24 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fa4839486ecd/ changeset: fa4839486ecd user: dan date: 2012-10-15 22:01:12 summary: Fix tabs to spaces. affected #: 1 file diff -r d79a4e48653d678a7f07e3ef6f5bf1169567b48e -r fa4839486ecd30c173920ca8cab8ec74e995e20d templates/display_base.mako --- a/templates/display_base.mako +++ b/templates/display_base.mako @@ -1,12 +1,12 @@ <%! - def inherit( context ): - if context.get('no_panels'): - return '/base.mako' - else: - return '/webapps/galaxy/base_panels.mako' - - from galaxy.model import History, StoredWorkflow, Page - from galaxy.web.framework.helpers import iff + def inherit( context ): + if context.get('no_panels'): + return '/base.mako' + else: + return '/webapps/galaxy/base_panels.mako' + + from galaxy.model import History, StoredWorkflow, Page + from galaxy.web.framework.helpers import iff %><%inherit file="${inherit( context )}"/><%namespace file="/tagging_common.mako" import="render_individual_tagging_element, render_community_tagging_element" /> @@ -23,11 +23,11 @@ <%def name="init()"><% - self.has_left_panel=False - self.has_right_panel=True - self.message_box_visible=False - self.active_view="shared" - self.overlay_visible=False + self.has_left_panel=False + self.has_right_panel=True + self.message_box_visible=False + self.active_view="shared" + self.overlay_visible=False %></%def> @@ -171,12 +171,12 @@ ## For base.mako <%def name="body()"> - ${self.render_content()} + ${self.render_content()} </%def> ## For base_panels.mako <%def name="center_panel()"> - ${self.render_content()} + ${self.render_content()} </%def> @@ -196,23 +196,23 @@ %><div class="unified-panel-header" unselectable="on"> - <div class="unified-panel-header-inner"> - %if item.published: - <a href="${href_to_all_items}">Published ${item_plural}</a> | - <a href="${href_to_user_items}">${item.user.username}</a> - %elif item.importable: - Accessible ${get_class_display_name( item.__class__ )} - %elif item.users_shared_with: - Shared ${get_class_display_name( item.__class__ )} - %else: - Private ${get_class_display_name( item.__class__ )} - %endif - | ${get_item_name( item )} - + <div class="unified-panel-header-inner"> + %if item.published: + <a href="${href_to_all_items}">Published ${item_plural}</a> | + <a href="${href_to_user_items}">${item.user.username}</a> + %elif item.importable: + Accessible ${get_class_display_name( item.__class__ )} + %elif item.users_shared_with: + Shared ${get_class_display_name( item.__class__ )} + %else: + Private ${get_class_display_name( item.__class__ )} + %endif + | ${get_item_name( item )} + <div style="float: right"> ${self.render_item_links( item )} </div> - </div> + </div></div><div class="unified-panel-body"> https://bitbucket.org/galaxy/galaxy-central/changeset/266be75675fc/ changeset: 266be75675fc user: dan date: 2012-10-15 22:01:12 summary: Fix tabs to spaces. affected #: 1 file diff -r fa4839486ecd30c173920ca8cab8ec74e995e20d -r 266be75675fc12ac7834919e00102a056f1c29c0 templates/display_common.mako --- a/templates/display_common.mako +++ b/templates/display_common.mako @@ -29,12 +29,12 @@ item_name = item.get_display_name() else: item_name = item.name - + # Encode in unicode. if type( item_name ) is str: item_name = unicode( item_name, 'utf-8' ) - return item_name - %> + return item_name + %></%def> ## Get plural display name for a class. @@ -65,7 +65,7 @@ ## Get plural term for item. <%def name="get_item_plural( item )"> - <% return get_class_plural( item.__class__ ) %> + <% return get_class_plural( item.__class__ ) %></%def> ## Get plural term for class. https://bitbucket.org/galaxy/galaxy-central/changeset/6cb9cc1daca5/ changeset: 6cb9cc1daca5 user: dan date: 2012-10-15 22:01:12 summary: Fix tabs to spaces. affected #: 1 file diff -r 266be75675fc12ac7834919e00102a056f1c29c0 -r 6cb9cc1daca52643dc9e68783247ac06e8c51069 templates/admin/external_service/common.mako --- a/templates/admin/external_service/common.mako +++ b/templates/admin/external_service/common.mako @@ -7,16 +7,16 @@ ##<a href="${h.url_for( controller='external_service', action='view_external_service', id=trans.security.encode_id( external_service.id ) )}">${external_service.name}</a><div style="clear: both"></div></div> - <div class="form-row"> - <label>Description:</label> - ${external_service.description} - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Version:</label> - ${external_service.version} - <div style="clear: both"></div> - </div> + <div class="form-row"> + <label>Description:</label> + ${external_service.description} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Version:</label> + ${external_service.version} + <div style="clear: both"></div> + </div><div class="form-row"><label>External service type:</label> %if trans.app.external_service_types.all_external_service_types.has_key( external_service.external_service_type_id ): https://bitbucket.org/galaxy/galaxy-central/changeset/fc6bbeae9549/ changeset: fc6bbeae9549 user: dan date: 2012-10-15 22:01:13 summary: Fix tabs to spaces. affected #: 1 file diff -r 6cb9cc1daca52643dc9e68783247ac06e8c51069 -r fc6bbeae9549fa33d860e09749c4194d51374404 templates/admin/external_service/create_external_service.mako --- a/templates/admin/external_service/create_external_service.mako +++ b/templates/admin/external_service/create_external_service.mako @@ -10,16 +10,16 @@ <div class="toolForm"><div class="toolFormTitle">New external service</div> %if widgets: - %for i, field in enumerate( widgets ): - <div class="form-row"> - <label>${field['label']}:</label> - ${field['widget'].get_html()} - <div class="toolParamHelp" style="clear: both;"> - ${field['helptext']} - </div> - <div style="clear: both"></div> - </div> - %endfor + %for i, field in enumerate( widgets ): + <div class="form-row"> + <label>${field['label']}:</label> + ${field['widget'].get_html()} + <div class="toolParamHelp" style="clear: both;"> + ${field['helptext']} + </div> + <div style="clear: both"></div> + </div> + %endfor %endif </div><div class="form-row"> https://bitbucket.org/galaxy/galaxy-central/changeset/c20374ea53db/ changeset: c20374ea53db user: dan date: 2012-10-15 22:01:13 summary: Fix tabs to spaces. affected #: 1 file diff -r fc6bbeae9549fa33d860e09749c4194d51374404 -r c20374ea53db879a05ad997878eb5592befb5879 templates/admin/external_service/reload_external_service_types.mako --- a/templates/admin/external_service/reload_external_service_types.mako +++ b/templates/admin/external_service/reload_external_service_types.mako @@ -8,15 +8,15 @@ ${render_msg( message, status )} %endif <form name="reload_external_service_types" action="${h.url_for( controller='external_service', action='reload_external_service_types' )}" method="post"> - <div class="toolForm"> - <div class="toolFormTitle">Reload external service types</div> - <div class="form-row"> - <label>Select external service type to reload:</label> - ${external_service_type_select_field.get_html()} - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="reload_external_service_type_button" value="Reload"/> - </div> - </div> + <div class="toolForm"> + <div class="toolFormTitle">Reload external service types</div> + <div class="form-row"> + <label>Select external service type to reload:</label> + ${external_service_type_select_field.get_html()} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <input type="submit" name="reload_external_service_type_button" value="Reload"/> + </div> + </div></form> \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/changeset/5f42a1ae038f/ changeset: 5f42a1ae038f user: dan date: 2012-10-15 22:01:13 summary: Fix tabs to spaces. affected #: 1 file diff -r c20374ea53db879a05ad997878eb5592befb5879 -r 5f42a1ae038f4cd296b5c71e537ef524bc5f92d1 templates/admin/forms/edit_form_definition.mako --- a/templates/admin/forms/edit_form_definition.mako +++ b/templates/admin/forms/edit_form_definition.mako @@ -55,23 +55,23 @@ </h4><div class="msg_body2"> %endif - <div class="repeat-group-item"> - %for field_attr in field: - <div class="form-row"> - <label>${field_attr[0]}</label> - ${field_attr[1].get_html()} - ${render_selectbox_options( index, field_attr )} + <div class="repeat-group-item"> + %for field_attr in field: + <div class="form-row"> + <label>${field_attr[0]}</label> + ${field_attr[1].get_html()} + ${render_selectbox_options( index, field_attr )} %if len(field_attr) == 3: - <div class="toolParamHelp" style="clear: both;"> - ${field_attr[2]} - </div> + <div class="toolParamHelp" style="clear: both;"> + ${field_attr[2]} + </div> %endif - </div> - %endfor - <div class="form-row"> - <input type="submit" name="remove_button" value="Remove field ${index+1}"/> - </div> - </div> + </div> + %endfor + <div class="form-row"> + <input type="submit" name="remove_button" value="Remove field ${index+1}"/> + </div> + </div></div></%def> @@ -96,7 +96,7 @@ <form id="edit_form_definition" name="edit_form_definition" action="${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 "${form_definition.name}" (${form_definition.type})</div> %if response_redirect: <input type="hidden" name="response_redirect" value="${response_redirect}" size="40" /> %endif @@ -112,20 +112,20 @@ </div> %endfor </div> - %if current_form_type == trans.app.model.FormDefinition.types.SAMPLE: - <p/> - <div class="toolForm"> - <div class="toolFormTitle">Form Layout</div> - <div class="form-row"> - <label>Layout grid names</label> - </div> - %for index, lg in enumerate( layout_grids ): - ${render_layout( index, lg )} - %endfor - <div class="form-row"> - <input type="submit" name="add_layout_grid_button" value="Add layout grid"/> - </div> - </div> + %if current_form_type == trans.app.model.FormDefinition.types.SAMPLE: + <p/> + <div class="toolForm"> + <div class="toolFormTitle">Form Layout</div> + <div class="form-row"> + <label>Layout grid names</label> + </div> + %for index, lg in enumerate( layout_grids ): + ${render_layout( index, lg )} + %endfor + <div class="form-row"> + <input type="submit" name="add_layout_grid_button" value="Add layout grid"/> + </div> + </div> %endif <p/><div class="toolForm"> https://bitbucket.org/galaxy/galaxy-central/changeset/14e69765b5cd/ changeset: 14e69765b5cd user: dan date: 2012-10-15 22:01:13 summary: Fix tabs to spaces. affected #: 1 file diff -r 5f42a1ae038f4cd296b5c71e537ef524bc5f92d1 -r 14e69765b5cd57c3ac3dd83b5e91052f04701224 templates/admin/request_type/edit_request_type.mako --- a/templates/admin/request_type/edit_request_type.mako +++ b/templates/admin/request_type/edit_request_type.mako @@ -60,20 +60,20 @@ <div class="toolForm"><div class="toolFormTitle">Sample states defined for this request