1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5f89fecb2f07/ Changeset: 5f89fecb2f07 User: carlfeberhard Date: 2014-05-01 15:17:19 Summary: History: remove unused server templates history_common, history_item, and history_annotation_table; Pages: remove unused dialog for annotated histories Affected #: 6 files diff -r 8ba0bd46e9fbd54fd6c525a276dd483daa9a79ba -r 5f89fecb2f0703ce237cc185b2ccbb2bc0fd2658 lib/galaxy/webapps/galaxy/controllers/page.py --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -697,16 +697,6 @@ return self._datasets_selection_grid( trans, **kwargs ) @web.expose - @web.require_login("get annotation table for history") - def get_history_annotation_table( self, trans, id ): - """ Returns HTML for an annotation table for a history. """ - history = self.get_history( trans, id, False, True ) - - if history: - datasets = self.get_history_datasets( trans, history ) - return trans.fill_template( "page/history_annotation_table.mako", history=history, datasets=datasets, show_deleted=False ) - - @web.expose def get_editor_iframe( self, trans ): """ Returns the document for the page editor's iframe. """ return trans.fill_template( "page/wymiframe.mako" ) diff -r 8ba0bd46e9fbd54fd6c525a276dd483daa9a79ba -r 5f89fecb2f0703ce237cc185b2ccbb2bc0fd2658 static/scripts/galaxy.pages.js --- a/static/scripts/galaxy.pages.js +++ b/static/scripts/galaxy.pages.js @@ -20,10 +20,7 @@ DIALOG_EMBED_DATASET : "embed_dataset", DIALOG_EMBED_WORKFLOW : "embed_workflow", DIALOG_EMBED_PAGE : "embed_page", - DIALOG_EMBED_VISUALIZATION : "embed_visualization", - - // Annotation dialogs. - DIALOG_HISTORY_ANNOTATE : "history_annotate", + DIALOG_EMBED_VISUALIZATION : "embed_visualization" }; // Initialize Galaxy elements. @@ -464,25 +461,8 @@ "</div>" ].join( '' ); // Insert embedded item into document. - //wym.insert(" "); // Needed to prevent insertion from occurring in child element in webkit browsers. wym.insert(item_embed_html); - // TODO: can we fix this? - // Due to oddities of wym.insert() [likely due to inserting a <div> and/or a complete paragraph], an - // empty paragraph (or two!) may be included either before an embedded item. Remove these paragraphs. - //$("#" + item_elt_id, wym._doc.body).each( function() { - // // Remove previous empty paragraphs. - // var removing = true; - // while (removing) - // { - // var prev_elt = $(this).prev(); - // if ( prev_elt.length != 0 && jQuery.trim(prev_elt.text()) == "" ) - // prev_elt.remove(); - // else - // removing = false; - // } - //}); - }); hide_modal(); }, @@ -495,55 +475,6 @@ } }); } - - // ANNOTATE HISTORY DIALOG - if ( dialogType == Galaxy.DIALOG_ANNOTATE_HISTORY ) { - $.ajax( - { - url: list_histories_for_selection_url, - data: {}, - error: function() { alert( "Grid refresh failed" ) }, - success: function(table_html) - { - show_modal( - "Insert Link to History", - table_html, - { - "Annotate": function() - { - // Insert links to history for each checked item. - var item_ids = new Array(); - $('input[name=id]:checked').each(function() { - var item_id = $(this).val(); - - // Get annotation table for history. - $.ajax( - { - url: get_history_annotation_table_url, - data: { id : item_id }, - error: function() { alert( "Grid refresh failed" ) }, - success: function(result) - { - // Insert into document. - wym.insert(result); - - init_galaxy_elts(wym); - - } - }); - }); - - hide_modal(); - }, - "Cancel": function() - { - hide_modal(); - } - } - ); - } - }); - } }; $(function(){ diff -r 8ba0bd46e9fbd54fd6c525a276dd483daa9a79ba -r 5f89fecb2f0703ce237cc185b2ccbb2bc0fd2658 templates/webapps/galaxy/page/editor.mako --- a/templates/webapps/galaxy/page/editor.mako +++ b/templates/webapps/galaxy/page/editor.mako @@ -19,7 +19,6 @@ set_accessible_url = "${h.url_for( controller='ITEM_CONTROLLER', action='set_accessible_async' )}", get_name_and_link_url = "${h.url_for( controller='ITEM_CONTROLLER', action='get_name_and_link_async' )}?id=", list_histories_for_selection_url = "${h.url_for(controller='page', action='list_histories_for_selection' )}", - get_history_annotation_table_url = "${h.url_for(controller='page', action='get_history_annotation_table' )}", editor_base_path = "${h.url_for('/static/wymeditor')}/", iframe_base_path = "${h.url_for('/static/wymeditor/iframe/galaxy')}/", save_url = "${h.url_for(controller='page', action='save' )}"; diff -r 8ba0bd46e9fbd54fd6c525a276dd483daa9a79ba -r 5f89fecb2f0703ce237cc185b2ccbb2bc0fd2658 templates/webapps/galaxy/page/history_annotation_table.mako --- a/templates/webapps/galaxy/page/history_annotation_table.mako +++ /dev/null @@ -1,61 +0,0 @@ -<%namespace