/templates/root/history_common.mako
Mako | 305 lines | 274 code | 19 blank | 12 comment | 2 complexity | c962b9a0b36366e97114953ea25b38c7 MD5 | raw file
1<% _=n_ %> 2 3<%def name="render_download_links( data, dataset_id )"> 4 <% 5 from galaxy.datatypes.metadata import FileParameter 6 %> 7 %if not data.purged: 8 ## Check for downloadable metadata files 9 <% meta_files = [ k for k in data.metadata.spec.keys() if isinstance( data.metadata.spec[k].param, FileParameter ) ] %> 10 %if meta_files: 11 <div popupmenu="dataset-${dataset_id}-popup"> 12 <a class="action-button" href="${h.url_for( controller='dataset', action='display', dataset_id=dataset_id, \ 13 to_ext=data.ext )}">Download Dataset</a> 14 <a>Additional Files</a> 15 %for file_type in meta_files: 16 <a class="action-button" href="${h.url_for( controller='dataset', action='get_metadata_file', \ 17 hda_id=dataset_id, metadata_name=file_type )}">Download ${file_type}</a> 18 %endfor 19 </div> 20 <div style="float:left;" class="menubutton split popup" id="dataset-${dataset_id}-popup"> 21 %endif 22 <a href="${h.url_for( controller='dataset', action='display', dataset_id=dataset_id, to_ext=data.ext )}" title="Download" class="icon-button disk tooltip"></a> 23 %if meta_files: 24 </div> 25 %endif 26 %endif 27</%def> 28 29## Render the dataset `data` as history item, using `hid` as the displayed id 30<%def name="render_dataset( data, hid, show_deleted_on_refresh = False, for_editing = True, display_structured = False )"> 31 <% 32 dataset_id = trans.security.encode_id( data.id ) 33 34 if data.state in ['no state','',None]: 35 data_state = "queued" 36 else: 37 data_state = data.state 38 current_user_roles = trans.get_current_user_roles() 39 can_edit = not ( data.deleted or data.purged ) 40 %> 41 %if not trans.user_is_admin() and not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): 42 <div class="historyItemWrapper historyItem historyItem-${data_state} historyItem-noPermission" id="historyItem-${dataset_id}"> 43 %else: 44 <div class="historyItemWrapper historyItem historyItem-${data_state}" id="historyItem-${dataset_id}"> 45 %endif 46 47 %if data.deleted or data.purged or data.dataset.purged: 48 <div class="warningmessagesmall"><strong> 49 %if data.dataset.purged or data.purged: 50 This dataset has been deleted and removed from disk. 51 %else: 52 This dataset has been deleted. 53 %if for_editing: 54 Click <a href="${h.url_for( controller='dataset', action='undelete', dataset_id=dataset_id )}" class="historyItemUndelete" id="historyItemUndeleter-${dataset_id}" target="galaxy_history">here</a> to undelete 55 %if trans.app.config.allow_user_dataset_purge: 56 or <a href="${h.url_for( controller='dataset', action='purge', dataset_id=dataset_id )}" class="historyItemPurge" id="historyItemPurger-${dataset_id}" target="galaxy_history">here</a> to immediately remove it from disk. 57 %else: 58 it. 59 %endif 60 %endif 61 %endif 62 </strong></div> 63 %endif 64 65 %if data.visible is False: 66 <div class="warningmessagesmall"> 67 <strong>This dataset has been hidden. Click <a href="${h.url_for( controller='dataset', action='unhide', dataset_id=dataset_id )}" class="historyItemUnhide" id="historyItemUnhider-${dataset_id}" target="galaxy_history">here</a> to unhide.</strong> 68 </div> 69 %endif 70 71 ## Header row for history items (name, state, action buttons) 72 <div style="overflow: hidden;" class="historyItemTitleBar"> 73 <div class="historyItemButtons"> 74 %if data_state == "upload": 75 ## TODO: Make these CSS, just adding a "disabled" class to the normal 76 ## links should be enough. However the number of datasets being uploaded 77 ## at a time is usually small so the impact of these images is also small. 78 <span title='Display Data' class='icon-button display_disabled tooltip'></span> 79 %if for_editing: 80 <span title='Edit Attributes' class='icon-button edit_disabled tooltip'></span> 81 %endif 82 %else: 83 <% 84 if for_editing: 85 display_url = h.url_for( controller='dataset', action='display', dataset_id=dataset_id, preview=True, filename='' ) 86 else: 87 # Get URL for display only. 88 if data.history.user and data.history.user.username: 89 display_url = h.url_for( controller='dataset', action='display_by_username_and_slug', 90 username=data.history.user.username, slug=dataset_id ) 91 else: 92 # HACK: revert to for_editing display URL when there is no user/username. This should only happen when 93 # there's no user/username because dataset is being displayed by history/view after error reported. 