)));var s=this._get_draw_coords(g.feature),p=this._get_draw_coords(x),j=this.start_end_dct[g.slot];for(var n=0;n<j.length;n++){var w=j[n];if(w[0]===s[0]&&w[1]===s[1]){j[n]=p}}}m=Math.max(m,this.slots[l].slot)}else{v.push(o)}}for(var o=0,t=v.length;o<t;o++){x=h[v[o]];l=x[0];var r=this._get_draw_coords(x);var u=this._find_slot(r);if(u>=0){if(q[u]===undefined){q[u]=[]}q[u].push(r);this.slots[l]=new a(u,x);m=Math.max(m,u)}}return m+1}});return{FeatureSlotter:e}}); \ No newline at end of file +define(["libs/underscore"],function(c){var f=c.extend;var d=2,b=5;var a=function(h,g){this.slot=h;this.feature=g};var e=function(j,i,g,h){this.slots={};this.start_end_dct={};this.w_scale=j;this.mode=i;this.include_label=(i==="Pack");this.max_rows=g;this.measureText=h};f(e.prototype,{_get_draw_coords:function(j){var h=Math.floor(j[1]*this.w_scale),i=Math.ceil(j[2]*this.w_scale),g=j[3],k;if(g!==undefined&&this.include_label){var l=this.measureText(g).width+(d+b);if(h-l>=0){h-=l;k="left"}else{i+=l;k="right"}}return[h,i]},_find_slot:function(j){var o=j[0],n=j[1];for(var l=0;l<=this.max_rows;l++){var p=false,m=this.start_end_dct[l];if(m!==undefined){for(var g=0,h=m.length;g<h;g++){var i=m[g];if(n>i[0]&&o<i[1]){p=true;break}}}if(!p){return l}}return -1},slot_features:function(h){var q=this.start_end_dct,v=[],m=0,x,l;for(var o=0,t=h.length;o<t;o++){x=h[o];l=x[0];var g=this.slots[l];if(g){if(x[1]<g.feature[1]||g.feature[2]<x[2]){var s=this._get_draw_coords(g.feature),p=this._get_draw_coords(x),j=this.start_end_dct[g.slot];for(var n=0;n<j.length;n++){var w=j[n];if(w[0]===s[0]&&w[1]===s[1]){j[n]=p}}}m=Math.max(m,this.slots[l].slot)}else{v.push(o)}}for(var o=0,t=v.length;o<t;o++){x=h[v[o]];l=x[0];var r=this._get_draw_coords(x);var u=this._find_slot(r);if(u>=0){if(q[u]===undefined){q[u]=[]}q[u].push(r);this.slots[l]=new a(u,x);m=Math.max(m,u)}}return m+1}});return{FeatureSlotter:e}}); \ No newline at end of file diff -r 1a2ef4a380ff35ca7f97ca2c50bab474400c6275 -r eb9d9ab34d23456d58f291b782b42724a83f711e static/scripts/viz/trackster/slotting.js --- a/static/scripts/viz/trackster/slotting.js +++ b/static/scripts/viz/trackster/slotting.js @@ -138,7 +138,6 @@ // Feature is slotted; if feature now has larger start/end coordinates, // update drawing coordinates. if (feature[1] < slotted_info.feature[1] || slotted_info.feature[2] < feature[2]) { - console.log(feature[3], slotted_info.slot, this._find_slot(this._get_draw_coords(feature))); // Feature has changed (e.g. a single read now has its pair), so recalculate its // drawing coordinates. var old_draw_coords = this._get_draw_coords(slotted_info.feature), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Merge
by commits-noreply＠bitbucket.org 02 Dec '14

02 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/447e69511115/ Changeset: 447e69511115 User: guerler Date: 2014-12-02 17:05:53+00:00 Summary: Merge Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 02 Dec '14

02 Dec '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/98a6cad91c3a/ Changeset: 98a6cad91c3a Branch: next-stable User: guerler Date: 2014-12-01 04:40:38+00:00 Summary: ToolForm: Add drill down element Affected #: 25 files diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -211,7 +211,7 @@ this.tree.matchModel(new_model, function(input_id, node) { var input = self.input_list[input_id]; if (input && input.options) { - if (JSON.stringify(input.options) != JSON.stringify(node.options)) { + if (!_.isEqual(input.options, node.options)) { // backup new options input.options = node.options; @@ -223,6 +223,9 @@ case 'data': new_options = input.options; break; + case 'drill_down': + new_options = input.options; + break; default: for (var i in node.options) { var opt = node.options[i]; diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -337,7 +337,12 @@ input_def.searchable = true; field = this._fieldSelect(input_def); break; - + + // drill down field + case 'drill_down': + field = this._fieldDrilldown(input_def); + break; + // field not found default: // flag @@ -417,6 +422,20 @@ }); }, + /** Drill down options field + */ + _fieldDrilldown : function (input_def) { + var self = this; + return new Ui.Drilldown.View({ + id : 'field-' + input_def.id, + data : input_def.options, + display : input_def.display, + onchange : function() { + self.app.refresh(); + } + }); + }, + /** Text input field */ _fieldText : function(input_def) { diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -90,6 +90,11 @@ // update options this.update(options.data); + // set initial value + if (this.options.value !== undefined) { + this.value(this.options.value); + } + // refresh view this.refresh(); diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 client/galaxy/scripts/mvc/ui/ui-drilldown.js --- /dev/null +++ b/client/galaxy/scripts/mvc/ui/ui-drilldown.js @@ -0,0 +1,102 @@ +// dependencies +define(['utils/utils', 'mvc/ui/ui-options'], function(Utils, Options) { + +/** + * This class creates/wraps a drill down element. + */ +var View = Options.Base.extend({ + // initialize + initialize: function(options) { + this.display = options.display || 'checkbox'; + options.multiple = (this.display == 'checkbox'); + Options.Base.prototype.initialize.call(this, options); + }, + + /** Template for input field + */ + _templateOption: function(name, value, selected) { + return '<div>' + + '<input name="' + this.options.id + '" class="ui-option" type="' + this.display + '" value="' + value + '">' + + Utils.sanitize(name) + + '<div/>'; + }, + + /** Template to create options tree + */ + _templateOptions: function(data, current) { + // link this + var self = this; + + // attach show/hide event + function attachEvents($button, $subgroup) { + function setVisibility (visible) { + if (visible) { + $subgroup.fadeIn('fast') + $button.removeClass('toggle-expand'); + $button.addClass('toggle'); + $button.is_expanded = true; + } else { + $subgroup.hide(); + $button.removeClass('toggle'); + $button.addClass('toggle-expand'); + $button.is_expanded = false; + } + }; + $button.on('click', function() { + setVisibility(!$button.is_expanded); + }); + } + + // recursive function which iterates through options + function iterate ($tmpl, data) { + for (i in data) { + // current option level in hierarchy + var level = data[i]; + + // check for options + var has_options = level.options.length > 0; + + // build template + var $group = $('<div/>'); + if (has_options) { + // create button and add flag + var $button = $('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>'); + + // add expand group + var $buttongroup = $('<div/>'); + $buttongroup.append($button); + $buttongroup.append(self._templateOption(level.name, level.value)); + $group.append($buttongroup); + + // add sub group + var $subgroup = $('<div style="display: none; margin-left: 25px;"/>'); + iterate($subgroup, level.options); + $group.append($subgroup); + + // attach click event to collapse/expand hierarchy + attachEvents($button, $subgroup); + } else { + $group.append(self._templateOption(level.name, level.value)); + } + $tmpl.append($group); + } + } + + // iterate through options and create dom + var $tmpl = $('<div/>'); + iterate($tmpl, data); + return $tmpl; + }, + + /** Template for drill down view + */ + _template: function(options) { + return '<div class="ui-options drilldown-container" id="' + options.id + '"/>'; + } +}); + +return { + View: View +} + +}); diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 client/galaxy/scripts/mvc/ui/ui-misc.js --- a/client/galaxy/scripts/mvc/ui/ui-misc.js +++ b/client/galaxy/scripts/mvc/ui/ui-misc.js @@ -1,6 +1,6 @@ // dependencies -define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-slider', 'mvc/ui/ui-options', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'], - function(Utils, Select, Slider, Options, ButtonMenu, Modal) { +define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-slider', 'mvc/ui/ui-options', 'mvc/ui/ui-drilldown', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'], + function(Utils, Select, Slider, Options, Drilldown, ButtonMenu, Modal) { /** * This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc. @@ -339,7 +339,6 @@ var Input = Backbone.View.extend({ // options optionsDefault: { - value : '', type : 'text', placeholder : '', disabled : false, @@ -356,6 +355,11 @@ // create new element this.setElement(this._template(this.options)); + // set initial value + if (this.options.value !== undefined) { + this.value(this.options.value); + } + // disable input field if (this.options.disabled) { this.$el.prop('disabled', true); @@ -395,18 +399,18 @@ // plugin var Hidden = Backbone.View.extend({ - // options - optionsDefault: { - value : '' - }, - // initialize initialize : function(options) { // configure options - this.options = Utils.merge(options, this.optionsDefault); + this.options = options; // create new element this.setElement(this._template(this.options)); + + // set initial value + if (this.options.value !== undefined) { + this.value(this.options.value); + } }, // value @@ -441,6 +445,7 @@ Searchbox : Searchbox, Select : Select, Hidden : Hidden, - Slider : Slider + Slider : Slider, + Drilldown : Drilldown } }); diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 client/galaxy/scripts/mvc/ui/ui-options.js --- a/client/galaxy/scripts/mvc/ui/ui-options.js +++ b/client/galaxy/scripts/mvc/ui/ui-options.js @@ -2,7 +2,7 @@ define(['utils/utils'], function(Utils) { /** Base class for options based ui elements **/ -var OptionsBase = Backbone.View.extend({ +var Base = Backbone.View.extend({ // initialize initialize: function(options) { // options @@ -56,16 +56,19 @@ var current = this._getValue(); // remove all options - this.$el.find('.ui-option').remove(); + this.$options.empty(); - // add new options - for (var key in options) { - // load option template - var $option = $(this._templateOption(options[key])); - $option.addClass('ui-option'); - - // append to dom - this.$options.append($option); + // add new options using single option templates or full template + if (this._templateOptions) { + // rebuild options using full template + this.$options.append(this._templateOptions(options)); + } else { + // rebuild options using single option templates + for (var key in options) { + var $option = $(this._templateOption(options[key])); + $option.addClass('ui-option'); + this.$options.append($option); + } } // add change events @@ -82,6 +85,29 @@ this.value(current); }, + /** Return/Set current value + */ + value: function (new_value) { + // check if its an array + if (typeof new_value === 'string') { + new_value = [new_value]; + } + + // set new value + if (new_value !== undefined) { + // reset selection + this.$el.find('input').prop('checked', false); + + // update to new selection + for (var i in new_value) { + this.$el.find('input[value="' + new_value[i] + '"]').first().prop('checked', true); + }; + } + + // get and return value + return this._getValue(); + }, + /** Check if selected value exists (or any if multiple) */ exists: function(value) { @@ -198,46 +224,6 @@ */ _messageHide: function() { this.$message.hide(); - } -}); - -/** Radio button field **/ -var Radio = {}; -Radio.View = OptionsBase.extend({ - // initialize - initialize: function(options) { - OptionsBase.prototype.initialize.call(this, options); - }, - - /** Return/Set current value - */ - value: function (new_val) { - // check if its an array - if (typeof new_val === 'string') { - new_val = [new_val]; - } - - // set new value - if (new_val !== undefined) { - // reset selection - this.$el.find('input').prop('checked', false); - - // update to new selection - for (var i in new_val) { - this.$el.find('input[value="' + new_val[i] + '"]').prop('checked', true); - }; - } - - // get and return value - return this._getValue(); - }, - - /** Template for options - */ - _templateOption: function(pair) { - return '<div>' + - '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' + - '</div>'; }, /** Main template function @@ -247,16 +233,33 @@ } }); +/** Radio button field **/ +var Radio = {}; +Radio.View = Base.extend({ + // initialize + initialize: function(options) { + Base.prototype.initialize.call(this, options); + }, + + /** Template for a single option + */ + _templateOption: function(pair) { + return '<div>' + + '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' + + '</div>'; + } +}); + /** Checkbox options field **/ var Checkbox = {}; -Checkbox.View = Radio.View.extend({ +Checkbox.View = Base.extend({ // initialize initialize: function(options) { options.multiple = true; - Radio.View.prototype.initialize.call(this, options); + Base.prototype.initialize.call(this, options); }, - /** Template for options + /** Template for a single option */ _templateOption: function(pair) { return '<div>' + @@ -267,27 +270,27 @@ /** Radio button options field styled as classic buttons **/ var RadioButton = {}; -RadioButton.View = OptionsBase.extend({ +RadioButton.View = Base.extend({ // initialize initialize: function(options) { - OptionsBase.prototype.initialize.call(this, options); + Base.prototype.initialize.call(this, options); }, /** Return/Set current value */ - value: function (new_val) { + value: function (new_value) { // set new value - if (new_val !== undefined) { + if (new_value !== undefined) { this.$el.find('input').prop('checked', false); this.$el.find('label').removeClass('active'); - this.$el.find('[value="' + new_val + '"]').prop('checked', true).closest('label').addClass('active'); + this.$el.find('[value="' + new_value + '"]').prop('checked', true).closest('label').addClass('active'); } // get and return value return this._getValue(); }, - /** Template for options + /** Template for a single option */ _templateOption: function(pair) { var tmpl = '<label class="btn btn-default">'; @@ -307,6 +310,7 @@ }); return { + Base : Base, Radio : Radio, RadioButton : RadioButton, Checkbox : Checkbox diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 client/galaxy/scripts/mvc/ui/ui-select-default.js --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -41,6 +41,11 @@ // refresh this.update(this.options.data); + // set initial value + if (this.options.value !== undefined) { + this.value(this.options.value); + } + // show/hide if (!this.options.visible) { this.hide(); diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 client/galaxy/scripts/mvc/ui/ui-slider.js --- a/client/galaxy/scripts/mvc/ui/ui-slider.js +++ b/client/galaxy/scripts/mvc/ui/ui-slider.js @@ -5,7 +5,6 @@ var View = Backbone.View.extend({ // options optionsDefault: { - value : '', min : null, max : null, step : null, @@ -49,6 +48,11 @@ // link text input field this.$text = this.$el.find('#text'); + // set initial value + if (this.options.value !== undefined) { + this.value(this.options.value); + } + // add text field event this.$text.on('change', function () { self.value($(this).val()); diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1606,19 +1606,20 @@ """ return self.filtered.keys() - def to_dict( self, trans, view='collection', value_mapper=None ): + def to_dict( self, trans, view='collection', value_mapper=None, context={} ): # skip SelectToolParameter (the immediate parent) bc we need to get options in a different way here d = ToolParameter.to_dict( self, trans ) options = [] try: - options = self.get_options( trans, {} ) + options = self.get_options( trans, context ) except KeyError: # will sometimes error if self.is_dynamic and self.filtered # bc we dont/cant fill out other_values above ({}) pass - d[ 'options' ] = options + d[ 'display' ] = self.display + d[ 'is_dynamic' ] = self.is_dynamic return d diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -211,7 +211,7 @@ this.tree.matchModel(new_model, function(input_id, node) { var input = self.input_list[input_id]; if (input && input.options) { - if (JSON.stringify(input.options) != JSON.stringify(node.options)) { + if (!_.isEqual(input.options, node.options)) { // backup new options input.options = node.options; @@ -223,6 +223,9 @@ case 'data': new_options = input.options; break; + case 'drill_down': + new_options = input.options; + break; default: for (var i in node.options) { var opt = node.options[i]; diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -337,7 +337,12 @@ input_def.searchable = true; field = this._fieldSelect(input_def); break; - + + // drill down field + case 'drill_down': + field = this._fieldDrilldown(input_def); + break; + // field not found default: // flag @@ -417,6 +422,20 @@ }); }, + /** Drill down options field + */ + _fieldDrilldown : function (input_def) { + var self = this; + return new Ui.Drilldown.View({ + id : 'field-' + input_def.id, + data : input_def.options, + display : input_def.display, + onchange : function() { + self.app.refresh(); + } + }); + }, + /** Text input field */ _fieldText : function(input_def) { diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -90,6 +90,11 @@ // update options this.update(options.data); + // set initial value + if (this.options.value !== undefined) { + this.value(this.options.value); + } + // refresh view this.refresh(); diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/mvc/ui/ui-drilldown.js --- /dev/null +++ b/static/scripts/mvc/ui/ui-drilldown.js @@ -0,0 +1,102 @@ +// dependencies +define(['utils/utils', 'mvc/ui/ui-options'], function(Utils, Options) { + +/** + * This class creates/wraps a drill down element. + */ +var View = Options.Base.extend({ + // initialize + initialize: function(options) { + this.display = options.display || 'checkbox'; + options.multiple = (this.display == 'checkbox'); + Options.Base.prototype.initialize.call(this, options); + }, + + /** Template for input field + */ + _templateOption: function(name, value, selected) { + return '<div>' + + '<input name="' + this.options.id + '" class="ui-option" type="' + this.display + '" value="' + value + '">' + + Utils.sanitize(name) + + '<div/>'; + }, + + /** Template to create options tree + */ + _templateOptions: function(data, current) { + // link this + var self = this; + + // attach show/hide event + function attachEvents($button, $subgroup) { + function setVisibility (visible) { + if (visible) { + $subgroup.fadeIn('fast') + $button.removeClass('toggle-expand'); + $button.addClass('toggle'); + $button.is_expanded = true; + } else { + $subgroup.hide(); + $button.removeClass('toggle'); + $button.addClass('toggle-expand'); + $button.is_expanded = false; + } + }; + $button.on('click', function() { + setVisibility(!$button.is_expanded); + }); + } + + // recursive function which iterates through options + function iterate ($tmpl, data) { + for (i in data) { + // current option level in hierarchy + var level = data[i]; + + // check for options + var has_options = level.options.length > 0; + + // build template + var $group = $('<div/>'); + if (has_options) { + // create button and add flag + var $button = $('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>'); + + // add expand group + var $buttongroup = $('<div/>'); + $buttongroup.append($button); + $buttongroup.append(self._templateOption(level.name, level.value)); + $group.append($buttongroup); + + // add sub group + var $subgroup = $('<div style="display: none; margin-left: 25px;"/>'); + iterate($subgroup, level.options); + $group.append($subgroup); + + // attach click event to collapse/expand hierarchy + attachEvents($button, $subgroup); + } else { + $group.append(self._templateOption(level.name, level.value)); + } + $tmpl.append($group); + } + } + + // iterate through options and create dom + var $tmpl = $('<div/>'); + iterate($tmpl, data); + return $tmpl; + }, + + /** Template for drill down view + */ + _template: function(options) { + return '<div class="ui-options drilldown-container" id="' + options.id + '"/>'; + } +}); + +return { + View: View +} + +}); diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/mvc/ui/ui-misc.js --- a/static/scripts/mvc/ui/ui-misc.js +++ b/static/scripts/mvc/ui/ui-misc.js @@ -1,6 +1,6 @@ // dependencies -define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-slider', 'mvc/ui/ui-options', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'], - function(Utils, Select, Slider, Options, ButtonMenu, Modal) { +define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-slider', 'mvc/ui/ui-options', 'mvc/ui/ui-drilldown', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'], + function(Utils, Select, Slider, Options, Drilldown, ButtonMenu, Modal) { /** * This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc. @@ -339,7 +339,6 @@ var Input = Backbone.View.extend({ // options optionsDefault: { - value : '', type : 'text', placeholder : '', disabled : false, @@ -356,6 +355,11 @@ // create new element this.setElement(this._template(this.options)); + // set initial value + if (this.options.value !== undefined) { + this.value(this.options.value); + } + // disable input field if (this.options.disabled) { this.$el.prop('disabled', true); @@ -395,18 +399,18 @@ // plugin var Hidden = Backbone.View.extend({ - // options - optionsDefault: { - value : '' - }, - // initialize initialize : function(options) { // configure options - this.options = Utils.merge(options, this.optionsDefault); + this.options = options; // create new element this.setElement(this._template(this.options)); + + // set initial value + if (this.options.value !== undefined) { + this.value(this.options.value); + } }, // value @@ -441,6 +445,7 @@ Searchbox : Searchbox, Select : Select, Hidden : Hidden, - Slider : Slider + Slider : Slider, + Drilldown : Drilldown } }); diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/mvc/ui/ui-options.js --- a/static/scripts/mvc/ui/ui-options.js +++ b/static/scripts/mvc/ui/ui-options.js @@ -2,7 +2,7 @@ define(['utils/utils'], function(Utils) { /** Base class for options based ui elements **/ -var OptionsBase = Backbone.View.extend({ +var Base = Backbone.View.extend({ // initialize initialize: function(options) { // options @@ -56,16 +56,19 @@ var current = this._getValue(); // remove all options - this.$el.find('.ui-option').remove(); + this.$options.empty(); - // add new options - for (var key in options) { - // load option template - var $option = $(this._templateOption(options[key])); - $option.addClass('ui-option'); - - // append to dom - this.$options.append($option); + // add new options using single option templates or full template + if (this._templateOptions) { + // rebuild options using full template + this.