mirror of
https://github.com/galaxyproject/galaxy.git
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History: remove unused server templates history_common, history_item, and history_annotation_table; Pages: remove unused dialog for annotated histories
This commit is contained in:
Carl Eberhard
@@ -696,16 +696,6 @@ class PageController( BaseUIController, SharableMixin, UsesHistoryMixin,
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# Render the list view
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return self._datasets_selection_grid( trans, **kwargs )
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@web.expose
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@web.require_login("get annotation table for history")
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def get_history_annotation_table( self, trans, id ):
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""" Returns HTML for an annotation table for a history. """
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history = self.get_history( trans, id, False, True )
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if history:
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datasets = self.get_history_datasets( trans, history )
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return trans.fill_template( "page/history_annotation_table.mako", history=history, datasets=datasets, show_deleted=False )
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@web.expose
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def get_editor_iframe( self, trans ):
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""" Returns the document for the page editor's iframe. """
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@@ -20,10 +20,7 @@ var Galaxy =
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DIALOG_EMBED_DATASET : "embed_dataset",
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DIALOG_EMBED_WORKFLOW : "embed_workflow",
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DIALOG_EMBED_PAGE : "embed_page",
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DIALOG_EMBED_VISUALIZATION : "embed_visualization",
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// Annotation dialogs.
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DIALOG_HISTORY_ANNOTATE : "history_annotate",
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DIALOG_EMBED_VISUALIZATION : "embed_visualization"
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};
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// Initialize Galaxy elements.
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@@ -464,25 +461,8 @@ WYMeditor.editor.prototype.dialog = function( dialogType, dialogFeatures, bodyHt
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"</div>" ].join( '' );
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// Insert embedded item into document.
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//wym.insert(" "); // Needed to prevent insertion from occurring in child element in webkit browsers.
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wym.insert(item_embed_html);
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// TODO: can we fix this?
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// Due to oddities of wym.insert() [likely due to inserting a <div> and/or a complete paragraph], an
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// empty paragraph (or two!) may be included either before an embedded item. Remove these paragraphs.
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//$("#" + item_elt_id, wym._doc.body).each( function() {
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// // Remove previous empty paragraphs.
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// var removing = true;
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// while (removing)
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// {
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// var prev_elt = $(this).prev();
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// if ( prev_elt.length != 0 && jQuery.trim(prev_elt.text()) == "" )
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// prev_elt.remove();
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// else
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// removing = false;
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// }
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//});
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});
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hide_modal();
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},
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@@ -495,55 +475,6 @@ WYMeditor.editor.prototype.dialog = function( dialogType, dialogFeatures, bodyHt
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}
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});
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}
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// ANNOTATE HISTORY DIALOG
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if ( dialogType == Galaxy.DIALOG_ANNOTATE_HISTORY ) {
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$.ajax(
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{
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url: list_histories_for_selection_url,
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data: {},
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error: function() { alert( "Grid refresh failed" ) },
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success: function(table_html)
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{
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show_modal(
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"Insert Link to History",
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table_html,
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{
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"Annotate": function()
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{
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// Insert links to history for each checked item.
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var item_ids = new Array();
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$('input[name=id]:checked').each(function() {
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var item_id = $(this).val();
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// Get annotation table for history.
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$.ajax(
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{
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url: get_history_annotation_table_url,
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data: { id : item_id },
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error: function() { alert( "Grid refresh failed" ) },
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success: function(result)
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{
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// Insert into document.
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wym.insert(result);
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init_galaxy_elts(wym);
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}
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});
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});
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hide_modal();
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},
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"Cancel": function()
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{
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hide_modal();
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}
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}
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);
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}
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});
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}
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};
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$(function(){
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@@ -19,7 +19,6 @@
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set_accessible_url = "${h.url_for( controller='ITEM_CONTROLLER', action='set_accessible_async' )}",
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get_name_and_link_url = "${h.url_for( controller='ITEM_CONTROLLER', action='get_name_and_link_async' )}?id=",
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list_histories_for_selection_url = "${h.url_for(controller='page', action='list_histories_for_selection' )}",
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get_history_annotation_table_url = "${h.url_for(controller='page', action='get_history_annotation_table' )}",
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editor_base_path = "${h.url_for('/static/wymeditor')}/",
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iframe_base_path = "${h.url_for('/static/wymeditor/iframe/galaxy')}/",
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save_url = "${h.url_for(controller='page', action='save' )}";
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@@ -1,61 +0,0 @@
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<%namespace file="../tagging_common.mako" import="render_tagging_element_html" />
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<%namespace file="../root/history_common.mako" import="render_dataset" />
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<div class="annotated_item">
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<table>
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## Table header.
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<tr>
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<th colspan='2'>History '${history.get_display_name()}'</th>
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</tr>
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<tr>
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## Status messages and tags.
