1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a5c906f0e8a0/ changeset: a5c906f0e8a0 user: greg date: 2013-03-16 17:43:20 summary: Relocate the tool shed's workflow utility component. affected #: 4 files
diff -r 3f2e8f5f0d7de7131aa878e867c12c352f1f79b5 -r a5c906f0e8a03b9ec884b224393c5cb767dcf37d lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -7,9 +7,8 @@ from galaxy.model.orm import or_ import tool_shed.util.shed_util_common as suc from tool_shed.util import common_install_util, data_manager_util, datatype_util, encoding_util, metadata_util -from tool_shed.util import readme_util, repository_dependency_util, tool_dependency_util, tool_util +from tool_shed.util import readme_util, repository_dependency_util, tool_dependency_util, tool_util, workflow_util from tool_shed.galaxy_install import repository_util -from galaxy.webapps.tool_shed.util import workflow_util import tool_shed.galaxy_install.grids.admin_toolshed_grids as admin_toolshed_grids import pkg_resources
diff -r 3f2e8f5f0d7de7131aa878e867c12c352f1f79b5 -r a5c906f0e8a03b9ec884b224393c5cb767dcf37d lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -11,9 +11,9 @@ from galaxy.util import json from galaxy.model.orm import and_, or_ import tool_shed.util.shed_util_common as suc -from tool_shed.util import encoding_util, metadata_util, readme_util, repository_dependency_util, review_util, tool_dependency_util, tool_util +from tool_shed.util import encoding_util, metadata_util, readme_util, repository_dependency_util, review_util, tool_dependency_util, tool_util, workflow_util from tool_shed.galaxy_install import repository_util -from galaxy.webapps.tool_shed.util import common_util, container_util, workflow_util +from galaxy.webapps.tool_shed.util import common_util, container_util import galaxy.tools import tool_shed.grids.repository_grids as repository_grids import tool_shed.grids.util as grids_util
diff -r 3f2e8f5f0d7de7131aa878e867c12c352f1f79b5 -r a5c906f0e8a03b9ec884b224393c5cb767dcf37d lib/galaxy/webapps/tool_shed/util/workflow_util.py --- a/lib/galaxy/webapps/tool_shed/util/workflow_util.py +++ /dev/null @@ -1,411 +0,0 @@ -from galaxy import eggs -import pkg_resources - -pkg_resources.require( "SVGFig" ) - -import logging, svgfig -from galaxy.util import json -import tool_shed.util.shed_util_common as suc -from tool_shed.util import encoding_util, metadata_util, tool_util -from galaxy.workflow.modules import InputDataModule, ToolModule, WorkflowModuleFactory -import galaxy.webapps.galaxy.controllers.workflow -import galaxy.tools -import galaxy.tools.parameters - -log = logging.getLogger( __name__ ) - -class RepoInputDataModule( InputDataModule ): - - type = "data_input" - name = "Input dataset" - - @classmethod - def new( Class, trans, tools_metadata=None, tool_id=None ): - module = Class( trans ) - module.state = dict( name="Input Dataset" ) - return module - @classmethod - def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata=None, secure=True ): - module = Class( trans ) - state = json.from_json_string( step_dict[ "tool_state" ] ) - module.state = dict( name=state.get( "name", "Input Dataset" ) ) - return module - @classmethod - def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ): - module = Class( trans ) - module.state = dict( name="Input Dataset" ) - if step.tool_inputs and "name" in step.tool_inputs: - module.state[ 'name' ] = step.tool_inputs[ 'name' ] - return module - -class RepoToolModule( ToolModule ): - - type = "tool" - - def __init__( self, trans, repository_id, changeset_revision, tools_metadata, tool_id ): - self.trans = trans - self.tools_metadata = tools_metadata - self.tool_id = tool_id - self.tool = None - self.errors = None - for tool_dict in tools_metadata: - if self.tool_id in [ tool_dict[ 'id' ], tool_dict[ 'guid' ] ]: - if trans.webapp.name == 'tool_shed': - # We're in the tool shed. - repository, self.tool, message = tool_util.