$options.append(this._templateOptions(options)); + } else { + // rebuild options using single option templates + for (var key in options) { + var $option = $(this._templateOption(options[key])); + $option.addClass('ui-option'); + this.$options.append($option); + } } // add change events @@ -82,6 +85,29 @@ this.value(current); }, + /** Return/Set current value + */ + value: function (new_value) { + // check if its an array + if (typeof new_value === 'string') { + new_value = [new_value]; + } + + // set new value + if (new_value !== undefined) { + // reset selection + this.$el.find('input').prop('checked', false); + + // update to new selection + for (var i in new_value) { + this.$el.find('input[value="' + new_value[i] + '"]').first().prop('checked', true); + }; + } + + // get and return value + return this._getValue(); + }, + /** Check if selected value exists (or any if multiple) */ exists: function(value) { @@ -198,46 +224,6 @@ */ _messageHide: function() { this.$message.hide(); - } -}); - -/** Radio button field **/ -var Radio = {}; -Radio.View = OptionsBase.extend({ - // initialize - initialize: function(options) { - OptionsBase.prototype.initialize.call(this, options); - }, - - /** Return/Set current value - */ - value: function (new_val) { - // check if its an array - if (typeof new_val === 'string') { - new_val = [new_val]; - } - - // set new value - if (new_val !== undefined) { - // reset selection - this.$el.find('input').prop('checked', false); - - // update to new selection - for (var i in new_val) { - this.$el.find('input[value="' + new_val[i] + '"]').prop('checked', true); - }; - } - - // get and return value - return this._getValue(); - }, - - /** Template for options - */ - _templateOption: function(pair) { - return '<div>' + - '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' + - '</div>'; }, /** Main template function @@ -247,16 +233,33 @@ } }); +/** Radio button field **/ +var Radio = {}; +Radio.View = Base.extend({ + // initialize + initialize: function(options) { + Base.prototype.initialize.call(this, options); + }, + + /** Template for a single option + */ + _templateOption: function(pair) { + return '<div>' + + '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' + + '</div>'; + } +}); + /** Checkbox options field **/ var Checkbox = {}; -Checkbox.View = Radio.View.extend({ +Checkbox.View = Base.extend({ // initialize initialize: function(options) { options.multiple = true; - Radio.View.prototype.initialize.call(this, options); + Base.prototype.initialize.call(this, options); }, - /** Template for options + /** Template for a single option */ _templateOption: function(pair) { return '<div>' + @@ -267,27 +270,27 @@ /** Radio button options field styled as classic buttons **/ var RadioButton = {}; -RadioButton.View = OptionsBase.extend({ +RadioButton.View = Base.extend({ // initialize initialize: function(options) { - OptionsBase.prototype.initialize.call(this, options); + Base.prototype.initialize.call(this, options); }, /** Return/Set current value */ - value: function (new_val) { + value: function (new_value) { // set new value - if (new_val !== undefined) { + if (new_value !== undefined) { this.$el.find('input').prop('checked', false); this.$el.find('label').removeClass('active'); - this.$el.find('[value="' + new_val + '"]').prop('checked', true).closest('label').addClass('active'); + this.$el.find('[value="' + new_value + '"]').prop('checked', true).closest('label').addClass('active'); } // get and return value return this._getValue(); }, - /** Template for options + /** Template for a single option */ _templateOption: function(pair) { var tmpl = '<label class="btn btn-default">'; @@ -307,6 +310,7 @@ }); return { + Base : Base, Radio : Radio, RadioButton : RadioButton, Checkbox : Checkbox diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -41,6 +41,11 @@ // refresh this.update(this.options.data); + // set initial value + if (this.options.value !== undefined) { + this.value(this.options.value); + } + // show/hide if (!this.options.visible) { this.hide(); diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/mvc/ui/ui-slider.js --- a/static/scripts/mvc/ui/ui-slider.js +++ b/static/scripts/mvc/ui/ui-slider.js @@ -5,7 +5,6 @@ var View = Backbone.View.extend({ // options optionsDefault: { - value : '', min : null, max : null, step : null, @@ -49,6 +48,11 @@ // link text input field this.$text = this.$el.find('#text'); + // set initial value + if (this.options.value !== undefined) { + this.value(this.options.value); + } + // add text field event this.$text.on('change', function () { self.value($(this).val()); diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(this.is_dynamic){var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})}},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var s=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){s.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});s.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}s.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+o.options.id)}});if(this.is_admin){s.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,cls:"ui-portlet-slim",operations:{menu:s},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var r=$("<div/>");var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({el:r,collection:n});q.render();n.fetch();this.$el.append(r)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(this.is_dynamic){var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})}},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(!_.isEqual(p.options,u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;case"drill_down":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var s=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){s.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});s.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}s.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+o.options.id)}});if(this.is_admin){s.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,cls:"ui-portlet-slim",operations:{menu:s},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var r=$("<div/>");var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({el:r,collection:n});q.render();n.fetch();this.$el.append(r)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;case"drill_down":i=this._fieldDrilldown(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldDrilldown:function(h){var i=this;return new g.Drilldown.View({id:"field-"+h.id,data:h.options,display:h.display,onchange:function(){i.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple&&this.current!="single",values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple&&this.current!="single",values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/packed/mvc/ui/ui-drilldown.js --- /dev/null +++ b/static/scripts/packed/mvc/ui/ui-drilldown.js @@ -0,0 +1,1 @@ +define(["utils/utils","mvc/ui/ui-options"],function(b,a){var c=a.Base.extend({initialize:function(d){this.display=d.display||"checkbox";d.multiple=(this.display=="checkbox");a.Base.prototype.initialize.call(this,d)},_templateOption:function(d,f,e){return'<div><input name="'+this.options.id+'" class="ui-option" type="'+this.display+'" value="'+f+'">'+b.sanitize(d)+"<div/>"},_templateOptions:function(g,h){var e=this;function f(l,m){function k(n){if(n){m.fadeIn("fast");l.removeClass("toggle-expand");l.addClass("toggle");l.is_expanded=true}else{m.hide();l.removeClass("toggle");l.addClass("toggle-expand");l.is_expanded=false}}l.on("click",function(){k(!l.is_expanded)})}function d(q,o){for(i in o){var r=o[i];var m=r.options.length>0;var l=$("<div/>");if(m){var n=$('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>');var k=$("<div/>");k.append(n);k.append(e._templateOption(r.name,r.value));l.append(k);var p=$('<div style="display: none; margin-left: 25px;"/>');d(p,r.options);l.append(p);f(n,p)}else{l.append(e._templateOption(r.name,r.value))}q.append(l)}}var j=$("<div/>");d(j,g);return j},_template:function(d){return'<div class="ui-options drilldown-container" id="'+d.id+'"/>'}});return{View:c}}); \ No newline at end of file diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/packed/mvc/ui/ui-misc.js --- a/static/scripts/packed/mvc/ui/ui-misc.js +++ b/static/scripts/packed/mvc/ui/ui-misc.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(k,b,e,n,p,l){var d=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(q){return'<img class="ui-image '+q.cls+'" src="'+q.url+'"/>'}});var j=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},title:function(q){this.$el.html(q)},_template:function(q){return'<label class="ui-label '+q.cls+'">'+q.title+"</label>"},value:function(){return options.title}});var c=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){return'<div><span class="fa '+q.icon+'" class="ui-icon"/> '+q.title+"</div>"}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",function(){$(".tooltip").hide();if(q.onclick){q.onclick()}});$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){var r='<button id="'+q.id+'" type="submit" style="float: '+q.floating+';" type="button" class="'+q.cls+'">';if(q.icon){r+='<i class="icon fa '+q.icon+'"></i> '}r+=q.title+"</button>";return r}});var h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));this.$button=this.$el.find(".button");var q=this;$(this.el).on("click",function(){$(".tooltip").hide();if(r.onclick&&!q.disabled){r.onclick()}});$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled");this.disabled=true},enable:function(){this.$button.removeClass("disabled");this.disabled=false},_template:function(q){var r="";if(q.title){r="width: auto;"}var s='<div id="'+q.id+'" style="float: '+q.floating+"; "+r+'" class="'+q.cls+'">';if(q.title){s+='<div class="button"><i class="icon fa '+q.icon+'"/> <span class="title">'+q.title+"</span></div>"}else{s+='<i class="icon fa '+q.icon+'"/>'}s+="</div>";return s}});var f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",q.onclick)},_template:function(q){return'<div><a href="javascript:void(0)" class="ui-anchor '+q.cls+'">'+q.title+"</a></div>"}});var m=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement("<div></div>")},update:function(r){this.options=k.merge(r,this.optionsDefault);if(r.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(r.message);this.$el.fadeIn();if(!r.persistent){var q=this;window.setTimeout(function(){if(q.$el.is(":visible")){q.$el.fadeOut()}else{q.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(q){return'<div class="ui-message alert alert-'+q.status+'"/>'}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));var q=this;if(this.options.onclick){this.$el.on("submit",function(t){var s=q.$el.find("#search");q.options.onclick(s.val())})}},_template:function(q){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+q.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var i=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:"",area:false},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var q=this;this.$el.on("input",function(){if(q.options.onchange){q.options.onchange(q.$el.val())}})},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){if(q.area){return'<textarea id="'+q.id+'" class="ui-textarea '+q.cls+'"></textarea>'}else{return'<input id="'+q.id+'" type="'+q.type+'" value="'+q.value+'" placeholder="'+q.placeholder+'" class="ui-input '+q.cls+'">'}}});var o=Backbone.View.extend({optionsDefault:{value:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){return'<hidden id="'+q.id+'" value="'+q.value+'"/>'}});return{Anchor:f,Button:g,ButtonIcon:h,ButtonMenu:p,Icon:c,Image:d,Input:i,Label:j,Message:m,Modal:l,RadioButton:n.RadioButton,Checkbox:n.Checkbox,Radio:n.Radio,Searchbox:a,Select:b,Hidden:o,Slider:e}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(k,b,e,o,l,q,m){var d=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(r){return'<img class="ui-image '+r.cls+'" src="'+r.url+'"/>'}});var j=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options))},title:function(r){this.$el.html(r)},_template:function(r){return'<label class="ui-label '+r.cls+'">'+r.title+"</label>"},value:function(){return options.title}});var c=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},_template:function(r){return'<div><span class="fa '+r.icon+'" class="ui-icon"/> '+r.title+"</div>"}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",function(){$(".tooltip").hide();if(r.onclick){r.onclick()}});$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},_template:function(r){var s='<button id="'+r.id+'" type="submit" style="float: '+r.floating+';" type="button" class="'+r.cls+'">';if(r.icon){s+='<i class="icon fa '+r.icon+'"></i> '}s+=r.title+"</button>";return s}});var h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(s){this.options=k.merge(s,this.optionsDefault);this.setElement(this._template(this.options));this.$button=this.$el.find(".button");var r=this;$(this.el).on("click",function(){$(".tooltip").hide();if(s.onclick&&!r.disabled){s.onclick()}});$(this.el).tooltip({title:s.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled");this.disabled=true},enable:function(){this.$button.removeClass("disabled");this.disabled=false},_template:function(r){var s="";if(r.title){s="width: auto;"}var t='<div id="'+r.id+'" style="float: '+r.floating+"; "+s+'" class="'+r.cls+'">';if(r.title){t+='<div class="button"><i class="icon fa '+r.icon+'"/> <span class="title">'+r.title+"</span></div>"}else{t+='<i class="icon fa '+r.icon+'"/>'}t+="</div>";return t}});var f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",r.onclick)},_template:function(r){return'<div><a href="javascript:void(0)" class="ui-anchor '+r.cls+'">'+r.title+"</a></div>"}});var n=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement("<div></div>")},update:function(s){this.options=k.merge(s,this.optionsDefault);if(s.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(s.message);this.$el.fadeIn();if(!s.persistent){var r=this;window.setTimeout(function(){if(r.$el.is(":visible")){r.$el.fadeOut()}else{r.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(r){return'<div class="ui-message alert alert-'+r.status+'"/>'}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(s){this.options=k.merge(s,this.optionsDefault);this.setElement(this._template(this.options));var r=this;if(this.options.onclick){this.$el.on("submit",function(u){var t=r.$el.find("#search");r.options.onclick(t.val())})}},_template:function(r){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+r.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var i=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:false,visible:true,cls:"",area:false},initialize:function(s){this.options=k.merge(s,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.value!==undefined){this.value(this.options.value)}if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var r=this;this.$el.on("input",function(){if(r.options.onchange){r.options.onchange(r.$el.val())}})},value:function(r){if(r!==undefined){this.$el.val(r)}return this.$el.val()},_template:function(r){if(r.area){return'<textarea id="'+r.id+'" class="ui-textarea '+r.cls+'"></textarea>'}else{return'<input id="'+r.id+'" type="'+r.type+'" value="'+r.value+'" placeholder="'+r.placeholder+'" class="ui-input '+r.cls+'">'}}});var p=Backbone.View.extend({initialize:function(r){this.options=r;this.setElement(this._template(this.options));if(this.options.value!==undefined){this.value(this.options.value)}},value:function(r){if(r!==undefined){this.$el.val(r)}return this.$el.val()},_template:function(r){return'<hidden id="'+r.id+'" value="'+r.value+'"/>'}});return{Anchor:f,Button:g,ButtonIcon:h,ButtonMenu:q,Icon:c,Image:d,Input:i,Label:j,Message:n,Modal:m,RadioButton:o.RadioButton,Checkbox:o.Checkbox,Radio:o.Radio,Searchbox:a,Select:b,Hidden:p,Slider:e,Drilldown:l}}); \ No newline at end of file diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/packed/mvc/ui/ui-options.js --- a/static/scripts/packed/mvc/ui/ui-options.js +++ b/static/scripts/packed/mvc/ui/ui-options.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$el.find(".ui-option").remove();for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(typeof f==="string"){f=[f]}if(f!==undefined){this.$el.find("input").prop("checked",false);for(var g in f){this.$el.find('input[value="'+f[g]+'"]').prop("checked",true)}}return this._getValue()},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"},_template:function(){return'<div class="ui-options"/>'}});var c={};c.View=d.View.extend({initialize:function(f){f.multiple=true;d.View.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file +define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(g))}else{for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},value:function(g){if(typeof g==="string"){g=[g]}if(g!==undefined){this.$el.find("input").prop("checked",false);for(var f in g){this.$el.find('input[value="'+g[f]+'"]').first().prop("checked",true)}}return this._getValue()},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options"/>'}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var c={};c.View=a.extend({initialize:function(f){f.multiple=true;a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:a,Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false,searchable:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}if(this.options.searchable){this.$button.hide();this.$select.select2("destroy");this.$select.select2()}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false,searchable:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}if(this.options.searchable){this.$button.hide();this.$select.select2("destroy");this.$select.select2()}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/packed/mvc/ui/ui-slider.js --- a/static/scripts/packed/mvc/ui/ui-slider.js +++ b/static/scripts/packed/mvc/ui/ui-slider.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",min:null,max:null,step:null,precise:false,split:10000},initialize:function(d){var c=this;this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min;if(this.options.step===null){this.options.step=1;if(this.options.precise&&this.useslider){this.options.step=(this.options.max-this.options.min)/this.options.split}}if(this.useslider){this.$slider=this.$el.find("#slider");this.$slider.slider(this.options);this.$slider.on("slide",function(f,g){c.value(g.value)})}else{this.$el.find(".ui-form-slider-text").css("width","100%")}this.$text=this.$el.find("#text");this.$text.on("change",function(){c.value($(this).val())});var e=[];this.$text.on("keyup",function(f){e[f.which]=false});this.$text.on("keydown",function(g){var f=g.which;e[f]=true;if(!(f==8||f==9||f==13||f==37||f==39||(f>=48&&f<=57)||(f==190&&$(this).val().indexOf(".")==-1&&c.options.precise)||(f==189&&$(this).val().indexOf("-")==-1)||e[91]||e[17])){event.preventDefault()}})},value:function(c){if(c!==undefined){if(isNaN(c)){c=0}if(this.options.max!==null){c=Math.min(c,this.options.max)}if(this.options.min!==null){c=Math.max(c,this.options.min)}if(this.options.onchange){this.options.onchange(c)}this.$slider&&this.$slider.slider("value",c);this.$text.val(c)}return this.$text.val()},_template:function(c){return'<div id="'+c.id+'" class="ui-form-slider"><input id="text" type="text" class="ui-form-slider-text"/><div id="slider" class="ui-form-slider-element"/></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{min:null,max:null,step:null,precise:false,split:10000},initialize:function(d){var c=this;this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min;if(this.options.step===null){this.options.step=1;if(this.options.precise&&this.useslider){this.options.step=(this.options.max-this.options.min)/this.options.split}}if(this.useslider){this.$slider=this.$el.find("#slider");this.$slider.slider(this.options);this.$slider.on("slide",function(f,g){c.value(g.value)})}else{this.$el.find(".ui-form-slider-text").css("width","100%")}this.$text=this.$el.find("#text");if(this.options.value!==undefined){this.value(this.options.value)}this.$text.on("change",function(){c.value($(this).val())});var e=[];this.$text.on("keyup",function(f){e[f.which]=false});this.$text.on("keydown",function(g){var f=g.which;e[f]=true;if(!(f==8||f==9||f==13||f==37||f==39||(f>=48&&f<=57)||(f==190&&$(this).val().indexOf(".")==-1&&c.options.precise)||(f==189&&$(this).val().indexOf("-")==-1)||e[91]||e[17])){event.preventDefault()}})},value:function(c){if(c!==undefined){if(isNaN(c)){c=0}if(this.options.max!==null){c=Math.min(c,this.options.max)}if(this.options.min!==null){c=Math.max(c,this.options.min)}if(this.options.onchange){this.options.onchange(c)}this.$slider&&this.$slider.slider("value",c);this.$text.val(c)}return this.$text.val()},_template:function(c){return'<div id="'+c.id+'" class="ui-form-slider"><input id="text" type="text" class="ui-form-slider-text"/><div id="slider" class="ui-form-slider-element"/></div>'}});return{View:b}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/8fefb0715524/ Changeset: 8fefb0715524 Branch: next-stable User: guerler Date: 2014-12-01 05:21:40+00:00 Summary: ToolForm: Fix select2 value selection Affected #: 9 files diff -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 -r 8fefb07155242c59a263a785cfef8e0b46560781 client/galaxy/scripts/mvc/ui/ui-drilldown.js --- a/client/galaxy/scripts/mvc/ui/ui-drilldown.js +++ b/client/galaxy/scripts/mvc/ui/ui-drilldown.js @@ -23,7 +23,7 @@ /** Template to create options tree */ - _templateOptions: function(data, current) { + _templateOptions: function(options) { // link this var self = this; @@ -48,10 +48,10 @@ } // recursive function which iterates through options - function iterate ($tmpl, data) { - for (i in data) { + function iterate ($tmpl, options) { + for (i in options) { // current option level in hierarchy - var level = data[i]; + var level = options[i]; // check for options var has_options = level.options.length > 0; @@ -84,7 +84,7 @@ // iterate through options and create dom var $tmpl = $('<div/>'); - iterate($tmpl, data); + iterate($tmpl, options); return $tmpl; }, diff -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 -r 8fefb07155242c59a263a785cfef8e0b46560781 client/galaxy/scripts/mvc/ui/ui-options.js --- a/client/galaxy/scripts/mvc/ui/ui-options.js +++ b/client/galaxy/scripts/mvc/ui/ui-options.js @@ -7,7 +7,6 @@ initialize: function(options) { // options this.optionsDefault = { - value : [], visible : true, data : [], id : Utils.uuid(), @@ -38,7 +37,7 @@ this.update(this.options.data); // set initial value - if (this.options.value) { + if (this.options.value !