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common.mako

リビジョン 2, 30.0 KB (コミッタ: hatakeyama, 14 年前)
import galaxy-central

行番号
1	<%def name="render_template_field( field, render_as_hidden=False )">
2	<%
3	from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, TextArea, TextField, WorkflowField
4
5	widget = field[ 'widget' ]
6	has_contents = False
7	label = field[ 'label' ]
8	value = ''
9	if isinstance( widget, TextArea ) and widget.value:
10	has_contents = True
11	if render_as_hidden:
12	value = widget.value
13	else:
14	value = '<pre>%s</pre>' % widget.value
15	elif isinstance( widget, TextField ) and widget.value:
16	has_contents = True
17	value = widget.value
18	elif isinstance( widget, SelectField ) and widget.options:
19	for option_label, option_value, selected in widget.options:
20	if selected:
21	has_contents = True
22	value = option_value
23	elif isinstance( widget, CheckboxField ) and widget.checked:
24	has_contents = True
25	if render_as_hidden:
26	value = 'true'
27	else:
28	value = 'checked'
29	elif isinstance( widget, WorkflowField ) and str( widget.value ).lower() not in [ 'none' ]:
30	has_contents = True
31	if render_as_hidden:
32	value = widget.value
33	else:
34	workflow_user = widget.user
35	if workflow_user:
36	for workflow in workflow_user.stored_workflows:
37	if not workflow.deleted and str( widget.value ) == str( workflow.id ):
38	value = workflow.name
39	break
40	else:
41	# If we didn't find the selected workflow option above, we'll just print the value
42	value = widget.value
43	elif isinstance( widget, AddressField ) and str( widget.value ).lower() not in [ 'none' ]:
44	has_contents = True
45	if render_as_hidden:
46	value = widget.value
47	else:
48	address = trans.sa_session.query( trans.model.UserAddress ).get( int( widget.value ) )
49	label = address.desc
50	value = address.get_html()
51	%>
52	%if has_contents:
53	% if render_as_hidden:
54	<input type="hidden" name="${widget.name}" value="${value}"/>
55	%else:
56	<div class="form-row">
57	<label>${label}</label>
58	${value}
59	<div class="toolParamHelp" style="clear: both;">
60	${field[ 'helptext' ]}
61	</div>
62	<div style="clear: both"></div>
63	</div>
64	%endif
65	%endif
66	</%def>
67
68	<%def name="render_template_fields( cntrller, item_type, library_id, widgets, widget_fields_have_contents, info_association, inherited, folder_id=None, ldda_id=None, editable=True )">
69	<%
70	if item_type == 'library':
71	item = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) )
72	elif item_type == 'folder':
73	item = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) )
74	elif item_type == 'ldda':
75	item = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) )
76	if trans.user_is_admin() and cntrller == 'library_admin':
77	can_modify = True
78	elif cntrller == 'library':
79	can_modify = trans.app.security_agent.can_modify_library_item( trans.get_current_user_roles(), item )
80	else:
81	can_modify = False
82	%>
83	%if editable and can_modify:
84	<p/>
85	<div class="toolForm">
86	<div class="toolFormTitle">Other information
87	<a id="item-${item.id}-popup" class="popup-arrow" style="display: none;">▼</a>
88	<div popupmenu="item-${item.id}-popup">
89	%if info_association and inherited and can_modify:
90	## "inherited" will be true only if the info_association is not associated with the current item,
91	## which means that the currently display template has not yet been saved for the current item.