type</div> %for element_count, state in enumerate( request_type.states ): - <div class="repeat-group-item"> - <div class="form-row"> - <label>${1+element_count}. State name:</label> - <input type="text" name="state_name_${trans.security.encode_id( state.id )}" value="${state.name}" size="40"/> - </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"/> - <div class="toolParamHelp" style="clear: both;"> - optional - </div> - </div> - <div style="clear: both"></div> - </div> + <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="${state.name}" size="40"/> + </div> + <div class="form-row"> + <label>Description:</label> + <input type="text" name="state_desc_${trans.security.encode_id( state.id )}" value="${state.desc}" size="40"/> + <div class="toolParamHelp" style="clear: both;"> + optional + </div> + </div> + <div style="clear: both"></div> + </div> %endfor </div><p/> https://bitbucket.org/galaxy/galaxy-central/changeset/551ca42085e6/ changeset: 551ca42085e6 user: dan date: 2012-10-15 22:01:14 summary: Fix tabs to spaces. affected #: 1 file diff -r 14e69765b5cd57c3ac3dd83b5e91052f04701224 -r 551ca42085e677dd5397c717759a653b9b249741 templates/admin/requests/rename_datasets.mako --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -15,45 +15,45 @@ %endif <div class="toolForm"> - <form name="rename_datasets" id="rename_datasets" action="${h.url_for( controller='requests_admin', action='rename_datasets', id_list=id_list, sample_id=trans.security.encode_id( sample.id ) )}" method="post" > + <form name="rename_datasets" id="rename_datasets" action="${h.url_for( controller='requests_admin', action='rename_datasets', id_list=id_list, sample_id=trans.security.encode_id( sample.id ) )}" method="post" > - <table class="grid"> - <thead> - <tr> - <th>Prepend directory name</th> - <th>Name</th> - <th>Path on external service</th> - </tr> - <thead> - <tbody> - %for id in id_list: - <% sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( id ) ) %> - %if sample_dataset.status == trans.app.model.SampleDataset.transfer_status.NOT_STARTED: - <tr> - <td> - <% rename_datasets_for_sample_select_field = build_rename_datasets_for_sample_select_field( trans, sample_dataset ) %> - ${rename_datasets_for_sample_select_field.get_html()} - </td> - <td> - <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id ) }" value="${sample_dataset.name}" size="100"/> - </td> - <td>${sample_dataset.file_path}</td> - </tr> - %endif - %endfor - </tbody> - </table> - <br/> + <table class="grid"> + <thead> + <tr> + <th>Prepend directory name</th> + <th>Name</th> + <th>Path on external service</th> + </tr> + <thead> + <tbody> + %for id in id_list: + <% sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( id ) ) %> + %if sample_dataset.status == trans.app.model.SampleDataset.transfer_status.NOT_STARTED: + <tr> + <td> + <% rename_datasets_for_sample_select_field = build_rename_datasets_for_sample_select_field( trans, sample_dataset ) %> + ${rename_datasets_for_sample_select_field.get_html()} + </td> + <td> + <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id ) }" value="${sample_dataset.name}" size="100"/> + </td> + <td>${sample_dataset.file_path}</td> + </tr> + %endif + %endfor + </tbody> + </table> + <br/><div class="form-row"> - <div class="toolParamHelp" style="clear: both;"> - A dataset name should only contain the alphanumeric characters or underscore(_). - If a dataset name contains any other character, it would be replaced by an underscore(_). - </div> + <div class="toolParamHelp" style="clear: both;"> + A dataset name should only contain the alphanumeric characters or underscore(_). + If a dataset name contains any other character, it would be replaced by an underscore(_). + </div></div> - <div class="form-row"> - <input type="submit" name="rename_datasets_button" value="Save"/> - <input type="submit" name="cancel_rename_datasets_button" value="Close"/> - </div> - </form> + <div class="form-row"> + <input type="submit" name="rename_datasets_button" value="Save"/> + <input type="submit" name="cancel_rename_datasets_button" value="Close"/> + </div> + </form></div> https://bitbucket.org/galaxy/galaxy-central/changeset/1eadee772d78/ changeset: 1eadee772d78 user: dan date: 2012-10-15 22:01:14 summary: Fix tabs to spaces. affected #: 1 file diff -r 551ca42085e677dd5397c717759a653b9b249741 -r 1eadee772d78e34c51e90fdc9980e780ff577e85 templates/admin/requests/select_datasets_to_transfer.mako --- a/templates/admin/requests/select_datasets_to_transfer.mako +++ b/templates/admin/requests/select_datasets_to_transfer.mako @@ -13,16 +13,16 @@ <script type="text/javascript"> $(function(){ - $("#tree").ajaxComplete(function(event, XMLHttpRequest, ajaxOptions) { - _log("debug", "ajaxComplete: %o", this); // dom element listening - }); + $("#tree").ajaxComplete(function(event, XMLHttpRequest, ajaxOptions) { + _log("debug", "ajaxComplete: %o", this); // dom element listening + }); // --- Initialize sample trees $("#tree").dynatree({ title: "${scp_configs['data_location']}", - rootVisible: true, - minExpandLevel: 0, // 1: root node is not collapsible - persist: false, - checkbox: true, + rootVisible: true, + minExpandLevel: 0, // 1: root node is not collapsible + persist: false, + checkbox: true, selectMode: 3, onPostInit: function(isReloading, isError) { //alert("reloading: "+isReloading+", error:"+isError); @@ -43,38 +43,38 @@ data: { request_id: "${trans.security.encode_id( request.id )}", external_service_id: "${trans.security.encode_id( external_service.id )}", key: dtnode.data.key }, }); }, - onSelect: function(select, dtnode) { + onSelect: function(select, dtnode) { // Display list of selected nodes - var selNodes = dtnode.tree.getSelectedNodes(); - // convert to title/key array - var selKeys = $.map(selNodes, function(node){ - return node.data.key; - }); - document.select_datasets_to_transfer.selected_datasets_to_transfer.value = selKeys.join(",") + var selNodes = dtnode.tree.getSelectedNodes(); + // convert to title/key array + var selKeys = $.map(selNodes, function(node){ + return node.data.key; + }); + document.select_datasets_to_transfer.selected_datasets_to_transfer.value = selKeys.join(",") }, - onActivate: function(dtnode) { - var cell = $("#file_details"); - var selected_value; - if (dtnode.data.key == 'root') { - selected_value = "${scp_configs['data_location']}/"; - } else { - selected_value = dtnode.data.key; - }; - if (selected_value.charAt(selected_value.length-1) != '/') { - // Make ajax call - $.ajax( { - type: "POST", - url: "${h.url_for( controller='requests_admin', action='get_file_details' )}", - dataType: "json", - data: { request_id: "${trans.security.encode_id(request.id)}", external_service_id: "${trans.security.encode_id(external_service.id)}", folder_path: selected_value }, - success : function ( data ) { - cell.html( '<label>'+data+'</label>' ) - } + onActivate: function(dtnode) { + var cell = $("#file_details"); + var selected_value; + if (dtnode.data.key == 'root') { + selected_value = "${scp_configs['data_location']}/"; + } else { + selected_value = dtnode.data.key; + }; + if (selected_value.charAt(selected_value.length-1) != '/') { + // Make ajax call + $.ajax( { + type: "POST", + url: "${h.url_for( controller='requests_admin', action='get_file_details' )}", + dataType: "json", + data: { request_id: "${trans.security.encode_id(request.id)}", external_service_id: "${trans.security.encode_id(external_service.id)}", folder_path: selected_value }, + success : function ( data ) { + cell.html( '<label>'+data+'</label>' ) + } }); } else { cell.html( '' ); }; - }, + }, }); }); </script> https://bitbucket.org/galaxy/galaxy-central/changeset/015f5962780f/ changeset: 015f5962780f user: dan date: 2012-10-15 22:01:14 summary: Fix tabs to spaces. affected #: 1 file diff -r 1eadee772d78e34c51e90fdc9980e780ff577e85 -r 015f5962780f8278d6c1d42b87d88ff93ed46d38 templates/dataset/embed.mako --- a/templates/dataset/embed.mako +++ b/templates/dataset/embed.mako @@ -1,6 +1,6 @@ <%inherit file="/embed_base.mako"/><%! - from galaxy.web.framework.helpers import iff + from galaxy.web.framework.helpers import iff %><%def name="render_item_links( dataset )"> https://bitbucket.org/galaxy/galaxy-central/changeset/878d4f3c89c6/ changeset: 878d4f3c89c6 user: dan date: 2012-10-15 22:01:15 summary: Fix tabs to spaces. affected #: 1 file diff -r 015f5962780f8278d6c1d42b87d88ff93ed46d38 -r 878d4f3c89c6e67655173385d484d007ad53e126 templates/history/display.mako --- a/templates/history/display.mako +++ b/templates/history/display.mako @@ -20,11 +20,11 @@ } .column { float: left; - padding: 10px; - margin: 20px; - background: #666; - border: 5px solid #ccc; - width: 300px; + padding: 10px; + margin: 20px; + background: #666; + border: 5px solid #ccc; + width: 300px; } </style> https://bitbucket.org/galaxy/galaxy-central/changeset/b5f54f1a1f79/ changeset: b5f54f1a1f79 user: dan date: 2012-10-15 22:01:17 summary: Fix tabs to spaces. affected #: 1 file diff -r 878d4f3c89c6e67655173385d484d007ad53e126 -r b5f54f1a1f79eae6ca0b82151c3be175ec7c6f30 templates/history/embed.mako --- a/templates/history/embed.mako +++ b/templates/history/embed.mako @@ -1,6 +1,6 @@ <%inherit file="/embed_base.mako"/><%! - from galaxy.web.framework.helpers import iff + from galaxy.web.framework.helpers import iff %><%def name="render_summary_content( history, datasets )"> https://bitbucket.org/galaxy/galaxy-central/changeset/43854cdbfd90/ changeset: 43854cdbfd90 user: dan date: 2012-10-15 22:01:17 summary: Fix tabs to spaces. affected #: 1 file diff -r b5f54f1a1f79eae6ca0b82151c3be175ec7c6f30 -r 43854cdbfd90951a3e7b4e2cc6bf69c9926c5dad templates/mobile/dataset/detail.mako --- a/templates/mobile/dataset/detail.mako +++ b/templates/mobile/dataset/detail.mako @@ -5,25 +5,25 @@ </div><div class="pad"> - <fieldset> - <div class="row"> - <label>State</label><span>${dataset.state}</span> - </div> - <div class="row"> - <label>Content</label><span>${dataset.blurb}</span> - </div> - <div class="row"> - <label>Format</label><span>${dataset.ext}</span> - </div> - <div class="row"> - <label>Info</label><span>${dataset.display_info()}</span> - </div> - %if dataset.state == "ok": - <div class="row"> - <a href="${h.url_for( action='dataset_peek', id=dataset.id )}">Peek</a> - </div> - %endif - </fieldset> + <fieldset> + <div class="row"> + <label>State</label><span>${dataset.state}</span> + </div> + <div class="row"> + <label>Content</label><span>${dataset.blurb}</span> + </div> + <div class="row"> + <label>Format</label><span>${dataset.ext}</span> + </div> + <div class="row"> + <label>Info</label><span>${dataset.display_info()}</span> + </div> + %if