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<td colspan='2'>
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%if history.deleted:
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<div class="warningmessagesmall">
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${_('This is a deleted history.')}
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</div>
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%endif
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## Tags come for free with community tagging, so not sure if this is necessary.
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##%if trans.get_user() is not None:
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## Tags: ${render_tagging_element_html( tags=history.tags, editable=False, use_toggle_link=False )}
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##%endif
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</td>
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</tr>
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<tr>
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<td colspan="2" class="annotation" item_class="History" item_id="${trans.security.encode_id( history.id )}">Description of History:
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<ol>
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<li>What was the motivation for this history?
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<li>What is the outcome of this history?
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<li>What are unresolved questions from this history?
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<li>What new questions arise from this history?
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</ol>
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</td>
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</tr>
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## Table body. For each dataset, there is an area to annotate the dataset.
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%if not datasets:
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<tr>
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<td>
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<div class="infomessagesmall" id="emptyHistoryMessage">
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${_("Your history is empty. Click 'Get Data' on the left pane to start")}
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</div>
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</td>
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</tr>
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%else:
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## Render requested datasets.
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%for data in datasets:
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%if data.visible:
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<tr>
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<td valign="top" class="annotation" item_class="HistoryDatasetAssociation" item_id="${trans.security.encode_id( data.id )}">Describe this step: why was it done? what data did it produce?</td>
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##<td valign="top" class="annotation">Describe this step: why was it done? what data does it produce?</td>
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<td>
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<div class="historyItemContainer" id="historyItemContainer-${data.id}">
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${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing = False )}
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</div>
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</td>
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</tr>
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%endif
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%endfor
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%endif
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</table>
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</div>
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@@ -1,337 +0,0 @@
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<% _=n_ %>
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<%def name="render_download_links( data, dataset_id )">
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<%
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from galaxy.datatypes.metadata import FileParameter
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%>
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%if not data.purged:
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## Check for downloadable metadata files
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<% meta_files = [ k for k in data.metadata.spec.keys() if isinstance( data.metadata.spec[k].param, FileParameter ) ] %>
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%if meta_files:
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<div popupmenu="dataset-${dataset_id}-popup">
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<a class="action-button" href="${h.url_for( controller='dataset', action='display', dataset_id=dataset_id, \
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to_ext=data.ext )}">Download Dataset</a>
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<a>Additional Files</a>
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%for file_type in meta_files:
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<a class="action-button" href="${h.url_for( controller='/dataset', action='get_metadata_file', \
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hda_id=dataset_id, metadata_name=file_type )}">Download ${file_type}</a>
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%endfor
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</div>
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<div style="float:left;" class="menubutton split popup" id="dataset-${dataset_id}-popup">
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%endif
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<a href="${h.url_for( controller='/dataset', action='display', dataset_id=dataset_id, to_ext=data.ext )}" title='${_("Download")}' class="icon-button disk"></a>
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%if meta_files:
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</div>
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%endif
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%endif
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</%def>
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## Render the dataset `data` as history item, using `hid` as the displayed id
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<%def name="render_dataset( data, hid, show_deleted_on_refresh = False, for_editing = True, display_structured = False )">
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<%
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dataset_id = trans.security.encode_id( data.id )
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if data.state in ['no state','',None]:
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data_state = "queued"
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else:
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data_state = data.state
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current_user_roles = trans.get_current_user_roles()
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can_edit = not ( data.deleted or data.purged )
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%>
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%if not trans.user_is_admin() and not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ):
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<div class="historyItemWrapper historyItem historyItem-${data_state} historyItem-noPermission" id="historyItem-${dataset_id}">
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%else:
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<div class="historyItemWrapper historyItem historyItem-${data_state}" id="historyItem-${dataset_id}">
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%endif
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%if data.deleted or data.purged or data.dataset.purged:
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<div class="warningmessagesmall"><strong>
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%if data.dataset.purged or data.purged:
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This dataset has been deleted and removed from disk.
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%else:
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This dataset has been deleted.
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%if for_editing:
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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
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%if trans.app.config.allow_user_dataset_purge:
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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.
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%else:
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it.
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%endif
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%endif
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%endif
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</strong></div>
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%endif
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%if data.visible is False:
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<div class="warningmessagesmall">
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<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>
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</div>
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%endif
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## Header row for history items (name, state, action buttons)
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<div style="overflow: hidden;" class="historyItemTitleBar">
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<div class="historyItemButtons">
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%if data_state == "upload":
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## TODO: Make these CSS, just adding a "disabled" class to the normal
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## links should be enough. However the number of datasets being uploaded
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## at a time is usually small so the impact of these images is also small.
