def delete_repository_metadata(self, trans, **kwd): params = util.Params(kwd) message = util.restore_text(params.get('message', '')) status = params.get('status', 'done') id = kwd.get('id', None) if id: ids = util.listify(id) count = 0 for repository_metadata_id in ids: repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id) trans.sa_session.delete(repository_metadata) trans.sa_session.flush() count += 1 if count: message = "Deleted %d repository metadata %s" % ( count, inflector.cond_plural(len(ids), "record")) else: message = "No repository metadata ids received for deleting." status = 'error' trans.response.send_redirect( web.url_for(controller='admin', action='browse_repository_metadata', message=util.sanitize_text(message), status=status))
def browse_repository_metadata( self, trans, **kwd ): if 'operation' in kwd: operation = kwd[ 'operation' ].lower() if operation == "delete": return self.delete_repository_metadata( trans, **kwd ) if operation == "view_or_manage_repository_revision": # The received id is a RepositoryMetadata object id, so we need to get the # associated Repository and redirect to view_or_manage_repository with the # changeset_revision. repository_metadata = suc.get_repository_metadata_by_id( trans, kwd[ 'id' ] ) repository = repository_metadata.repository kwd[ 'id' ] = trans.security.encode_id( repository.id ) kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision kwd[ 'operation' ] = 'view_or_manage_repository' return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', **kwd ) ) return self.repository_metadata_grid( trans, **kwd )
def browse_repository_metadata(self, trans, **kwd): if 'operation' in kwd: operation = kwd['operation'].lower() if operation == "delete": return self.delete_repository_metadata(trans, **kwd) if operation == "view_or_manage_repository_revision": # The received id is a RepositoryMetadata object id, so we need to get the # associated Repository and redirect to view_or_manage_repository with the # changeset_revision. repository_metadata = suc.get_repository_metadata_by_id( trans, kwd['id']) repository = repository_metadata.repository kwd['id'] = trans.security.encode_id(repository.id) kwd['changeset_revision'] = repository_metadata.changeset_revision kwd['operation'] = 'view_or_manage_repository' return trans.response.send_redirect( web.url_for(controller='repository', action='browse_repositories', **kwd)) return self.repository_metadata_grid(trans, **kwd)
def delete_repository_metadata( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) id = kwd.get( 'id', None ) if id: ids = util.listify( id ) count = 0 for repository_metadata_id in ids: repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) trans.sa_session.delete( repository_metadata ) trans.sa_session.flush() count += 1 if count: message = "Deleted %d repository metadata %s" % ( count, inflector.cond_plural( len( ids ), "record" ) ) else: message = "No repository metadata ids received for deleting." status = 'error' trans.response.send_redirect( web.url_for( controller='admin', action='browse_repository_metadata', message=util.sanitize_text( message ), status=status ) )
def generate_workflow_image( trans, workflow_name, repository_metadata_id=None, repository_id=None ): """ Return an svg image representation of a workflow dictionary created when the workflow was exported. This method is called from both Galaxy and the tool shed. When called from the tool shed, repository_metadata_id will have a value and repository_id will be None. When called from Galaxy, repository_metadata_id will be None and repository_id will have a value. """ workflow_name = encoding_util.tool_shed_decode( workflow_name ) if trans.webapp.name == 'community': # We're in the tool shed. repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) repository_id = trans.security.encode_id( repository_metadata.repository_id ) changeset_revision = repository_metadata.changeset_revision metadata = repository_metadata.metadata else: # We're in Galaxy. repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) changeset_revision = repository.changeset_revision metadata = repository.metadata # metadata[ 'workflows' ] is a list of tuples where each contained tuple is # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] for workflow_tup in metadata[ 'workflows' ]: workflow_dict = workflow_tup[1] if workflow_dict[ 'name' ] == workflow_name: break if 'tools' in metadata: tools_metadata = metadata[ 'tools' ] else: tools_metadata = [] workflow, missing_tool_tups = get_workflow_from_dict( trans=trans, workflow_dict=workflow_dict, tools_metadata=tools_metadata, repository_id=repository_id, changeset_revision=changeset_revision ) data = [] canvas = svgfig.canvas( style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left" ) text = svgfig.SVG( "g" ) connectors = svgfig.SVG( "g" ) boxes = svgfig.SVG( "g" ) svgfig.Text.defaults[ "font-size" ] = "10px" in_pos = {} out_pos = {} margin = 5 # Spacing between input/outputs. line_px = 16 # Store px width for boxes of each step. widths = {} max_width, max_x, max_y = 0, 0, 0 for step in workflow.steps: step.upgrade_messages = {} module = module_factory.from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step ) tool_errors = module.type == 'tool' and not module.tool module_data_inputs = get_workflow_data_inputs( step, module ) module_data_outputs = get_workflow_data_outputs( step, module, workflow.steps ) step_dict = { 'id' : step.order_index, 'data_inputs' : module_data_inputs, 'data_outputs' : module_data_outputs, 'position' : step.position, 'tool_errors' : tool_errors } input_conn_dict = {} for conn in step.input_connections: input_conn_dict[ conn.input_name ] = dict( id=conn.output_step.order_index, output_name=conn.output_name ) step_dict[ 'input_connections' ] = input_conn_dict data.append( step_dict ) x, y = step.position[ 'left' ], step.position[ 'top' ] count = 0 module_name = get_workflow_module_name( module, missing_tool_tups ) max_len = len( module_name ) * 1.5 text.append( svgfig.Text( x, y + 20, module_name, **{ "font-size": "14px" } ).SVG() ) y += 45 for di in module_data_inputs: cur_y = y + count * line_px if step.order_index not in in_pos: in_pos[ step.order_index ] = {} in_pos[ step.order_index ][ di[ 'name' ] ] = ( x, cur_y ) text.append( svgfig.Text( x, cur_y, di[ 'label' ] ).SVG() ) count += 1 max_len = max( max_len, len( di[ 'label' ] ) ) if len( module.get_data_inputs() ) > 0: y += 15 for do in module_data_outputs: cur_y = y + count * line_px if step.order_index not in out_pos: out_pos[ step.order_index ] = {} out_pos[ step.order_index ][ do[ 'name' ] ] = ( x, cur_y ) text.append( svgfig.Text( x, cur_y, do[ 'name' ] ).SVG() ) count += 1 max_len = max( max_len, len( do['name' ] ) ) widths[ step.order_index ] = max_len * 5.5 max_x = max( max_x, step.position[ 'left' ] ) max_y = max( max_y, step.position[ 'top' ] ) max_width = max( max_width, widths[ step.order_index ] ) for step_dict in data: tool_unavailable = step_dict[ 'tool_errors' ] width = widths[ step_dict[ 'id' ] ] x, y = step_dict[ 'position' ][ 'left' ], step_dict[ 'position' ][ 'top' ] # Only highlight missing tools if displaying in the tool shed. if trans.webapp.name == 'community' and tool_unavailable: fill = "#EBBCB2" else: fill = "#EBD9B2" boxes.append( svgfig.Rect( x - margin, y, x + width - margin, y + 30, fill=fill ).SVG() ) box_height = ( len( step_dict[ 'data_inputs' ] ) + len( step_dict[ 'data_outputs' ] ) ) * line_px + margin # Draw separator line. if len( step_dict[ 'data_inputs' ] ) > 0: box_height += 15 sep_y = y + len( step_dict[ 'data_inputs' ] ) * line_px + 40 text.append( svgfig.Line( x - margin, sep_y, x + width - margin, sep_y ).SVG() ) # Define an input/output box. boxes.append( svgfig.Rect( x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff" ).SVG() ) for conn, output_dict in step_dict[ 'input_connections' ].iteritems(): in_coords = in_pos[ step_dict[ 'id' ] ][ conn ] # out_pos_index will be a step number like 1, 2, 3... out_pos_index = output_dict[ 'id' ] # out_pos_name will be a string like 'o', 'o2', etc. out_pos_name = output_dict[ 'output_name' ] if out_pos_index in out_pos: # out_conn_index_dict will be something like: # 7: {'o': (824.5, 618)} out_conn_index_dict = out_pos[ out_pos_index ] if out_pos_name in out_conn_index_dict: out_conn_pos = out_pos[ out_pos_index ][ out_pos_name ] else: # Take any key / value pair available in out_conn_index_dict. # A problem will result if the dictionary is empty. if out_conn_index_dict.keys(): key = out_conn_index_dict.keys()[0] out_conn_pos = out_pos[ out_pos_index ][ key ] adjusted = ( out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ], out_conn_pos[ 1 ] ) text.append( svgfig.SVG( "circle", cx=out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ] - margin, cy=out_conn_pos[ 1 ] - margin, r = 5, fill="#ffffff" ) ) connectors.append( svgfig.Line( adjusted[ 0 ], adjusted[ 1 ] - margin, in_coords[ 0 ] - 10, in_coords[ 1 ], arrow_end = "true" ).SVG() ) canvas.append( connectors ) canvas.append( boxes ) canvas.append( text ) width, height = ( max_x + max_width + 50 ), max_y + 300 canvas[ 'width' ] = "%s px" % width canvas[ 'height' ] = "%s px" % height canvas[ 'viewBox' ] = "0 0 %s %s" % ( width, height ) trans.response.set_content_type( "image/svg+xml" ) return canvas.standalone_xml()
def generate_workflow_image(trans, workflow_name, repository_metadata_id=None, repository_id=None): """ Return an svg image representation of a workflow dictionary created when the workflow was exported. This method is called from both Galaxy and the tool shed. When called from the tool shed, repository_metadata_id will have a value and repository_id will be None. When called from Galaxy, repository_metadata_id will be None and repository_id will have a value. """ workflow_name = encoding_util.tool_shed_decode(workflow_name) if trans.webapp.name == "community": # We're in the tool shed. repository_metadata = suc.get_repository_metadata_by_id(trans, repository_metadata_id) repository_id = trans.security.encode_id(repository_metadata.repository_id) changeset_revision = repository_metadata.changeset_revision metadata = repository_metadata.metadata else: # We're in Galaxy. repository = suc.get_tool_shed_repository_by_id(trans, repository_id) changeset_revision = repository.changeset_revision metadata = repository.metadata # metadata[ 'workflows' ] is a list of tuples where each contained tuple is # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] for workflow_tup in metadata["workflows"]: workflow_dict = workflow_tup[1] if workflow_dict["name"] == workflow_name: break if "tools" in metadata: tools_metadata = metadata["tools"] else: tools_metadata = [] workflow, missing_tool_tups = get_workflow_from_dict( trans=trans, workflow_dict=workflow_dict, tools_metadata=tools_metadata, repository_id=repository_id, changeset_revision=changeset_revision, ) data = [] canvas = svgfig.canvas(style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left") text = svgfig.SVG("g") connectors = svgfig.SVG("g") boxes = svgfig.SVG("g") svgfig.Text.defaults["font-size"] = "10px" in_pos = {} out_pos = {} margin = 5 # Spacing between input/outputs. line_px = 16 # Store px width for boxes of each step. widths = {} max_width, max_x, max_y = 0, 0, 0 for step in workflow.steps: step.upgrade_messages = {} module = module_factory.from_workflow_step(trans, repository_id, changeset_revision, tools_metadata, step) tool_errors = module.type == "tool" and not module.tool