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commit/galaxy-central: dannon: Merged in dan/galaxy-central-prs/stable (pull request #613)
by commits-noreply＠bitbucket.org 16 Dec '14

16 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7086b87d83a9/ Changeset: 7086b87d83a9 Branch: stable User: dannon Date: 2014-12-16 06:31:43+00:00 Summary: Merged in dan/galaxy-central-prs/stable (pull request #613) [STABLE] Do not |h escape tool dependency error message, as it is escaped and formated by tool_shed.util.basic_util.to_html_string Affected #: 1 file diff -r b930c6d7157889fd7f3dc7393e7b8961875a5eb3 -r 7086b87d83a9092cbece0fec6f3e3ed03266be0c templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako --- a/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako +++ b/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako @@ -57,7 +57,7 @@ <td>${tool_dependency.version|h}</td><td>${tool_dependency.type|h}</td><td>${tool_dependency.status|h}</td> - <td>${error_message|h}</td> + <td>${error_message}</td></tr> %endfor </table> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 18 new changesets
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

18 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ff54ae664024/ Changeset: ff54ae664024 User: jmchilton Date: 2014-12-16 03:20:11+00:00 Summary: Code de-dup in workflow controller. Affected #: 1 file diff -r 4f767bb3989f2ee9b7e3fdb47fa4cdf716205fc6 -r ff54ae664024274bb876d54930f6c3e8786f629d lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -666,12 +666,8 @@ encode it as a json string that can be read by the workflow editor web interface. """ - user = trans.get_user() - id = trans.security.decode_id( id ) trans.workflow_building_mode = True - # Load encoded workflow from database - stored = trans.sa_session.query( model.StoredWorkflow ).get( id ) - assert stored.user == user + stored = self.get_stored_workflow( trans, id, check_ownership=True, check_accessible=False ) workflow = stored.latest_workflow # Pack workflow data into a dictionary and return data = {} @@ -898,12 +894,8 @@ """ Exports a workflow to myExperiment website. """ - - # Load encoded workflow from database - id = trans.security.decode_id( id ) trans.workflow_building_mode = True - stored = trans.sa_session.query( model.StoredWorkflow ).get( id ) - self.security_check( trans, stored, False, True ) + stored = self.get_stored_workflow( trans, id, check_ownership=False, check_accessible=True ) # Convert workflow to dict. workflow_dict = self._workflow_to_dict( trans, stored ) https://bitbucket.org/galaxy/galaxy-central/commits/e89cb5a78e20/ Changeset: e89cb5a78e20 User: jmchilton Date: 2014-12-16 03:20:11+00:00 Summary: Refactor helper out for detailed encoding of a workflow for API. Affected #: 2 files diff -r ff54ae664024274bb876d54930f6c3e8786f629d -r e89cb5a78e209b8a9c1209603a357b10194e377e lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -75,44 +75,8 @@ if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: message = "Workflow is neither importable, nor owned by or shared with current user" raise exceptions.ItemAccessibilityException( message ) - - item = stored_workflow.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } ) - item['url'] = url_for('workflow', id=id) - item['owner'] = stored_workflow.user.username latest_workflow = stored_workflow.latest_workflow - inputs = {} - for step in latest_workflow.steps: - step_type = step.type - if step_type in ['data_input', 'data_collection_input']: - if step.tool_inputs and "name" in step.tool_inputs: - label = step.tool_inputs['name'] - elif step_type == "data_input": - label = "Input Dataset" - elif step_type == "data_collection_input": - label = "Input Dataset Collection" - else: - raise ValueError("Invalid step_type %s" % step_type) - inputs[step.id] = {'label': label, 'value': ""} - else: - pass - # Eventually, allow regular tool parameters to be inserted and modified at runtime. - # p = step.get_required_parameters() - item['inputs'] = inputs - item['annotation'] = self.get_item_annotation_str( trans.sa_session, stored_workflow.user, stored_workflow ) - steps = {} - for step in latest_workflow.steps: - steps[step.id] = {'id': step.id, - 'type': step.type, - 'tool_id': step.tool_id, - 'tool_version': step.tool_version, - 'annotation': self.get_item_annotation_str( trans.sa_session, stored_workflow.user, step ), - 'tool_inputs': step.tool_inputs, - 'input_steps': {}} - for conn in step.input_connections: - steps[step.id]['input_steps'][conn.input_name] = {'source_step': conn.output_step_id, - 'step_output': conn.output_name} - item['steps'] = steps - return item + return self.