92	<a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type=item_type, library_id=library_id, folder_id=folder_id, ldda_id=ldda_id, show_deleted=show_deleted )}">Select a different template</a>
93	%elif info_association and not inherited and can_modify:
94	<a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type=item_type, library_id=library_id, folder_id=folder_id, ldda_id=ldda_id, show_deleted=show_deleted )}">Edit template</a>
95	<a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type=item_type, library_id=library_id, folder_id=folder_id, ldda_id=ldda_id, show_deleted=show_deleted )}">Delete template</a>
96	%if item_type not in [ 'ldda', 'library_dataset' ]:
97	%if info_association.inheritable:
98	<a class="action-button" href="${h.url_for( controller='library_common', action='manage_template_inheritance', cntrller=cntrller, item_type=item_type, library_id=library_id, folder_id=folder_id, ldda_id=ldda_id, show_deleted=show_deleted )}">Dis-inherit template</a>
99	%else:
100	<a class="action-button" href="${h.url_for( controller='library_common', action='manage_template_inheritance', cntrller=cntrller, item_type=item_type, library_id=library_id, folder_id=folder_id, ldda_id=ldda_id, show_deleted=show_deleted )}">Inherit template</a>
101	%endif
102	%endif
103	%endif
104	</div>
105	</div>
106	<div class="toolFormBody">
107	%if inherited:
108	<div class="form-row">
109	<font color="red">
110	<b>
111	This is an inherited template and is not required to be used with this ${item_type}. You can
112	<a href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type=item_type, library_id=library_id, folder_id=folder_id, ldda_id=ldda_id, show_deleted=show_deleted )}"><font color="red">select a different template</font></a>
113	or fill in the desired fields and save this one. This template will not be assocaiated with this ${item_type} until you click the Save button.
114	</b>
115	</font>
116	</div>
117	%endif
118	<form name="edit_info" id="edit_info" action="${h.url_for( controller='library_common', action='edit_template_info', cntrller=cntrller, item_type=item_type, library_id=library_id, folder_id=folder_id, ldda_id=ldda_id, show_deleted=show_deleted )}" method="post">
119	%for i, field in enumerate( widgets ):
120	<div class="form-row">
121	<label>${field[ 'label' ]}</label>
122	${field[ 'widget' ].get_html()}
123	<div class="toolParamHelp" style="clear: both;">
124	${field[ 'helptext' ]}
125	</div>
126	<div style="clear: both"></div>
127	</div>
128	%endfor
129	<div class="form-row">
130	<input type="submit" name="edit_info_button" value="Save"/>
131	</div>
132	</form>
133	</div>
134	</div>
135	<p/>
136	%elif widget_fields_have_contents:
137	<p/>
138	<div class="toolForm">
139	<div class="toolFormTitle">Other information about ${item.name}</div>
140	<div class="toolFormBody">
141	%for i, field in enumerate( widgets ):
142	${render_template_field( field )}
143	%endfor
144	</div>
145	</div>
146	<p/>
147	%endif
148	</%def>
149
150	<%def name="render_upload_form( cntrller, upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, space_to_tab, link_data_only, widgets, roles_select_list, history, show_deleted )">
151	<%
152	import os, os.path
153	from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, TextArea, TextField, WorkflowField
154	%>
155	%if upload_option in [ 'upload_file', 'upload_directory', 'upload_paths' ]:
156	<div class="toolForm" id="upload_library_dataset_tool_form">
157	<%
158	if upload_option == 'upload_directory':
159	tool_form_title = 'Upload a directory of files'
160	elif upload_option == 'upload_paths':
161	tool_form_title = 'Upload files from filesystem paths'
162	else:
163	tool_form_title = 'Upload files'
164	%>
165	<div class="toolFormTitle">${tool_form_title}</div>
166	<div class="toolFormBody">
167	<form name="upload_library_dataset" id="upload_library_dataset" action="${action}" enctype="multipart/form-data" method="post">
168	<input type="hidden" name="tool_id" value="upload1"/>
169	<input type="hidden" name="tool_state" value="None"/>
170	<input type="hidden" name="cntrller" value="${cntrller}"/>
171	<input type="hidden" name="library_id" value="${library_id}"/>
172	<input type="hidden" name="folder_id" value="${folder_id}"/>
173	<input type="hidden" name="show_deleted" value="${show_deleted}"/>
174	%if replace_dataset not in [ None, 'None' ]:
175	<input type="hidden" name="replace_id" value="${trans.security.encode_id( replace_dataset.id )}"/>
176	<div class="form-row">
177	You are currently selecting a new file to replace '<a href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=library_id, folder_id=folder_id, id=trans.security.encode_id( replace_dataset.library_dataset_dataset_association.id ) )}">${replace_dataset.name}</a>'.
