def check_for_tool_dependencies( self, trans, migration_stage ): # Get the 000x_tools.xml file associated with migration_stage. tools_xml_file_path = os.path.abspath( os.path.join( trans.app.config.root, 'scripts', 'migrate_tools', '%04d_tools.xml' % migration_stage ) ) tree = util.parse_xml( tools_xml_file_path ) root = tree.getroot() tool_shed = root.get( 'name' ) tool_shed_url = self.get_tool_shed_url_from_tools_xml_file_path( trans, tool_shed ) repo_name_dependency_tups = [] if tool_shed_url: for elem in root: if elem.tag == 'repository': tool_dependencies = [] tool_dependencies_dict = {} repository_name = elem.get( 'name' ) changeset_revision = elem.get( 'changeset_revision' ) url = '%s/repository/get_tool_dependencies?name=%s&owner=devteam&changeset_revision=%s&from_install_manager=True' % \ ( tool_shed_url, repository_name, changeset_revision ) response = urllib2.urlopen( url ) text = response.read() response.close() if text: tool_dependencies_dict = encoding_util.tool_shed_decode( text ) for dependency_key, requirements_dict in tool_dependencies_dict.items(): tool_dependency_name = requirements_dict[ 'name' ] tool_dependency_version = requirements_dict[ 'version' ] tool_dependency_type = requirements_dict[ 'type' ] tool_dependency_readme = requirements_dict.get( 'readme', '' ) tool_dependencies.append( ( tool_dependency_name, tool_dependency_version, tool_dependency_type, tool_dependency_readme ) ) repo_name_dependency_tups.append( ( repository_name, tool_dependencies ) ) return repo_name_dependency_tups
def check_for_missing_tools( app, tool_panel_configs, latest_tool_migration_script_number ): # Get the 000x_tools.xml file associated with the current migrate_tools version number. tools_xml_file_path = os.path.abspath( os.path.join( 'scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number ) ) # Parse the XML and load the file attributes for later checking against the proprietary tool_panel_config. migrated_tool_configs_dict = odict() tree = util.parse_xml( tools_xml_file_path ) root = tree.getroot() tool_shed = root.get( 'name' ) tool_shed_url = get_tool_shed_url_from_tools_xml_file_path( app, tool_shed ) # The default behavior is that the tool shed is down. tool_shed_accessible = False if tool_shed_url: for elem in root: if elem.tag == 'repository': tool_dependencies = [] tool_dependencies_dict = {} repository_name = elem.get( 'name' ) changeset_revision = elem.get( 'changeset_revision' ) url = '%s/repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s&from_install_manager=True' % \ ( tool_shed_url, repository_name, REPOSITORY_OWNER, changeset_revision ) try: response = urllib2.urlopen( url ) text = response.read() response.close() tool_shed_accessible = True except Exception, e: # Tool shed may be unavailable - we have to set tool_shed_accessible since we're looping. tool_shed_accessible = False print "The URL\n%s\nraised the exception:\n%s\n" % ( url, str( e ) ) if tool_shed_accessible: if text: tool_dependencies_dict = encoding_util.tool_shed_decode( text ) for dependency_key, requirements_dict in tool_dependencies_dict.items(): tool_dependency_name = requirements_dict[ 'name' ] tool_dependency_version = requirements_dict[ 'version' ] tool_dependency_type = requirements_dict[ 'type' ] tool_dependency_readme = requirements_dict.get( 'readme', '' ) tool_dependencies.append( ( tool_dependency_name, tool_dependency_version, tool_dependency_type, tool_dependency_readme ) ) for tool_elem in elem.findall( 'tool' ): migrated_tool_configs_dict[ tool_elem.get( 'file' ) ] = tool_dependencies if tool_shed_accessible: # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names. missing_tool_configs_dict = odict() for tool_panel_config in tool_panel_configs: tree = util.parse_xml( tool_panel_config ) root = tree.getroot() for elem in root: if elem.tag == 'tool': missing_tool_configs_dict = check_tool_tag_set( elem, migrated_tool_configs_dict, missing_tool_configs_dict ) elif elem.tag == 'section': for section_elem in elem: if section_elem.tag == 'tool': missing_tool_configs_dict = check_tool_tag_set( section_elem, migrated_tool_configs_dict, missing_tool_configs_dict )