file="../tagging_common.mako" import="render_tagging_element_html" /> -<%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 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}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing = False )} - </div> - </td> - </tr> - %endif - %endfor - %endif - </table> -</div> \ No newline at end of file diff -r 8ba0bd46e9fbd54fd6c525a276dd483daa9a79ba -r 5f89fecb2f0703ce237cc185b2ccbb2bc0fd2658 templates/webapps/galaxy/root/history_common.mako --- a/templates/webapps/galaxy/root/history_common.mako +++ /dev/null @@ -1,337 +0,0 @@ -<% _=n_ %> - -<%def name="render_download_links( data, dataset_id )"> - <% - from galaxy.datatypes.metadata import FileParameter - %> - %if not data.purged: - ## Check for downloadable metadata files - <% meta_files = [ k for k in data.metadata.spec.keys() if isinstance( data.metadata.spec[k].param, FileParameter ) ] %> - %if meta_files: - <div popupmenu="dataset-${dataset_id}-popup"> - <a class="action-button" href="${h.url_for( controller='dataset', action='display', dataset_id=dataset_id, \ - to_ext=data.ext )}">Download Dataset</a> - <a>Additional Files</a> - %for file_type in meta_files: - <a class="action-button" href="${h.url_for( controller='/dataset', action='get_metadata_file', \ - hda_id=dataset_id, metadata_name=file_type )}">Download ${file_type}</a> - %endfor - </div> - <div style="float:left;" class="menubutton split popup" id="dataset-${dataset_id}-popup"> - %endif - <a href="${h.url_for( controller='/dataset', action='display', dataset_id=dataset_id, to_ext=data.ext )}" title='${_("Download")}' class="icon-button disk"></a> - %if meta_files: - </div> - %endif - %endif -</%def> - -## Render the dataset `data` as history item, using `hid` as the displayed id -<%def name="render_dataset( data, hid, show_deleted_on_refresh = False, for_editing = True, display_structured = False )"> - <% - dataset_id = trans.security.encode_id( data.id ) - - if data.state in ['no state','',None]: - data_state = "queued" - else: - data_state = data.state - current_user_roles = trans.get_current_user_roles() - can_edit = not ( data.deleted or data.purged ) - %> - %if not trans.user_is_admin() and not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): - <div class="historyItemWrapper historyItem historyItem-${data_state} historyItem-noPermission" id="historyItem-${dataset_id}"> - %else: - <div class="historyItemWrapper historyItem historyItem-${data_state}" id="historyItem-${dataset_id}"> - %endif - - %if data.deleted or data.purged or data.dataset.purged: - <div class="warningmessagesmall"><strong> - %if data.dataset.purged or data.purged: - This dataset has been deleted and removed from disk. - %else: - This dataset has been deleted. - %if for_editing: - Click <a href="${h.url_for( controller='dataset', action='undelete', dataset_id=dataset_id )}" class="historyItemUndelete" id="historyItemUndeleter-${dataset_id}" target="galaxy_history">here</a> to undelete - %if trans.app.config.allow_user_dataset_purge: - or <a href="${h.url_for( controller='dataset', action='purge', dataset_id=dataset_id )}" class="historyItemPurge" id="historyItemPurger-${dataset_id}" target="galaxy_history">here</a> to immediately remove it from disk. - %else: - it. - %endif - %endif - %endif - </strong></div> - %endif - - %if data.visible is False: - <div class="warningmessagesmall"> - <strong>This dataset has been hidden. Click <a href="${h.url_for( controller='dataset', action='unhide', dataset_id=dataset_id )}" class="historyItemUnhide" id="historyItemUnhider-${dataset_id}" target="galaxy_history">here</a> to unhide.</strong> - </div> - %endif - - ## Header row for history items (name, state, action buttons) - <div style="overflow: hidden;" class="historyItemTitleBar"> - <div class="historyItemButtons"> - %if data_state == "upload": - ## TODO: Make these CSS, just adding a "disabled" class to the normal - ## links should be enough. However the number of datasets being uploaded - ## at a time is usually small so the impact of these images is also small. - <span title='${_("Display Data")}' class='icon-button display_disabled'></span> - %if for_editing: - <span title='Edit Attributes' class='icon-button edit_disabled'></span> - %endif - %else: - <% - if for_editing: - display_url = h.url_for( controller='dataset', action='display', dataset_id=dataset_id, preview=True, filename='' ) - else: - # Get URL for display only. - if data.history.user and data.history.user.username: - display_url = h.url_for( controller='dataset', action='display_by_username_and_slug', - username=data.history.user.username, slug=dataset_id, filename='' ) - else: - # HACK: revert to for_editing display URL when there is no user/username. This should only happen when - # there's no user/username because dataset is being displayed by history/view after error reported. - # There are no security concerns here because both dataset/display and dataset/display_by_username_and_slug - # check user permissions (to the same degree) before displaying. - display_url = h.url_for( controller='dataset', action='display', dataset_id=dataset_id, preview=True, filename='' ) - %> - %if data.purged: - <span class="icon-button display_disabled" title="Cannot display datasets removed from disk"></span> - %else: - <a class="icon-button display" dataset_id="${dataset_id}" title='${_("View data")}' href="${display_url}" - %if for_editing: - target="galaxy_main" - %endif - ></a> - %endif - - ## edit attr button - %if for_editing: - %if data.deleted and not data.purged: - <span title="Undelete dataset to edit attributes" class="icon-button edit_disabled"></span> - %elif data.purged: - <span title="Cannot edit attributes of datasets removed from disk" class="icon-button edit_disabled"></span> - %else: - <a class="icon-button edit" title='${_("Edit attributes")}' href="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" target="galaxy_main"></a> - %endif - %endif - - %endif - - ## delete button - %if for_editing: - %if can_edit: - <a class="icon-button delete" title='${_("Delete")}' href="${h.url_for( controller='dataset', action='delete', dataset_id=dataset_id, show_deleted_on_refresh=show_deleted_on_refresh )}" id="historyItemDeleter-${dataset_id}"></a> - %else: - <span title="Dataset is already deleted" class="icon-button delete_disabled"></span> - %endif - %endif - </div> - ## Hack, do it in css - %if data_state == "paused": - <span class="fa fa-pause"></span> - %else: - <span class="state-icon"></span> - %endif - <span class="historyItemTitle">${hid}: ${data.display_name()}</span> - </div> - - ## Body for history items, extra info and actions, data "peek" - - <div id="info${data.id}" class="historyItemBody"> - %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 == "upload": - <div>Dataset is uploading</div> - %elif data_state == "queued": - <div>${_('Job is waiting to run')}</div> - <div> - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information"></a> - %if for_editing: - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle"></a> - %endif - </div> - %elif data_state == "paused": - <div> - ${_('Job is currently paused:')} <i>${data.display_info().strip().rstrip('.')}.</i> ${_('Use the history menu to resume.')}</div> - <div> - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information"></a> - %if for_editing: - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle"></a> - %endif - </div> - %elif data_state == "running": - <div>${_('Job is currently running')}</div> - <div> - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information"></a> - %if for_editing: - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle"></a> - %endif - </div> - %elif data_state == "error": - %if not data.purged: - <div>${data.get_size( nice_size=True )}</div> - %endif - <div> - An error occurred running this job: <i>${data.display_info().strip()}</i> - </div> - <div> - %if for_editing: - <a href="${h.url_for( controller='dataset', action='errors', id=data.id )}" target="galaxy_main" title="View or report this error" class="icon-button bug"></a> - %endif - %if data.has_data(): - ${render_download_links( data, dataset_id )} - %endif - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information"></a> - %if for_editing: - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle"></a> - %endif - </div> - %elif data_state == "discarded": - <div> - The job creating this dataset was cancelled before completion. - </div> - <div> - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information"></a> - %if for_editing: - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle"></a> - %endif - </div> - %elif data_state == 'setting_metadata': - <div>${_('Metadata is being Auto-Detected.')