94 # There are no security concerns here because both dataset/display and dataset/display_by_username_and_slug 95 # check user permissions (to the same degree) before displaying. 96 display_url = h.url_for( controller='dataset', action='display', dataset_id=dataset_id, preview=True, filename='' ) 97 %> 98 %if data.purged: 99 <span class="icon-button display_disabled tooltip" title="Cannoy display datasets removed from disk"></span> 100 %else: 101 <a class="icon-button display tooltip" title="Display data in browser" href="${display_url}" 102 %if for_editing: 103 target="galaxy_main" 104 %endif 105 ></a> 106 %endif 107 %if for_editing: 108 %if data.deleted and not data.purged: 109 <span title="Undelete dataset to edit attributes" class="icon-button edit_disabled tooltip"></span> 110 %elif data.purged: 111 <span title="Cannot edit attributes of datasets removed from disk" class="icon-button edit_disabled tooltip"></span> 112 %else: 113 <a class="icon-button edit tooltip" title="Edit attributes" href="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" target="galaxy_main"></a> 114 %endif 115 %endif 116 %endif 117 %if for_editing: 118 %if can_edit: 119 <a class="icon-button delete tooltip" title="Delete" href="${h.url_for( controller='dataset', action='delete', dataset_id=dataset_id, show_deleted_on_refresh=show_deleted_on_refresh )}" id="historyItemDeleter-${dataset_id}"></a> 120 %else: 121 <span title="Dataset is already deleted" class="icon-button delete_disabled tooltip"></span> 122 %endif 123 %endif 124 </div> 125 <span class="state-icon"></span> 126 <span class="historyItemTitle">${hid}: ${data.display_name()}</span> 127 </div> 128 129 ## Body for history items, extra info and actions, data "peek" 130 131 <div id="info${data.id}" class="historyItemBody"> 132 %if not trans.user_is_admin() and not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): 133 <div>You do not have permission to view this dataset.</div> 134 %elif data_state == "upload": 135 <div>Dataset is uploading</div> 136 %elif data_state == "queued": 137 <div>${_('Job is waiting to run')}</div> 138 <div> 139 <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a> 140 %if for_editing: 141 <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a> 142 %endif 143 </div> 144 %elif data_state == "running": 145 <div>${_('Job is currently running')}</div> 146 <div> 147 <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a> 148 %if for_editing: 149 <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a> 150 %endif 151 </div> 152 %elif data_state == "error": 153 <div> 154 An error occurred running this job: <i>${data.display_info().strip()}</i> 155 </div> 156 <div> 157 %if for_editing: 158 <a href="${h.url_for( controller='dataset', action='errors', id=data.id )}" target="galaxy_main" title="View or report this error" class="icon-button bug tooltip"></a> 159 %endif 160 %if data.has_data(): 161 ${render_download_links( data, dataset_id )} 162 %endif 163 <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a> 164 %if for_editing: 165 <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a> 166 %endif 167 </div> 168 %elif data_state == "discarded": 169 <div> 170 The job creating this dataset was cancelled before completion. 171 </div> 172 %elif data_state == 'setting_metadata': 173 <div>${_('Metadata is being Auto-Detected.')}</div> 174 %elif data_state == "empty": 175 <div>${_('No data: ')}<i>${data.display_info()}</i></div> 176 <div> 177 <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a> 178 %if for_editing: 179 <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a> 180 %endif 181 </div> 182 %elif data_state in [ "ok", "failed_metadata" ]: 183 %if data_state == "failed_metadata": 184 <div class="warningmessagesmall" style="margin: 4px 0 4px 0"> 185 An error occurred setting the metadata for this dataset. 186 %if can_edit: 187 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>. 