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<span title='${_("Display Data")}' class='icon-button display_disabled'></span>
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%if for_editing:
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<span title='Edit Attributes' class='icon-button edit_disabled'></span>
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%endif
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%else:
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<%
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if for_editing:
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display_url = h.url_for( controller='dataset', action='display', dataset_id=dataset_id, preview=True, filename='' )
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else:
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# Get URL for display only.
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if data.history.user and data.history.user.username:
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display_url = h.url_for( controller='dataset', action='display_by_username_and_slug',
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username=data.history.user.username, slug=dataset_id, filename='' )
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else:
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# HACK: revert to for_editing display URL when there is no user/username. This should only happen when
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# there's no user/username because dataset is being displayed by history/view after error reported.
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# There are no security concerns here because both dataset/display and dataset/display_by_username_and_slug
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# check user permissions (to the same degree) before displaying.
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display_url = h.url_for( controller='dataset', action='display', dataset_id=dataset_id, preview=True, filename='' )
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%>
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%if data.purged:
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<span class="icon-button display_disabled" title="Cannot display datasets removed from disk"></span>
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%else:
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<a class="icon-button display" dataset_id="${dataset_id}" title='${_("View data")}' href="${display_url}"
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%if for_editing:
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target="galaxy_main"
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%endif
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></a>
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%endif
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## edit attr button
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%if for_editing:
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%if data.deleted and not data.purged:
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<span title="Undelete dataset to edit attributes" class="icon-button edit_disabled"></span>
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%elif data.purged:
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<span title="Cannot edit attributes of datasets removed from disk" class="icon-button edit_disabled"></span>
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%else:
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<a class="icon-button edit" title='${_("Edit attributes")}' href="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" target="galaxy_main"></a>
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%endif
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%endif
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%endif
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## delete button
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%if for_editing:
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%if can_edit:
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<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-${dataset_id}"></a>
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%else:
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<span title="Dataset is already deleted" class="icon-button delete_disabled"></span>
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%endif
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%endif
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</div>
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## Hack, do it in css
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%if data_state == "paused":
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<span class="fa fa-pause"></span>
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%else:
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<span class="state-icon"></span>
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%endif
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<span class="historyItemTitle">${hid}: ${data.display_name()}</span>
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</div>
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## Body for history items, extra info and actions, data "peek"
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<div id="info${data.id}" class="historyItemBody">
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%if not trans.user_is_admin() and not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ):
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<div>You do not have permission to view this dataset.</div>
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%elif data_state == "upload":
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<div>Dataset is uploading</div>
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%elif data_state == "queued":
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<div>${_('Job is waiting to run')}</div>
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<div>
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<a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information"></a>
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%if for_editing:
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<a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle"></a>
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%endif
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</div>
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%elif data_state == "paused":
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<div>
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${_('Job is currently paused:')} <i>${data.display_info().strip().rstrip('.')}.</i> ${_('Use the history menu to resume.')}</div>
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<div>
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<a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information"></a>
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%if for_editing:
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<a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle"></a>
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%endif
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</div>
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%elif data_state == "running":
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<div>${_('Job is currently running')}</div>
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<div>
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<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>
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%if for_editing:
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<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>
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%endif
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</div>
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%elif data_state == "error":
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%if not data.purged:
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<div>${data.get_size( nice_size=True )}</div>
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%endif
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<div>
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An error occurred running this job: <i>${data.display_info().strip()}</i>
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</div>
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<div>
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%if for_editing:
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<a href="${h.url_for( controller='dataset', action='errors', id=data.id )}" target="galaxy_main" title="View or report this error" class="icon-button bug"></a>
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%endif
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%if data.has_data():
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${render_download_links( data, dataset_id )}
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%endif
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<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>
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%if for_editing:
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<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>
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%endif
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</div>
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%elif data_state == "discarded":
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<div>
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The job creating this dataset was cancelled before completion.
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</div>
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<div>
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<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>
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%if for_editing:
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<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>
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%endif
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</div>
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%elif data_state == 'setting_metadata':
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<div>${_('Metadata is being Auto-Detected.')}</div>
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%elif data_state == "empty":
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<div>${_('No data: ')}<i>${data.display_info()}</i></div>
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<div>
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<a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information"></a>
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%if for_editing:
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<a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle"></a>
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%endif
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</div>
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%elif data_state in [ "ok", "failed_metadata" ]:
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%if data_state == "failed_metadata":
|
||||
<div class="warningmessagesmall" style="margin: 4px 0 4px 0">
|
||||
An error occurred setting the metadata for this dataset.
|
||||
%if can_edit:
|
||||
You may be able to <a href="${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>
|
||||
@@ -1,3 +0,0 @@
|
||||
<%namespace file="history_common.mako" import="render_dataset" />
|
||||
|
||||
${render_dataset( data, hid )}
|
||||
Reference in New Issue
Block a user