dataset.state == "ok": + <div class="row"> + <a href="${h.url_for( action='dataset_peek', id=dataset.id )}">Peek</a> + </div> + %endif + </fieldset></div></body> https://bitbucket.org/galaxy/galaxy-central/changeset/37339d7b4354/ changeset: 37339d7b4354 user: dan date: 2012-10-15 22:01:18 summary: Fix tabs to spaces. affected #: 1 file diff -r 43854cdbfd90951a3e7b4e2cc6bf69c9926c5dad -r 37339d7b4354705caf7f403d76958c57353ac604 templates/mobile/history/detail.mako --- a/templates/mobile/history/detail.mako +++ b/templates/mobile/history/detail.mako @@ -6,73 +6,73 @@ <ul class="edgetoedge"> %for data in history.active_datasets: - %if data.visible: + %if data.visible: - <% - if data.state in ['no state','',None]: - data_state = "queued" - else: - data_state = data.state - %> + <% + if data.state in ['no state','',None]: + data_state = "queued" + else: + data_state = data.state + %> - <li id="historyItemContainer-${data.id}"> + <li id="historyItemContainer-${data.id}"> + + <div style="float: left; padding-right: 8px;"> + <div style='display: none;' id="progress-${data.id}"> + <img src="${h.url_for('/static/style/data_running.gif')}" border="0"> + </div> + %if data_state == 'running': + <div><img src="${h.url_for('/static/style/data_running.gif')}" border="0"></div> + %elif data_state == 'upload': + <div><img src="${h.url_for('/static/style/data_upload.gif')}" border="0"></div> + %else: + <div><img src="${h.url_for( "/static/style/data_%s.png" % data_state )}" border="0"></div> + %endif + </div> + + <a href="${h.url_for( action="dataset_detail", id=data.id )}"> + + <div>${data.hid}: ${data.display_name()}</div> + + <div class="secondary"> + ## Body for history items, extra info and actions, data "peek" + <% current_user_roles = trans.get_current_user_roles() %> + %if not trans.user_is_admin() and not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): + <div>You do not have permission to view this dataset.</div> + %elif data_state == "queued": + <div>Job is waiting to run</div> + %elif data_state == "running": + <div>Job is currently running</div> + %elif data_state == "error": + <div> + An error occurred running this job. + </div> + %elif data_state == "discarded": + <div> + The job creating this dataset was cancelled before completion. + </div> + %elif data_state == 'setting_metadata': + <div>Metadata is being Auto-Detected.</div> + %elif data_state == "empty": + <div>No data: <i>${data.display_info()}</i></div> + %elif data_state in [ "ok", "failed_metadata" ]: + <div> + %if data_state == "failed_metadata": + Warning: setting metadata failed, + %endif + ${data.blurb}, + format: <span class="${data.ext}">${data.ext}</span>, + database: <span class="${data.dbkey}">${data.dbkey}</span> + </div> + %else: + <div>Error: unknown dataset state "${data_state}".</div> + %endif + </div> + + </a> - <div style="float: left; padding-right: 8px;"> - <div style='display: none;' id="progress-${data.id}"> - <img src="${h.url_for('/static/style/data_running.gif')}" border="0"> - </div> - %if data_state == 'running': - <div><img src="${h.url_for('/static/style/data_running.gif')}" border="0"></div> - %elif data_state == 'upload': - <div><img src="${h.url_for('/static/style/data_upload.gif')}" border="0"></div> - %else: - <div><img src="${h.url_for( "/static/style/data_%s.png" % data_state )}" border="0"></div> - %endif - </div> - - <a href="${h.url_for( action="dataset_detail", id=data.id )}"> - - <div>${data.hid}: ${data.display_name()}</div> - - <div class="secondary"> - ## Body for history items, extra info and actions, data "peek" - <% current_user_roles = trans.get_current_user_roles() %> - %if not trans.user_is_admin() and not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): - <div>You do not have permission to view this dataset.</div> - %elif data_state == "queued": - <div>Job is waiting to run</div> - %elif data_state == "running": - <div>Job is currently running</div> - %elif data_state == "error": - <div> - An error occurred running this job. - </div> - %elif data_state == "discarded": - <div> - The job creating this dataset was cancelled before completion. - </div> - %elif data_state == 'setting_metadata': - <div>Metadata is being Auto-Detected.</div> - %elif data_state == "empty": - <div>No data: <i>${data.display_info()}</i></div> - %elif data_state in [ "ok", "failed_metadata" ]: - <div> - %if data_state == "failed_metadata": - Warning: setting metadata failed, - %endif - ${data.blurb}, - format: <span class="${data.ext}">${data.ext}</span>, - database: <span class="${data.dbkey}">${data.dbkey}</span> - </div> - %else: - <div>Error: unknown dataset state "${data_state}".</div> - %endif - </div> - - </a> - - </li> - %endif + </li> + %endif %endfor https://bitbucket.org/galaxy/galaxy-central/changeset/fd7644e67b3d/ changeset: fd7644e67b3d user: dan date: 2012-10-15 22:01:18 summary: Fix tabs to spaces. affected #: 1 file diff -r 37339d7b4354705caf7f403d76958c57353ac604 -r fd7644e67b3d9129c5487d28817ec54585d4493e templates/page/history_annotation_table.mako --- a/templates/page/history_annotation_table.mako +++ b/templates/page/history_annotation_table.mako @@ -2,60 +2,60 @@ <%namespace file="../root/history_common.mako" import="render_dataset" /><div class="annotated_item"> - <table> - ## Table header. - <tr> - <th colspan='2'>History '${history.get_display_name()}'</th> - </tr> - <tr> - ## Status messages and tags. - <td colspan='2'> - %if history.deleted: - <div class="warningmessagesmall"> - ${_('This is a deleted history.')