== undefined) { this.value(this.options.value); } @@ -88,13 +87,13 @@ /** Return/Set current value */ value: function (new_value) { - // check if its an array - if (typeof new_value === 'string') { - new_value = [new_value]; - } - - // set new value + // set new value if provided if (new_value !== undefined) { + // check if its an array + if (!(new_value instanceof Array)) { + new_value = [new_value]; + } + // reset selection this.$el.find('input').prop('checked', false); @@ -111,12 +110,14 @@ /** Check if selected value exists (or any if multiple) */ exists: function(value) { - if (typeof value === 'string') { - value = [value]; - } - for (var i in value) { - if (this.$el.find('input[value="' + value[i] + '"]').length > 0) { - return true; + if (value !== undefined) { + if (!(value instanceof Array)) { + value = [value]; + } + for (var i in value) { + if (this.$el.find('input[value="' + value[i] + '"]').length > 0) { + return true; + } } } return false; diff -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 -r 8fefb07155242c59a263a785cfef8e0b46560781 client/galaxy/scripts/mvc/ui/ui-select-default.js --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -75,6 +75,9 @@ value : function (new_value) { if (new_value !== undefined) { this.$select.val(new_value); + if (this.$select.select2) { + this.$select.select2('val', new_value); + } } return this.$select.val(); }, diff -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 -r 8fefb07155242c59a263a785cfef8e0b46560781 static/scripts/mvc/ui/ui-drilldown.js --- a/static/scripts/mvc/ui/ui-drilldown.js +++ b/static/scripts/mvc/ui/ui-drilldown.js @@ -23,7 +23,7 @@ /** Template to create options tree */ - _templateOptions: function(data, current) { + _templateOptions: function(options) { // link this var self = this; @@ -48,10 +48,10 @@ } // recursive function which iterates through options - function iterate ($tmpl, data) { - for (i in data) { + function iterate ($tmpl, options) { + for (i in options) { // current option level in hierarchy - var level = data[i]; + var level = options[i]; // check for options var has_options = level.options.length > 0; @@ -84,7 +84,7 @@ // iterate through options and create dom var $tmpl = $('<div/>'); - iterate($tmpl, data); + iterate($tmpl, options); return $tmpl; }, diff -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 -r 8fefb07155242c59a263a785cfef8e0b46560781 static/scripts/mvc/ui/ui-options.js --- a/static/scripts/mvc/ui/ui-options.js +++ b/static/scripts/mvc/ui/ui-options.js @@ -7,7 +7,6 @@ initialize: function(options) { // options this.optionsDefault = { - value : [], visible : true, data : [], id : Utils.uuid(), @@ -38,7 +37,7 @@ this.update(this.options.data); // set initial value - if (this.options.value) { + if (this.options.value !== undefined) { this.value(this.options.value); } @@ -88,13 +87,13 @@ /** Return/Set current value */ value: function (new_value) { - // check if its an array - if (typeof new_value === 'string') { - new_value = [new_value]; - } - - // set new value + // set new value if provided if (new_value !== undefined) { + // check if its an array + if (!(new_value instanceof Array)) { + new_value = [new_value]; + } + // reset selection this.$el.find('input').prop('checked', false); @@ -111,12 +110,14 @@ /** Check if selected value exists (or any if multiple) */ exists: function(value) { - if (typeof value === 'string') { - value = [value]; - } - for (var i in value) { - if (this.$el.find('input[value="' + value[i] + '"]').length > 0) { - return true; + if (value !== undefined) { + if (!(value instanceof Array)) { + value = [value]; + } + for (var i in value) { + if (this.$el.find('input[value="' + value[i] + '"]').length > 0) { + return true; + } } } return false; diff -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 -r 8fefb07155242c59a263a785cfef8e0b46560781 static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -75,6 +75,9 @@ value : function (new_value) { if (new_value !== undefined) { this.$select.val(new_value); + if (this.$select.select2) { + this.$select.select2('val', new_value); + } } return this.$select.val(); }, diff -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 -r 8fefb07155242c59a263a785cfef8e0b46560781 static/scripts/packed/mvc/ui/ui-drilldown.js --- a/static/scripts/packed/mvc/ui/ui-drilldown.js +++ b/static/scripts/packed/mvc/ui/ui-drilldown.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-options"],function(b,a){var c=a.Base.extend({initialize:function(d){this.display=d.display||"checkbox";d.multiple=(this.display=="checkbox");a.Base.prototype.initialize.call(this,d)},_templateOption:function(d,f,e){return'<div><input name="'+this.options.id+'" class="ui-option" type="'+this.display+'" value="'+f+'">'+b.sanitize(d)+"<div/>"},_templateOptions:function(g,h){var e=this;function f(l,m){function k(n){if(n){m.fadeIn("fast");l.removeClass("toggle-expand");l.addClass("toggle");l.is_expanded=true}else{m.hide();l.removeClass("toggle");l.addClass("toggle-expand");l.is_expanded=false}}l.on("click",function(){k(!l.is_expanded)})}function d(q,o){for(i in o){var r=o[i];var m=r.options.length>0;var l=$("<div/>");if(m){var n=$('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>');var k=$("<div/>");k.append(n);k.append(e._templateOption(r.name,r.value));l.append(k);var p=$('<div style="display: none; margin-left: 25px;"/>');d(p,r.options);l.append(p);f(n,p)}else{l.append(e._templateOption(r.name,r.value))}q.append(l)}}var j=$("<div/>");d(j,g);return j},_template:function(d){return'<div class="ui-options drilldown-container" id="'+d.id+'"/>'}});return{View:c}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-options"],function(b,a){var c=a.Base.extend({initialize:function(d){this.display=d.display||"checkbox";d.multiple=(this.display=="checkbox");a.Base.prototype.initialize.call(this,d)},_templateOption:function(d,f,e){return'<div><input name="'+this.options.id+'" class="ui-option" type="'+this.display+'" value="'+f+'">'+b.sanitize(d)+"<div/>"},_templateOptions:function(f){var e=this;function g(k,l){function j(m){if(m){l.fadeIn("fast");k.removeClass("toggle-expand");k.addClass("toggle");k.is_expanded=true}else{l.hide();k.removeClass("toggle");k.addClass("toggle-expand");k.is_expanded=false}}k.on("click",function(){j(!k.is_expanded)})}function d(p,k){for(i in k){var q=k[i];var m=q.options.length>0;var l=$("<div/>");if(m){var n=$('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>');var j=$("<div/>");j.append(n);j.append(e._templateOption(q.name,q.value));l.append(j);var o=$('<div style="display: none; margin-left: 25px;"/>');d(o,q.options);l.append(o);g(n,o)}else{l.append(e._templateOption(q.name,q.value))}p.append(l)}}var h=$("<div/>");d(h,f);return h},_template:function(d){return'<div class="ui-options drilldown-container" id="'+d.id+'"/>'}});return{View:c}}); \ No newline at end of file diff -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 -r 8fefb07155242c59a263a785cfef8e0b46560781 static/scripts/packed/mvc/ui/ui-options.js --- a/static/scripts/packed/mvc/ui/ui-options.js +++ b/static/scripts/packed/mvc/ui/ui-options.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(g))}else{for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},value:function(g){if(typeof g==="string"){g=[g]}if(g!==undefined){this.$el.find("input").prop("checked",false);for(var f in g){this.$el.find('input[value="'+g[f]+'"]').first().prop("checked",true)}}return this._getValue()},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options"/>'}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var c={};c.View=a.extend({initialize:function(f){f.multiple=true;a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:a,Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file +define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(g))}else{for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},value:function(g){if(g!==undefined){if(!(g instanceof Array)){g=[g]}this.$el.find("input").prop("checked",false);for(var f in g){this.$el.find('input[value="'+g[f]+'"]').first().prop("checked",true)}}return this._getValue()},exists:function(g){if(g!==undefined){if(!(g instanceof Array)){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options"/>'}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var c={};c.View=a.extend({initialize:function(f){f.multiple=true;a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:a,Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file diff -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 -r 8fefb07155242c59a263a785cfef8e0b46560781 static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false,searchable:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}if(this.options.searchable){this.$button.hide();this.$select.select2("destroy");this.$select.select2()}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false,searchable:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}if(this.options.searchable){this.$button.hide();this.$select.select2("destroy");this.$select.select2()}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/1a2ef4a380ff/ Changeset: 1a2ef4a380ff Branch: next-stable User: guerler Date: 2014-12-01 06:18:16+00:00 Summary: ToolForm: Add baseurl, fix dynamic drill down options Affected #: 7 files diff -r 8fefb07155242c59a263a785cfef8e0b46560781 -r 1a2ef4a380ff35ca7f97ca2c50bab474400c6275 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -342,6 +342,11 @@ case 'drill_down': field = this._fieldDrilldown(input_def); break; + + // base url field + case 'baseurl': + field = this._fieldHidden(input_def); + break; // field not found default: diff -r 8fefb07155242c59a263a785cfef8e0b46560781 -r 1a2ef4a380ff35ca7f97ca2c50bab474400c6275 client/galaxy/scripts/mvc/ui/ui-drilldown.js --- a/client/galaxy/scripts/mvc/ui/ui-drilldown.js +++ b/client/galaxy/scripts/mvc/ui/ui-drilldown.js @@ -16,8 +16,7 @@ */ _templateOption: function(name, value, selected) { return '<div>' + - '<input name="' + this.options.id + '" class="ui-option" type="' + this.display + '" value="' + value + '">' + - Utils.sanitize(name) + + '<input name="' + this.options.id + '" class="ui-option" type="' + this.display + '" value="' + value + '">' + name + '<div/>'; }, diff -r 8fefb07155242c59a263a785cfef8e0b46560781 -r 1a2ef4a380ff35ca7f97ca2c50bab474400c6275 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -650,6 +650,11 @@ def get_label( self ): # BaseURLToolParameters are ultimately "hidden" parameters return None + + def to_dict( self, trans, view='collection', value_mapper=None ): + d = super( BaseURLToolParameter, self ).to_dict( trans ) + d['value'] = self.get_value( trans ) + return d DEFAULT_VALUE_MAP = lambda x: x @@ -1606,13 +1611,13 @@ """ return self.filtered.keys() - def to_dict( self, trans, view='collection', value_mapper=None, context={} ): + def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ): # skip SelectToolParameter (the immediate parent) bc we need to get options in a different way here d = ToolParameter.to_dict( self, trans ) options = [] try: - options = self.get_options( trans, context ) + options = self.get_options( trans=trans, other_values=other_values ) except KeyError: # will sometimes error if self.is_dynamic and self.filtered # bc we dont/cant fill out other_values above ({}) diff -r 8fefb07155242c59a263a785cfef8e0b46560781 -r 1a2ef4a380ff35ca7f97ca2c50bab474400c6275 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -342,6 +342,11 @@ case 'drill_down': field = this._fieldDrilldown(input_def); break; + + // base url field + case 'baseurl': + field = this._fieldHidden(input_def); + break; // field not found default: diff -r 8fefb07155242c59a263a785cfef8e0b46560781 -r 1a2ef4a380ff35ca7f97ca2c50bab474400c6275 static/scripts/mvc/ui/ui-drilldown.js --- a/static/scripts/mvc/ui/ui-drilldown.js +++ b/static/scripts/mvc/ui/ui-drilldown.js @@ -16,8 +16,7 @@ */ _templateOption: function(name, value, selected) { return '<div>' + - '<input name="' + this.options.id + '" class="ui-option" type="' + this.display + '" value="' + value + '">' + - Utils.sanitize(name) + + '<input name="' + this.options.id + '" class="ui-option" type="' + this.display + '" value="' + value + '">' + name + '<div/>'; }, diff -r 8fefb07155242c59a263a785cfef8e0b46560781 -r 1a2ef4a380ff35ca7f97ca2c50bab474400c6275 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;case"drill_down":i=this._fieldDrilldown(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldDrilldown:function(h){var i=this;return new g.Drilldown.View({id:"field-"+h.id,data:h.options,display:h.display,onchange:function(){i.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;case"drill_down":i=this._fieldDrilldown(h);break;case"baseurl":i=this._fieldHidden(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldDrilldown:function(h){var i=this;return new g.Drilldown.View({id:"field-"+h.id,data:h.options,display:h.display,onchange:function(){i.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file diff -r 8fefb07155242c59a263a785cfef8e0b46560781 -r 1a2ef4a380ff35ca7f97ca2c50bab474400c6275 static/scripts/packed/mvc/ui/ui-drilldown.js --- a/static/scripts/packed/mvc/ui/ui-drilldown.js +++ b/static/scripts/packed/mvc/ui/ui-drilldown.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-options"],function(b,a){var c=a.Base.extend({initialize:function(d){this.display=d.display||"checkbox";d.multiple=(this.display=="checkbox");a.Base.prototype.initialize.call(this,d)},_templateOption:function(d,f,e){return'<div><input name="'+this.options.id+'" class="ui-option" type="'+this.display+'" value="'+f+'">'+b.sanitize(d)+"<div/>"},_templateOptions:function(f){var e=this;function g(k,l){function j(m){if(m){l.fadeIn("fast");k.removeClass("toggle-expand");k.addClass("toggle");k.is_expanded=true}else{l.hide();k.removeClass("toggle");k.addClass("toggle-expand");k.is_expanded=false}}k.on("click",function(){j(!k.is_expanded)})}function d(p,k){for(i in k){var q=k[i];var m=q.options.length>0;var l=$("<div/>");if(m){var n=$('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>');var j=$("<div/>");j.append(n);j.append(e._templateOption(q.name,q.value));l.append(j);var o=$('<div style="display: none; margin-left: 25px;"/>');d(o,q.options);l.append(o);g(n,o)}else{l.append(e._templateOption(q.name,q.value))}p.append(l)}}var h=$("<div/>");d(h,f);return h},_template:function(d){return'<div class="ui-options drilldown-container" id="'+d.id+'"/>'}});return{View:c}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-options"],function(b,a){var c=a.Base.extend({initialize:function(d){this.display=d.display||"checkbox";d.multiple=(this.display=="checkbox");a.Base.prototype.initialize.call(this,d)},_templateOption:function(d,f,e){return'<div><input name="'+this.options.id+'" class="ui-option" type="'+this.display+'" value="'+f+'">'+d+"<div/>"},_templateOptions:function(f){var e=this;function g(k,l){function j(m){if(m){l.fadeIn("fast");k.removeClass("toggle-expand");k.addClass("toggle");k.is_expanded=true}else{l.hide();k.removeClass("toggle");k.addClass("toggle-expand");k.is_expanded=false}}k.on("click",function(){j(!k.is_expanded)})}function d(p,k){for(i in k){var q=k[i];var m=q.options.length>0;var l=$("<div/>");if(m){var n=$('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>');var j=$("<div/>");j.append(n);j.append(e._templateOption(q.name,q.value));l.append(j);var o=$('<div style="display: none; margin-left: 25px;"/>');d(o,q.options);l.append(o);g(n,o)}else{l.append(e._templateOption(q.name,q.value))}p.append(l)}}var h=$("<div/>");d(h,f);return h},_template:function(d){return'<div class="ui-options drilldown-container" id="'+d.id+'"/>'}});return{View:c}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 02 Dec '14

02 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/20e0db2511e5/ Changeset: 20e0db2511e5 Branch: next-stable User: guerler Date: 2014-12-02 16:47:59+00:00 Summary: Charts: Use most recent select field style Affected #: 1 file diff -r 1034c973ec1d2ce424f711d750ecc6de582d02aa -r 20e0db2511e555b9a168a96dee1ff75180aabbdf config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var 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r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div id="'+e.id+'" class="'+e.cls+'">';return e.title&&(t+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><div class="portlet-title">',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span id="portlet-title-text" class="portlet-title-text">'+e.title+"</span>"+"</div>"+"</div>"),t+='<div id="portlet-content" class="portlet-content">',e.placement=="top"&&(t+='<div id="buttons" class="buttons"></div>'),t+='<div id="content" class="content"></div>',e.placement=="bottom"&&(t+='<div id="buttons" class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("mvc/ui/ui-select-default",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1,multiple:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.options.multiple?(this.$select.prop("multiple",!0),this.$select.addClass("ui-select-multiple"),this.$icon.remove()):this.$el.addClass("ui-select"),this.update(this.options.data),this.options.visible||this.hide(),this.options.wait?this.wait():this.show();var n=this;this.$select.on("change",function(){n._change()}),this.on("change",function(){n._change()})},value:function(e){return e!==undefined&&this.$select.val(e),this.$select.val()},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},validate:function(){var e=this.value();e instanceof Array||(e=[e]);for(var t in e)if([null,"null",undefined].indexOf(e[t])>-1)return!1;return!0},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait(),this.$select.show(),this.$el.css("display","inline-block")},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){var t=this.$select.val();this.$select.find("option").remove();for(var n in e)this.$select.append(this._templateOption(e[n]));this._refresh(),this.$select.val(t),this.$select.val()||this.$select.val(this.first())},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find('option[value="'+e+'"]').length>0},_change:function(){this.options.onchange&&this.options.onchange(this.$select.val())},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable()},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){return'<div id="'+e.id+'">'+'<select id="select" class="select '+e.cls+" "+e.id+'"></select>'+'<div class="button">'+'<i id="icon"/>'+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-slider",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{value:"",min:null,max:null,step:null,precise:!1,split:1e4},initialize:function(t){var n=this;this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min,this.options.step===null&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$el.find("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(e,t){n.value(t.value)})):this.$el.find(".ui-form-slider-text").css("width","100%"),this.$text=this.$el.find("#text"),this.$text.on("change",function(){n.value($(this).val())}),this.$text.on("keydown",function(e){var t=e.which;t==8||t==9||t==13||t==37||t==39||t==189||t>=48&&t<=57||n.options.precise&&$(this).val().indexOf(".")==-1&&t==190||e.preventDefault()})},value:function(e){return e!==undefined&&(this.options.max!==null&&(e=Math.min(e,this.options.max)),this.options.min!==null&&(e=Math.max(e,this.options.min)),this.options.onchange&&this.options.onchange(e),this.$slider&&this.$slider.slider("value",e),this.$text.val(e)),this.$text.val()},_template:function(e){return'<div id="'+e.id+'" class="ui-form-slider">'+'<input id="text" type="text" class="ui-form-slider-text"/>'+'<div id="slider" class="ui-form-slider-element"/>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-options",["utils/utils"],function(e){var t=Backbone.View.extend({initialize:function(t){this.optionsDefault={value:[],visible:!0,data:[],id:e.uuid(),errorText:"No data available.",waitText:"Please wait..."},this.options=e.merge(t,this.optionsDefault),this.setElement("<div/>"),this.$message=$("<div/>"),this.$options=$(this._template(t)),this.$el.append(this.$message),this.$el.append(this.$options),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value&&this.value(this.options.value);var n=this;this.on("change",function(){n._change()})},update:function(e){var t=this._getValue();this.$el.find(".ui-option").remove();for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),this.$options.append(r)}var i=this;this.$el.find("input").on("change",function(){i.value(i._getValue()),i._change()}),this._refresh(),this.value(t)},exists:function(e){typeof e=="string"&&(e=[e]);for(var t in e)if(this.$el.find('input[value="'+e[t]+'"]').length>0)return!0;return!1},first:function(){var e=this.$el.find("input");return e.length>0?e.val():undefined},validate:function(){var e=this.value();e instanceof Array||(e=[e]);for(var t in e)if([null,"null",undefined].indexOf(e[t])>-1)return!1;return!0},wait:function(){this._size()==0&&(this._messageShow(this.options.waitText,"info"),this.$options.hide())},unwait:function(){this._messageHide(),this._refresh()},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){this._size()==0?(this._messageShow(this.options.errorText,"danger"),this.$options.hide()):(this._messageHide(),this.$options.css("display","inline-block"))},_getValue:function(){var e=this.$el.find(":checked");if(e.length==0)return"null";if(this.options.multiple){var t=[];return e.each(function(){t.push($(this).val())}),t}return e.val()},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert alert-"+t),this.$message.html(e)},_messageHide:function(){this.$message.hide()}}),n={};n.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){typeof e=="string"&&(e=[e]);if(e!==undefined){this.$el.find("input").prop("checked",!1);for(var t in e)this.$el.find("input[value="+e[t]+"]").prop("checked",!0)}return this._getValue()},_templateOption:function(e){return'<div><input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"},_template:function(){return'<div class="ui-options"/>'}});var r={};r.View=n.View.extend({initialize:function(e){e.multiple=!0,n.View.prototype.initialize.call(this,e)},_templateOption:function(e){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"}});var i={};return i.