module_data_inputs = get_workflow_data_inputs(step, module) module_data_outputs = get_workflow_data_outputs(step, module, workflow.steps) step_dict = { "id": step.order_index, "data_inputs": module_data_inputs, "data_outputs": module_data_outputs, "position": step.position, "tool_errors": tool_errors, } input_conn_dict = {} for conn in step.input_connections: input_conn_dict[conn.input_name] = dict(id=conn.output_step.order_index, output_name=conn.output_name) step_dict["input_connections"] = input_conn_dict data.append(step_dict) x, y = step.position["left"], step.position["top"] count = 0 module_name = get_workflow_module_name(module, missing_tool_tups) max_len = len(module_name) * 1.5 text.append(svgfig.Text(x, y + 20, module_name, **{"font-size": "14px"}).SVG()) y += 45 for di in module_data_inputs: cur_y = y + count * line_px if step.order_index not in in_pos: in_pos[step.order_index] = {} in_pos[step.order_index][di["name"]] = (x, cur_y) text.append(svgfig.Text(x, cur_y, di["label"]).SVG()) count += 1 max_len = max(max_len, len(di["label"])) if len(module.get_data_inputs()) > 0: y += 15 for do in module_data_outputs: cur_y = y + count * line_px if step.order_index not in out_pos: out_pos[step.order_index] = {} out_pos[step.order_index][do["name"]] = (x, cur_y) text.append(svgfig.Text(x, cur_y, do["name"]).SVG()) count += 1 max_len = max(max_len, len(do["name"])) widths[step.order_index] = max_len * 5.5 max_x = max(max_x, step.position["left"]) max_y = max(max_y, step.position["top"]) max_width = max(max_width, widths[step.order_index]) for step_dict in data: tool_unavailable = step_dict["tool_errors"] width = widths[step_dict["id"]] x, y = step_dict["position"]["left"], step_dict["position"]["top"] # Only highlight missing tools if displaying in the tool shed. if trans.webapp.name == "community" and tool_unavailable: fill = "#EBBCB2" else: fill = "#EBD9B2" boxes.append(svgfig.Rect(x - margin, y, x + width - margin, y + 30, fill=fill).SVG()) box_height = (len(step_dict["data_inputs"]) + len(step_dict["data_outputs"])) * line_px + margin # Draw separator line. if len(step_dict["data_inputs"]) > 0: box_height += 15 sep_y = y + len(step_dict["data_inputs"]) * line_px + 40 text.append(svgfig.Line(x - margin, sep_y, x + width - margin, sep_y).SVG()) # Define an input/output box. boxes.append(svgfig.Rect(x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff").SVG()) for conn, output_dict in step_dict["input_connections"].iteritems(): in_coords = in_pos[step_dict["id"]][conn] # out_pos_index will be a step number like 1, 2, 3... out_pos_index = output_dict["id"] # out_pos_name will be a string like 'o', 'o2', etc. out_pos_name = output_dict["output_name"] if out_pos_index in out_pos: # out_conn_index_dict will be something like: # 7: {'o': (824.5, 618)} out_conn_index_dict = out_pos[out_pos_index] if out_pos_name in out_conn_index_dict: out_conn_pos = out_pos[out_pos_index][out_pos_name] else: # Take any key / value pair available in out_conn_index_dict. # A problem will result if the dictionary is empty. if out_conn_index_dict.keys(): key = out_conn_index_dict.keys()[0] out_conn_pos = out_pos[out_pos_index][key] adjusted = (out_conn_pos[0] + widths[output_dict["id"]], out_conn_pos[1]) text.append( svgfig.SVG( "circle", cx=out_conn_pos[0] + widths[output_dict["id"]] - margin, cy=out_conn_pos[1] - margin, r=5, fill="#ffffff", ) ) connectors.append( svgfig.Line(adjusted[0], adjusted[1] - margin, in_coords[0] - 10, in_coords[1], arrow_end="true").SVG() ) canvas.append(connectors) canvas.append(boxes) canvas.append(text) width, height = (max_x + max_width + 50), max_y + 300 canvas["width"] = "%s px" % width canvas["height"] = "%s px" % height canvas["viewBox"] = "0 0 %s %s" % (width, height) trans.response.set_content_type("image/svg+xml") return canvas.standalone_xml()