def editor(self, trans, id=None, workflow_id=None, version=None):
"""
Render the main workflow editor interface. The canvas is embedded as
an iframe (necessary for scrolling to work properly), which is
rendered by `editor_canvas`.
"""
if not id:
if workflow_id:
workflow = trans.sa_session.query(model.Workflow).get(trans.security.decode_id(workflow_id))
stored_workflow = workflow.stored_workflow
self.security_check(trans, stored_workflow, True, False)
stored_workflow_id = trans.security.encode_id(stored_workflow.id)
return trans.response.send_redirect(f'{url_for("/")}workflow/editor?id={stored_workflow_id}')
error("Invalid workflow id")
stored = self.get_stored_workflow(trans, id)
# The following query loads all user-owned workflows,
# So that they can be copied or inserted in the workflow editor.
workflows = trans.sa_session.query(model.StoredWorkflow) \
.filter_by(user=trans.user, deleted=False, hidden=False) \
.order_by(desc(model.StoredWorkflow.table.c.update_time)) \
.options(joinedload('latest_workflow').joinedload('steps')) \
.all()
if version is None:
version = len(stored.workflows) - 1
else:
version = int(version)
# create workflow module models
module_sections = []
for module_section in load_module_sections(trans).values():
module_sections.append({
"title": module_section.get("title"),
"name": module_section.get("name"),
"elems": [{
"name": elem.get("name"),
"title": elem.get("title"),
"description": elem.get("description")
} for elem in module_section.get("modules")]
})
# create data manager tool models
data_managers = []
if trans.user_is_admin and trans.app.data_managers.data_managers:
for data_manager_val in trans.app.data_managers.data_managers.values():
tool = data_manager_val.tool
if not tool.hidden:
data_managers.append({
"id": tool.id,
"name": tool.name,
"hidden": tool.hidden,
"description": tool.description,
"is_workflow_compatible": tool.is_workflow_compatible
})
# create workflow models
workflows = [{
'id': trans.security.encode_id(workflow.id),
'latest_id': trans.security.encode_id(workflow.latest_workflow.id),
'step_count': len(workflow.latest_workflow.steps),
'name': workflow.name
} for workflow in workflows if workflow.id != stored.id]
# identify item tags
item_tags = [tag for tag in stored.tags if tag.user == trans.user]
item_tag_names = []
for ta in item_tags:
item_tag_names.append(escape(ta.tag.name))
# build workflow editor model
editor_config = {
'id': trans.security.encode_id(stored.id),
'name': stored.name,
'tags': item_tag_names,
'initialVersion': version,
'annotation': self.get_item_annotation_str(trans.sa_session, trans.user, stored),
'toolbox': trans.app.toolbox.to_dict(trans),
'moduleSections': module_sections,
'dataManagers': data_managers,
'workflows': workflows
}
# parse to mako
return trans.fill_template("workflow/editor.mako", editor_config=editor_config)
def render_left_panel(context):
context.caller_stack._push_frame()
try:
_import_ns = {}
_mako_get_namespace(context, '__anon_0x11ade8d50')._populate(_import_ns, [u'render_individual_tagging_element'])
trans = _import_ns.get('trans', context.get('trans', UNDEFINED))
h = _import_ns.get('h', context.get('h', UNDEFINED))
app = _import_ns.get('app', context.get('app', UNDEFINED))
def render_label(label):
return render_render_label(context,label)
n_ = _import_ns.get('n_', context.get('n_', UNDEFINED))
isinstance = _import_ns.get('isinstance', context.get('isinstance', UNDEFINED))
def render_tool(tool,section):
return render_render_tool(context,tool,section)
__M_writer = context.writer()
# SOURCE LINE 262
__M_writer(u'\n ')
# SOURCE LINE 263
from galaxy.tools import Tool
from galaxy.tools.toolbox import ToolSection, ToolSectionLabel
