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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. 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