def check_for_tool_dependencies(self, trans, migration_stage): # Get the 000x_tools.xml file associated with migration_stage. tools_xml_file_path = os.path.abspath( os.path.join(trans.app.config.root, 'scripts', 'migrate_tools', '%04d_tools.xml' % migration_stage)) tree = util.parse_xml(tools_xml_file_path) root = tree.getroot() tool_shed = root.get('name') tool_shed_url = self.get_tool_shed_url_from_tools_xml_file_path( trans, tool_shed) repo_name_dependency_tups = [] if tool_shed_url: for elem in root: if elem.tag == 'repository': tool_dependencies = [] tool_dependencies_dict = {} repository_name = elem.get('name') changeset_revision = elem.get('changeset_revision') url = '%s/repository/get_tool_dependencies?name=%s&owner=devteam&changeset_revision=%s&from_install_manager=True' % \ ( tool_shed_url, repository_name, changeset_revision ) response = urllib2.urlopen(url) text = response.read() response.close() if text: tool_dependencies_dict = encoding_util.tool_shed_decode( text) for dependency_key, requirements_dict in tool_dependencies_dict.items( ): tool_dependency_name = requirements_dict['name'] tool_dependency_version = requirements_dict[ 'version'] tool_dependency_type = requirements_dict['type'] tool_dependency_readme = requirements_dict.get( 'readme', '') tool_dependencies.append( (tool_dependency_name, tool_dependency_version, tool_dependency_type, tool_dependency_readme)) repo_name_dependency_tups.append( (repository_name, tool_dependencies)) return repo_name_dependency_tups
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()
def check_for_missing_tools(app, tool_panel_configs, latest_tool_migration_script_number): # Get the 000x_tools.xml file associated with the current migrate_tools version number. tools_xml_file_path = os.path.abspath( os.path.join('scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number)) # Parse the XML and load the file attributes for later checking against the proprietary tool_panel_config. migrated_tool_configs_dict = odict() tree = util.parse_xml(tools_xml_file_path) root = tree.getroot() tool_shed = root.get('name') tool_shed_url = get_tool_shed_url_from_tools_xml_file_path(app, tool_shed) # The default behavior is that the tool shed is down. tool_shed_accessible = False if tool_shed_url: for elem in root: if elem.tag == 'repository': tool_dependencies = [] tool_dependencies_dict = {} repository_name = elem.get('name') changeset_revision = elem.get('changeset_revision') url = '%s/repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s&from_install_manager=True' % \ ( tool_shed_url, repository_name, REPOSITORY_OWNER, changeset_revision ) try: response = urllib2.urlopen(url) text = response.read() response.close() tool_shed_accessible = True except Exception, e: # Tool shed may be unavailable - we have to set tool_shed_accessible since we're looping. tool_shed_accessible = False print "The URL\n%s\nraised the exception:\n%s\n" % (url, str(e)) if tool_shed_accessible: if text: tool_dependencies_dict = encoding_util.tool_shed_decode( text) for dependency_key, requirements_dict in tool_dependencies_dict.items( ): tool_dependency_name = requirements_dict['name'] tool_dependency_version = requirements_dict[ 'version'] tool_dependency_type = requirements_dict['type'] tool_dependency_readme = requirements_dict.get( 'readme', '') tool_dependencies.append( (tool_dependency_name, tool_dependency_version, tool_dependency_type, tool_dependency_readme)) for tool_elem in elem.findall('tool'): migrated_tool_configs_dict[tool_elem.get( 'file')] = tool_dependencies if tool_shed_accessible: # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names. missing_tool_configs_dict = odict() for tool_panel_config in tool_panel_configs: tree = util.parse_xml(tool_panel_config) root = tree.getroot() for elem in root: if elem.tag == 'tool': missing_tool_configs_dict = check_tool_tag_set( elem, migrated_tool_configs_dict, missing_tool_configs_dict) elif elem.tag == 'section': for section_elem in elem: if section_elem.tag == 'tool': missing_tool_configs_dict = check_tool_tag_set( section_elem, migrated_tool_configs_dict, missing_tool_configs_dict)