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$el.find("input").prop("checked",!1),this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t='<label class="btn btn-default">';return e.icon&&(t+='<i class="fa '+e.icon+'"/>'),t+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'">'+e.label+"</label>",t},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Radio:n,RadioButton:i,Checkbox:r}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r,i,s){var o=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),u=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),p=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success:function(){n._refreshHdas()}}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request({type:"POST",url:config.root+"api/tools",data:data,success:function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),o.app.storage.save(),o._wait(t,i,s)}},error:function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()}})},_wait:function(t,n,r){var i=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success:function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))}})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)}})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","mvc/ui/ui-misc","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e4,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"radiobutton",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},use_panels:{title:"Use multi-panels",info:"Would you like to separate your data into individual panels?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),function(){function t(e,t){return(new Date(t,e+1,0)).getDate()}function n(e,t,n){return function(r,i,s){var o=e(r),u=[];o<r&&t(o);if(s>1)while(o<i){var a=new Date(+o);n(a)%s===0&&u.push(a),t(o)}else while(o<i)u.push(new Date(+o)),t(o);return u}}var e=window.nv||{};e.version="1.1.15b",e.dev=!0,window.nv=e,e.tooltip=e.tooltip||{},e.utils=e.utils||{},e.models=e.models||{},e.charts={},e.graphs=[],e.logs={},e.dispatch=d3.dispatch("render_start","render_end"),e.dev&&(e.dispatch.on("render_start",function(t){e.logs.startTime=+(new Date)}),e.dispatch.on("render_end",function(t){e.logs.endTime=+(new Date),e.logs.totalTime=e.logs.endTime-e.logs.startTime,e.log("total",e.logs.totalTime)})),e.log=function(){if(e.dev&&console.log&&console.log.apply)console.log.apply(console,arguments);else if(e.dev&&typeof console.log=="function"&&Function.prototype.bind){var t=Function.prototype.bind.call(console.log,console);t.apply(console,arguments)}return arguments[arguments.length-1]},e.render=function(n){n=n||1,e.render.active=!0,e.dispatch.render_start(),setTimeout(function(){var t,r;for(var i=0;i<n&&(r=e.render.queue[i]);i++)t=r.generate(),typeof r.callback==typeof Function&&r.callback(t),e.graphs.push(t);e.render.queue.splice(0,i),e.render.queue.length?setTimeout(arguments.callee,0):(e.dispatch.render_end(),e.render.active=!1)},0)},e.render.active=!1,e.render.queue=[],e.addGraph=function(t){typeof arguments[0]==typeof Function&&(t={generate:arguments[0],callback:arguments[1]}),e.render.queue.push(t),e.render.active||e.render()},e.identity=function(e){return e},e.strip=function(e){return 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t=e.models.line(),n=e.models.historicalBar(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.legend(),u={top:30,right:60,bottom:50,left:60},a=null,f=null,l=function(e){return e.x},c=function(e){return e.y},h=e.utils.defaultColor(),p=!0,d=!0,v=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},m,g,y,b={},w=null,E="No Data Available.",S=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState");n.padData(!0),t.clipEdge(!1).padData(!0),r.orient("bottom").tickPadding(7).highlightZero(!1),i.orient("left"),s.orient("right");var x=function(n,o){var u=n.pos[0]+(o.offsetLeft||0),a=n.pos[1]+(o.offsetTop||0),f=r.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?i:s).tickFormat()(t.y()(n.point,n.pointIndex)),c=v(n.series.key,f,l,n,T);e.tooltip.show([u,a],c,n.value<0?"n":"s",null,o)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=0;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return arguments.length?(h=e,k):h},k.height=function(e){return arguments.length?(p=e,k):p},k.height2=function(e){return arguments.length?(d=e,k):d},k.color=function(t){return arguments.length?(c=e.utils.getColor(t),u.color(c),k):c},k.showLegend=function(e){return arguments.length?(b=e,k):b},k.tooltips=function(e){return arguments.length?(E=e,k):E},k.tooltipContent=function(e){return arguments.length?(S=e,k):S},k.interpolate=function(e){return arguments.length?(t.interpolate(e),n.interpolate(e),k):t.interpolate()},k.noData=function(e){return arguments.length?(x=e,k):x},k.xTickFormat=function(e){return arguments.length?(r.tickFormat(e),s.tickFormat(e),k):r.tickFormat()},k.yTickFormat=function(e){return arguments.length?(i.tickFormat(e),o.tickFormat(e),k):i.tickFormat()},k.brushExtent=function(e){return arguments.length?(w=e,k):w},k.transitionDuration=function(e){return arguments.length?(N=e,k):N},k},e.models.linePlusBarWithFocusChart=function(){function B(e){return e.each(function(e){function tt(e){var t=+(e=="e"),n=t?1:-1,r=I/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function nt(){h.empty()||h.extent(x),Y.data([h.empty()?k.domain():x]).each(function(e,t){var n=k(e[0])-k.range()[0],r=k.range()[1]-k(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",k(e[1])).attr("width",r<0?0:r)})}function rt(){x=h.empty()?null:h.extent(),S=h.empty()?k.domain():h.extent(),D.brush({extent:S,brush:h}),nt(),r.width(j).height(F).color(e.map(function(e,t){return e.color||w(e,t)}).filter(function(t,n){return!e[n].disabled&&e[n].bar})),t.width(j).height(F).color(e.map(function(e,t){return e.color||w(e,t)}).filter(function(t,n){return!e[n].disabled&&!e[n].bar}));var n=$.select(".nv-focus .nv-barsWrap").datum(R.length?R.map(function(e,t){return{key:e.key,values:e.values.filter(function(e,t){return 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arguments.length?(m=e,F):m},F.showDistY=function(e){return arguments.length?(g=e,F):g},F.showControls=function(e){return arguments.length?(S=e,F):S},F.showLegend=function(e){return arguments.length?(y=e,F):y},F.showXAxis=function(e){return arguments.length?(b=e,F):b},F.showYAxis=function(e){return arguments.length?(w=e,F):w},F.rightAlignYAxis=function(e){return arguments.length?(E=e,r.orient(e?"right":"left"),F):E},F.fisheye=function(e){return arguments.length?(x=e,F):x},F.xPadding=function(e){return arguments.length?(d=e,F):d},F.yPadding=function(e){return arguments.length?(v=e,F):v},F.tooltips=function(e){return arguments.length?(N=e,F):N},F.tooltipContent=function(e){return arguments.length?(L=e,F):L},F.tooltipXContent=function(e){return arguments.length?(C=e,F):C},F.tooltipYContent=function(e){return arguments.length?(k=e,F):k},F.state=function(e){return arguments.length?(A=e,F):A},F.defaultState=function(e){return arguments.length?(O=e,F):O},F.noData=function(e){return 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t=e.models.scatter(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.models.distribution(),u=e.models.distribution(),a={top:30,right:20,bottom:50,left:75},f=null,l=null,c=e.utils.defaultColor(),h=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.xScale(),p=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.yScale(),d=!1,v=!1,m=!0,g=!0,y=!0,b=!1,w=!!d3.fisheye,E=0,S=!1,x=!0,T=function(e,t,n){return"<strong>"+t+"</strong>"},N=function(e,t,n){return"<strong>"+n+"</strong>"},C=function(e,t,n,r){return"<h3>"+e+"</h3>"+"<p>"+r+"</p>"},k={},L=null,A=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),O="No Data Available.",M=0;t.xScale(h).yScale(p),n.orient("bottom").tickPadding(10),r.orient(b?"right":"left").tickPadding(10),o.axis("x"),u.axis("y"),s.updateState(!1);var _,D,P=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(d=e,B):d},B.showDistY=function(e){return arguments.length?(v=e,B):v},B.showControls=function(e){return arguments.length?(w=e,B):w},B.showLegend=function(e){return arguments.length?(m=e,B):m},B.showXAxis=function(e){return arguments.length?(g=e,B):g},B.showYAxis=function(e){return arguments.length?(y=e,B):y},B.rightAlignYAxis=function(e){return arguments.length?(b=e,r.orient(e?"right":"left"),B):b},B.fisheye=function(e){return arguments.length?(E=e,B):E},B.tooltips=function(e){return arguments.length?(x=e,B):x},B.tooltipContent=function(e){return arguments.length?(C=e,B):C},B.tooltipXContent=function(e){return arguments.length?(T=e,B):T},B.tooltipYContent=function(e){return arguments.length?(N=e,B):N},B.state=function(e){return arguments.length?(k=e,B):k},B.defaultState=function(e){return arguments.length?(L=e,B):L},B.noData=function(e){return arguments.length?(O=e,B):O},B.transitionDuration=function(e){return arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var e=d3.mouse(this)[0]-n.left;u=[r(c,Math.round(s.invert(e)))],O()}var m=d3.select(this),g=(r||parseInt(m.style("width"))||960)-n.left-n.right,b=(i||parseInt(m.style("height"))||400)-n.top-n.bottom;v.update=function(){v(e)},v.container=this;if(!c||!c.length){var w=m.selectAll(".nv-noData").data([d]);return w.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),w.attr("x",n.left+g/2).attr("y",n.top+b/2).text(function(e){return e}),v}m.selectAll(".nv-noData").remove();var E=t.y()(c[c.length-1],c.length-1);s=t.xScale(),o=t.yScale();var S=m.selectAll("g.nv-wrap.nv-sparklineplus").data([c]),T=S.enter().append("g").attr("class","nvd3 nv-wrap nv-sparklineplus"),N=T.append("g"),C=S.select("g");N.append("g").attr("class","nv-sparklineWrap"),N.append("g").attr("class","nv-valueWrap"),N.append("g").attr("class","nv-hoverArea"),S.attr("transform","translate("+n.left+","+n.top+")");var k=C.select(".nv-sparklineWrap");t.width(g).height(b),k.call(t);var L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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src="'+e.url+'"/>'}}),u=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),p=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success:function(){n._refreshHdas()}}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request({type:"POST",url:config.root+"api/tools",data:data,success:function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),o.app.storage.save(),o._wait(t,i,s)}},error:function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()}})},_wait:function(t,n,r){var i=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success:function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))}})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)}})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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v.size(2.2).sizeDomain([2.2,2.2]),v.dispatch.on("elementClick.area",function(e){m.areaClick(e)}),v.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+t.left,e.pos[1]+t.top],m.tooltipShow(e)}),v.dispatch.on("elementMouseout.tooltip",function(e){m.tooltipHide(e)}),g.dispatch=m,g.scatter=v,d3.rebind(g,v,"interactive","size","xScale","yScale","zScale","xDomain","yDomain","xRange","yRange","sizeDomain","forceX","forceY","forceSize","clipVoronoi","useVoronoi","clipRadius","highlightPoint","clearHighlights"),g.options=e.utils.optionsFunc.bind(g),g.x=function(e){return arguments.length?(o=d3.functor(e),g):o},g.y=function(e){return arguments.length?(u=d3.functor(e),g):u},g.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,g):t},g.width=function(e){return 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Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:c,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:f,nvd3_scatter:l,nvd3_histogram:a,jqplot_bar:h,jqplot_histogram_discrete:m,jqplot_line:p,jqplot_scatter:d,jqplot_boxplot:v,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","utils/deferred","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c,h){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new l,this.types=new h,this.chart=new c,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.deferred=new u,this.viewer_view=new a(this),this.editor_view=new f(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)}})}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/d857f25c1114/ Changeset: d857f25c1114 User: guerler Date: 2014-12-02 16:48:17+00:00 Summary: Merge Affected #: 1 file diff -r 82b95de1f7bd2db44900c2d85c14dc49fa683502 -r d857f25c111411359a977366d446cd0a78768595 config/plugins/visualizations/charts/static/build-app.js --- 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this.$select.find('option[value="'+e+'"]').length>0},_change:function(){this.options.onchange&&this.options.onchange(this.$select.val())},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable()},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){return'<div id="'+e.id+'">'+'<select id="select" class="select '+e.cls+" "+e.id+'"></select>'+'<div class="button">'+'<i id="icon"/>'+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-slider",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{value:"",min:null,max:null,step:null,precise:!1,split:1e4},initialize:function(t){var n=this;this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min,this.options.step===null&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$el.find("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(e,t){n.value(t.value)})):this.$el.find(".ui-form-slider-text").css("width","100%"),this.$text=this.$el.find("#text"),this.$text.on("change",function(){n.value($(this).val())}),this.$text.on("keydown",function(e){var t=e.which;t==8||t==9||t==13||t==37||t==39||t==189||t>=48&&t<=57||n.options.precise&&$(this).val().indexOf(".")==-1&&t==190||e.preventDefault()})},value:function(e){return 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e!==undefined&&(this.$el.find("input").prop("checked",!1),this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t='<label class="btn btn-default">';return e.icon&&(t+='<i class="fa '+e.icon+'"/>'),t+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'">'+e.label+"</label>",t},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Radio:n,RadioButton:i,Checkbox:r}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r,i,s){var o=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),u=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor 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onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success:function(){n._refreshHdas()}}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request({type:"POST",url:config.root+"api/tools",data:data,success:function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),o.app.storage.save(),o._wait(t,i,s)}},error:function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()}})},_wait:function(t,n,r){var i=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success:function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))}})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)}})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","mvc/ui/ui-misc","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e4,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["x_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["x_axis_precision"]}},{label:"Float",value:"f",operations:{show:["x_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["x_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["x_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["x_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["x_axis_precision"]}}]},x_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_y:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"radiobutton",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},use_panels:{title:"Use multi-panels",info:"Would you like to separate your data into individual panels?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),function(){function t(e,t){return(new Date(t,e+1,0)).getDate()}function n(e,t,n){return function(r,i,s){var o=e(r),u=[];o<r&&t(o);if(s>1)while(o<i){var a=new Date(+o);n(a)%s===0&&u.push(a),t(o)}else while(o<i)u.push(new Date(+o)),t(o);return u}}var e=window.nv||{};e.version="1.1.15b",e.dev=!0,window.nv=e,e.tooltip=e.tooltip||{},e.utils=e.utils||{},e.models=e.models||{},e.charts={},e.graphs=[],e.logs={},e.dispatch=d3.dispatch("render_start","render_end"),e.dev&&(e.dispatch.on("render_start",function(t){e.logs.startTime=+(new Date)}),e.dispatch.on("render_end",function(t){e.logs.endTime=+(new 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E=d3.select(this),T=this,N=(u||parseInt(E.style("width"))||960)-s.left-s.right,C=(a||parseInt(E.style("height"))||400)-s.top-s.bottom;x.update=function(){E.call(x)},x.container=this,g.disabled=d.map(function(e){return!!e.disabled});if(!y){var k;y={};for(k in g)g[k]instanceof Array?y[k]=g[k].slice(0):y[k]=g[k]}if(!d||!d.length||!d.filter(function(e){return e.values.length}).length){var L=E.selectAll(".nv-noData").data([b]);return L.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),L.attr("x",s.left+N/2).attr("y",s.top+C/2).text(function(e){return e}),x}E.selectAll(".nv-noData").remove(),v=t.xScale(),m=t.yScale();var A=E.selectAll("g.nv-wrap.nv-historicalBarChart").data([d]),O=A.enter().append("g").attr("class","nvd3 nv-wrap nv-historicalBarChart").append("g"),M=A.select("g");O.append("g").attr("class","nv-x nv-axis"),O.append("g").attr("class","nv-y 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t=e.models.historicalBar(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s={top:30,right:90,bottom:50,left:90},o=e.utils.defaultColor(),u=null,a=null,f=!1,l=!0,c=!0,h=!1,p=!0,d=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},v,m,g={},y=null,b="No Data Available.",w=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),E=0;n.orient("bottom").tickPadding(7),r.orient(h?"right":"left");var S=function(i,s){if(s){var o=d3.select(s).select("svg"),u=o.node()?o.attr("viewBox"):null;if(u){u=u.split(" ");var a=parseInt(o.style("width"))/u[2];i.pos[0]=i.pos[0]*a,i.pos[1]=i.pos[1]*a}}var f=i.pos[0]+(s.offsetLeft||0),l=i.pos[1]+(s.offsetTop||0),c=n.tickFormat()(t.x()(i.point,i.pointIndex)),h=r.tickFormat()(t.y()(i.point,i.pointIndex)),p=d(i.series.key,c,h,i,x);e.tooltip.show([f,l],p,null,null,s)};return 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=0;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),C.dispatch=S,C.multibar=t,C.legend=i,C.xAxis=n,C.yAxis=r,d3.rebind(C,t,"x","y","xDomain","yDomain","xRange","yRange","forceX","forceY","clipEdge","id","delay","showValues","showBarLabels","valueFormat","stacked","barColor"),C.options=e.utils.optionsFunc.bind(C),C.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,C):o},C.width=function(e){return arguments.length?(u=e,C):u},C.height=function(e){return arguments.length?(a=e,C):a},C.color=function(t){return arguments.length?(f=e.utils.getColor(t),i.color(f),C):f},C.showControls=function(e){return 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arguments.length?(m=e,F):m},F.showDistY=function(e){return arguments.length?(g=e,F):g},F.showControls=function(e){return arguments.length?(S=e,F):S},F.showLegend=function(e){return arguments.length?(y=e,F):y},F.showXAxis=function(e){return arguments.length?(b=e,F):b},F.showYAxis=function(e){return arguments.length?(w=e,F):w},F.rightAlignYAxis=function(e){return arguments.length?(E=e,r.orient(e?"right":"left"),F):E},F.fisheye=function(e){return arguments.length?(x=e,F):x},F.xPadding=function(e){return arguments.length?(d=e,F):d},F.yPadding=function(e){return arguments.length?(v=e,F):v},F.tooltips=function(e){return arguments.length?(N=e,F):N},F.tooltipContent=function(e){return arguments.length?(L=e,F):L},F.tooltipXContent=function(e){return arguments.length?(C=e,F):C},F.tooltipYContent=function(e){return arguments.length?(k=e,F):k},F.state=function(e){return arguments.length?(A=e,F):A},F.defaultState=function(e){return arguments.length?(O=e,F):O},F.noData=function(e){return 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t=e.models.scatter(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.models.distribution(),u=e.models.distribution(),a={top:30,right:20,bottom:50,left:75},f=null,l=null,c=e.utils.defaultColor(),h=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.xScale(),p=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.yScale(),d=!1,v=!1,m=!0,g=!0,y=!0,b=!1,w=!!d3.fisheye,E=0,S=!1,x=!0,T=function(e,t,n){return"<strong>"+t+"</strong>"},N=function(e,t,n){return"<strong>"+n+"</strong>"},C=function(e,t,n,r){return"<h3>"+e+"</h3>"+"<p>"+r+"</p>"},k={},L=null,A=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),O="No Data Available.",M=0;t.xScale(h).yScale(p),n.orient("bottom").tickPadding(10),r.orient(b?"right":"left").tickPadding(10),o.axis("x"),u.axis("y"),s.updateState(!1);var _,D,P=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var e=d3.mouse(this)[0]-n.left;u=[r(c,Math.round(s.invert(e)))],O()}var m=d3.select(this),g=(r||parseInt(m.style("width"))||960)-n.left-n.right,b=(i||parseInt(m.style("height"))||400)-n.top-n.bottom;v.update=function(){v(e)},v.container=this;if(!c||!c.length){var w=m.selectAll(".nv-noData").data([d]);return w.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),w.attr("x",n.left+g/2).attr("y",n.top+b/2).text(function(e){return e}),v}m.selectAll(".nv-noData").remove();var E=t.y()(c[c.length-1],c.length-1);s=t.xScale(),o=t.yScale();var S=m.selectAll("g.nv-wrap.nv-sparklineplus").data([c]),T=S.enter().append("g").attr("class","nvd3 nv-wrap nv-sparklineplus"),N=T.append("g"),C=S.select("g");N.append("g").attr("class","nv-sparklineWrap"),N.append("g").attr("class","nv-valueWrap"),N.append("g").attr("class","nv-hoverArea"),S.attr("transform","translate("+n.left+","+n.top+")");var k=C.select(".nv-sparklineWrap");t.width(g).height(b),k.call(t);var 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e!==undefined&&(this.$el.find("input").prop("checked",!1),this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t='<label class="btn btn-default">';return e.icon&&(t+='<i class="fa '+e.icon+'"/>'),t+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'">'+e.label+"</label>",t},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Radio:n,RadioButton:i,Checkbox:r}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r,i,s){var o=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),u=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),p=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success:function(){n._refreshHdas()}}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request({type:"POST",url:config.root+"api/tools",data:data,success:function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),o.app.storage.save(),o._wait(t,i,s)}},error:function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()}})},_wait:function(t,n,r){var i=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success:function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))}})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)}})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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v.size(2.2).sizeDomain([2.2,2.2]),v.dispatch.on("elementClick.area",function(e){m.areaClick(e)}),v.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+t.left,e.pos[1]+t.top],m.tooltipShow(e)}),v.dispatch.on("elementMouseout.tooltip",function(e){m.tooltipHide(e)}),g.dispatch=m,g.scatter=v,d3.rebind(g,v,"interactive","size","xScale","yScale","zScale","xDomain","yDomain","xRange","yRange","sizeDomain","forceX","forceY","forceSize","clipVoronoi","useVoronoi","clipRadius","highlightPoint","clearHighlights"),g.options=e.utils.optionsFunc.bind(g),g.x=function(e){return arguments.length?(o=d3.functor(e),g):o},g.y=function(e){return arguments.length?(u=d3.functor(e),g):u},g.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,g):t},g.width=function(e){return 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You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Merged in BjoernGruening/galaxy-central-1 (pull request #578)