} - </div> - %endif - ## Tags come for free with community tagging, so not sure if this is necessary. - ##%if trans.get_user() is not None: - ## Tags: ${render_tagging_element_html( tags=history.tags, editable=False, use_toggle_link=False )} - ##%endif - </td> - </tr> - <tr> - <td colspan="2" class="annotation" item_class="History" item_id="${trans.security.encode_id( history.id )}">Description of History: - <ol> - <li>What was the motivation for this history? - <li>What is the outcome of this history? - <li>What are unresolved questions from this history? - <li>What new questions arise from this history? - </ol> - </td> - </tr> + <table> + ## Table header. + <tr> + <th colspan='2'>History '${history.get_display_name()}'</th> + </tr> + <tr> + ## Status messages and tags. + <td colspan='2'> + %if history.deleted: + <div class="warningmessagesmall"> + ${_('This is a deleted history.')} + </div> + %endif + ## Tags come for free with community tagging, so not sure if this is necessary. + ##%if trans.get_user() is not None: + ## Tags: ${render_tagging_element_html( tags=history.tags, editable=False, use_toggle_link=False )} + ##%endif + </td> + </tr> + <tr> + <td colspan="2" class="annotation" item_class="History" item_id="${trans.security.encode_id( history.id )}">Description of History: + <ol> + <li>What was the motivation for this history? + <li>What is the outcome of this history? + <li>What are unresolved questions from this history? + <li>What new questions arise from this history? + </ol> + </td> + </tr> - ## Table body. For each dataset, there is an area to annotate the dataset. - %if not datasets: - <tr> - <td> - <div class="infomessagesmall" id="emptyHistoryMessage"> - ${_("Your history is empty. Click 'Get Data' on the left pane to start")} - </div> - </td> - </tr> - %else: - ## Render requested datasets. - %for data in datasets: - %if data.visible: - <tr> - <td valign="top" class="annotation" item_class="HistoryDatasetAssociation" item_id="${trans.security.encode_id( data.id )}">Describe this step: why was it done? what data did it produce?</td> - ##<td valign="top" class="annotation">Describe this step: why was it done? what data does it produce?</td> - <td> - <div class="historyItemContainer" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing = False )} - </div> - </td> - </tr> - %endif - %endfor - %endif - </table> + ## Table body. For each dataset, there is an area to annotate the dataset. + %if not datasets: + <tr> + <td> + <div class="infomessagesmall" id="emptyHistoryMessage"> + ${_("Your history is empty. Click 'Get Data' on the left pane to start")} + </div> + </td> + </tr> + %else: + ## Render requested datasets. + %for data in datasets: + %if data.visible: + <tr> + <td valign="top" class="annotation" item_class="HistoryDatasetAssociation" item_id="${trans.security.encode_id( data.id )}">Describe this step: why was it done? what data did it produce?</td> + ##<td valign="top" class="annotation">Describe this step: why was it done? what data does it produce?</td> + <td> + <div class="historyItemContainer" id="historyItemContainer-${data.id}"> + ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing = False )} + </div> + </td> + </tr> + %endif + %endfor + %endif + </table></div> \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/changeset/47668884fcc3/ changeset: 47668884fcc3 user: dan date: 2012-10-15 22:01:18 summary: Fix tabs to spaces. affected #: 1 file diff -r fd7644e67b3d9129c5487d28817ec54585d4493e -r 47668884fcc331e32703ff8772a2ca8003852fac templates/page/index.mako --- a/templates/page/index.mako +++ b/templates/page/index.mako @@ -15,36 +15,36 @@ <div class="page-container" style="padding: 10px;"> ${h.to_unicode( grid )} - <br><br> - <h2>Pages shared with you by others</h2> + <br><br> + <h2>Pages shared with you by others</h2> - %if shared_by_others: - <table class="colored" border="0" cellspacing="0" cellpadding="0" width="100%"> - <tr class="header"> - <th>Title</th> - <th>Owner</th> - <th></th> - </tr> - %for i, association in enumerate( shared_by_others ): - <% page = association.page %> - <tr> - <td> - <a class="menubutton" id="shared-${i}-popup" href="${h.url_for( action='display_by_username_and_slug', username=page.user.username, slug=page.slug)}">${page.title}</a> - </td> - <td>${page.user.username}</td> - <td> - <div popupmenu="shared-${i}-popup"> - <a class="action-button" href="${h.url_for( action='display_by_username_and_slug', username=page.user.username, slug=page.slug)}" target="_top">View</a> - </div> - </td> - </tr> - %endfor - </table> - %else: + %if shared_by_others: + <table class="colored" border="0" cellspacing="0" cellpadding="0" width="100%"> + <tr class="header"> + <th>Title</th> + <th>Owner</th> + <th></th> + </tr> + %for i, association in enumerate( shared_by_others ): + <% page = association.page %> + <tr> + <td> + <a class="menubutton" id="shared-${i}-popup" href="${h.url_for( action='display_by_username_and_slug', username=page.user.username, slug=page.slug)}">${page.title}</a> + </td> + <td>${page.user.username}</td> + <td> + <div