__encode_workflow( trans, stored_workflow, latest_workflow ) @expose_api def create(self, trans, payload, **kwd): @@ -512,6 +476,44 @@ ) return self.__encode_invocation_step( trans, invocation_step ) + def __encode_workflow( self, trans, stored_workflow, workflow ): + item = stored_workflow.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } ) + item['url'] = url_for('workflow', id=item['id']) + item['owner'] = stored_workflow.user.username + inputs = {} + for step in workflow.steps: + step_type = step.type + if step_type in ['data_input', 'data_collection_input']: + if step.tool_inputs and "name" in step.tool_inputs: + label = step.tool_inputs['name'] + elif step_type == "data_input": + label = "Input Dataset" + elif step_type == "data_collection_input": + label = "Input Dataset Collection" + else: + raise ValueError("Invalid step_type %s" % step_type) + inputs[step.id] = {'label': label, 'value': ""} + else: + pass + # Eventually, allow regular tool parameters to be inserted and modified at runtime. + # p = step.get_required_parameters() + item['inputs'] = inputs + item['annotation'] = self.get_item_annotation_str( trans.sa_session, stored_workflow.user, stored_workflow ) + steps = {} + for step in workflow.steps: + steps[step.id] = {'id': step.id, + 'type': step.type, + 'tool_id': step.tool_id, + 'tool_version': step.tool_version, + 'annotation': self.get_item_annotation_str( trans.sa_session, stored_workflow.user, step ), + 'tool_inputs': step.tool_inputs, + 'input_steps': {}} + for conn in step.input_connections: + steps[step.id]['input_steps'][conn.input_name] = {'source_step': conn.output_step_id, + 'step_output': conn.output_name} + item['steps'] = steps + return item + def __encode_invocation_step( self, trans, invocation_step ): return self.encode_all_ids( trans, diff -r ff54ae664024274bb876d54930f6c3e8786f629d -r e89cb5a78e209b8a9c1209603a357b10194e377e test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -181,6 +181,13 @@ def setUp( self ): super( WorkflowsApiTestCase, self ).setUp() + def test_show_valid( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_regular" ) + show_response = self._get( "workflows/%s" % workflow_id ) + workflow = show_response.json() + self._assert_looks_like_instance_workflow_representation( workflow ) + assert len(workflow["steps"]) == 3 + def test_show_invalid_key_is_400( self ): show_response = self._get( "workflows/%s" % self._random_key() ) self._assert_status_code_is( show_response, 400 ) @@ -731,4 +738,25 @@ self._assert_status_code_is( show_response, 200 ) return show_response.json() + def _assert_looks_like_instance_workflow_representation(self, workflow): + self._assert_has_keys( + workflow, + 'url', + 'owner', + 'inputs', + 'annotation', + 'steps' + ) + for step in workflow["steps"].values(): + self._assert_has_keys( + step, + 'id', + 'type', + 'tool_id', + 'tool_version', + 'annotation', + 'tool_inputs', + 'input_steps', + ) + RunJobsSummary = namedtuple('RunJobsSummary', ['history_id', 'workflow_id', 'inputs', 'jobs']) https://bitbucket.org/galaxy/galaxy-central/commits/448c66ad21e0/ Changeset: 448c66ad21e0 User: jmchilton Date: 2014-12-16 03:20:11+00:00 Summary: Move building workflows from dictionaries into new WorkflowContentsManager. Going to build up a WorkflowContentsManager that is reponsible for slightly more complex operations involving step logic, etc... and keep the WorkflowsManager focused on CRUD-like and sharing operations. Affected #: 2 files diff -r e89cb5a78e209b8a9c1209603a357b10194e377e -r 448c66ad21e012c7b18f1edfd7729527dc8cd507 lib/galaxy/managers/workflows.py --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -1,7 +1,18 @@ +from __future__ import absolute_import + +from collections import namedtuple +import json + from galaxy import model from galaxy import exceptions +from galaxy.model.item_attrs import UsesAnnotations from galaxy.workflow import modules +# For WorkflowContentManager +from galaxy.util.sanitize_html import sanitize_html +from galaxy.workflow.steps import attach_ordered_steps +from galaxy.workflow.modules import module_factory + class WorkflowsManager( object ): """ Handle CRUD type operaitons related to workflows. More interesting @@ -103,3 +114,124 @@ ).filter_by( workflow_id=stored_workflow.latest_workflow_id ) + + +CreatedWorkflow = namedtuple("CreatedWorkflow", ["stored_workflow", "missing_tools"]) + + +class WorkflowContentsManager(UsesAnnotations): + + def build_workflow_from_dict( + self, + trans, + data, + source=None, + add_to_menu=False, + publish=False + ): + # Put parameters in workflow mode + trans.workflow_building_mode = True + # Create new workflow from incoming dict + workflow = model.Workflow() + # If there's a source, put it in the workflow name. + if source: + name = "%s (imported from %s)" % ( data['name'], source ) + else: + name = data['name'] + workflow.name = name + if 'uuid' in data: + workflow.uuid = data['uuid'] + # Assume no errors until we find a step that has some + workflow.has_errors = False + # Create each step + steps = [] + # The editor will provide ids for each step that we don't need to save, + # but do need to use to make connections + steps_by_external_id = {} + # Keep track of tools required by the workflow that are not available in + # the local Galaxy instance. Each tuple in the list of missing_tool_tups + # will be ( tool_id, tool_name, tool_version ). + missing_tool_tups = [] + supplied_steps = data[ 'steps' ] + # Try to iterate through imported workflow in such a way as to + # preserve step order. + step_indices = supplied_steps.keys() + try: + step_indices = sorted( step_indices, key=int ) + except ValueError: + # to defensive, were these ever or will they ever not be integers? + pass + # First pass to build step objects and populate basic values + for step_index in step_indices: + step_dict = supplied_steps[ step_index ] + # Create the model class for the step + step = model.WorkflowStep() + steps.append( step ) + steps_by_external_id[ step_dict['id' ] ] = step + # FIXME: Position should be handled inside module + step.position = step_dict['position'] + module = module_factory.from_dict( trans, step_dict, secure=False ) + module.save_to_step( step ) + if module.type == 'tool' and module.tool is None: + # A required tool is not available in the local Galaxy instance. + 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 ) + # Save the entire step_dict in the unused config field, be parsed later + # when we do have the tool + step.config = json.dumps(step_dict) + if step.tool_errors: + workflow.has_errors = True + # Stick this in the step temporarily + step.temp_input_connections = step_dict['input_connections'] + # Save step annotation. + annotation = step_dict[ 'annotation' ] + if annotation: + annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) + self.add_item_annotation( trans.sa_session, trans.get_user(), step, annotation ) + # Second pass to deal with connections between steps + for step in steps: + # Input connections + for input_name, conn_list in step.temp_input_connections.iteritems(): + if not conn_list: + continue + if not isinstance(conn_list, list): # Older style singleton connection + conn_list = [conn_list] + for conn_dict in conn_list: + conn = model.WorkflowStepConnection() + conn.input_step = step + conn.input_name = input_name + conn.output_name = conn_dict['output_name'] + conn.output_step = steps_by_external_id[ conn_dict['id'] ] + del step.temp_input_connections + + # Order the steps if possible + attach_ordered_steps( workflow, steps ) + + # Connect up + stored = model.StoredWorkflow() + stored.name = workflow.name + workflow.stored_workflow = stored + stored.latest_workflow = workflow + stored.user = trans.user + stored.published = publish + if data[ 