by commits-noreply＠bitbucket.org 02 Dec '14

02 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/82b95de1f7bd/ Changeset: 82b95de1f7bd User: dannon Date: 2014-12-02 13:26:09+00:00 Summary: Merged in BjoernGruening/galaxy-central-1 (pull request #578) Update the Dockerfile template to the latest version our Galaxy Docker Container. Affected #: 1 file diff -r 74e82c604d026307fa8d72a7850ddd33c5f9259b -r 82b95de1f7bd2db44900c2d85c14dc49fa683502 lib/tool_shed/util/basic_util.py --- a/lib/tool_shed/util/basic_util.py +++ b/lib/tool_shed/util/basic_util.py @@ -27,24 +27,25 @@ MAINTAINER Bjoern A. Gruning, bjoern.gruening(a)gmail.com -RUN sed -i 's|brand.*|brand = deepTools|g' ~/galaxy-central/universe_wsgi.ini - WORKDIR /galaxy-central ${selected_repositories} -# Mark one folder as imported from the host. -VOLUME ["/export/"] +# Mark folders as imported from the host. +VOLUME ["/export/", "/data/", "/var/lib/docker"] -# Expose port 80 to the host +# Expose port 80 (webserver), 21 (FTP server), 8800 (Proxy), 9001 (Galaxy report app) EXPOSE :80 +EXPOSE :21 +EXPOSE :8800 +EXPOSE :9001 # Autostart script that is invoked during container start CMD ["/usr/bin/startup"] ''' SELECTED_REPOSITORIES_TEMPLATE = ''' -RUN service postgresql start && service apache2 start && ./run.sh --daemon && sleep 120 && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:8080 --url ${tool_shed_url} -o ${repository_owner} --name ${repository_name} --tool-deps --repository-deps --panel-section-name 'Docker' +RUN install-repository "--url ${tool_shed_url} -o ${repository_owner} --name ${repository_name}" ''' def evaluate_template( text, install_environment ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 02 Dec '14

02 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/88d434f15cd4/ Changeset: 88d434f15cd4 User: BjoernGruening Date: 2014-11-28 19:18:58+00:00 Summary: Update the Dockerfile template to the latest version our Galaxy Docker Container. The new container will be release together with Galaxy next week. Affected #: 1 file diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 88d434f15cd4042df6b4fb22c9861cbd42bb2a77 lib/tool_shed/util/basic_util.py --- a/lib/tool_shed/util/basic_util.py +++ b/lib/tool_shed/util/basic_util.py @@ -27,24 +27,25 @@ MAINTAINER Bjoern A. Gruning, bjoern.gruening(a)gmail.com -RUN sed -i 's|brand.*|brand = deepTools|g' ~/galaxy-central/universe_wsgi.ini - WORKDIR /galaxy-central ${selected_repositories} -# Mark one folder as imported from the host. -VOLUME ["/export/"] +# Mark folders as imported from the host. +VOLUME ["/export/", "/data/", "/var/lib/docker"] -# Expose port 80 to the host +# Expose port 80 (webserver), 21 (FTP server), 8800 (Proxy), 9001 (Galaxy report app) EXPOSE :80 +EXPOSE :21 +EXPOSE :8800 +EXPOSE :9001 # Autostart script that is invoked during container start CMD ["/usr/bin/startup"] ''' SELECTED_REPOSITORIES_TEMPLATE = ''' -RUN service postgresql start && service apache2 start && ./run.sh --daemon && sleep 120 && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:8080 --url ${tool_shed_url} -o ${repository_owner} --name ${repository_name} --tool-deps --repository-deps --panel-section-name 'Docker' +RUN install-repository "--url ${tool_shed_url} -o ${repository_owner} --name ${repository_name}" ''' def evaluate_template( text, install_environment ): https://bitbucket.org/galaxy/galaxy-central/commits/82b95de1f7bd/ Changeset: 82b95de1f7bd User: dannon Date: 2014-12-02 13:26:09+00:00 Summary: Merged in BjoernGruening/galaxy-central-1 (pull request #578) Update the Dockerfile template to the latest version our Galaxy Docker Container. Affected #: 1 file diff -r 74e82c604d026307fa8d72a7850ddd33c5f9259b -r 82b95de1f7bd2db44900c2d85c14dc49fa683502 lib/tool_shed/util/basic_util.py --- a/lib/tool_shed/util/basic_util.py +++ b/lib/tool_shed/util/basic_util.py @@ -27,24 +27,25 @@ MAINTAINER Bjoern A. Gruning, bjoern.gruening(a)gmail.com -RUN sed -i 's|brand.*|brand = deepTools|g' ~/galaxy-central/universe_wsgi.ini - WORKDIR /galaxy-central ${selected_repositories} -# Mark one folder as imported from the host. -VOLUME ["/export/"] +# Mark folders as imported from the host. +VOLUME ["/export/", "/data/", "/var/lib/docker"] -# Expose port 80 to the host +# Expose port 80 (webserver), 21 (FTP server), 8800 (Proxy), 9001 (Galaxy report app) EXPOSE :80 +EXPOSE :21 +EXPOSE :8800 +EXPOSE :9001 # Autostart script that is invoked during container start CMD ["/usr/bin/startup"] ''' SELECTED_REPOSITORIES_TEMPLATE = ''' -RUN service postgresql start && service apache2 start && ./run.sh --daemon && sleep 120 && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:8080 --url ${tool_shed_url} -o ${repository_owner} --name ${repository_name} --tool-deps --repository-deps --panel-section-name 'Docker' +RUN install-repository "--url ${tool_shed_url} -o ${repository_owner} --name ${repository_name}" ''' def evaluate_template( text, install_environment ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 18 new changesets
by commits-noreply＠bitbucket.org 02 Dec '14

02 Dec '14

18 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1037d12c3005/ Changeset: 1037d12c3005 User: jmchilton Date: 2014-12-02 02:18:56+00:00 Summary: PEP-8 fixes for lib/galaxy/tools/parameters/output_collect.py Affected #: 1 file diff -r 5393f6389105d22bc8791f908075c152f11a4d2e -r 1037d12c30058f318014efea19898b209dc8ba8a lib/galaxy/tools/parameters/output_collect.py --- a/lib/galaxy/tools/parameters/output_collect.py +++ b/lib/galaxy/tools/parameters/output_collect.py @@ -119,7 +119,8 @@ for root, dirs, files in os.walk( extra_files_path_joined ): extra_dir = os.path.join( primary_data.extra_files_path, root.replace( extra_files_path_joined, '', 1 ).lstrip( os.path.sep ) ) for f in files: - app.object_store.update_from_file( primary_data.dataset, + app.object_store.update_from_file( + primary_data.dataset, extra_dir=extra_dir, alt_name=f, file_name=os.path.join( root, f ), @@ -127,7 +128,7 @@ dir_only=True, preserve_symlinks=True ) - # FIXME: + # FIXME: # since these are placed into the job working dir, let the standard # Galaxy cleanup methods handle this (for now?) # there was an extra_files_path dir, attempt to remove it https://bitbucket.org/galaxy/galaxy-central/commits/fd043fbe00ab/ Changeset: fd043fbe00ab User: jmchilton Date: 2014-12-02 02:18:56+00:00 Summary: Refactor output_collect for reuse. Reduces cyclomatic complexity slightly as well. Affected #: 1 file diff -r 1037d12c30058f318014efea19898b209dc8ba8a -r fd043fbe00abd3f2ee6b6b2f8ffc3271c44cbce0 lib/galaxy/tools/parameters/output_collect.py --- a/lib/galaxy/tools/parameters/output_collect.py +++ b/lib/galaxy/tools/parameters/output_collect.py @@ -43,20 +43,8 @@ for filename in glob.glob(os.path.join(app.config.new_file_path, "primary_%i_*" % outdata.id) ): filenames[ filename ] = DEFAULT_DATASET_COLLECTOR if 'job_working_directory' in app.config.collect_outputs_from: - for extra_file_collector in dataset_collectors: - directory = job_working_directory - if extra_file_collector.directory: - directory = os.path.join( directory, extra_file_collector.directory ) - if not util.in_directory( directory, job_working_directory ): - raise Exception( "Problem with tool configuration, attempting to pull in datasets from outside working directory." ) - if not os.path.isdir( directory ): - continue - for filename in sorted( os.listdir( directory ) ): - path = os.path.join( directory, filename ) - if not os.path.isfile( path ): - continue - if extra_file_collector.match( outdata, filename ): - filenames[ path ] = extra_file_collector + for path, extra_file_collector in walk_over_extra_files( dataset_collectors, job_working_directory, outdata ): + filenames[ path ] = extra_file_collector for filename_index, ( filename, extra_file_collector ) in enumerate( filenames.iteritems() ): fields_match = extra_file_collector.match( outdata, os.path.basename( filename ) ) if not fields_match: @@ -163,6 +151,22 @@ return primary_datasets +def walk_over_extra_files( extra_file_collectors, job_working_directory, matchable ): + for extra_file_collector in extra_file_collectors: + directory = job_working_directory + if extra_file_collector.directory: + directory = os.path.join( directory, extra_file_collector.directory ) + if not util.in_directory( directory, job_working_directory ): + raise Exception( "Problem with tool configuration, attempting to pull in datasets from outside working directory." ) + if not os.path.isdir( directory ): + continue + for filename in sorted( os.listdir( directory ) ): + path = os.path.join( directory, filename ) + if not os.path.isfile( path ): + continue + if extra_file_collector.match( matchable, filename ): + yield path, extra_file_collector + # XML can describe custom patterns, but these literals describe named # patterns that will be replaced. NAMED_PATTERNS = { https://bitbucket.org/galaxy/galaxy-central/commits/2022044556ca/ Changeset: 2022044556ca User: jmchilton Date: 2014-12-02 02:18:56+00:00 Summary: Refactor small helper out of get_work_dir_outputs for reuse. Leave comment about not understanding the complexity :). Affected #: 1 file diff -r fd043fbe00abd3f2ee6b6b2f8ffc3271c44cbce0 -r 2022044556ca064d879cacbdeae07f2a8ae6f1fc lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -214,23 +214,31 @@ # Walk job's output associations to find and use from_work_dir attributes. job = job_wrapper.get_job() job_tool = job_wrapper.tool + for (joda, dataset) in self._walk_dataset_outputs( job ): + if joda and job_tool: + hda_tool_output = job_tool.outputs.get( joda.name, None ) + if hda_tool_output and hda_tool_output.from_work_dir: + # Copy from working dir to HDA. + # TODO: move instead of copy to save time? + source_file = os.path.join( job_working_directory, hda_tool_output.from_work_dir ) + destination = job_wrapper.get_output_destination( output_paths[ dataset.dataset_id ] ) + if in_directory( source_file, job_working_directory ): + output_pairs.append( ( source_file, destination ) ) + else: + # Security violation. + log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, job_wrapper.working_directory ) ) + return output_pairs + + def _walk_dataset_outputs( self, job ): for dataset_assoc in job.output_datasets + job.output_library_datasets: for dataset in dataset_assoc.dataset.dataset.history_associations + dataset_assoc.dataset.dataset.library_associations: if isinstance( dataset, self.app.model.HistoryDatasetAssociation ): joda = self.sa_session.query( self.app.model.JobToOutputDatasetAssociation ).filter_by( job=job, dataset=dataset ).first() - if joda and job_tool: - hda_tool_output = job_tool.outputs.get( joda.name, None ) - if hda_tool_output and hda_tool_output.from_work_dir: - # Copy from working dir to HDA. - # TODO: move instead of copy to save time? - source_file = os.path.join( job_working_directory, hda_tool_output.from_work_dir ) - destination = job_wrapper.get_output_destination( output_paths[ dataset.dataset_id ] ) - if in_directory( source_file, job_working_directory ): - output_pairs.append( ( source_file, destination ) ) - else: - # Security violation. - log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, job_wrapper.working_directory ) ) - return output_pairs + yield (joda, dataset) + # TODO: why is this not just something easy like: + # for dataset_assoc in job.output_datasets + job.output_library_datasets: + # yield (dataset_assoc, dataset_assoc.dataset) + # I don't understand the reworking it backwards. -John def _handle_metadata_externally( self, job_wrapper, resolve_requirements=False ): """ https://bitbucket.org/galaxy/galaxy-central/commits/691584d72c7c/ Changeset: 691584d72c7c User: jmchilton Date: 2014-12-02 02:18:56+00:00 Summary: Rename variable for clarity post output collections. After tools can explicitly create collections the term created_collections becomes ambigious - these are history collection instances (HDCA) implicitly created by mapping over collections so renaming this field implicit_collections. Affected #: 3 files diff -r 2022044556ca064d879cacbdeae07f2a8ae6f1fc -r 691584d72c7c74e92d5756358a723b8f2064ef91 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2216,7 +2216,7 @@ num_jobs=len( execution_tracker.successful_jobs ), job_errors=execution_tracker.execution_errors, jobs=execution_tracker.successful_jobs, - implicit_collections=execution_tracker.created_collections, + implicit_collections=execution_tracker.implicit_collections, ) else: template = 'message.mako' diff -r 2022044556ca064d879cacbdeae07f2a8ae6f1fc -r 691584d72c7c74e92d5756358a723b8f2064ef91 lib/galaxy/tools/execute.py --- a/lib/galaxy/tools/execute.py +++ b/lib/galaxy/tools/execute.py @@ -47,7 +47,7 @@ self.execution_errors = [] self.output_datasets = [] self.outputs_by_output_name = collections.defaultdict(list) - self.created_collections = {} + self.implicit_collections = {} def record_success( self, job, outputs ): self.successful_jobs.append( job ) @@ -122,6 +122,6 @@ ) collections[ output_name ] = collection - self.created_collections = collections + self.implicit_collections = collections __all__ = [ execute ] diff -r 2022044556ca064d879cacbdeae07f2a8ae6f1fc -r 691584d72c7c74e92d5756358a723b8f2064ef91 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -784,7 +784,7 @@ workflow_invocation_uuid=invocation.uuid.hex ) if collection_info: - step_outputs = dict( execution_tracker.created_collections ) + step_outputs = dict( execution_tracker.implicit_collections ) else: step_outputs = dict( execution_tracker.output_datasets ) progress.set_step_outputs( step, step_outputs ) https://bitbucket.org/galaxy/galaxy-central/commits/1e2fbca80715/ Changeset: 1e2fbca80715 User: jmchilton Date: 2014-12-02 02:18:56+00:00 Summary: Rename variable for clarity. This method does not just return datasets. Affected #: 1 file diff -r 691584d72c7c74e92d5756358a723b8f2064ef91 -r 1e2fbca807151860c54f84b14ba6285b39aaf6a7 test/base/interactor.py --- a/test/base/interactor.py +++ b/test/base/interactor.py @@ -207,12 +207,12 @@ if isinstance(value, list) and len(value) == 1: inputs_tree[key] = value[0] - datasets = self.__submit_tool( history_id, tool_id=testdef.tool.id, tool_input=inputs_tree ) - datasets_object = datasets.json() + submit_response = self.__submit_tool( history_id, tool_id=testdef.tool.id, tool_input=inputs_tree ) + submit_response_object = submit_response.json() try: - return self.__dictify_outputs( datasets_object ), datasets_object[ 'jobs' ] + return self.__dictify_outputs( submit_response_object ), submit_response_object[ 'jobs' ] except KeyError: - raise Exception( datasets_object[ 'message' ] ) + raise Exception( submit_response_object[ 'message' ] ) def _create_collection( self, history_id, collection_def ): create_payload = dict( https://bitbucket.org/galaxy/galaxy-central/commits/cd9eb06bb5f7/ Changeset: cd9eb06bb5f7 User: jmchilton Date: 2014-12-02 02:18:56+00:00 Summary: Add file missed with pull request 505. Affected #: 1 file diff -r 1e2fbca807151860c54f84b14ba6285b39aaf6a7 -r cd9eb06bb5f7da306031ef62f6c538a5816ef08e test/api/test_workflow_map_reduce_pause.ga --- /dev/null +++ b/test/api/test_workflow_map_reduce_pause.ga @@ -0,0 +1,198 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "map_reduce_pause", + "steps": { + "0": { + "annotation": "", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Input Dataset" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 172.83680772781372, + "top": 200.96180772781372 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Input Dataset\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "1": { + "annotation": "", + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Input Dataset Collection" + } + ], + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 161.46528673171997, + "top": 422.5764012336731 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}", + "tool_version": null, + "type": "data_collection_input", + "user_outputs": [] + }, + "2": { + "annotation": "", + "id": 2, + "input_connections": { + "input": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "Select first", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 410.9444432258606, + "top": 195.05903673171997 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "head", + "tool_state": "{\"__job_resource\": \"{\\\"__job_resource__select\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"lineNum\": \"\\\"1\\\"\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "3": { + "annotation": "", + "id": 3, + "input_connections": { + "input": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "name": "Select first", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 632.9756932258606, + "top": 360.57988023757935 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "head", + "tool_state": "{\"__job_resource\": \"{\\\"__job_resource__select\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"lineNum\": \"\\\"1\\\"\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "4": { + "annotation": "", + "id": 4, + "input_connections": { + "input": { + "id": 2, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "Pause for dataset review", + "outputs": [], + "position": { + "left": 657.0903172492981, + "top": 197.71528673171997 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Pause for Dataset Review\"}", + "tool_version": null, + "type": "pause", + "user_outputs": [] + }, + "5": { + "annotation": "", + "id": 5, + "input_connections": { + "input1": { + "id": 4, + "output_name": "output" + }, + "queries_0|input2": { + "id": 3, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "Concatenate datasets (for test workflows)", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 977.8889012336731, + "top": 228.01042222976685 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "cat", + "tool_state": "{\"__job_resource\": \"{\\\"__job_resource__select\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "6": { + "annotation": "", + "id": 6, + "input_connections": { + "input1": { + "id": 5, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "Concatenate multiple datasets (for test workflows)", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 1342.545150756836, + "top": 233.55210876464844 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "cat_list", + "tool_state": "{\"__job_resource\": \"{\\\"__job_resource__select\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + } + }, + "uuid": "a27044e7-2efe-4661-9a09-00708d3520f1" +} \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/0a809bab2180/ Changeset: 0a809bab2180 User: jmchilton Date: 2014-12-02 02:18:56+00:00 Summary: Refactor dataset collection creation into reusable pieces. In downstream output collection work this allows creating elements after initial construction - which is useful for output collections composed of dynamically discovered datasets after a job has completed. Affected #: 5 files diff -r cd9eb06bb5f7da306031ef62f6c538a5816ef08e -r 0a809bab2180137fd7c6cf25a53bfa93fe1b0dcd lib/galaxy/dataset_collections/builder.py --- /dev/null +++ b/lib/galaxy/dataset_collections/builder.py @@ -0,0 +1,26 @@ +from galaxy import model + + +def build_collection( type, dataset_instances ): + """ + Build DatasetCollection with populated DatasetcollectionElement objects + corresponding to the supplied dataset instances or throw exception if + this is not a valid collection of the specified type. + """ + dataset_collection = model.DatasetCollection( ) + set_collection_elements( dataset_collection, type, dataset_instances ) + return dataset_collection + + +def set_collection_elements( dataset_collection, type, dataset_instances ): + element_index = 0 + elements = [] + for element in type.generate_elements( dataset_instances ): + element.element_index = element_index + element.collection = dataset_collection + elements.append( element ) + + element_index += 1 + + dataset_collection.elements = elements + return dataset_collection diff -r cd9eb06bb5f7da306031ef62f6c538a5816ef08e -r 0a809bab2180137fd7c6cf25a53bfa93fe1b0dcd lib/galaxy/dataset_collections/types/__init__.py --- a/lib/galaxy/dataset_collections/types/__init__.py +++ b/lib/galaxy/dataset_collections/types/__init__.py @@ -12,10 +12,9 @@ __metaclass__ = ABCMeta @abstractmethod - def build_collection( self, dataset_instances ): - """ - Build DatasetCollection with populated DatasetcollectionElement objects - corresponding to the supplied dataset instances or throw exception if + def generate_elements( self, dataset_instances ): + """ Generate DatasetCollectionElements with corresponding + to the supplied dataset instances or throw exception if this is not a valid collection of the specified type. """ @@ -24,11 +23,3 @@ def _validation_failed( self, message ): raise exceptions.ObjectAttributeInvalidException( message ) - - def _new_collection_for_elements( self, elements ): - dataset_collection = model.DatasetCollection( ) - for index, element in enumerate( elements ): - element.element_index = index - element.collection = dataset_collection - dataset_collection.elements = elements - return dataset_collection diff -r cd9eb06bb5f7da306031ef62f6c538a5816ef08e -r 0a809bab2180137fd7c6cf25a53bfa93fe1b0dcd lib/galaxy/dataset_collections/types/list.py --- a/lib/galaxy/dataset_collections/types/list.py +++ b/lib/galaxy/dataset_collections/types/list.py @@ -11,13 +11,10 @@ def __init__( self ): pass - def build_collection( self, elements ): - associations = [] + def generate_elements( self, elements ): for identifier, element in elements.iteritems(): association = DatasetCollectionElement( element=element, element_identifier=identifier, ) - associations.append( association ) - - return self._new_collection_for_elements( associations ) + yield association diff -r cd9eb06bb5f7da306031ef62f6c538a5816ef08e -r 0a809bab2180137fd7c6cf25a53bfa93fe1b0dcd lib/galaxy/dataset_collections/types/paired.py --- a/lib/galaxy/dataset_collections/types/paired.py +++ b/lib/galaxy/dataset_collections/types/paired.py @@ -17,7 +17,7 @@ def __init__( self ): pass - def build_collection( self, elements ): + def generate_elements( self, elements ): forward_dataset = elements.get( FORWARD_IDENTIFIER, None ) reverse_dataset = elements.get( REVERSE_IDENTIFIER, None ) if not forward_dataset or not reverse_dataset: @@ -30,4 +30,5 @@ element=reverse_dataset, element_identifier=REVERSE_IDENTIFIER, ) - return self._new_collection_for_elements([left_association, right_association]) + yield left_association + yield right_association diff -r cd9eb06bb5f7da306031ef62f6c538a5816ef08e -r 0a809bab2180137fd7c6cf25a53bfa93fe1b0dcd lib/galaxy/managers/collections.py --- a/lib/galaxy/managers/collections.py +++ b/lib/galaxy/managers/collections.py @@ -1,6 +1,7 @@ from galaxy.dataset_collections.registry import DatasetCollectionTypesRegistry from galaxy.dataset_collections.matching import MatchingCollections from galaxy.dataset_collections.type_description import CollectionTypeDescriptionFactory +from galaxy.dataset_collections import builder from galaxy import model from galaxy.exceptions import MessageException @@ -113,7 +114,7 @@ # else if elements is set, it better be an ordered dict! type_plugin = collection_type_description.rank_type_plugin() - dataset_collection = type_plugin.build_collection( elements ) + dataset_collection = builder.build_collection( type_plugin, elements ) dataset_collection.collection_type = collection_type return dataset_collection https://bitbucket.org/galaxy/galaxy-central/commits/9fba811dd8f9/ Changeset: 9fba811dd8f9 User: jmchilton Date: 2014-12-02 02:18:56+00:00 Summary: Rearrange verify method to make duplication more obvious. Affected #: 1 file diff -r 0a809bab2180137fd7c6cf25a53bfa93fe1b0dcd -r 9fba811dd8f919d6ae24795f17e1f269556cee9e test/base/interactor.py --- a/test/base/interactor.py +++ b/test/base/interactor.py @@ -64,6 +64,7 @@ fetcher = self.