188 %endif 189 </div> 190 %endif 191 <div> 192 ${data.blurb}<br /> 193 format: <span class="${data.ext}">${data.ext}</span>, 194 database: 195 %if data.dbkey == '?' and can_edit: 196 <a href="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" target="galaxy_main">${_(data.dbkey)}</a> 197 %else: 198 <span class="${data.dbkey}">${_(data.dbkey)}</span> 199 %endif 200 </div> 201 %if data.display_info(): 202 <div class="info">${_('Info: ')}${data.display_info()}</div> 203 %endif 204 <div> 205 %if data.has_data(): 206 ${render_download_links( data, dataset_id )} 207 208 <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a> 209 210 %if for_editing: 211 <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a> 212 %if app.config.get_bool( 'enable_tracks', False ) and data.ext in app.datatypes_registry.get_available_tracks(): 213 <% 214 if data.dbkey != '?': 215 data_url = h.url_for( controller='tracks', action='list_tracks', dbkey=data.dbkey ) 216 data_url = data_url.replace( 'dbkey', 'f-dbkey' ) 217 else: 218 data_url = h.url_for( controller='tracks', action='list_tracks' ) 219 %> 220 <a data-url="${data_url}" class="icon-button vis-chart tooltip trackster-add" 221 action-url="${h.url_for( controller='tracks', action='browser', dataset_id=dataset_id)}" 222 new-url="${h.url_for( controller='tracks', action='index', dataset_id=dataset_id, default_dbkey=data.dbkey)}" title="Visualize in Trackster"></a> 223 %endif 224 %if trans.user: 225 %if not display_structured: 226 <div style="float: right"> 227 <a href="${h.url_for( controller='tag', action='retag', item_class=data.__class__.__name__, item_id=dataset_id )}" target="galaxy_main" title="Edit dataset tags" class="icon-button tags tooltip"></a> 228 <a href="${h.url_for( controller='dataset', action='annotate', id=dataset_id )}" target="galaxy_main" title="Edit dataset annotation" class="icon-button annotate tooltip"></a> 229 </div> 230 %endif 231 <div style="clear: both"></div> 232 <div class="tag-area" style="display: none"> 233 <strong>Tags:</strong> 234 <div class="tag-elt"></div> 235 </div> 236 <div id="${dataset_id}-annotation-area" class="annotation-area" style="display: none"> 237 <strong>Annotation:</strong> 238 <div id="${dataset_id}-annotation-elt" style="margin: 1px 0px 1px 0px" class="annotation-elt tooltip editable-text" title="Edit dataset annotation"></div> 239 </div> 240 241 %endif 242 %else: 243 ## When displaying datasets for viewing, this is often needed to prevent peek from overlapping 244 ## icons. 245 <div style="clear: both"></div> 246 %endif 247 <div style="clear: both"></div> 248 %for display_app in data.datatype.get_display_types(): 249 <% target_frame, display_links = data.datatype.get_display_links( data, display_app, app, request.base ) %> 250 %if len( display_links ) > 0: 251 ${data.datatype.get_display_label(display_app)} 252 %for display_name, display_link in display_links: 253 <a target="${target_frame}" href="${display_link}">${_(display_name)}</a> 254 %endfor 255 <br /> 256 %endif 257 %endfor 258 %for display_app in data.get_display_applications( trans ).itervalues(): 259 ${display_app.name} 260 %for link_app in display_app.links.itervalues(): 261 <a target="${link_app.url.get( 'target_frame', '_blank' )}" href="${link_app.get_display_url( data, trans )}">${_(link_app.name)}</a> 262 %endfor 263 <br /> 264 %endfor 265 %elif for_editing: 266 <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a> 267 %endif 268 269 </div> 270 %if data.peek != "no peek": 271 <div><pre id="peek${data.id}" class="peek">${_(h.to_unicode(data.display_peek()))}</pre></div> 272 %endif 273 %else: 274 <div>${_('Error: unknown dataset state "%s".') % data_state}</div> 275 %endif 276 277 ## Recurse for child datasets 278 279 %if len( data.children ) > 0: 280 ## FIXME: This should not be in the template, there should 281 ## be a 'visible_children' method on dataset. 282 <% 283 children = [] 284 for child in data.children: 285 if child.visible: 286 children.append( child ) 287 %> 288 %if len( children ) > 0: 289 <div> 290 There are ${len( children )} secondary datasets. 291 %for idx, child in enumerate(children): 292 ${render_dataset( child, idx + 1, show_deleted_on_refresh = show_deleted_on_refresh )} 293 %endfor 294 </div> 295 %endif 296 %endif 297 298 <div style="clear: both;"></div> 299 300 </div> 301 302 303 </div> 304 305</%def>