'annotation' ]: + annotation = sanitize_html( data[ 'annotation' ], 'utf-8', 'text/html' ) + self.add_item_annotation( trans.sa_session, stored.user, stored, annotation ) + + # Persist + trans.sa_session.add( stored ) + trans.sa_session.flush() + + if add_to_menu: + if trans.user.stored_workflow_menu_entries is None: + trans.user.stored_workflow_menu_entries = [] + menuEntry = model.StoredWorkflowMenuEntry() + menuEntry.stored_workflow = stored + trans.user.stored_workflow_menu_entries.append( menuEntry ) + trans.sa_session.flush() + + return CreatedWorkflow( + stored_workflow=stored, + missing_tools=missing_tool_tups + ) diff -r e89cb5a78e209b8a9c1209603a357b10194e377e -r 448c66ad21e012c7b18f1edfd7729527dc8cd507 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -38,14 +38,13 @@ from galaxy.managers import api_keys from galaxy.managers import tags +from galaxy.managers import workflows from galaxy.managers import base as managers_base from galaxy.datatypes.metadata import FileParameter from galaxy.tools.parameters import visit_input_values from galaxy.tools.parameters.basic import DataToolParameter from galaxy.tools.parameters.basic import DataCollectionToolParameter -from galaxy.util.json import dumps from galaxy.workflow.modules import ToolModule -from galaxy.workflow.steps import attach_ordered_steps from galaxy.util import validation @@ -1576,110 +1575,15 @@ """ Creates a workflow from a dict. Created workflow is stored in the database and returned. """ - - # Put parameters in workflow mode - trans.workflow_building_mode = True - # Create new workflow from incoming dict - workflow = model.Workflow() - # If there's a source, put it in the workflow name. - if source: - name = "%s (imported from %s)" % ( data['name'], source ) - else: - name = data['name'] - workflow.name = name - if 'uuid' in data: - workflow.uuid = data['uuid'] - # Assume no errors until we find a step that has some - workflow.has_errors = False - # Create each step - steps = [] - # The editor will provide ids for each step that we don't need to save, - # but do need to use to make connections - steps_by_external_id = {} - # Keep track of tools required by the workflow that are not available in - # the local Galaxy instance. Each tuple in the list of missing_tool_tups - # will be ( tool_id, tool_name, tool_version ). - missing_tool_tups = [] - supplied_steps = data[ 'steps' ] - # Try to iterate through imported workflow in such a way as to - # preserve step order. - step_indices = supplied_steps.keys() - try: - step_indices = sorted( step_indices, key=int ) - except ValueError: - # to defensive, were these ever or will they ever not be integers? - pass - # First pass to build step objects and populate basic values - for step_index in step_indices: - step_dict = supplied_steps[ step_index ] - # Create the model class for the step - step = model.WorkflowStep() - steps.append( step ) - steps_by_external_id[ step_dict['id' ] ] = step - # FIXME: Position should be handled inside module - step.position = step_dict['position'] - module = module_factory.from_dict( trans, step_dict, secure=False ) - module.save_to_step( step ) - if module.type == 'tool' and module.tool is None: - # A required tool is not available in the local Galaxy instance. - 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 ) - # Save the entire step_dict in the unused config field, be parsed later - # when we do have the tool - step.config = dumps(step_dict) - if step.tool_errors: - workflow.has_errors = True - # Stick this in the step temporarily - step.temp_input_connections = step_dict['input_connections'] - # Save step annotation. - annotation = step_dict[ 'annotation' ] - if annotation: - annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) - self.add_item_annotation( trans.sa_session, trans.get_user(), step, annotation ) - # Second pass to deal with connections between steps - for step in steps: - # Input connections - for input_name, conn_list in step.temp_input_connections.iteritems(): - if not conn_list: - continue - if not isinstance(conn_list, list): # Older style singleton connection - conn_list = [conn_list] - for