__dataset_fetcher( history_id ) ## TODO: Twill version verifys dataset is 'ok' in here. self.twill_test_case.verify_hid( outfile, hda_id=hid, attributes=attributes, dataset_fetcher=fetcher, shed_tool_id=shed_tool_id ) + self._verify_metadata( history_id, hid, attributes ) primary_datasets = attributes.get( 'primary_datasets', {} ) if primary_datasets: @@ -86,8 +87,6 @@ self.twill_test_case.verify_hid( primary_outfile, hda_id=primary_hda_id, attributes=primary_attributes, dataset_fetcher=fetcher, shed_tool_id=shed_tool_id ) self._verify_metadata( history_id, primary_hda_id, primary_attributes ) - self._verify_metadata( history_id, hid, attributes ) - def _verify_metadata( self, history_id, hid, attributes ): metadata = attributes.get( 'metadata', {} ).copy() for key, value in metadata.copy().iteritems(): https://bitbucket.org/galaxy/galaxy-central/commits/4ac25385dfc6/ Changeset: 4ac25385dfc6 User: jmchilton Date: 2014-12-02 02:18:56+00:00 Summary: Break up a couple test methods for reuse downstream. Remove duplication related to verifying a single dataset in tests - allows reuse in downstream when verifying the content of explicitly defined tool output collections. Refactor out waiting for jobs - seems wrong place to put that logic this should allow easier moving. Affected #: 1 file diff -r 9fba811dd8f919d6ae24795f17e1f269556cee9e -r 4ac25385dfc69a72744e8593200696c499d60eaa test/base/interactor.py --- a/test/base/interactor.py +++ b/test/base/interactor.py @@ -58,13 +58,10 @@ outfile = output_testdef.outfile attributes = output_testdef.attributes name = output_testdef.name - for job in jobs: - self.wait_for_job( job[ 'id' ], history_id, maxseconds ) + self.wait_for_jobs( history_id, jobs, maxseconds ) hid = self.__output_id( output_data ) - fetcher = self.__dataset_fetcher( history_id ) ## TODO: Twill version verifys dataset is 'ok' in here. - self.twill_test_case.verify_hid( outfile, hda_id=hid, attributes=attributes, dataset_fetcher=fetcher, shed_tool_id=shed_tool_id ) - self._verify_metadata( history_id, hid, attributes ) + self.verify_output_dataset( history_id=history_id, hda_id=hid, outfile=outfile, attributes=attributes, shed_tool_id=shed_tool_id ) primary_datasets = attributes.get( 'primary_datasets', {} ) if primary_datasets: @@ -84,8 +81,16 @@ raise Exception( msg_template % msg_args ) primary_hda_id = primary_output[ "dataset" ][ "id" ] - self.twill_test_case.verify_hid( primary_outfile, hda_id=primary_hda_id, attributes=primary_attributes, dataset_fetcher=fetcher, shed_tool_id=shed_tool_id ) - self._verify_metadata( history_id, primary_hda_id, primary_attributes ) + self.verify_output_dataset( history_id, primary_hda_id, primary_outfile, primary_attributes, shed_tool_id=shed_tool_id ) + + def wait_for_jobs( self, history_id, jobs, maxseconds ): + for job in jobs: + self.wait_for_job( job[ 'id' ], history_id, maxseconds ) + + def verify_output_dataset( self, history_id, hda_id, outfile, attributes, shed_tool_id ): + fetcher = self.__dataset_fetcher( history_id ) + self.twill_test_case.verify_hid( outfile, hda_id=hda_id, attributes=attributes, dataset_fetcher=fetcher, shed_tool_id=shed_tool_id ) + self._verify_metadata( history_id, hda_id, attributes ) def _verify_metadata( self, history_id, hid, attributes ): metadata = attributes.get( 'metadata', {} ).copy() https://bitbucket.org/galaxy/galaxy-central/commits/e5be58d2ae87/ Changeset: e5be58d2ae87 User: jmchilton Date: 2014-12-02 02:18:56+00:00 Summary: Script to build workflows from simpler YAML description. Affected #: 3 files diff -r 4ac25385dfc69a72744e8593200696c499d60eaa -r e5be58d2ae874cdeb697e1a367ea18652ca93fdc test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -8,24 +8,54 @@ from .helpers import DatasetCollectionPopulator from .helpers import skip_without_tool +from .yaml_to_workflow import yaml_to_workflow + from requests import delete from requests import put from galaxy.exceptions import error_codes +class BaseWorkflowsApiTestCase( api.ApiTestCase ): + # TODO: Find a new file for this class. + + def setUp( self ): + super( BaseWorkflowsApiTestCase, self ).setUp() + self.workflow_populator = WorkflowPopulator( self.galaxy_interactor ) + self.dataset_populator = DatasetPopulator( self.galaxy_interactor ) + self.dataset_collection_populator = DatasetCollectionPopulator( self.galaxy_interactor ) + + def _assert_user_has_workflow_with_name( self, name ): + names = self._workflow_names() + assert name in names, "No workflows with name %s in users workflows <%s>" % ( name, names ) + + def _workflow_names( self ): + index_response = self._get( "workflows" ) + self._assert_status_code_is( index_response, 200 ) + names = map( lambda w: w[ "name" ], index_response.json() ) + return names + + def _upload_yaml_workflow(self, has_yaml): + workflow = yaml_to_workflow(has_yaml) + workflow_str = dumps(workflow, indent=4) + data = { + 'workflow': workflow_str + } + upload_response = self._post( "workflows", data=data ) + self._assert_status_code_is( upload_response, 200 ) + self._assert_user_has_workflow_with_name( "%s (imported from API)" % ( workflow[ "name" ] ) ) + return upload_response.json()[ "id" ] + + # Workflow API TODO: # - Allow history_id as param to workflow run action. (hist_id) # - Allow post to workflows/<workflow_id>/run in addition to posting to # /workflows with id in payload. # - Much more testing obviously, always more testing. -class WorkflowsApiTestCase( api.ApiTestCase ): +class WorkflowsApiTestCase( BaseWorkflowsApiTestCase ): def setUp( self ): super( WorkflowsApiTestCase, self ).setUp() - self.workflow_populator = WorkflowPopulator( self.galaxy_interactor ) - self.dataset_populator = DatasetPopulator( self.galaxy_interactor ) - self.dataset_collection_populator = DatasetCollectionPopulator( self.galaxy_interactor ) def test_show_invalid_key_is_400( self ): show_response = self._get( "workflows/%s" % self._random_key() ) @@ -45,7 +75,7 @@ delete_response = delete( workflow_url ) self._assert_status_code_is( delete_response, 200 ) # Make sure workflow is no longer in index by default. - assert workflow_name not in self.__workflow_names() + assert workflow_name not in self._workflow_names() def test_other_cannot_delete( self ): workflow_id = self.workflow_populator.simple_workflow( "test_other_delete" ) @@ -825,10 +855,6 @@ src = 'hdca' return dict( src=src, id=hda[ "id" ] ) - def _assert_user_has_workflow_with_name( self, name ): - names = self.__workflow_names() - assert name in names, "No workflows with name %s in users workflows <%s>" % ( name, names ) - def __review_paused_steps( self, uploaded_workflow_id, invocation_id, order_index, action=True ): invocation = self._invocation_details( uploaded_workflow_id, invocation_id ) invocation_steps = invocation[ "steps" ] @@ -863,12 +889,6 @@ else: return invocation_response - def __workflow_names( self ): - index_response = self._get( "workflows" ) - self._assert_status_code_is( index_response, 200 ) - names = map( lambda w: w[ "name" ], index_response.json() ) - return names - def __import_workflow( self, workflow_id, deprecated_route=False ): if deprecated_route: route = "workflows/import" diff -r 4ac25385dfc69a72744e8593200696c499d60eaa -r e5be58d2ae874cdeb697e1a367ea18652ca93fdc test/api/test_workflows_from_yaml.py --- /dev/null +++ b/test/api/test_workflows_from_yaml.py @@ -0,0 +1,32 @@ +import json + +from .test_workflows import BaseWorkflowsApiTestCase + + +class WorkflowsFromYamlApiTestCase( BaseWorkflowsApiTestCase ): + + def setUp( self ): + super( WorkflowsFromYamlApiTestCase, self ).setUp() + + def test_simple_upload(self): + workflow_id = self._upload_yaml_workflow(""" +- type: input +- tool_id: cat1 + state: + input1: + $link: 0 +- tool_id: cat1 + state: + input1: + $link: 1#out_file1 +- tool_id: random_lines1 + state: + num_lines: 10 + input: + $link: 2#out_file1 + seed_source: + seed_source_selector: set_seed + seed: asdf + __current_case__: 1 +""") + self._get("workflows/%s/download" % workflow_id).content diff -r 4ac25385dfc69a72744e8593200696c499d60eaa -r e5be58d2ae874cdeb697e1a367ea18652ca93fdc test/api/yaml_to_workflow.py --- /dev/null +++ b/test/api/yaml_to_workflow.py @@ -0,0 +1,220 @@ +import sys + +import yaml +import json + +try: + from collections import OrderedDict +except ImportError: + from galaxy.util.odict import odict as OrderedDict + + +STEP_TYPE_ALIASES = { + 'input': 'data_input', + 'input_collection': 'data_collection_input', +} + + +def yaml_to_workflow(has_yaml): + as_python = yaml.load(has_yaml) + + if isinstance(as_python, list): + as_python = {"steps": as_python} + + __ensure_defaults(as_python, { + "a_galaxy_workflow": "true", + "format-version": "0.1", + "annotation": "", + "name": "Workflow" + }) + + steps = as_python["steps"] + + conversion_context = ConversionContext() + if isinstance(steps, list): + steps_as_dict = OrderedDict() + for i, step in enumerate(steps): + steps_as_dict[ str(i) ] = step + if "id" not in step: + step["id"] = i + + if "label" in step: + label = step["label"] + conversion_context.labels[label] = i + + if "position" not in step: + # TODO: this really should be optional in Galaxy API. + step["position"] = { + "left": 10 * i, + "top": 10 * i + } + + as_python["steps"] = steps_as_dict + steps = steps_as_dict + + for i, step in steps.iteritems(): + step_type = step.get("type", "tool") + step_type = STEP_TYPE_ALIASES.get(step_type, step_type) + if step_type not in [ "data_input", "data_collection_input", "tool", "pause"]: + raise Exception("Unknown step type encountered %s" % step_type) + step["type"] = step_type + eval("transform_%s" % step_type)(conversion_context, step) + + return as_python + + +def transform_data_input(context, step): + transform_input(context, step, default_name="Input dataset") + + +def transform_data_collection_input(context, step): + transform_input(context, step, default_name="Input dataset collection") + + +def transform_input(context, step, default_name): + default_name = step.get("label", default_name) + __ensure_defaults( step, { + "annotation": "", + }) + + __ensure_inputs_connections(step) + + if not "inputs" in step: + step["inputs"] = [{}] + + step_inputs = step["inputs"][0] + if "name" in step_inputs: + name = step_inputs["name"] + else: + name = default_name + + __ensure_defaults( step_inputs, { + "name": name, + "description": "", + }) + tool_state = { + "name": name + } + if "collection_type" in step: + tool_state["collection_type"] = step["collection_type"] + + __populate_tool_state(step, tool_state) + + +def transform_tool(context, step): + if "tool_id" not in step: + raise Exception("Tool steps must define a tool_id.") + + __ensure_defaults( step, { + "annotation": "", + } ) + __ensure_inputs_connections(step) + + tool_state = { + # TODO: Galaxy should not require tool state actually specify a __page__. + "__page__": 0, + } + + if "connect" not in step: + step["connect"] = {} + + connect = step["connect"] + del step["connect"] + + def append_link(key, value): + if key not in connect: + connect[key] = [] + connect[key].append(value["$link"]) + + def replace_links(value, key=""): + if __is_link(value): + append_link(key, value) + return None + if isinstance(value, dict): + new_values = {} + for k, v in value.iteritems(): + new_key = __join_prefix(key, k) + new_values[k] = replace_links(v, new_key) + return new_values + elif isinstance(value, list): + new_values = [] + for i, v in enumerate(value): + # If we are a repeat we need to modify the key + # but not if values are actually $links. + if __is_link(v): + append_link(key, v) + new_values.append(None) + else: + new_key = "%s_%d" % ( key, i ) + new_values.append(replace_links(v, new_key)) + return new_values + else: + return value + + if "state" in step: + step_state = step["state"] + step_state = replace_links(step_state) + + for key, value in step_state.iteritems(): + tool_state[key] = json.dumps(value) + del step["state"] + + for key, values in connect.iteritems(): + input_connection_value = [] + if not isinstance(values, list): + values = [ values ] + for value in values: + if not isinstance(value, dict): + value_parts = str(value).split("#") + if len(value_parts) == 1: + value_parts.append("output") + id = value_parts[0] + if id in context.labels: + id = context.labels[id] + value = {"id": int(id), "output_name": value_parts[1]} + input_connection_value.append(value) + # TODO: this should be a list + step["input_connections"][key] = input_connection_value[0] + + __populate_tool_state(step, tool_state) + + +class ConversionContext(object): + + def __init__(self): + self.labels = {} + + +def __is_link(value): + return isinstance(value, dict) and "$link" in value + + +def __join_prefix(prefix, key): + if prefix: + new_key = "%s|%s" % (prefix, key) + else: + new_key = key + return new_key + + +def __ensure_inputs_connections(step): + if "input_connections" not in step: + step["input_connections"] = {} + + +def __ensure_defaults(in_dict, defaults): + for key, value in defaults.items(): + if key not in in_dict: + in_dict[ key ] = value + + +def __populate_tool_state(step, tool_state): + step["tool_state"] = json.dumps(tool_state) + + +def main(argv): + print json.dumps(yaml_to_workflow(argv[0])) + + +if __name__ == "__main__": + main(sys.argv) https://bitbucket.org/galaxy/galaxy-central/commits/c214c2f07f3b/ Changeset: c214c2f07f3b User: jmchilton Date: 2014-12-02 02:18:56+00:00 Summary: Split all workflow extraction testing out of test/api/test_workflows.py. test_workflows.py was pretty unwieldy and the workflow extraction tests were very different than the other tests in that file (e.g. very different helper functions). Affected #: 2 files diff -r e5be58d2ae874cdeb697e1a367ea18652ca93fdc -r c214c2f07f3bf7d86db8ee14188765c9aabdb22e test/api/test_workflow_extraction.py --- /dev/null +++ b/test/api/test_workflow_extraction.py @@ -0,0 +1,269 @@ +from json import dumps, loads +import operator + +from .helpers import skip_without_tool +from .test_workflows import BaseWorkflowsApiTestCase + + +class WorkflowExtractionApiTestCase( BaseWorkflowsApiTestCase ): + + def setUp( self ): + super( WorkflowExtractionApiTestCase, self ).setUp() + + @skip_without_tool( "cat1" ) + def test_extract_from_history( self ): + history_id = self.dataset_populator.new_history() + # Run the simple test workflow and extract it back out from history + cat1_job_id = self.__setup_and_run_cat1_workflow( history_id=history_id ) + contents_response = self._get( "histories/%s/contents" % history_id ) + input_hids = map( lambda c: c[ "hid" ], contents_response.json()[ 0:2 ] ) + downloaded_workflow = self._extract_and_download_workflow( + from_history_id=history_id, + dataset_ids=dumps( input_hids ), + job_ids=dumps( [ cat1_job_id ] ), + workflow_name="test import from history", + ) + self.assertEquals( downloaded_workflow[ "name" ], "test import from history" ) + self.__assert_looks_like_cat1_example_workflow( downloaded_workflow ) + + def test_extract_with_copied_inputs( self ): + old_history_id = self.dataset_populator.new_history() + # Run the simple test workflow and extract it back out from history + self.__setup_and_run_cat1_workflow( history_id=old_history_id ) + + history_id = self.dataset_populator.new_history() + + # Bug cannot mess up hids or these don't extract correctly. See Trello card here: + # https://trello.com/c/mKzLbM2P + # # create dummy dataset to complicate hid mapping + # self.dataset_populator.new_dataset( history_id, content="dummydataset" ) + # offset = 1 + + offset = 0 + old_contents = self._get( "histories/%s/contents" % old_history_id ).json() + for old_dataset in old_contents: + self.__copy_content_to_history( history_id, old_dataset ) + new_contents = self._get( "histories/%s/contents" % history_id ).json() + input_hids = map( lambda c: c[ "hid" ], new_contents[ (offset + 0):(offset + 2) ] ) + cat1_job_id = self.__job_id( history_id, new_contents[ (offset + 2) ][ "id" ] ) + downloaded_workflow = self._extract_and_download_workflow( + from_history_id=history_id, + dataset_ids=dumps( input_hids ), + job_ids=dumps( [ cat1_job_id ] ), + workflow_name="test import from history", + ) + self.__assert_looks_like_cat1_example_workflow( downloaded_workflow ) + + @skip_without_tool( "random_lines1" ) + def test_extract_mapping_workflow_from_history( self ): + history_id = self.dataset_populator.new_history() + hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair( history_id ) + downloaded_workflow = self._extract_and_download_workflow( + from_history_id=history_id, + dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ), + job_ids=dumps( [ job_id1, job_id2 ] ), + workflow_name="test import from mapping history", + ) + self.__assert_looks_like_randomlines_mapping_workflow( downloaded_workflow ) + + def test_extract_copied_mapping_from_history( self ): + old_history_id = self.dataset_populator.new_history() + hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair( old_history_id ) + + history_id = self.dataset_populator.new_history() + old_contents = self._get( "histories/%s/contents" % old_history_id ).json() + for old_content in old_contents: + self.__copy_content_to_history( history_id, old_content ) + # API test is somewhat contrived since there is no good way + # to retrieve job_id1, job_id2 like this for copied dataset + # collections I don't think. + downloaded_workflow = self._extract_and_download_workflow( + from_history_id=history_id, + dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ), + job_ids=dumps( [ job_id1, job_id2 ] ), + workflow_name="test import from history", + ) + self.