178	<div style="clear: both"></div>
179	</div>
180	%endif
181	%if replace_dataset in [ None, 'None' ]:
182	## Don't allow multiple datasets to be uploaded when replacing a dataset with a new version
183	<div class="form-row">
184	<label>Upload option:</label>
185	<div class="form-row-input">
186	${upload_option_select_list.get_html()}
187	</div>
188	<div class="toolParamHelp" style="clear: both;">
189	Choose upload option (file, directory, filesystem paths, current history).
190	</div>
191	<div style="clear: both"></div>
192	</div>
193	%else:
194	<input type="hidden" name="upload_option" value="upload_file"/>
195	%endif
196	<div class="form-row">
197	<label>File Format:</label>
198	<div class="form-row-input">
199	<select name="file_type">
200	<option value="auto" selected>Auto-detect</option>
201	%for file_format in file_formats:
202	<option value="${file_format}">${file_format}</option>
203	%endfor
204	</select>
205	</div>
206	<div style="clear: both"></div>
207	</div>
208	%if upload_option == 'upload_file':
209	<div class="form-row">
210	<input type="hidden" name="async_datasets" value="None"/>
211	<div style="clear: both"></div>
212	</div>
213	<div class="form-row">
214	<label>File:</label>
215	<div class="form-row-input">
216	<input type="file" name="files_0\|file_data" galaxy-ajax-upload="true"/>
217	</div>
218	<div style="clear: both"></div>
219	</div>
220	<div class="form-row">
221	<label>URL/Text:</label>
222	<div class="form-row-input">
223	<textarea name="files_0\|url_paste" rows="5" cols="35"></textarea>
224	</div>
225	<div class="toolParamHelp" style="clear: both;">
226	Specify a list of URLs (one per line) or paste the contents of a file.
227	</div>
228	<div style="clear: both"></div>
229	</div>
230	%elif upload_option == 'upload_directory':
231	<%
232	if ( trans.user_is_admin() and cntrller == 'library_admin' ):
233	import_dir = trans.app.config.library_import_dir
234	else:
235	# Directories of files from the Data Libraries view are restricted to a
236	# sub-directory named the same as the current user's email address
237	# contained within the configured setting for user_library_import_dir
238	import_dir = os.path.join( trans.app.config.user_library_import_dir, trans.user.email )
239	%>
240	<div class="form-row">
241	<%
242	# See if we have any contained sub-directories, if not the only option
243	# in the server_dir select list will be library_import_dir
244	contains_directories = False
245	for entry in os.listdir( import_dir ):
246	if os.path.isdir( os.path.join( import_dir, entry ) ):
247	contains_directories = True
248	break
249	%>
250	<label>Server Directory</label>
251	<div class="form-row-input">
252	<select name="server_dir">
253	%if contains_directories:
254	<option>None</option>
255	%for entry in os.listdir( import_dir ):
256	## Do not include entries that are not directories
257	%if os.path.isdir( os.path.join( import_dir, entry ) ):
258	<option>${entry}</option>
259	%endif
260	%endfor
261	%else:
262	%if ( trans.user_is_admin() and cntrller == 'library_admin' ):
263	<option>${import_dir}</option>
264	%else:
265	<option>${trans.user.email}</option>
266	%endif
267	%endif
268	</select>
269	</div>
270	<div class="toolParamHelp" style="clear: both;">
271	%if contains_directories:
272	Upload all files in a sub-directory of <strong>${import_dir}</strong> on the Galaxy server.
273	%else:
274	Upload all files in <strong>${import_dir}</strong> on the Galaxy server.
275	%endif
276	</div>
277	<div style="clear: both"></div>
278	</div>
279	%elif upload_option == 'upload_paths':
280	<div class="form-row">
281	<label>Paths to upload</label>
282	<div class="form-row-input">
283	<textarea name="filesystem_paths" rows="10" cols="35"></textarea>
284	</div>
285	<div class="toolParamHelp" style="clear: both;">
286	Upload all files pasted in the box. The (recursive) contents of any pasted directories will be added as well.
287	</div>
288	</div>
289	<div class="form-row">
290	<label>Preserve directory structure?</label>
291	<div class="form-row-input">
292	<input type="checkbox" name="dont_preserve_dirs" value="No"/>No
293	</div>
294	<div class="toolParamHelp" style="clear: both;">
295	If checked, all files in subdirectories on the filesystem will be placed at the top level of the folder, instead of into subfolders.