}</div> - %elif data_state == "empty": - <div>${_('No data: ')}<i>${data.display_info()}</i></div> - <div> - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information"></a> - %if for_editing: - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle"></a> - %endif - </div> - %elif data_state in [ "ok", "failed_metadata" ]: - %if data_state == "failed_metadata": - <div class="warningmessagesmall" style="margin: 4px 0 4px 0"> - An error occurred setting the metadata for this dataset. - %if can_edit: - You may be able to <a href="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" target="galaxy_main">set it manually or retry auto-detection</a>. - %endif - </div> - %endif - <div> - ${data.blurb}<br /> - ${_("format: ")} <span class="${data.ext}">${data.ext}</span>, - ${_("database: ")} - %if data.dbkey == '?' and can_edit: - <a href="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" target="galaxy_main">${_(data.dbkey)}</a> - %else: - <span class="${data.dbkey}">${_(data.dbkey)}</span> - %endif - </div> - %if data.display_info(): - <div class="info">${_('Info: ')}${data.display_info()}</div> - %endif - <div> - %if data.has_data(): - ${render_download_links( data, dataset_id )} - - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information"></a> - - %if for_editing: - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle"></a> - ## Visualization icon + visualizations. Using anchor attributes is a HACK to encode needed - ## information--URL base, dataset id, dbkey, visualizations--in anchor. - <% - visualizations = data.get_visualizations() - %> - %if visualizations: - <a href="${h.url_for( controller='visualization' )}" - class="icon-button chart_curve visualize-icon" - title="Visualize" - dataset_id="${dataset_id}" - %if data.dbkey != '?': - dbkey="${data.dbkey}" - %endif - visualizations="${','.join(visualizations)}"></a> - %endif - %if trans.user: - %if not display_structured: - <div style="float: right"> - <a href="${h.url_for( controller='tag', action='retag', item_class=data.__class__.__name__, item_id=dataset_id )}" target="galaxy_main" title="Edit dataset tags" class="icon-button tags"></a> - <a href="${h.url_for( controller='dataset', action='annotate', id=dataset_id )}" target="galaxy_main" title="Edit dataset annotation" class="icon-button annotate"></a> - </div> - %endif - <div style="clear: both"></div> - <div class="tag-area" style="display: none"> - <strong>Tags:</strong> - <div class="tag-elt"></div> - </div> - <div id="${dataset_id}-annotation-area" class="annotation-area" style="display: none"> - <strong>Annotation:</strong> - <div id="${dataset_id}-annotation-elt" style="margin: 1px 0px 1px 0px" class="annotation-elt editable-text" title="Edit dataset annotation"></div> - </div> - - %endif - %else: - ## When displaying datasets for viewing, this is often needed to prevent peek from overlapping - ## icons. - <div style="clear: both"></div> - %endif - <div style="clear: both"></div> - %for display_app in data.datatype.get_display_types(): - <% target_frame, display_links = data.datatype.get_display_links( data, display_app, app, request.base ) %> - %if len( display_links ) > 0: - ${data.datatype.get_display_label(display_app)} - %for display_name, display_link in display_links: - <a target="${target_frame}" href="${display_link}">${_(display_name)}</a> - %endfor - <br /> - %endif - %endfor - %for display_app in data.get_display_applications( trans ).itervalues(): - ${display_app.name} - %for link_app in display_app.links.itervalues(): - <a target="${link_app.url.get( 'target_frame', '_blank' )}" href="${link_app.get_display_url( data, trans )}">${_(link_app.name)}</a> - %endfor - <br /> - %endfor - %elif for_editing: - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information"></a> - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle"></a> - %endif - - </div> - %if data.peek != "no peek": - <div><pre id="peek${data.id}" class="peek">${_(h.to_unicode(data.display_peek()))}</pre></div> - %endif - %else: - <div>${_('Error: unknown dataset state "%s".') % data_state}</div> - %endif - - ## Recurse for child datasets - - %if len( data.children ) > 0: - ## FIXME: This should not be in the template, there should - ## be a 'visible_children' method on dataset. - <% - children = [] - for child in data.children: - if child.visible: - children.append( child ) - %> - %if len( children ) > 0: - <div> - There are ${len( children )} secondary datasets. - %for idx, child in enumerate(children): - ${render_dataset( child, idx + 1, show_deleted_on_refresh = show_deleted_on_refresh )} - %endfor - </div> - %endif - %endif - - <div style="clear: both;"></div> - - </div> - - - </div> - -</%def> diff -r 8ba0bd46e9fbd54fd6c525a276dd483daa9a79ba -r 5f89fecb2f0703ce237cc185b2ccbb2bc0fd2658 templates/webapps/galaxy/root/history_item.mako --- a/templates/webapps/galaxy/root/history_item.mako +++ /dev/null @@ -1,3 +0,0 @@ -<%namespace file="history_common.mako" import="render_dataset" /> - -${render_dataset( data, hid )} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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