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_dict[ 'tool_config' ] ) - if message and self.tool is None: - self.errors = 'unavailable' - break - else: - # We're in Galaxy. - self.tool = trans.app.toolbox.tools_by_id.get( self.tool_id, None ) - if self.tool is None: - self.errors = 'unavailable' - self.post_job_actions = {} - self.workflow_outputs = [] - self.state = None - @classmethod - def new( Class, trans, repository_id, changeset_revision, tools_metadata, tool_id=None ): - module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id ) - module.state = module.tool.new_state( trans, all_pages=True ) - return module - @classmethod - def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata, secure=True ): - tool_id = step_dict[ 'tool_id' ] - module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id ) - module.state = galaxy.tools.DefaultToolState() - if module.tool is not None: - module.state.decode( step_dict[ "tool_state" ], module.tool, module.trans.app, secure=secure ) - module.errors = step_dict.get( "tool_errors", None ) - return module - @classmethod - def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ): - module = Class( trans, repository_id, changeset_revision, tools_metadata, step.tool_id ) - module.state = galaxy.tools.DefaultToolState() - if module.tool: - module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) - else: - module.state.inputs = {} - module.errors = step.tool_errors - return module - def get_data_inputs( self ): - data_inputs = [] - def callback( input, value, prefixed_name, prefixed_label ): - if isinstance( input, galaxy.tools.parameters.DataToolParameter ): - data_inputs.append( dict( name=prefixed_name, - label=prefixed_label, - extensions=input.extensions ) ) - if self.tool: - galaxy.tools.parameters.visit_input_values( self.tool.inputs, self.state.inputs, callback ) - return data_inputs - def get_data_outputs( self ): - data_outputs = [] - if self.tool: - data_inputs = None - for name, tool_output in self.tool.outputs.iteritems(): - if tool_output.format_source != None: - # Default to special name "input" which remove restrictions on connections - formats = [ 'input' ] - if data_inputs == None: - data_inputs = self.get_data_inputs() - # Find the input parameter referenced by format_source - for di in data_inputs: - # Input names come prefixed with conditional and repeat names separated by '|', - # so remove prefixes when comparing with format_source. - if di[ 'name' ] != None and di[ 'name' ].split( '|' )[ -1 ] == tool_output.format_source: - formats = di[ 'extensions' ] - else: - formats = [ tool_output.format ] - for change_elem in tool_output.change_format: - for when_elem in change_elem.findall( 'when' ): - format = when_elem.get( 'format', None ) - if format and format not in formats: - formats.append( format ) - data_outputs.append( dict( name=name, extensions=formats ) ) - return data_outputs - -class RepoWorkflowModuleFactory( WorkflowModuleFactory ): - def __init__( self, module_types ): - self.module_types = module_types - def new( self, trans, type, tools_metadata=None, tool_id=None ): - """Return module for type and (optional) tool_id initialized with new / default state.""" - assert type in self.module_types - return self.module_types[type].new( trans, tool_id ) - def from_dict( self, trans, repository_id, changeset_revision, step_dict, **kwd ): - """Return module initialized from the data in dictionary `step_dict`.""" - type = step_dict[ 'type' ] - assert type in self.module_types - return self.module_types[ type ].from_dict( trans, repository_id, changeset_revision, step_dict, **kwd ) - def from_workflow_step( self, trans, repository_id, changeset_revision, tools_metadata, step ): - """Return module initialized from the WorkflowStep object `step`.""" - type = step.type - return self.module_types[ type ].from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step ) - -module_factory = RepoWorkflowModuleFactory( dict( data_input=RepoInputDataModule, tool=RepoToolModule ) ) - -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 == 'tool_shed': - # We're in the tool shed. - repository_metadata = metadata_util.