popupmenu="shared-${i}-popup"> + <a class="action-button" href="${h.url_for( action='display_by_username_and_slug', username=page.user.username, slug=page.slug)}" target="_top">View</a> + </div> + </td> + </tr> + %endfor + </table> + %else: - No pages have been shared with you. + No pages have been shared with you. - %endif + %endif </div></div> https://bitbucket.org/galaxy/galaxy-central/changeset/260a77340a97/ changeset: 260a77340a97 user: dan date: 2012-10-15 22:01:18 summary: Fix tabs to spaces. affected #: 1 file diff -r 47668884fcc331e32703ff8772a2ca8003852fac -r 260a77340a97cd213374c8048ad5c9cdbaa88e6b templates/requests/common/create_request.mako --- a/templates/requests/common/create_request.mako +++ b/templates/requests/common/create_request.mako @@ -32,10 +32,10 @@ ## The request_type_select_field is a SelectField named request_type_id ${request_type_select_field.get_html()} %if cntrller != 'requests_admin': - <div class="toolParamHelp" style="clear: both;"> - Contact the lab manager if you are not sure about the request type configuration. - </div> - %endif + <div class="toolParamHelp" style="clear: both;"> + Contact the lab manager if you are not sure about the request type configuration. + </div> + %endif </div> %if request_type_select_field_selected != 'none': ## If a request_type has been selected, display the associated form using received widgets. @@ -54,7 +54,7 @@ <input type="submit" name="add_sample_button" value="Add samples"/></div> %endif - </form> - </div> + </form> + </div> %endif </div> https://bitbucket.org/galaxy/galaxy-central/changeset/738e7d290f75/ changeset: 738e7d290f75 user: dan date: 2012-10-15 22:01:19 summary: Fix tabs to spaces. affected #: 1 file diff -r 260a77340a97cd213374c8048ad5c9cdbaa88e6b -r 738e7d290f75287c3bae8374f2a69b2bbedf8d8d templates/requests/common/edit_samples.mako --- a/templates/requests/common/edit_samples.mako +++ b/templates/requests/common/edit_samples.mako @@ -18,15 +18,15 @@ <%def name="local_javascripts()"><script type="text/javascript"> - // This function stops the form from getting submitted when return key is pressed - // This is needed in this form as the barcode scanner (when in keyboard emulation mode) - // may send a return key appended to the scanned barcode string. - function stopRKey(evt) { - var evt = (evt) ? evt : ((event) ? event : null); - var node = (evt.target) ? evt.target : ((evt.srcElement) ? evt.srcElement : null); - if ((evt.keyCode == 13) && (node.type=="text")) {return false;} - } - document.onkeypress = stopRKey + // This function stops the form from getting submitted when return key is pressed + // This is needed in this form as the barcode scanner (when in keyboard emulation mode) + // may send a return key appended to the scanned barcode string. + function stopRKey(evt) { + var evt = (evt) ? evt : ((event) ? event : null); + var node = (evt.target) ? evt.target : ((evt.srcElement) ? evt.srcElement : null); + if ((evt.keyCode == 13) && (node.type=="text")) {return false;} + } + document.onkeypress = stopRKey </script></%def> @@ -100,14 +100,14 @@ %elif sample_operation_selected_value == trans.app.model.Sample.bulk_operations.SELECT_LIBRARY: <% libraries_selected_value = libraries_select_field.get_selected( return_value=True ) %><div class="form-row"> - <label>Select data library:</label> - ${libraries_select_field.get_html()} + <label>Select data library:</label> + ${libraries_select_field.get_html()} </div> %if libraries_selected_value != 'none': <div class="form-row"> - <label>Select folder:</label> - ${folders_select_field.get_html()} - </div> + <label>Select folder:</label> + ${folders_select_field.get_html()} + </div> %endif %endif </div> https://bitbucket.org/galaxy/galaxy-central/changeset/208c6a3af3c3/ changeset: 208c6a3af3c3 user: dan date: 2012-10-15 22:01:19 summary: Fix tabs to spaces. affected #: 1 file diff -r 738e7d290f75287c3bae8374f2a69b2bbedf8d8d -r 208c6a3af3c38b1a79076f88210bf688124cb48a templates/requests/common/find_samples.mako --- a/templates/requests/common/find_samples.mako +++ b/templates/requests/common/find_samples.mako @@ -59,19 +59,19 @@ </div></div> %if results: - <div class="form-row"> + <div class="form-row"><label><i>${results}</i></label> %if samples: - <div class="toolParamHelp" style="clear: both;"> - The search results are sorted by the date the samples where created. - </div> - %endif - </div> - %endif + <div class="toolParamHelp" style="clear: both;"> + The search results are sorted by the date the samples where created. + </div> + %endif + </div> + %endif <div class="form-row"> - %if samples: - %for sample in samples: - <div class="form-row"> + %if samples: + %for sample in samples: + <div class="form-row"> Sample: <b>${sample.name}</b> | Barcode: ${sample.bar_code}<br/> %if sample.request.is_new or not sample.state: State: Unsubmitted<br/> @@ -90,10 +90,10 @@ <div class="toolParamHelp" style="clear: both;"><a href="${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></div> - </div> - <br/> - %endfor - %endif + </div> + <br/> + %endfor + %endif </div></form></div> https://bitbucket.org/galaxy/galaxy-central/changeset/5fe5e8a15484/ changeset: 5fe5e8a15484 user: dan date: 2012-10-15 22:01:19 summary: Fix tabs to spaces. affected #: 1 file diff -r 208c6a3af3c38b1a79076f88210bf688124cb48a -r 5fe5e8a154844f9d9b146023b13480024825420f templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -298,10 +298,10 @@ 'name' : history.name, 'status' : status, - 'showDeleted' : show_deleted, - 'showHidden' : show_hidden, - 'quotaMsg' : over_quota, - 'message' : message, ##'go outside' + 'showDeleted' : show_deleted, + 'showHidden' : show_hidden, + 'quotaMsg' : over_quota, + 'message' : message, ##'go outside' 'deleted' : history.deleted, 'diskSize' : history.get_disk_size( nice_size=True ), @@ -336,7 +336,7 @@ 'hdas' : [ prep_hda( hda, for_editing ) for hda in datasets ], # some of these may be unneeded when all is said and done... - 'hdaId' : hda_id, + 'hdaId' : hda_id, 'forEditing' : for_editing, } %> @@ -418,43 +418,43 @@ <%def name="stylesheets()"> ${parent.stylesheets()} ${h.css("base", "history", "autocomplete_tagging" )} - <style> + <style> ## TODO: move to base.less - .historyItemBody { - display: none; - } - div.form-row { - padding: 5px 5px 5px 0px; - } - #top-links { - margin-bottom: 15px; - } - #history-name-container { - color: gray; - font-weight: bold; - } - #history-name { - word-wrap: break-word; - } - .editable-text { - border: solid transparent 1px; - padding: 3px; - margin: -4px; - } - </style> - - <noscript> - ## js disabled: degrade gracefully - <style> - .historyItemBody { - display: block; - } - </style> - </noscript> + .historyItemBody { + display: none; + } + div.form-row { + padding: 5px 5px 5px 0px; + } + #top-links { + margin-bottom: 15px; + } + #history-name-container { + color: gray; + font-weight: bold; + } + #history-name { + word-wrap: break-word; + } + .editable-text { + border: solid transparent 1px; + padding: 3px; + margin: -4px; + } + </style> + + <noscript> + ## js disabled: degrade gracefully + <style> + .historyItemBody { + display: block; + } + </style> + </noscript></%def><%def name="title()"> - ${_('Galaxy History')} + ${_('Galaxy History')} </%def><body class="historyPage"></body> https://bitbucket.org/galaxy/galaxy-central/changeset/eb786c2aeae2/ changeset: eb786c2aeae2 user: dan date: 2012-10-15 22:01:19 summary: Fix tabs to spaces. affected #: 1 file diff -r 5fe5e8a154844f9d9b146023b13480024825420f -r eb786c2aeae22b1a82d4983d4433c35adf0b4ce7 templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -44,7 +44,7 @@ search_url: "${h.url_for( controller='root', action='tool_search' )}", hidden: false }); - + // Set up tool panel. tool_panel = new tools.ToolPanel( { tool_search: tool_search } ); tool_panel.reset( tool_panel.parse( ${h.to_json_string( dictified_panel )} ) ); @@ -73,8 +73,8 @@ JSON.stringify({"search_active" : search_active})); }); */ - - $( '.tooltip' ).tooltip(); + + $( '.tooltip' ).tooltip(); // TODO: is this necessary? $( "a[minsizehint]" ).click( function() { https://bitbucket.org/galaxy/galaxy-central/changeset/ea9804d67d9c/ changeset: ea9804d67d9c user: dan date: 2012-10-15 22:01:20 summary: Fix tabs to spaces. affected #: 1 file diff -r eb786c2aeae22b1a82d4983d4433c35adf0b4ce7 -r ea9804d67d9c37129dac746ca7143a54ef60828f templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -14,12 +14,12 @@ /* -------------------------------------------- layout */ .column { - position:relative; + position:relative; overflow: auto; } .left-column { - float: left; + float: left; width: 40%; } https://bitbucket.org/galaxy/galaxy-central/changeset/4ce39ea921a2/ changeset: 4ce39ea921a2 user: dan date: 2012-10-15 22:01:20 summary: Fix tabs to spaces. affected #: 1 file diff -r ea9804d67d9c37129dac746ca7143a54ef60828f -r 4ce39ea921a24ef5e2c5a456aeb40b409805b693 templates/visualization/trackster_common.mako --- a/templates/visualization/trackster_common.mako +++ b/templates/visualization/trackster_common.mako @@ -4,14 +4,14 @@ ## Render needed CSS files. <%def name="render_trackster_css_files()"> - ${h.css( "history", "autocomplete_tagging", "trackster", "library", - "jquery-ui/smoothness/jquery-ui-1.8.23.custom" )} + ${h.css( "history", "autocomplete_tagging", "trackster", "library", + "jquery-ui/smoothness/jquery-ui-1.8.23.custom" )} </%def> ## Render needed JavaScript files. <%def name="render_trackster_js_files()"> - ${h.js( "galaxy.panels", "libs/jquery/jstorage", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel", "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/require", "libs/farbtastic" )} + ${h.js( "galaxy.panels", "libs/jquery/jstorage", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel", "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/require", "libs/farbtastic" )} </%def> ## Render a block of JavaScript that contains all necessary variables for Trackster. https://bitbucket.org/galaxy/galaxy-central/changeset/98b196af6c3e/ changeset: 98b196af6c3e user: dan date: 2012-10-15 22:01:20 summary: Fix tabs to spaces. affected #: 1 file diff -r 4ce39ea921a24ef5e2c5a456aeb40b409805b693 -r 98b196af6c3ed8c34c3dc05ba1fd9242a29f640d templates/workflow/embed.mako --- a/templates/workflow/embed.mako +++ b/templates/workflow/embed.mako @@ -1,6 +1,6 @@ <%inherit file="/embed_base.mako"/><%! - from galaxy.web.framework.helpers import iff + from galaxy.web.framework.helpers import iff %><%def name="render_summary_content( workflow, steps )"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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