__assert_looks_like_randomlines_mapping_workflow( downloaded_workflow ) + + @skip_without_tool( "random_lines1" ) + @skip_without_tool( "multi_data_param" ) + def test_extract_reduction_from_history( self ): + history_id = self.dataset_populator.new_history() + hdca = self.dataset_collection_populator.create_pair_in_history( history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"] ).json() + hdca_id = hdca[ "id" ] + inputs1 = { + "input": { "batch": True, "values": [ { "src": "hdca", "id": hdca_id } ] }, + "num_lines": 2 + } + implicit_hdca1, job_id1 = self._run_tool_get_collection_and_job_id( history_id, "random_lines1", inputs1 ) + inputs2 = { + "f1": { "src": "hdca", "id": implicit_hdca1[ "id" ] }, + "f2": { "src": "hdca", "id": implicit_hdca1[ "id" ] }, + } + reduction_run_output = self.dataset_populator.run_tool( + tool_id="multi_data_param", + inputs=inputs2, + history_id=history_id, + ) + job_id2 = reduction_run_output[ "jobs" ][ 0 ][ "id" ] + self.dataset_populator.wait_for_history( history_id, assert_ok=True, timeout=20 ) + downloaded_workflow = self._extract_and_download_workflow( + from_history_id=history_id, + dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ), + job_ids=dumps( [ job_id1, job_id2 ] ), + workflow_name="test import reduction", + ) + assert len( downloaded_workflow[ "steps" ] ) == 3 + collect_step_idx = self._assert_first_step_is_paired_input( downloaded_workflow ) + tool_steps = self._get_steps_of_type( downloaded_workflow, "tool", expected_len=2 ) + random_lines_map_step = tool_steps[ 0 ] + reduction_step = tool_steps[ 1 ] + random_lines_input = random_lines_map_step[ "input_connections" ][ "input" ] + assert random_lines_input[ "id" ] == collect_step_idx + reduction_step_input = reduction_step[ "input_connections" ][ "f1" ] + assert reduction_step_input[ "id"] == random_lines_map_step[ "id" ] + + @skip_without_tool( "collection_paired_test" ) + def test_extract_workflows_with_dataset_collections( self ): + history_id = self.dataset_populator.new_history() + hdca = self.dataset_collection_populator.create_pair_in_history( history_id ).json() + hdca_id = hdca[ "id" ] + inputs = { + "f1": dict( src="hdca", id=hdca_id ) + } + run_output = self.dataset_populator.run_tool( + tool_id="collection_paired_test", + inputs=inputs, + history_id=history_id, + ) + job_id = run_output[ "jobs" ][ 0 ][ "id" ] + self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + downloaded_workflow = self._extract_and_download_workflow( + from_history_id=history_id, + dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ), + job_ids=dumps( [ job_id ] ), + workflow_name="test import from history", + ) + collection_steps = self._get_steps_of_type( downloaded_workflow, "data_collection_input", expected_len=1 ) + collection_step = collection_steps[ 0 ] + collection_step_state = loads( collection_step[ "tool_state" ] ) + self.assertEquals( collection_step_state[ "collection_type" ], u"paired" ) + + def __run_random_lines_mapped_over_pair( self, history_id ): + hdca = self.dataset_collection_populator.create_pair_in_history( history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"] ).json() + hdca_id = hdca[ "id" ] + inputs1 = { + "input": { "batch": True, "values": [ { "src": "hdca", "id": hdca_id } ] }, + "num_lines": 2 + } + implicit_hdca1, job_id1 = self._run_tool_get_collection_and_job_id( history_id, "random_lines1", inputs1 ) + inputs2 = { + "input": { "batch": True, "values": [ { "src": "hdca", "id": implicit_hdca1[ "id" ] } ] }, + "num_lines": 1 + } + _, job_id2 = self._run_tool_get_collection_and_job_id( history_id, "random_lines1", inputs2 ) + return hdca, job_id1, job_id2 + + def __assert_looks_like_randomlines_mapping_workflow( self, downloaded_workflow ): + # Assert workflow is input connected to a tool step with one output + # connected to another tool step. + assert len( downloaded_workflow[ "steps" ] ) == 3 + collect_step_idx = self._assert_first_step_is_paired_input( downloaded_workflow ) + tool_steps = self._get_steps_of_type( downloaded_workflow, "tool", expected_len=2 ) + tool_step_idxs = [] + tool_input_step_idxs = [] + for tool_step in tool_steps: + self._assert_has_key( tool_step[ "input_connections" ], "input" ) + input_step_idx = tool_step[ "input_connections" ][ "input" ][ "id" ] + tool_step_idxs.append( tool_step[ "id" ] ) + tool_input_step_idxs.append( input_step_idx ) + + assert collect_step_idx not in tool_step_idxs + assert tool_input_step_idxs[ 0 ] == collect_step_idx + assert tool_input_step_idxs[ 1 ] == tool_step_idxs[ 0 ] + + def __assert_looks_like_cat1_example_workflow( self, downloaded_workflow ): + assert len( downloaded_workflow[ "steps" ] ) == 3 + input_steps = self._get_steps_of_type( downloaded_workflow, "data_input", expected_len=2 ) + tool_step = self._get_steps_of_type( downloaded_workflow, "tool", expected_len=1 )[ 0 ] + + input1 = tool_step[ "input_connections" ][ "input1" ] + input2 = tool_step[ "input_connections" ][ "queries_0|input2" ] + + self.assertEquals( input_steps[ 0 ][ "id" ], input1[ "id" ] ) + self.assertEquals( input_steps[ 1 ][ "id" ], input2[ "id" ] ) + + def __copy_content_to_history( self, history_id, content ): + if content[ "history_content_type" ] == "dataset": + payload = dict( + source="hda", + content=content["id"] + ) + response = self._post( "histories/%s/contents/datasets" % history_id, payload ) + + else: + payload = dict( + source="hdca", + content=content["id"] + ) + response = self._post( "histories/%s/contents/dataset_collections" % history_id, payload ) + self._assert_status_code_is( response, 200 ) + return response.json() + + def __setup_and_run_cat1_workflow( self, history_id ): + workflow = self.workflow_populator.load_workflow( name="test_for_extract" ) + workflow_request, history_id = self._setup_workflow_run( workflow, history_id=history_id ) + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 200 ) + + self.dataset_populator.wait_for_history( history_id, assert_ok=True, timeout=10 ) + return self.__cat_job_id( history_id ) + + def _assert_first_step_is_paired_input( self, downloaded_workflow ): + collection_steps = self._get_steps_of_type( downloaded_workflow, "data_collection_input", expected_len=1 ) + collection_step = collection_steps[ 0 ] + collection_step_state = loads( collection_step[ "tool_state" ] ) + self.assertEquals( collection_step_state[ "collection_type" ], u"paired" ) + collect_step_idx = collection_step[ "id" ] + return collect_step_idx + + def _extract_and_download_workflow( self, **extract_payload ): + create_workflow_response = self._post( "workflows", data=extract_payload ) + self._assert_status_code_is( create_workflow_response, 200 ) + + new_workflow_id = create_workflow_response.json()[ "id" ] + download_response = self._get( "workflows/%s/download" % new_workflow_id ) + self._assert_status_code_is( download_response, 200 ) + downloaded_workflow = download_response.json() + return downloaded_workflow + + def _get_steps_of_type( self, downloaded_workflow, type, expected_len=None ): + steps = [ s for s in downloaded_workflow[ "steps" ].values() if s[ "type" ] == type ] + if expected_len is not None: + n = len( steps ) + assert n == expected_len, "Expected %d steps of type %s, found %d" % ( expected_len, type, n ) + return sorted( steps, key=operator.itemgetter("id") ) + + def __job_id( self, history_id, dataset_id ): + url = "histories/%s/contents/%s/provenance" % ( history_id, dataset_id ) + prov_response = self._get( url, data=dict( follow=False ) ) + self._assert_status_code_is( prov_response, 200 ) + return prov_response.json()[ "job_id" ] + + def __cat_job_id( self, history_id ): + data = dict( history_id=history_id, tool_id="cat1" ) + jobs_response = self._get( "jobs", data=data ) + self._assert_status_code_is( jobs_response, 200 ) + cat1_job_id = jobs_response.json()[ 0 ][ "id" ] + return cat1_job_id + + def _run_tool_get_collection_and_job_id( self, history_id, tool_id, inputs ): + run_output1 = self.dataset_populator.run_tool( + tool_id=tool_id, + inputs=inputs, + history_id=history_id, + ) + implicit_hdca = run_output1[ "implicit_collections" ][ 0 ] + job_id = run_output1[ "jobs" ][ 0 ][ "id" ] + self.dataset_populator.wait_for_history( history_id, assert_ok=True, timeout=20 ) + return implicit_hdca, job_id diff -r e5be58d2ae874cdeb697e1a367ea18652ca93fdc -r c214c2f07f3bf7d86db8ee14188765c9aabdb22e test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -1,7 +1,5 @@ from base import api from json import dumps -from json import loads -import operator import time from .helpers import WorkflowPopulator from .helpers import DatasetPopulator @@ -46,6 +44,57 @@ self._assert_user_has_workflow_with_name( "%s (imported from API)" % ( workflow[ "name" ] ) ) return upload_response.json()[ "id" ] + def _setup_workflow_run( self, workflow, inputs_by='step_id', history_id=None ): + uploaded_workflow_id = self.workflow_populator.create_workflow( workflow ) + if not history_id: + history_id = self.dataset_populator.new_history() + hda1 = self.dataset_populator.new_dataset( history_id, content="1 2 3" ) + hda2 = self.dataset_populator.new_dataset( history_id, content="4 5 6" ) + workflow_request = dict( + history="hist_id=%s" % history_id, + workflow_id=uploaded_workflow_id, + ) + label_map = { + 'WorkflowInput1': self._ds_entry(hda1), + 'WorkflowInput2': self._ds_entry(hda2) + } + if inputs_by == 'step_id': + ds_map = self._build_ds_map( uploaded_workflow_id, label_map ) + workflow_request[ "ds_map" ] = ds_map + elif inputs_by == "step_index": + index_map = { + '0': self._ds_entry(hda1), + '1': self._ds_entry(hda2) + } + workflow_request[ "inputs" ] = dumps( index_map ) + workflow_request[ "inputs_by" ] = 'step_index' + elif inputs_by == "name": + workflow_request[ "inputs" ] = dumps( label_map ) + workflow_request[ "inputs_by" ] = 'name' + + return workflow_request, history_id + + def _build_ds_map( self, workflow_id, label_map ): + workflow_inputs = self._workflow_inputs( workflow_id ) + ds_map = {} + for key, value in workflow_inputs.iteritems(): + label = value[ "label" ] + if label in label_map: + ds_map[ key ] = label_map[ label ] + return dumps( ds_map ) + + def _ds_entry( self, hda ): + src = 'hda' + if 'history_content_type' in hda and hda[ 'history_content_type' ] == "dataset_collection": + src = 'hdca' + return dict( src=src, id=hda[ "id" ] ) + + def _workflow_inputs( self, uploaded_workflow_id ): + workflow_show_resposne = self._get( "workflows/%s" % uploaded_workflow_id ) + self._assert_status_code_is( workflow_show_resposne, 200 ) + workflow_inputs = workflow_show_resposne.json()[ "inputs" ] + return workflow_inputs + # Workflow API TODO: # - Allow history_id as param to workflow run action. (hist_id) @@ -358,109 +407,6 @@ step_map[step_index] = step["inputs"][0]["name"] return step_map - @skip_without_tool( "cat1" ) - def test_extract_from_history( self ): - history_id = self.dataset_populator.new_history() - # Run the simple test workflow and extract it back out from history - cat1_job_id = self.__setup_and_run_cat1_workflow( history_id=history_id ) - contents_response = self._get( "histories/%s/contents" % history_id ) - input_hids = map( lambda c: c[ "hid" ], contents_response.json()[ 0:2 ] ) - downloaded_workflow = self._extract_and_download_workflow( - from_history_id=history_id, - dataset_ids=dumps( input_hids ), - job_ids=dumps( [ cat1_job_id ] ), - workflow_name="test import from history", - ) - self.assertEquals( downloaded_workflow[ "name" ], "test import from history" ) - self.__assert_looks_like_cat1_example_workflow( downloaded_workflow ) - - def test_extract_with_copied_inputs( self ): - old_history_id = self.dataset_populator.new_history() - # Run the simple test workflow and extract it back out from history - self.__setup_and_run_cat1_workflow( history_id=old_history_id ) - - history_id = self.dataset_populator.new_history() - - # Bug cannot mess up hids or these don't extract correctly. See Trello card here: - # https://trello.com/c/mKzLbM2P - # # create dummy dataset to complicate hid mapping - # self.dataset_populator.new_dataset( history_id, content="dummydataset" ) - # offset = 1 - - offset = 0 - old_contents = self._get( "histories/%s/contents" % old_history_id ).json() - for old_dataset in old_contents: - self.__copy_content_to_history( history_id, old_dataset ) - new_contents = self._get( "histories/%s/contents" % history_id ).json() - input_hids = map( lambda c: c[ "hid" ], new_contents[ (offset + 0):(offset + 2) ] ) - cat1_job_id = self.__job_id( history_id, new_contents[ (offset + 2) ][ "id" ] ) - downloaded_workflow = self._extract_and_download_workflow( - from_history_id=history_id, - dataset_ids=dumps( input_hids ), - job_ids=dumps( [ cat1_job_id ] ), - workflow_name="test import from history", - ) - self.__assert_looks_like_cat1_example_workflow( downloaded_workflow ) - - def __assert_looks_like_cat1_example_workflow( self, downloaded_workflow ): - assert len( downloaded_workflow[ "steps" ] ) == 3 - input_steps = self._get_steps_of_type( downloaded_workflow, "data_input", expected_len=2 ) - tool_step = self._get_steps_of_type( downloaded_workflow, "tool", expected_len=1 )[ 0 ] - - input1 = tool_step[ "input_connections" ][ "input1" ] - input2 = tool_step[ "input_connections" ][ "queries_0|input2" ] - - self.assertEquals( input_steps[ 0 ][ "id" ], input1[ "id" ] ) - self.assertEquals( input_steps[ 1 ][ "id" ], input2[ "id" ] ) - - def __setup_and_run_cat1_workflow( self, history_id ): - workflow = self.workflow_populator.load_workflow( name="test_for_extract" ) - workflow_request, history_id = self._setup_workflow_run( workflow, history_id=history_id ) - run_workflow_response = self._post( "workflows", data=workflow_request ) - self._assert_status_code_is( run_workflow_response, 200 ) - - self.dataset_populator.wait_for_history( history_id, assert_ok=True, timeout=10 ) - return self.__cat_job_id( history_id ) - - def __cat_job_id( self, history_id ): - data = dict( history_id=history_id, tool_id="cat1" ) - jobs_response = self._get( "jobs", data=data ) - self._assert_status_code_is( jobs_response, 200 ) - cat1_job_id = jobs_response.json()[ 0 ][ "id" ] - return cat1_job_id - - def __job_id( self, history_id, dataset_id ): - url = "histories/%s/contents/%s/provenance" % ( history_id, dataset_id ) - prov_response = self._get( url, data=dict( follow=False ) ) - self._assert_status_code_is( prov_response, 200 ) - return prov_response.json()[ "job_id" ] - - @skip_without_tool( "collection_paired_test" ) - def test_extract_workflows_with_dataset_collections( self ): - history_id = self.dataset_populator.new_history() - hdca = self.dataset_collection_populator.create_pair_in_history( history_id ).json() - hdca_id = hdca[ "id" ] - inputs = { - "f1": dict( src="hdca", id=hdca_id ) - } - run_output = self.dataset_populator.run_tool( - tool_id="collection_paired_test", - inputs=inputs, - history_id=history_id, - ) - job_id = run_output[ "jobs" ][ 0 ][ "id" ] - self.dataset_populator.wait_for_history( history_id, assert_ok=True ) - downloaded_workflow = self._extract_and_download_workflow( - from_history_id=history_id, - dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ), - job_ids=dumps( [ job_id ] ), - workflow_name="test import from history", - ) - collection_steps = self._get_steps_of_type( downloaded_workflow, "data_collection_input", expected_len=1 ) - collection_step = collection_steps[ 0 ] - collection_step_state = loads( collection_step[ "tool_state" ] ) - self.assertEquals( collection_step_state[ "collection_type" ], u"paired" ) - def test_empty_create( self ): response = self._post( "workflows" ) self._assert_status_code_is( response, 400 ) @@ -475,161 +421,6 @@ self._assert_status_code_is( response, 400 ) self._assert_error_code_is( response, error_codes.USER_REQUEST_INVALID_PARAMETER ) - @skip_without_tool( "random_lines1" ) - def test_extract_mapping_workflow_from_history( self ): - history_id = self.dataset_populator.new_history() - hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair( history_id ) - downloaded_workflow = self._extract_and_download_workflow( - from_history_id=history_id, - dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ), - job_ids=dumps( [ job_id1, job_id2 ] ), - workflow_name="test import from mapping history", - ) - self.__assert_looks_like_randomlines_mapping_workflow( downloaded_workflow ) - - def test_extract_copied_mapping_from_history( self ): - old_history_id = self.dataset_populator.new_history() - hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair( old_history_id ) - - history_id = self.dataset_populator.new_history() - old_contents = self._get( "histories/%s/contents" % old_history_id ).json() - for old_content in old_contents: - self.__copy_content_to_history( history_id, old_content ) - # API test is somewhat contrived since there is no good way - # to retrieve job_id1, job_id2 like this for copied dataset - # collections I don't think. - downloaded_workflow = self._extract_and_download_workflow( - from_history_id=history_id, - dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ), - job_ids=dumps( [ job_id1, job_id2 ] ), - workflow_name="test import from history", - ) - self.__assert_looks_like_randomlines_mapping_workflow( downloaded_workflow ) - - @skip_without_tool( "random_lines1" ) - @skip_without_tool( "multi_data_param" ) - def test_extract_reduction_from_history( self ): - history_id = self.dataset_populator.new_history() - hdca = self.dataset_collection_populator.create_pair_in_history( history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"] ).json() - hdca_id = hdca[ "id" ] - inputs1 = { - "input": { "batch": True, "values": [ { "src": "hdca", "id": hdca_id } ] }, - "num_lines": 2 - } - implicit_hdca1, job_id1 = self._run_tool_get_collection_and_job_id( history_id, "random_lines1", inputs1 ) - inputs2 = { - "f1": { "src": "hdca", "id": implicit_hdca1[ "id" ] }, - "f2": { "src": "hdca", "id": implicit_hdca1[ "id" ] }, - } - reduction_run_output = self.dataset_populator.run_tool( - tool_id="multi_data_param", - inputs=inputs2, - history_id=history_id, - ) - job_id2 = reduction_run_output[ "jobs" ][ 0 ][ "id" ] - self.dataset_populator.wait_for_history( history_id, assert_ok=True, timeout=20 ) - downloaded_workflow = self._extract_and_download_workflow( - from_history_id=history_id, - dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ), - job_ids=dumps( [ job_id1, job_id2 ] ), - workflow_name="test import reduction", - ) - assert len( downloaded_workflow[ "steps" ] ) == 3 - collect_step_idx = self._assert_first_step_is_paired_input( downloaded_workflow ) - tool_steps = self._get_steps_of_type( downloaded_workflow, "tool", expected_len=2 ) - random_lines_map_step = tool_steps[ 0 ] - reduction_step = tool_steps[ 1 ] - random_lines_input = random_lines_map_step[ "input_connections" ][ "input" ] - assert random_lines_input[ "id" ] == collect_step_idx - reduction_step_input = reduction_step[ "input_connections" ][ "f1" ] - assert reduction_step_input[ "id"] == random_lines_map_step[ "id" ] - - def __copy_content_to_history( self, history_id, content ): - if content[ "history_content_type" ] == "dataset": - payload = dict( - source="hda", - content=content["id"] - ) - response = self._post( "histories/%s/contents/datasets" % history_id, payload ) - - else: - payload = dict( - source="hdca", - content=content["id"] - ) - response = self._post( "histories/%s/contents/dataset_collections" % history_id, payload ) - self._assert_status_code_is( response, 200 ) - return response.json() - - def __run_random_lines_mapped_over_pair( self, history_id ): - hdca = self.dataset_collection_populator.create_pair_in_history( history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"] ).json() - hdca_id = hdca[ "id" ] - inputs1 = { - "input": { "batch": True, "values": [ { "src": "hdca", "id": hdca_id } ] }, - "num_lines": 2 - } - implicit_hdca1, job_id1 = self._run_tool_get_collection_and_job_id( history_id, "random_lines1", inputs1 ) - inputs2 = { - "input": { "batch": True, "values": [ { "src": "hdca", "id": implicit_hdca1[ "id" ] } ] }, - "num_lines": 1 - } - _, job_id2 = self._run_tool_get_collection_and_job_id( history_id, "random_lines1", inputs2 ) - return hdca, job_id1, job_id2 - - def __assert_looks_like_randomlines_mapping_workflow( self, downloaded_workflow ): - # Assert workflow is input connected to a tool step with one output - # connected to another tool step. - assert len( downloaded_workflow[ "steps" ] ) == 3 - collect_step_idx = self._assert_first_step_is_paired_input( downloaded_workflow ) - tool_steps = self._get_steps_of_type( downloaded_workflow, "tool", expected_len=2 ) - tool_step_idxs = [] - tool_input_step_idxs = [] - for tool_step in tool_steps: - self._assert_has_key( tool_step[ "input_connections" ], "input" ) - input_step_idx = tool_step[ "input_connections" ][ "input" ][ "id" ] - tool_step_idxs.append( tool_step[ "id" ] ) - tool_input_step_idxs.append( input_step_idx ) - - assert collect_step_idx not in tool_step_idxs - assert tool_input_step_idxs[ 0 ] == collect_step_idx - assert tool_input_step_idxs[ 1 ] == tool_step_idxs[ 0 ] - - def _run_tool_get_collection_and_job_id( self, history_id, tool_id, inputs ): - run_output1 = self.dataset_populator.run_tool( - tool_id=tool_id, - inputs=inputs, - history_id=history_id, - ) - implicit_hdca = run_output1[ "implicit_collections" ][ 0 ] - job_id = run_output1[ "jobs" ][ 0 ][ "id" ] - self.dataset_populator.wait_for_history( history_id, assert_ok=True, timeout=20 ) - return implicit_hdca, job_id - - def _assert_first_step_is_paired_input( self, downloaded_workflow ): - collection_steps = self._get_steps_of_type( downloaded_workflow, "data_collection_input", expected_len=1 ) - collection_step = collection_steps[ 0 ] - collection_step_state = loads( collection_step[ "tool_state" ] ) - self.assertEquals( collection_step_state[ "collection_type" ], u"paired" ) - collect_step_idx = collection_step[ "id" ] - return collect_step_idx - - def _extract_and_download_workflow( self, **extract_payload ): - create_workflow_response = self._post( "workflows", data=extract_payload ) - self._assert_status_code_is( create_workflow_response, 200 ) - - new_workflow_id = create_workflow_response.json()[ "id" ] - download_response = self._get( "workflows/%s/download" % new_workflow_id ) - self._assert_status_code_is( download_response, 200 ) - downloaded_workflow = download_response.json() - return downloaded_workflow - - def _get_steps_of_type( self, downloaded_workflow, type, expected_len=None ): - steps = [ s for s in downloaded_workflow[ "steps" ].values() if s[ "type" ] == type ] - if expected_len is not None: - n = len( steps ) - assert n == expected_len, "Expected %d steps of type %s, found %d" % ( expected_len, type, n ) - return sorted( steps, key=operator.itemgetter("id") ) - @skip_without_tool( "cat1" ) def test_run_with_pja( self ): workflow = self.workflow_populator.load_workflow( name="test_for_pja_run", add_pja=True ) @@ -776,45 +567,6 @@ assert len( usages ) == 1 return workflow_id, usages[ 0 ] - def _setup_workflow_run( self, workflow, inputs_by='step_id', history_id=None ): - uploaded_workflow_id = self.workflow_populator.create_workflow( workflow ) - if not history_id: - history_id = self.dataset_populator.new_history() - hda1 = self.dataset_populator.new_dataset( history_id, content="1 2 3" ) - hda2 = self.dataset_populator.new_dataset( history_id, content="4 5 6" ) - workflow_request = dict( - history="hist_id=%s" % history_id, - workflow_id=uploaded_workflow_id, - ) - label_map = { - 'WorkflowInput1': self._ds_entry(hda1), - 'WorkflowInput2': self._ds_entry(hda2) - } - if inputs_by == 'step_id': - ds_map = self._build_ds_map( uploaded_workflow_id, label_map ) - workflow_request[ "ds_map" ] = ds_map - elif inputs_by == "step_index": - index_map = { - '0': self._ds_entry(hda1), - '1': self._ds_entry(hda2) - } - workflow_request[ "inputs" ] = dumps( index_map ) - workflow_request[ "inputs_by" ] = 'step_index' - elif inputs_by == "name": - workflow_request[ "inputs" ] = dumps( label_map ) - workflow_request[ "inputs_by" ] = 'name' - - return workflow_request, history_id - - def _build_ds_map( self, workflow_id, label_map ): - workflow_inputs = self._workflow_inputs( workflow_id ) - ds_map = {} - for key, value in workflow_inputs.iteritems(): - label = value[ "label" ] - if label in label_map: - ds_map[ key ] = label_map[ label ] - return dumps( ds_map ) - def _setup_random_x2_workflow_steps( self, name ): workflow_request, history_id = self._setup_random_x2_workflow( "test_for_replace_step_params" ) random_line_steps = self._random_lines_steps( workflow_request ) @@ -843,18 +595,6 @@ ) return workflow_request, history_id - def _workflow_inputs( self, uploaded_workflow_id ): - workflow_show_resposne = self._get( "workflows/%s" % uploaded_workflow_id ) - self._assert_status_code_is( workflow_show_resposne, 200 ) - workflow_inputs = workflow_show_resposne.json()[ "inputs" ] - return workflow_inputs - - def _ds_entry( self, hda ): - src = 'hda' - if 'history_content_type' in hda and hda[ 'history_content_type' ] == "dataset_collection": - src = 'hdca' - return dict( src=src, id=hda[ "id" ] ) - def __review_paused_steps( self, uploaded_workflow_id, invocation_id, order_index, action=True ): invocation = self._invocation_details( uploaded_workflow_id, invocation_id ) invocation_steps = invocation[ "steps" ] https://bitbucket.org/galaxy/galaxy-central/commits/415221281212/ Changeset: 415221281212 User: jmchilton Date: 2014-12-02 02:18:56+00:00 Summary: Simplify new test_workflow_extraction.py. Now makes sense to assume all tests consume a history. Affected #: 1 file diff -r c214c2f07f3bf7d86db8ee14188765c9aabdb22e -r 415221281212483cdad6213e284c03e0698dbf63 test/api/test_workflow_extraction.py --- a/test/api/test_workflow_extraction.py +++ b/test/api/test_workflow_extraction.py @@ -9,16 +9,16 @@ def setUp( self ): super( WorkflowExtractionApiTestCase, self ).setUp() + self.history_id = self.dataset_populator.new_history() @skip_without_tool( "cat1" ) def test_extract_from_history( self ): - history_id = self.dataset_populator.new_history() # Run the simple test workflow and extract it back out from history - cat1_job_id = self.