conn_dict in conn_list: - conn = model.WorkflowStepConnection() - conn.input_step = step - conn.input_name = input_name - conn.output_name = conn_dict['output_name'] - conn.output_step = steps_by_external_id[ conn_dict['id'] ] - del step.temp_input_connections - - # Order the steps if possible - attach_ordered_steps( workflow, steps ) - - # Connect up - stored = model.StoredWorkflow() - stored.name = workflow.name - workflow.stored_workflow = stored - stored.latest_workflow = workflow - stored.user = trans.user - stored.published = publish - if data[ 'annotation' ]: - annotation = sanitize_html( data[ 'annotation' ], 'utf-8', 'text/html' ) - self.add_item_annotation( trans.sa_session, stored.user, stored, annotation ) - - # Persist - trans.sa_session.add( stored ) - trans.sa_session.flush() - - if add_to_menu: - if trans.user.stored_workflow_menu_entries == None: - trans.user.stored_workflow_menu_entries = [] - menuEntry = model.StoredWorkflowMenuEntry() - menuEntry.stored_workflow = stored - trans.user.stored_workflow_menu_entries.append( menuEntry ) - trans.sa_session.flush() - - return stored, missing_tool_tups + workflow_contents_manager = workflows.WorkflowContentsManager() + created_workflow = workflow_contents_manager.build_workflow_from_dict( + trans, + data, + source=source, + add_to_menu=add_to_menu, + publish=publish + ) + return created_workflow.stored_workflow, created_workflow.missing_tools def _workflow_to_dict( self, trans, stored ): """ https://bitbucket.org/galaxy/galaxy-central/commits/a81fd56c879d/ Changeset: a81fd56c879d User: jmchilton Date: 2014-12-16 03:20:11+00:00 Summary: Refactor updating workflow contents out of mixin into manager. Introduce an API endpoint for this operation with test case. Affected #: 5 files diff -r 448c66ad21e012c7b18f1edfd7729527dc8cd507 -r a81fd56c879dc517dd61e6bcd9bae0b9dd5bca7b lib/galaxy/managers/workflows.py --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -11,7 +11,7 @@ # For WorkflowContentManager from galaxy.util.sanitize_html import sanitize_html from galaxy.workflow.steps import attach_ordered_steps -from galaxy.workflow.modules import module_factory +from galaxy.workflow.modules import module_factory, is_tool_module_type class WorkflowsManager( object ): @@ -235,3 +235,86 @@ stored_workflow=stored, missing_tools=missing_tool_tups ) + + def update_workflow_from_dict(self, trans, stored_workflow, workflow_data, from_editor=False): + # Put parameters in workflow mode + trans.workflow_building_mode = True + # Convert incoming workflow data from json if coming from editor + data = json.loads(workflow_data) if from_editor else workflow_data + # Create new workflow from incoming data + workflow = model.Workflow() + # Just keep the last name (user can rename later) + workflow.name = stored_workflow.name + # Assume no errors until we find a step that has some + workflow.has_errors = False + # Create each step + steps = [] + # The editor will provide ids for each step that we don't need to save, + # but do need to use to make connections + steps_by_external_id = {} + errors = [] + for key, step_dict in data['steps'].iteritems(): + is_tool = is_tool_module_type( step_dict[ 'type' ] ) + if is_tool and step_dict['tool_id'] not in trans.app.toolbox.tools_by_id: + errors.append("Step %s requires tool '%s'." % (step_dict['id'], step_dict['tool_id'])) + if errors: + raise MissingToolsException(workflow, errors) + + # First pass to build step objects and populate basic values + for key, step_dict in data['steps'].iteritems(): + # Create the model class for the step + step = model.WorkflowStep() + steps.append( step ) + steps_by_external_id[ step_dict['id' ] ] = step + # FIXME: Position should be handled inside module + step.position = step_dict['position'] + module = module_factory.from_dict( trans, step_dict, secure=from_editor ) + module.save_to_step( step ) + if 'workflow_outputs' in step_dict: + for output_name in step_dict['workflow_outputs']: + m = model.WorkflowOutput(workflow_step=step, output_name=output_name) + trans.sa_session.add(m) + if step.tool_errors: + # DBTODO Check for conditional inputs