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 == 'tool_shed' 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 get_workflow_data_inputs( step, module ): - if module.type == 'tool': - if module.tool: - return module.get_data_inputs() - else: - data_inputs = [] - for wfsc in step.input_connections: - data_inputs_dict = {} - data_inputs_dict[ 'extensions' ] = [ '' ] - data_inputs_dict[ 'name' ] = wfsc.input_name - data_inputs_dict[ 'label' ] = 'Unknown' - data_inputs.append( data_inputs_dict ) - return data_inputs - return module.get_data_inputs() -def get_workflow_data_outputs( step, module, steps ): - if module.type == 'tool': - if module.tool: - return module.get_data_outputs() - else: - data_outputs = [] - data_outputs_dict = {} - data_outputs_dict[ 'extensions' ] = [ 'input' ] - found = False - for workflow_step in steps: - for wfsc in workflow_step.input_connections: - if step.name == wfsc.output_step.name: - data_outputs_dict[ 'name' ] = wfsc.output_name - found = True - break - if found: - break - if not found: - # We're at the last step of the workflow. - data_outputs_dict[ 'name' ] = 'output' - data_outputs.append( data_outputs_dict ) - return data_outputs - return module.get_data_outputs() -def get_workflow_from_dict( trans, workflow_dict, tools_metadata, repository_id, changeset_revision ): - """ - Return an in-memory Workflow object from the dictionary object created when it was exported. This method is called from - both Galaxy and the tool shed to retrieve a Workflow object that can be displayed as an SVG image. This method is also - called from Galaxy to retrieve a Workflow object that can be used for saving to the Galaxy database. - """ - trans.workflow_building_mode = True - workflow = trans.model.Workflow() - workflow.name = workflow_dict[ 'name' ] - workflow.has_errors = False - steps = [] - # Keep ids for each step that we need to use to make connections. - steps_by_external_id = {} - # Keep track of tools required by the workflow that are not available in - # the tool shed repository. Each tuple in the list of missing_tool_tups - # will be ( tool_id, tool_name, tool_version ). - missing_tool_tups = [] - # First pass to build step objects and populate basic values - for key, step_dict in workflow_dict[ 'steps' ].iteritems(): - # Create the model class for the step - step = trans.model.WorkflowStep() - step.name = step_dict[ 'name' ] - step.position = step_dict[ 'position' ] - module = module_factory.from_dict( trans, repository_id, changeset_revision, step_dict, tools_metadata=tools_metadata, secure=False ) - if module.type == 'tool' and module.tool is None: - # A required tool is not available in the current repository. - step.tool_errors = 'unavailable' - missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) - if missing_tool_tup not in missing_tool_tups: - missing_tool_tups.append( missing_tool_tup ) - module.save_to_step( step ) - if step.tool_errors: - workflow.has_errors = True - # Stick this in the step temporarily. - step.temp_input_connections = step_dict[ 'input_connections' ] - steps.append( step ) - steps_by_external_id[ step_dict[ 'id' ] ] = step - # Second pass to deal with connections between steps. - for step in steps: - # Input connections. - for input_name, conn_dict in step.temp_input_connections.iteritems(): - if conn_dict: - output_step = steps_by_external_id[ conn_dict[ 'id' ] ] - conn = trans.model.WorkflowStepConnection() - conn.input_step = step - conn.input_name = input_name - conn.output_step = output_step - conn.output_name = conn_dict[ 'output_name' ] - step.input_connections.append( conn ) - del step.temp_input_connections - # Order the steps if possible. - galaxy.webapps.galaxy.controllers.workflow.attach_ordered_steps( workflow, steps ) - # Return the in-memory Workflow object for display or later persistence to the Galaxy database. - return workflow, missing_tool_tups -def get_workflow_module_name( module, missing_tool_tups ): - module_name = module.get_name() - if module.type == 'tool' and module_name == 'unavailable': - for