__setup_and_run_cat1_workflow( history_id=history_id ) - contents_response = self._get( "histories/%s/contents" % history_id ) + cat1_job_id = self.__setup_and_run_cat1_workflow( history_id=self.history_id ) + contents_response = self._get( "histories/%s/contents" % self.history_id ) input_hids = map( lambda c: c[ "hid" ], contents_response.json()[ 0:2 ] ) downloaded_workflow = self._extract_and_download_workflow( - from_history_id=history_id, + from_history_id=self.history_id, dataset_ids=dumps( input_hids ), job_ids=dumps( [ cat1_job_id ] ), workflow_name="test import from history", @@ -31,8 +31,6 @@ # Run the simple test workflow and extract it back out from history self.__setup_and_run_cat1_workflow( history_id=old_history_id ) - history_id = self.dataset_populator.new_history() - # Bug cannot mess up hids or these don't extract correctly. See Trello card here: # https://trello.com/c/mKzLbM2P # # create dummy dataset to complicate hid mapping @@ -42,12 +40,12 @@ offset = 0 old_contents = self._get( "histories/%s/contents" % old_history_id ).json() for old_dataset in old_contents: - self.__copy_content_to_history( history_id, old_dataset ) - new_contents = self._get( "histories/%s/contents" % history_id ).json() + self.__copy_content_to_history( self.history_id, old_dataset ) + new_contents = self._get( "histories/%s/contents" % self.history_id ).json() input_hids = map( lambda c: c[ "hid" ], new_contents[ (offset + 0):(offset + 2) ] ) - cat1_job_id = self.__job_id( history_id, new_contents[ (offset + 2) ][ "id" ] ) + cat1_job_id = self.__job_id( self.history_id, new_contents[ (offset + 2) ][ "id" ] ) downloaded_workflow = self._extract_and_download_workflow( - from_history_id=history_id, + from_history_id=self.history_id, dataset_ids=dumps( input_hids ), job_ids=dumps( [ cat1_job_id ] ), workflow_name="test import from history", @@ -56,10 +54,9 @@ @skip_without_tool( "random_lines1" ) def test_extract_mapping_workflow_from_history( self ): - history_id = self.dataset_populator.new_history() - hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair( history_id ) + hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair( self.history_id ) downloaded_workflow = self._extract_and_download_workflow( - from_history_id=history_id, + from_history_id=self.history_id, dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ), job_ids=dumps( [ job_id1, job_id2 ] ), workflow_name="test import from mapping history", @@ -70,15 +67,14 @@ old_history_id = self.dataset_populator.new_history() hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair( old_history_id ) - history_id = self.dataset_populator.new_history() old_contents = self._get( "histories/%s/contents" % old_history_id ).json() for old_content in old_contents: - self.__copy_content_to_history( history_id, old_content ) + self.__copy_content_to_history( self.history_id, old_content ) # API test is somewhat contrived since there is no good way # to retrieve job_id1, job_id2 like this for copied dataset # collections I don't think. downloaded_workflow = self._extract_and_download_workflow( - from_history_id=history_id, + from_history_id=self.history_id, dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ), job_ids=dumps( [ job_id1, job_id2 ] ), workflow_name="test import from history", @@ -88,14 +84,13 @@ @skip_without_tool( "random_lines1" ) @skip_without_tool( "multi_data_param" ) def test_extract_reduction_from_history( self ): - history_id = self.dataset_populator.new_history() - hdca = self.dataset_collection_populator.create_pair_in_history( history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"] ).json() + hdca = self.dataset_collection_populator.create_pair_in_history( self.history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"] ).json() hdca_id = hdca[ "id" ] inputs1 = { "input": { "batch": True, "values": [ { "src": "hdca", "id": hdca_id } ] }, "num_lines": 2 } - implicit_hdca1, job_id1 = self._run_tool_get_collection_and_job_id( history_id, "random_lines1", inputs1 ) + implicit_hdca1, job_id1 = self._run_tool_get_collection_and_job_id( self.history_id, "random_lines1", inputs1 ) inputs2 = { "f1": { "src": "hdca", "id": implicit_hdca1[ "id" ] }, "f2": { "src": "hdca", "id": implicit_hdca1[ "id" ] }, @@ -103,12 +98,12 @@ reduction_run_output = self.dataset_populator.run_tool( tool_id="multi_data_param", inputs=inputs2, - history_id=history_id, + history_id=self.history_id, ) job_id2 = reduction_run_output[ "jobs" ][ 0 ][ "id" ] - self.dataset_populator.wait_for_history( history_id, assert_ok=True, timeout=20 ) + self.dataset_populator.wait_for_history( self.history_id, assert_ok=True, timeout=20 ) downloaded_workflow = self._extract_and_download_workflow( - from_history_id=history_id, + from_history_id=self.history_id, dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ), job_ids=dumps( [ job_id1, job_id2 ] ), workflow_name="test import reduction", @@ -125,8 +120,7 @@ @skip_without_tool( "collection_paired_test" ) def test_extract_workflows_with_dataset_collections( self ): - history_id = self.dataset_populator.new_history() - hdca = self.dataset_collection_populator.create_pair_in_history( history_id ).json() + hdca = self.dataset_collection_populator.create_pair_in_history( self.history_id ).json() hdca_id = hdca[ "id" ] inputs = { "f1": dict( src="hdca", id=hdca_id ) @@ -134,12 +128,12 @@ run_output = self.dataset_populator.run_tool( tool_id="collection_paired_test", inputs=inputs, - history_id=history_id, + history_id=self.history_id, ) job_id = run_output[ "jobs" ][ 0 ][ "id" ] - self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + self.dataset_populator.wait_for_history( self.history_id, assert_ok=True ) downloaded_workflow = self._extract_and_download_workflow( - from_history_id=history_id, + from_history_id=self.history_id, dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ), job_ids=dumps( [ job_id ] ), workflow_name="test import from history", https://bitbucket.org/galaxy/galaxy-central/commits/b8a2150cfea0/ Changeset: b8a2150cfea0 User: jmchilton Date: 2014-12-02 02:18:56+00:00 Summary: Simplify interface to test helper _extract_and_download_workflow. Makes tests in this file marginally more readable. Affected #: 1 file diff -r 415221281212483cdad6213e284c03e0698dbf63 -r b8a2150cfea0a925cd21f7de71e1547b3b118025 test/api/test_workflow_extraction.py --- a/test/api/test_workflow_extraction.py +++ b/test/api/test_workflow_extraction.py @@ -18,10 +18,8 @@ contents_response = self._get( "histories/%s/contents" % self.history_id ) input_hids = map( lambda c: c[ "hid" ], contents_response.json()[ 0:2 ] ) downloaded_workflow = self._extract_and_download_workflow( - from_history_id=self.history_id, - dataset_ids=dumps( input_hids ), - job_ids=dumps( [ cat1_job_id ] ), - workflow_name="test import from history", + dataset_ids=input_hids, + job_ids=[ cat1_job_id ], ) self.assertEquals( downloaded_workflow[ "name" ], "test import from history" ) self.__assert_looks_like_cat1_example_workflow( downloaded_workflow ) @@ -45,10 +43,8 @@ input_hids = map( lambda c: c[ "hid" ], new_contents[ (offset + 0):(offset + 2) ] ) cat1_job_id = self.__job_id( self.history_id, new_contents[ (offset + 2) ][ "id" ] ) downloaded_workflow = self._extract_and_download_workflow( - from_history_id=self.history_id, - dataset_ids=dumps( input_hids ), - job_ids=dumps( [ cat1_job_id ] ), - workflow_name="test import from history", + dataset_ids=input_hids, + job_ids=[ cat1_job_id ], ) self.__assert_looks_like_cat1_example_workflow( downloaded_workflow ) @@ -56,10 +52,8 @@ def test_extract_mapping_workflow_from_history( self ): hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair( self.history_id ) downloaded_workflow = self._extract_and_download_workflow( - from_history_id=self.history_id, - dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ), - job_ids=dumps( [ job_id1, job_id2 ] ), - workflow_name="test import from mapping history", + dataset_collection_ids=[ hdca[ "hid" ] ], + job_ids=[ job_id1, job_id2 ], ) self.__assert_looks_like_randomlines_mapping_workflow( downloaded_workflow ) @@ -74,10 +68,8 @@ # to retrieve job_id1, job_id2 like this for copied dataset # collections I don't think. downloaded_workflow = self._extract_and_download_workflow( - from_history_id=self.history_id, - dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ), - job_ids=dumps( [ job_id1, job_id2 ] ), - workflow_name="test import from history", + dataset_collection_ids=[ hdca[ "hid" ] ], + job_ids=[ job_id1, job_id2 ], ) self.__assert_looks_like_randomlines_mapping_workflow( downloaded_workflow ) @@ -103,10 +95,8 @@ job_id2 = reduction_run_output[ "jobs" ][ 0 ][ "id" ] self.dataset_populator.wait_for_history( self.history_id, assert_ok=True, timeout=20 ) downloaded_workflow = self._extract_and_download_workflow( - from_history_id=self.history_id, - dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ), - job_ids=dumps( [ job_id1, job_id2 ] ), - workflow_name="test import reduction", + dataset_collection_ids=[ hdca[ "hid" ] ], + job_ids=[ job_id1, job_id2 ], ) assert len( downloaded_workflow[ "steps" ] ) == 3 collect_step_idx = self._assert_first_step_is_paired_input( downloaded_workflow ) @@ -133,10 +123,8 @@ job_id = run_output[ "jobs" ][ 0 ][ "id" ] self.dataset_populator.wait_for_history( self.history_id, assert_ok=True ) downloaded_workflow = self._extract_and_download_workflow( - from_history_id=self.history_id, - dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ), - job_ids=dumps( [ job_id ] ), - workflow_name="test import from history", + dataset_collection_ids=[ hdca[ "hid" ] ], + job_ids=[ job_id ], ) collection_steps = self._get_steps_of_type( downloaded_workflow, "data_collection_input", expected_len=1 ) collection_step = collection_steps[ 0 ] @@ -222,6 +210,18 @@ return collect_step_idx def _extract_and_download_workflow( self, **extract_payload ): + if "from_history_id" not in extract_payload: + extract_payload[ "from_history_id" ] = self.history_id + + if "workflow_name" not in extract_payload: + extract_payload[ "workflow_name" ] = "test import from history" + + for key in "job_ids", "dataset_ids", "dataset_collection_ids": + if key in extract_payload: + value = extract_payload[ key ] + if isinstance(value, list): + extract_payload[ key ] = dumps( value ) + create_workflow_response = self._post( "workflows", data=extract_payload ) self._assert_status_code_is( create_workflow_response, 200 ) https://bitbucket.org/galaxy/galaxy-central/commits/47195be80a9f/ Changeset: 47195be80a9f User: jmchilton Date: 2014-12-02 02:18:56+00:00 Summary: Introduce another helper to simplify test_workflow_extraction.py. Affected #: 1 file diff -r b8a2150cfea0a925cd21f7de71e1547b3b118025 -r 47195be80a9fa06c4777103d74dcbb2a18a8c33b test/api/test_workflow_extraction.py --- a/test/api/test_workflow_extraction.py +++ b/test/api/test_workflow_extraction.py @@ -15,8 +15,8 @@ def test_extract_from_history( self ): # Run the simple test workflow and extract it back out from history cat1_job_id = self.__setup_and_run_cat1_workflow( history_id=self.history_id ) - contents_response = self._get( "histories/%s/contents" % self.history_id ) - input_hids = map( lambda c: c[ "hid" ], contents_response.json()[ 0:2 ] ) + contents = self._history_contents() + input_hids = map( lambda c: c[ "hid" ], contents[ 0:2 ] ) downloaded_workflow = self._extract_and_download_workflow( dataset_ids=input_hids, job_ids=[ cat1_job_id ], @@ -36,10 +36,10 @@ # offset = 1 offset = 0 - old_contents = self._get( "histories/%s/contents" % old_history_id ).json() + old_contents = self._history_contents( old_history_id ) for old_dataset in old_contents: self.__copy_content_to_history( self.history_id, old_dataset ) - new_contents = self._get( "histories/%s/contents" % self.history_id ).json() + new_contents = self._history_contents() input_hids = map( lambda c: c[ "hid" ], new_contents[ (offset + 0):(offset + 2) ] ) cat1_job_id = self.__job_id( self.history_id, new_contents[ (offset + 2) ][ "id" ] ) downloaded_workflow = self._extract_and_download_workflow( @@ -61,7 +61,7 @@ old_history_id = self.dataset_populator.new_history() hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair( old_history_id ) - old_contents = self._get( "histories/%s/contents" % old_history_id ).json() + old_contents = self._history_contents( old_history_id ) for old_content in old_contents: self.__copy_content_to_history( self.history_id, old_content ) # API test is somewhat contrived since there is no good way @@ -175,6 +175,11 @@ self.assertEquals( input_steps[ 0 ][ "id" ], input1[ "id" ] ) self.assertEquals( input_steps[ 1 ][ "id" ], input2[ "id" ] ) + def _history_contents( self, history_id=None ): + if history_id is None: + history_id = self.history_id + return self._get( "histories/%s/contents" % history_id ).json() + def __copy_content_to_history( self, history_id, content ): if content[ "history_content_type" ] == "dataset": payload = dict( https://bitbucket.org/galaxy/galaxy-central/commits/d0dc9272a481/ Changeset: d0dc9272a481 User: jmchilton Date: 2014-12-02 02:18:56+00:00 Summary: Fix for running test_extract_workflow.py stand-alone. Affected #: 1 file diff -r 47195be80a9fa06c4777103d74dcbb2a18a8c33b -r d0dc9272a4819e2fb8867b45b782ac2e6d3d8861 test/unit/workflows/test_extract_summary.py --- a/test/unit/workflows/test_extract_summary.py +++ b/test/unit/workflows/test_extract_summary.py @@ -1,5 +1,6 @@ import unittest +import galaxy.model.mapping from galaxy import model from galaxy.workflow import extract https://bitbucket.org/galaxy/galaxy-central/commits/bc4086a04bef/ Changeset: bc4086a04bef User: jmchilton Date: 2014-12-02 02:18:56+00:00 Summary: Remove dated TODO from workflow extraction code. Affected #: 1 file diff -r d0dc9272a4819e2fb8867b45b782ac2e6d3d8861 -r bc4086a04beff9b1530e3093a15e15ffd8faa6b0 lib/galaxy/workflow/extract.py --- a/lib/galaxy/workflow/extract.py +++ b/lib/galaxy/workflow/extract.py @@ -205,8 +205,6 @@ else: dataset_collection = content # TODO: Optimize db call - # TODO: Ensure this is deterministic, must get same job - # for each dataset collection. dataset_instance = dataset_collection.collection.dataset_instances[ 0 ] if not self.__check_state( dataset_instance ): # Just checking the state of one instance, don't need more but https://bitbucket.org/galaxy/galaxy-central/commits/172c82454647/ Changeset: 172c82454647 User: jmchilton Date: 2014-12-02 02:18:56+00:00 Summary: More unit tests for workflow extraction summarize method. Affected #: 1 file diff -r bc4086a04beff9b1530e3093a15e15ffd8faa6b0 -r 172c824546478705dfc108310bd5db88254f5798 test/unit/workflows/test_extract_summary.py --- a/test/unit/workflows/test_extract_summary.py +++ b/test/unit/workflows/test_extract_summary.py @@ -46,7 +46,7 @@ assert len( job_dict ) == 1 self.assertEquals( job_dict[ hda.job ], [ ('out1', derived_hda_2 ) ] ) - def test_fake_job( self ): + def test_fake_job_hda( self ): """ Fakes job if creating_job_associations is empty. """ hda = MockHda( job=UNDEFINED_JOB ) @@ -59,6 +59,28 @@ datasets = job_dict.values()[ 0 ] assert datasets == [ ( None, hda ) ] + def test_fake_job_hdca( self ): + hdca = MockHdca( ) + self.history.active_datasets.append( hdca ) + job_dict, warnings = extract.summarize( trans=self.trans ) + assert not warnings + assert len( job_dict ) == 1 + fake_job = job_dict.keys()[ 0 ] + assert fake_job.id.startswith( "fake_" ) + assert fake_job.is_fake + content_instances = job_dict.values()[ 0 ] + assert content_instances == [ ( None, hdca ) ] + + def test_implicit_map_job_hdca( self ): + creating_job = model.Job() + hdca = MockHdca( implicit_output_name="out1", job=creating_job ) + self.history.active_datasets.append( hdca ) + job_dict, warnings = extract.summarize( trans=self.trans ) + assert not warnings + assert len( job_dict ) == 1 + job = job_dict.keys()[ 0 ] + assert job is creating_job + def test_warns_and_skips_datasets_if_not_finished( self ): hda = MockHda( state='queued' ) self.history.active_datasets.append( hda ) @@ -102,3 +124,31 @@ self.creating_job_associations = [ assoc ] else: self.creating_job_associations = [] + + +class MockHdca( object ): + + def __init__( self, implicit_output_name=None, job=None, hid=1 ): + self.id = 124 + self.copied_from_history_dataset_collection_association = None + self.history_content_type = "dataset_collection" + self.implicit_output_name = implicit_output_name + self.hid = 1 + self.collection = model.DatasetCollection() + element = model.DatasetCollectionElement( + collection=self.collection, + element=model.HistoryDatasetAssociation(), + element_index=0, + element_identifier="moocow", + ) + element.dataset_instance.dataset = model.Dataset() + element.dataset_instance.dataset.state = "ok" + creating = model.JobToOutputDatasetAssociation( + implicit_output_name, + element.dataset_instance, + ) + creating.job = job + element.dataset_instance.creating_job_associations = [ + creating, + ] + self.collection.elements = [element] https://bitbucket.org/galaxy/galaxy-central/commits/74e82c604d02/ Changeset: 74e82c604d02 User: jmchilton Date: 2014-12-02 02:18:56+00:00 Summary: Refactor lib/galaxy/workflow/extract.py to breakup big loop. Affected #: 1 file diff -r 172c824546478705dfc108310bd5db88254f5798 -r 74e82c604d026307fa8d72a7850ddd33c5f9259b lib/galaxy/workflow/extract.py --- a/lib/galaxy/workflow/extract.py +++ b/lib/galaxy/workflow/extract.py @@ -195,39 +195,48 @@ # needed because cannot allow selection of individual datasets from an implicit # mapping during extraction - you get the collection or nothing. for content in self.history.active_contents: - if content.history_content_type == "dataset_collection": - hid = content.hid - content = self.__original_hdca( content ) - self.collection_types[ hid ] = content.collection.collection_type - if not content.implicit_output_name: - job = DatasetCollectionCreationJob( content ) - self.jobs[ job ] = [ ( None, content ) ] + self.__summarize_content( content ) + + def __summarize_content( self, content ): + # Update internal state for history content (either an HDA or + # an HDCA). + if content.history_content_type == "dataset_collection": + self.__summarize_dataset_collection( content ) + else: + self.__summarize_dataset( content ) + + def __summarize_dataset_collection( self, content ): + content = self.__original_hdca( content ) + dataset_collection = content + hid = content.hid + self.collection_types[ hid ] = content.collection.collection_type + if not content.implicit_output_name: + job = DatasetCollectionCreationJob( content ) + self.jobs[ job ] = [ ( None, content ) ] + else: + dataset_collection = content + # TODO: Optimize db call + dataset_instance = dataset_collection.collection.dataset_instances[ 0 ] + if not self.__check_state( dataset_instance ): + # Just checking the state of one instance, don't need more but + # makes me wonder if even need this check at all? + return + + job_hda = self.__original_hda( dataset_instance ) + if not job_hda.creating_job_associations: + log.warn( "An implicitly create output dataset collection doesn't have a creating_job_association, should not happen!" ) + job = DatasetCollectionCreationJob( dataset_collection ) + self.jobs[ job ] = [ ( None, dataset_collection ) ] + + for assoc in job_hda.creating_job_associations: + job = assoc.job + if job not in self.jobs or self.jobs[ job ][ 0 ][ 1 ].history_content_type == "dataset": + self.jobs[ job ] = [ ( assoc.name, dataset_collection ) ] + self.implicit_map_jobs.append( job ) else: - dataset_collection = content - # TODO: Optimize db call - dataset_instance = dataset_collection.collection.dataset_instances[ 0 ] - if not self.__check_state( dataset_instance ): - # Just checking the state of one instance, don't need more but - # makes me wonder if even need this check at all? - continue + self.jobs[ job ].append( ( assoc.name, dataset_collection ) ) - job_hda = self.__original_hda( dataset_instance ) - if not job_hda.creating_job_associations: - log.warn( "An implicitly create output dataset collection doesn't have a creating_job_association, should not happen!" ) - job = DatasetCollectionCreationJob( dataset_collection ) - self.jobs[ job ] = [ ( None, dataset_collection ) ] - - for assoc in job_hda.creating_job_associations: - job = assoc.job - if job not in self.jobs or self.jobs[ job ][ 0 ][ 1 ].history_content_type == "dataset": - self.jobs[ job ] = [ ( assoc.name, dataset_collection ) ] - self.implicit_map_jobs.append( job ) - else: - self.jobs[ job ].append( ( assoc.name, dataset_collection ) ) - else: - self.__append_dataset( content ) - - def __append_dataset( self, dataset ): + def __summarize_dataset( self, dataset ): if not self.__check_state( dataset ): return Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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[galaxyproject/usegalaxy-playbook] ecd10d: Update readme w/ instructions for updating Galaxy ...
by GitHub 01 Dec '14

01 Dec '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ecd10db580aa8f39812ba06ba977d0ab5df8ba5e https://github.com/galaxyproject/usegalaxy-playbook/commit/ecd10db580aa8f39… Author: Dannon <dannon.baker(a)gmail.com> Date: 2014-12-01 (Mon, 01 Dec 2014) Changed paths: M README.md Log Message: ----------- Update readme w/ instructions for updating Galaxy playbook.

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