here. + workflow.has_errors = True + # Stick this in the step temporarily + step.temp_input_connections = step_dict['input_connections'] + # Save step annotation. + annotation = step_dict[ 'annotation' ] + if annotation: + annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) + self.add_item_annotation( trans.sa_session, trans.get_user(), step, annotation ) + # Second pass to deal with connections between steps + for step in steps: + # Input connections + for input_name, conns in step.temp_input_connections.iteritems(): + if conns: + conn_dicts = conns if isinstance(conns, list) else [ conns ] + for conn_dict in conn_dicts: + conn = model.WorkflowStepConnection() + conn.input_step = step + conn.input_name = input_name + conn.output_name = conn_dict['output_name'] + conn.output_step = steps_by_external_id[ conn_dict['id'] ] + del step.temp_input_connections + # Order the steps if possible + attach_ordered_steps( workflow, steps ) + # Connect up + workflow.stored_workflow = stored_workflow + stored_workflow.latest_workflow = workflow + # Persist + trans.sa_session.flush() + # Return something informative + errors = [] + if workflow.has_errors: + errors.append( "Some steps in this workflow have validation errors" ) + if workflow.has_cycles: + errors.append( "This workflow contains cycles" ) + return workflow, errors + + +class MissingToolsException(object): + + def __init__(self, workflow, errors): + self.workflow = workflow + self.errors = errors diff -r 448c66ad21e012c7b18f1edfd7729527dc8cd507 -r a81fd56c879dc517dd61e6bcd9bae0b9dd5bca7b lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1575,6 +1575,7 @@ """ Creates a workflow from a dict. Created workflow is stored in the database and returned. """ + # TODO: replace this method with direct access to manager. workflow_contents_manager = workflows.WorkflowContentsManager() created_workflow = workflow_contents_manager.build_workflow_from_dict( trans, diff -r 448c66ad21e012c7b18f1edfd7729527dc8cd507 -r a81fd56c879dc517dd61e6bcd9bae0b9dd5bca7b lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -271,6 +271,38 @@ """ return self.__api_import_new_workflow( trans, payload, **kwd ) + @expose_api + def update( self, trans, id, payload, **kwds ): + """ + * PUT /api/workflows/{id} + updates the workflow stored with ``id`` + + :type id: str + :param id: the encoded id of the workflow to update + :type payload: dict + :param payload: a dictionary containing any or all the + * workflow the json description of the workflow as would be + produced by GET workflows/<id>/download or + given to `POST workflows` + + The workflow contents will be updated to target + this. + :rtype: dict + :returns: serialized version of the workflow + """ + stored_workflow = self.__get_stored_workflow( trans, id ) + if 'workflow' in payload: + workflow_contents_manager = workflows.WorkflowContentsManager() + workflow, errors = workflow_contents_manager.update_workflow_from_dict( + trans, + stored_workflow, + payload['workflow'], + ) + else: + message = "Updating workflow requires dictionary containing 'workflow' attribute with new JSON description." + raise exceptions.RequestParameterInvalidException( message ) + return self.__encode_workflow( trans, stored_workflow, workflow ) + def __api_import_new_workflow( self, trans, payload, **kwd ): data = payload['workflow'] diff -r 448c66ad21e012c7b18f1edfd7729527dc8cd507 -r a81fd56c879dc517dd61e6bcd9bae0b9dd5bca7b lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -22,7 +22,8 @@ from galaxy.web import error, url_for from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin from galaxy.web.framework.formbuilder import form -from galaxy.web.framework.helpers import grids, time_ago, to_unicode +from galaxy.web.framework.helpers import grids, time_ago, to_unicode, escape +from galaxy.managers import workflows from galaxy.workflow.modules import WorkflowModuleInjector from galaxy.workflow.modules import MissingToolException from galaxy.workflow.modules import module_factory, is_tool_module_type @@ -796,76 +797,21 @@ """ # Get the stored workflow stored = self.get_stored_workflow( trans, id ) - # Put parameters in