missing_tool_tup in missing_tool_tups: - missing_tool_id, missing_tool_name, missing_tool_version = missing_tool_tup - if missing_tool_id == module.tool_id: - module_name = '%s' % missing_tool_name - break - return module_name -def save_workflow( trans, workflow ): - """Use the received in-memory Workflow object for saving to the Galaxy database.""" - stored = trans.model.StoredWorkflow() - stored.name = workflow.name - workflow.stored_workflow = stored - stored.latest_workflow = workflow - stored.user = trans.user - trans.sa_session.add( stored ) - trans.sa_session.flush() - # Add a new entry to the Workflows menu. - if trans.user.stored_workflow_menu_entries is None: - trans.user.stored_workflow_menu_entries = [] - menuEntry = trans.model.StoredWorkflowMenuEntry() - menuEntry.stored_workflow = stored - trans.user.stored_workflow_menu_entries.append( menuEntry ) - trans.sa_session.flush() - return stored
diff -r 3f2e8f5f0d7de7131aa878e867c12c352f1f79b5 -r a5c906f0e8a03b9ec884b224393c5cb767dcf37d lib/tool_shed/util/workflow_util.py --- /dev/null +++ b/lib/tool_shed/util/workflow_util.py @@ -0,0 +1,411 @@ +from galaxy import eggs +import pkg_resources + +pkg_resources.require( "SVGFig" ) + +import logging, svgfig +from galaxy.util import json +import tool_shed.util.shed_util_common as suc +from tool_shed.util import encoding_util, metadata_util, tool_util +from galaxy.workflow.modules import InputDataModule, ToolModule, WorkflowModuleFactory +import galaxy.webapps.galaxy.controllers.workflow +import galaxy.tools +import galaxy.tools.parameters + +log = logging.getLogger( __name__ ) + +class RepoInputDataModule( InputDataModule ): + + type = "data_input" + name = "Input dataset" + + @classmethod + def new( Class, trans, tools_metadata=None, tool_id=None ): + module = Class( trans ) + module.state = dict( name="Input Dataset" ) + return module + @classmethod + def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata=None, secure=True ): + module = Class( trans ) + state = json.from_json_string( step_dict[ "tool_state" ] ) + module.state = dict( name=state.get( "name", "Input Dataset" ) ) + return module + @classmethod + def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ): + module = Class( trans ) + module.state = dict( name="Input Dataset" ) + if step.tool_inputs and "name" in step.tool_inputs: + module.state[ 'name' ] = step.tool_inputs[ 'name' ] + return module + +class RepoToolModule( ToolModule ): + + type = "tool" + + def __init__( self, trans, repository_id, changeset_revision, tools_metadata, tool_id ): + self.trans = trans + self.tools_metadata = tools_metadata + self.tool_id = tool_id + self.tool = None + self.errors = None + for tool_dict in tools_metadata: + if self.tool_id in [ tool_dict[ 'id' ], tool_dict[ 'guid' ] ]: + if trans.webapp.name == 'tool_shed': + # We're in the tool shed. + repository, self.tool, message = tool_util.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_dict[ 'tool_config' ] ) + if message and self.tool is None: + self.errors = 'unavailable' + break + else: + # We're in Galaxy. + self.tool = trans.app.toolbox.tools_by_id.get( self.tool_id, None ) + if self.tool is None: + self.errors = 'unavailable' + self.post_job_actions = {} + self.workflow_outputs = [] + self.state = None + @classmethod + def new( Class, trans, repository_id, changeset_revision, tools_metadata, tool_id=None ): + module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id ) + module.state = module.tool.new_state( trans, all_pages=True ) + return module + @classmethod + def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata, secure=True ): + tool_id = step_dict[ 'tool_id' ] + module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id ) + module.state = galaxy.tools.DefaultToolState() + if module.tool is not None: + module.state.decode( step_dict[ "tool_state" ], module.tool, module.trans.app, secure=secure ) + module.errors = step_dict.get( "tool_errors", None ) + return module + @classmethod + def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ): + module = Class( trans, repository_id, changeset_revision, tools_metadata, step.tool_id ) + module.state = galaxy.tools.DefaultToolState() + if module.tool: + module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) + else: + module.state.inputs = {} + module.errors = step.tool_errors + return module + def get_data_inputs( self ): + data_inputs = [] + def callback( input, value, prefixed_name, prefixed_label ): + if isinstance( input, galaxy.tools.parameters.DataToolParameter ): + data_inputs.append( dict( name=prefixed_name, + label=prefixed_label, + extensions=input.extensions ) ) + if self.tool: + galaxy.tools.parameters.visit_input_values( self.tool.inputs, self.state.inputs, callback ) + return data_inputs + def get_data_outputs( self ): + data_outputs = [] + if self.tool: + data_inputs = None + for name, tool_output in self.tool.outputs.iteritems(): + if tool_output.format_source != None: + # Default to special name "input" which remove restrictions on connections + formats = [ 'input' ] + if data_inputs == None: + data_inputs = self.get_data_inputs() + # Find the input parameter referenced by format_source + for di in data_inputs: + # Input names come prefixed with conditional and repeat names separated by '|', + # so remove prefixes when comparing with format_source. + if di[ 'name' ] != None and di[ 'name' ].split( '|' )[ -1 ] == tool_output.format_source: + formats = di[ 'extensions' ] + else: + formats = [ tool_output.format ] + for change_elem in tool_output.change_format: + for when_elem in change_elem.findall( 'when' ): + format = when_elem.get( 'format', None ) + if format and format not in formats: + formats.append( format ) + data_outputs.append( dict( name=name, extensions=formats ) ) + return data_outputs + +class RepoWorkflowModuleFactory( WorkflowModuleFactory ): + def __init__( self, module_types ): + self.module_types = module_types + def new( self, trans, type, tools_metadata=None, tool_id=None ): + """Return module for type and (optional) tool_id initialized with new / default state.""" + assert type in self.module_types + return self.module_types[type].new( trans, tool_id ) + def from_dict( self, trans, repository_id, changeset_revision, step_dict, **kwd ): + """Return module initialized from the data in dictionary `step_dict`.""" + type = step_dict[ 'type' ] + assert type in self.module_types + return self.module_types[ type ].from_dict( trans, repository_id, changeset_revision, step_dict, **kwd ) + def from_workflow_step( self, trans, repository_id, changeset_revision, tools_metadata, step ): + """Return module initialized from the WorkflowStep object `step`.""" + type = step.type + return self.module_types[ type ].from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step ) + +module_factory = RepoWorkflowModuleFactory( dict( data_input=RepoInputDataModule, tool=RepoToolModule ) ) + +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 == 'tool_shed': + # We're in the tool shed. + repository_metadata = metadata_util.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 == 'tool_shed' 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 get_workflow_data_inputs( step, module ): + if module.type == 'tool': + if module.tool: + return module.get_data_inputs() + else: + data_inputs = [] + for wfsc in step.input_connections: + data_inputs_dict = {} + data_inputs_dict[ 'extensions' ] = [ '' ] + data_inputs_dict[ 'name' ] = wfsc.input_name + data_inputs_dict[ 'label' ] = 'Unknown' + data_inputs.append( data_inputs_dict ) + return data_inputs + return module.get_data_inputs() +def get_workflow_data_outputs( step, module, steps ): + if module.type == 'tool': + if module.tool: + return module.get_data_outputs() + else: + data_outputs = [] + data_outputs_dict = {} + data_outputs_dict[ 'extensions' ] = [ 'input' ] + found = False + for workflow_step in steps: + for wfsc in workflow_step.input_connections: + if step.name == wfsc.output_step.name: + data_outputs_dict[ 'name' ] = wfsc.output_name + found = True + break + if found: + break + if not found: + # We're at the last step of the workflow. + data_outputs_dict[ 'name' ] = 'output' + data_outputs.append( data_outputs_dict ) + return data_outputs + return module.get_data_outputs() +def get_workflow_from_dict( trans, workflow_dict, tools_metadata, repository_id, changeset_revision ): + """ + Return an in-memory Workflow object from the dictionary object created when it was exported. This method is called from + both Galaxy and the tool shed to retrieve a Workflow object that can be displayed as an SVG image. This method is also + called from Galaxy to retrieve a Workflow object that can be used for saving to the Galaxy database. + """ + trans.workflow_building_mode = True + workflow = trans.model.Workflow() + workflow.name = workflow_dict[ 'name' ] + workflow.has_errors = False + steps = [] + # Keep ids for each step that we need to use to make connections. + steps_by_external_id = {} + # Keep track of tools required by the workflow that are not available in + # the tool shed repository. Each tuple in the list of missing_tool_tups + # will be ( tool_id, tool_name, tool_version ). + missing_tool_tups = [] + # First pass to build step objects and populate basic values + for key, step_dict in workflow_dict[ 'steps' ].iteritems(): + # Create the model class for the step + step = trans.model.WorkflowStep() + step.name = step_dict[ 'name' ] + step.position = step_dict[ 'position' ] + module = module_factory.from_dict( trans, repository_id, changeset_revision, step_dict, tools_metadata=tools_metadata, secure=False ) + if module.type == 'tool' and module.tool is None: + # A required tool is not available in the current repository. + step.tool_errors = 'unavailable' + missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) + if missing_tool_tup not in missing_tool_tups: + missing_tool_tups.append( missing_tool_tup ) + module.save_to_step( step ) + if step.tool_errors: + workflow.has_errors = True + # Stick this in the step temporarily. + step.temp_input_connections = step_dict[ 'input_connections' ] + steps.append( step ) + steps_by_external_id[ step_dict[ 'id' ] ] = step + # Second pass to deal with connections between steps. + for step in steps: + # Input connections. + for input_name, conn_dict in step.temp_input_connections.iteritems(): + if conn_dict: + output_step = steps_by_external_id[ conn_dict[ 'id' ] ] + conn = trans.model.WorkflowStepConnection() + conn.input_step = step + conn.input_name = input_name + conn.output_step = output_step + conn.output_name = conn_dict[ 'output_name' ] + step.input_connections.append( conn ) + del step.temp_input_connections + # Order the steps if possible. + galaxy.webapps.galaxy.controllers.workflow.attach_ordered_steps( workflow, steps ) + # Return the in-memory Workflow object for display or later persistence to the Galaxy database. + return workflow, missing_tool_tups +def get_workflow_module_name( module, missing_tool_tups ): + module_name = module.get_name() + if module.type == 'tool' and module_name == 'unavailable': + for missing_tool_tup in missing_tool_tups: + missing_tool_id, missing_tool_name, missing_tool_version = missing_tool_tup + if missing_tool_id == module.tool_id: + module_name = '%s' % missing_tool_name + break + return module_name +def save_workflow( trans, workflow ): + """Use the received in-memory Workflow object for saving to the Galaxy database.""" + stored = trans.model.StoredWorkflow() + stored.name = workflow.name + workflow.stored_workflow = stored + stored.latest_workflow = workflow + stored.user = trans.user + trans.sa_session.add( stored ) + trans.sa_session.flush() + # Add a new entry to the Workflows menu. + if trans.user.stored_workflow_menu_entries is None: + trans.user.stored_workflow_menu_entries = [] + menuEntry = trans.model.StoredWorkflowMenuEntry() + menuEntry.stored_workflow = stored + trans.user.stored_workflow_menu_entries.append( menuEntry ) + trans.sa_session.flush() + return stored
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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