296	</div>
297	</div>
298	%endif
299	%if upload_option in ( 'upload_directory', 'upload_paths' ):
300	<div class="form-row">
301	<%
302	if link_data_only == 'No':
303	checked = ' checked'
304	else:
305	checked = ''
306	link_data_only_field = '<input type="checkbox" name="link_data_only" value="No"%s/>No' % checked
307	%>
308	<label>Copy data into Galaxy?</label>
309	<div class="form-row-input">
310	${link_data_only_field}
311	</div>
312	<div class="toolParamHelp" style="clear: both;">
313	Normally data uploaded with this tool is copied into Galaxy's "files" directory
314	so any later changes to the data will not affect Galaxy. However, this may not
315	be desired (especially for large NGS datasets), so use of this option will
316	force Galaxy to always read the data from its original path.
317	%if upload_option == 'upload_directory':
318	Any symlinks encountered in the upload directory will be dereferenced once -
319	that is, Galaxy will point directly to the file that is linked, but no other
320	symlinks further down the line will be dereferenced.
321	%endif
322	</div>
323	</div>
324	%endif
325	<div class="form-row">
326	<label>
327	Convert spaces to tabs:
328	</label>
329	<div class="form-row-input">
330	<%
331	if space_to_tab == 'true':
332	checked = ' checked'
333	else:
334	checked = ''
335	if upload_option == 'upload_file':
336	name = 'files_0\|space_to_tab'
337	else:
338	name = 'space_to_tab'
339	space2tab = '<input type="checkbox" name="%s" value="true"%s/>Yes' % ( name, checked )
340	%>
341	${space2tab}
342	</div>
343	<div class="toolParamHelp" style="clear: both;">
344	Use this option if you are entering intervals by hand.
345	</div>
346	</div>
347	<div style="clear: both"></div>
348	<div class="form-row">
349	<label>Genome:</label>
350	<div class="form-row-input">
351	<select name="dbkey" last_selected_value="?">
352	%for dbkey in dbkeys:
353	%if dbkey[1] == last_used_build:
354	<option value="${dbkey[1]}" selected>${dbkey[0]}</option>
355	%else:
356	<option value="${dbkey[1]}">${dbkey[0]}</option>
357	%endif
358	%endfor
359	</select>
360	</div>
361	<div style="clear: both"></div>
362	</div>
363	<div class="form-row">
364	<label>Message:</label>
365	<div class="form-row-input">
366	%if ldda_message:
367	<textarea name="ldda_message" rows="3" cols="35">${ldda_message}</textarea>
368	%else:
369	<textarea name="ldda_message" rows="3" cols="35"></textarea>
370	%endif
371	</div>
372	<div class="toolParamHelp" style="clear: both;">
373	This information will be displayed in the "Information" column for this dataset in the data library browser
374	</div>
375	<div style="clear: both"></div>
376	</div>
377	%if roles_select_list:
378	<div class="form-row">
379	<label>Restrict dataset access to specific roles:</label>
380	<div class="form-row-input">
381	${roles_select_list.get_html()}
382	</div>
383	<div class="toolParamHelp" style="clear: both;">
384	Multi-select list - hold the appropriate key while clicking to select multiple roles. More restrictions can be applied after the upload is complete. Selecting no roles makes a dataset public.
385	</div>
386	</div>
387	<div style="clear: both"></div>
388	%endif
389	%if widgets:
390	%for i, field in enumerate( widgets ):
391	<div class="form-row">
392	<label>${field[ 'label' ]}</label>
393	<div class="form-row-input">
394	${field[ 'widget' ].get_html()}
395	</div>
396	<div class="toolParamHelp" style="clear: both;">
397	%if field[ 'helptext' ]:
398	${field[ 'helptext' ]}<br/>
399	%endif
400	*Inherited template field
401	</div>
402	<div style="clear: both"></div>
403	</div>
404	%endfor
405	%endif
406	<div class="form-row">
407	<input type="submit" class="primary-button" name="runtool_btn" value="Upload to library"/>
408	</div>
409	</form>
410	</div>
411	</div>
412	## Script to replace dbkey select with select+search.
413	<script type="text/javascript">
414	// Replace dbkey select with search+select.