# SOURCE LINE 266
__M_writer(u'\n\n <div class="unified-panel-header" unselectable="on">\n <div class=\'unified-panel-header-inner\'>\n ')
# SOURCE LINE 270
__M_writer(unicode(n_('Tools')))
__M_writer(u'\n </div>\n </div>\n\n <div class="unified-panel-body" style="overflow: auto;">\n <div class="toolMenu">\n <div id="tool-search" style="padding-bottom: 5px; position: relative; display: block; width: 100%">\n <input type="text" name="query" placeholder="search tools" id="tool-search-query" class="search-query parent-width" />\n <img src="')
# SOURCE LINE 278
__M_writer(unicode(h.url_for('/static/images/loading_small_white_bg.gif')))
__M_writer(u'" id="search-spinner" class="search-spinner" />\n </div>\n <div class="toolSectionList">\n')
# SOURCE LINE 281
for val in app.toolbox.tool_panel_contents( trans ):
# SOURCE LINE 282
__M_writer(u' <div class="toolSectionWrapper">\n')
# SOURCE LINE 283
if isinstance( val, Tool ):
# SOURCE LINE 284
__M_writer(u' ')
__M_writer(unicode(render_tool( val, False )))
__M_writer(u'\n')
# SOURCE LINE 285
elif isinstance( val, ToolSection ) and val.elems:
# SOURCE LINE 286
__M_writer(u' ')
section = val
__M_writer(u'\n <div class="toolSectionTitle" id="title_')
# SOURCE LINE 287
__M_writer(unicode(section.id))
__M_writer(u'">\n <span>')
# SOURCE LINE 288
__M_writer(unicode(section.name))
__M_writer(u'</span>\n </div>\n <div id="')
# SOURCE LINE 290
__M_writer(unicode(section.id))
__M_writer(u'" class="toolSectionBody">\n <div class="toolSectionBg">\n')
# SOURCE LINE 292
for section_key, section_val in section.elems.items():
# SOURCE LINE 293
if isinstance( section_val, Tool ):
# SOURCE LINE 294
__M_writer(u' ')
__M_writer(unicode(render_tool( section_val, True )))
__M_writer(u'\n')
# SOURCE LINE 295
elif isinstance( section_val, ToolSectionLabel ):
# SOURCE LINE 296
__M_writer(u' ')
__M_writer(unicode(render_label( section_val )))
__M_writer(u'\n')
pass
pass
# SOURCE LINE 299
__M_writer(u' </div>\n </div>\n')
# SOURCE LINE 301
elif isinstance( val, ToolSectionLabel ):
# SOURCE LINE 302
__M_writer(u' ')
__M_writer(unicode(render_label( val )))
__M_writer(u'\n')
pass
# SOURCE LINE 304
__M_writer(u' </div>\n')
pass
# SOURCE LINE 307
if trans.user_is_admin() and trans.app.data_managers.data_managers:
# SOURCE LINE 308
__M_writer(u' <div> </div>\n <div class="toolSectionWrapper">\n <div class="toolSectionTitle" id="title___DATA_MANAGER_TOOLS__">\n <span>Data Manager Tools</span>\n </div>\n <div id="__DATA_MANAGER_TOOLS__" class="toolSectionBody">\n <div class="toolSectionBg">\n')
# SOURCE LINE 315
for data_manager_id, data_manager_val in trans.app.data_managers.data_managers.items():
# SOURCE LINE 316
__M_writer(u' ')
__M_writer(unicode( render_tool( data_manager_val.tool, True ) ))
__M_writer(u'\n')
pass
# SOURCE LINE 318
__M_writer(u' </div>\n </div>\n </div>\n')
pass
# SOURCE LINE 323
__M_writer(u' </div>\n')
# SOURCE LINE 325
__M_writer(u' <div id="search-no-results" style="display: none; padding-top: 5px">\n <em><strong>Search did not match any tools.</strong></em>\n </div>\n <div> </div>\n\n <div class="toolMenuGroupHeader">Workflow control</div>\n ')
# SOURCE LINE 331
from galaxy.workflow.modules import load_module_sections
# SOURCE LINE 333
__M_writer(u'\n')
# SOURCE LINE 334
for module_section in load_module_sections( trans ):
# SOURCE LINE 335
__M_writer(u' ')
section_title = module_section["title"]
__M_writer(u'\n ')
# SOURCE LINE 336
section_name = module_section["name"]
__M_writer(u'\n <div class="toolSectionTitle" id="title___workflow__')
# SOURCE LINE 337
__M_writer(unicode(section_name))
__M_writer(u'__">\n <span>')
# SOURCE LINE 338
__M_writer(unicode(section_title))
__M_writer(u'</span>\n </div>\n <div id="__workflow__')
# SOURCE LINE 340
__M_writer(unicode(section_name))
__M_writer(u'__" class="toolSectionBody">\n <div class="toolSectionBg">\n')
# SOURCE LINE 342
for module in module_section["modules"]:
# SOURCE LINE 343
__M_writer(u' <div class="toolTitle">\n <a href="#" onclick="workflow_view.add_node_for_module( \'')
# SOURCE LINE 344
__M_writer(unicode(module['name']))
__M_writer(u"', '")
__M_writer(unicode(module['title']))
__M_writer(u'\' )">')
__M_writer(unicode(module['description']))
__M_writer(u'</a>\n </div><!-- end toolTitle -->\n')
pass
# SOURCE LINE 347
__M_writer(u' </div>\n </div>\n')
pass
# SOURCE LINE 350
__M_writer(u' </div>\n </div>\n\n')
return ''
finally:
context.caller_stack._pop_frame()