415	jQuery(document).ready( function() {
416	replace_big_select_inputs();
417	});
418	</script>
419	%elif upload_option == 'import_from_history':
420	<div class="toolForm">
421	<div class="toolFormTitle">Active datasets in your current history (${history.name})</div>
422	<div class="toolFormBody">
423	%if history and history.active_datasets:
424	<form name="add_history_datasets_to_library" action="${h.url_for( controller='library_common', action='add_history_datasets_to_library', cntrller=cntrller, library_id=library_id )}" enctype="multipart/form-data" method="post">
425	<input type="hidden" name="folder_id" value="${folder_id}"/>
426	<input type="hidden" name="show_deleted" value="${show_deleted}"/>
427	<input type="hidden" name="upload_option" value="import_from_history"/>
428	<input type="hidden" name="ldda_message" value="${ldda_message}"/>
429	<%
430	if roles_select_list:
431	role_ids_selected = roles_select_list.get_selected( return_value=True, multi=True )
432	if role_ids_selected:
433	role_ids_selected = ','.join( role_ids_selected )
434	else:
435	role_ids_selected = ''
436	else:
437	role_ids_selected = ''
438	%>
439	<input type="hidden" name="roles" value="${role_ids_selected}"/>
440	%if replace_dataset not in [ None, 'None' ]:
441	<input type="hidden" name="replace_id" value="${trans.security.encode_id( replace_dataset.id )}"/>
442	<div class="form-row">
443	You are currently selecting a new file to replace '<a href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=library_id, folder_id=folder_id, id=trans.security.encode_id( replace_dataset.library_dataset_dataset_association.id ) )}">${replace_dataset.name}</a>'.
444	<div style="clear: both"></div>
445	</div>
446	%endif
447	## Render hidden template fields so the contents will be associated with the dataset
448	%if widgets:
449	%for i, field in enumerate( widgets ):
450	${render_template_field( field, render_as_hidden=True )}
451	%endfor
452	%endif
453	%for hda in history.active_datasets:
454	<div class="form-row">
455	<input name="hda_ids" value="${trans.security.encode_id( hda.id )}" type="checkbox"/>${hda.hid}: ${hda.name}
456	</div>
457	%endfor
458	<div class="form-row">
459	<input type="submit" name="add_history_datasets_to_library_button" value="Import to library"/>
460	</div>
461	</form>
462	%else:
463	<p/>
464	Your current history is empty
465	<p/>
466	%endif
467	</div>
468	</div>
469	%endif
470	</%def>
471
472	<%def name="render_actions_on_multiple_items()">
473	<tfoot>
474	<tr>
475	<td colspan="5" style="padding-left: 42px;">
476	For selected items:
477	<select name="do_action" id="action_on_selected_items">
478	%if ( trans.user_is_admin() and cntrller=='library_admin' ):
479	<option value="manage_permissions">Edit permissions</option>
480	<option value="delete">Delete</option>
481	%elif cntrller=='library':
482	%if default_action == 'add':
483	<option value="add" selected>Import into your current history</option>
484	%else:
485	<option value="add">Import into your current history</option>
486	%endif
487	%if default_action == 'manage_permissions':
488	<option value="manage_permissions" selected>Edit permissions</option>
489	# This condition should not contain an else clause because the user is not authorized
490	# to manage dataset permissions unless the default action is 'manage_permissions'
491	%endif
492	%if 'gz' in comptypes:
493	<option value="tgz"
494	%if default_action == 'download':
495	selected
496	%endif>
497	>Download as a .tar.gz file</option>
498	%endif
499	%if 'bz2' in comptypes:
500	<option value="tbz">Download as a .tar.bz2 file</option>
501	%endif
502	%if 'zip' in comptypes:
503	<option value="zip">Download as a .zip file</option>
504	%endif
505	%if 'ngxzip' in comptypes:
506	## We can safely have two default selected items since ngxzip, if present, will always be the only available type.
507	<option value="ngxzip"
508	%if default_action == 'download':
509	selected
510	%endif>
511	>Download as a .zip file</option>
512	%endif
513	%endif
514	</select>
515	<input type="submit" class="primary-button" name="action_on_datasets_button" id="action_on_datasets_button" value="Go"/>
516	</td>
517	</tr>
518	</tfoot>
519	</%def>

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