workflow mode - trans.workflow_building_mode = True - # Convert incoming workflow data from json - data = json.loads( workflow_data ) - # Create new workflow from incoming data - workflow = model.Workflow() - # Just keep the last name (user can rename later) - workflow.name = stored.name - # Assume no errors until we find a step that has some - workflow.has_errors = False - # Create each step - steps = [] - # The editor will provide ids for each step that we don't need to save, - # but do need to use to make connections - steps_by_external_id = {} - errors = [] - for key, step_dict in data['steps'].iteritems(): - is_tool = is_tool_module_type( step_dict[ 'type' ] ) - if is_tool and step_dict['tool_id'] not in trans.app.toolbox.tools_by_id: - errors.append("Step %s requires tool '%s'." % (step_dict['id'], step_dict['tool_id'])) - if errors: - return dict( name=workflow.name, - message="This workflow includes missing or invalid tools. It cannot be saved until the following steps are removed or the missing tools are enabled.", - errors=errors ) - # First pass to build step objects and populate basic values - for key, step_dict in data['steps'].iteritems(): - # Create the model class for the step - step = model.WorkflowStep() - steps.append( step ) - steps_by_external_id[ step_dict['id' ] ] = step - # FIXME: Position should be handled inside module - step.position = step_dict['position'] - module = module_factory.from_dict( trans, step_dict ) - module.save_to_step( step ) - if 'workflow_outputs' in step_dict: - for output_name in step_dict['workflow_outputs']: - m = model.WorkflowOutput(workflow_step=step, output_name=output_name) - trans.sa_session.add(m) - if step.tool_errors: - # DBTODO Check for conditional inputs here. - workflow.has_errors = True - # Stick this in the step temporarily - step.temp_input_connections = step_dict['input_connections'] - # Save step annotation. - annotation = step_dict[ 'annotation' ] - if annotation: - annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) - self.add_item_annotation( trans.sa_session, trans.get_user(), step, annotation ) - # Second pass to deal with connections between steps - for step in steps: - # Input connections - for input_name, conns in step.temp_input_connections.iteritems(): - if conns: - conn_dicts = conns if isinstance(conns, list) else [ conns ] - for conn_dict in conn_dicts: - conn = model.WorkflowStepConnection() - conn.input_step = step - conn.input_name = input_name - conn.output_name = conn_dict['output_name'] - conn.output_step = steps_by_external_id[ conn_dict['id'] ] - del step.temp_input_connections - # Order the steps if possible - attach_ordered_steps( workflow, steps ) - # Connect up - workflow.stored_workflow = stored - stored.latest_workflow = workflow - # Persist - trans.sa_session.flush() - # Return something informative - errors = [] + workflow_contents_manager = workflows.WorkflowContentsManager() + try: + workflow, errors = workflow_contents_manager.update_workflow_from_dict( + trans, + stored, + workflow_data, + from_editor=True, + ) + except workflows.MissingToolsException as e: + return dict( + name=e.workflow.name, + message="This workflow includes missing or invalid tools. It cannot be saved until the following steps are removed or the missing tools are enabled.", + errors=e.errors, + ) + if workflow.has_errors: errors.append( "Some steps in this workflow have validation errors" ) if workflow.has_cycles: diff -r 448c66ad21e012c7b18f1edfd7729527dc8cd507 -r a81fd56c879dc517dd61e6bcd9bae0b9dd5bca7b test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -226,9 +226,9 @@ def test_upload_deprecated( self ): self.__test_upload( use_deprecated_route=True ) - def __test_upload( self, use_deprecated_route ): + def __test_upload( self, use_deprecated_route=False, name="test_import" ): data = dict( - workflow=dumps( self.workflow_populator.load_workflow( name="test_import" ) ), + workflow=dumps( self.workflow_populator.load_workflow( name=name ) ), ) if use_deprecated_route: route = "workflows/upload" @@ -236,7 +236,51 @@ route = "workflows" upload_response = self._post( route, data=data ) self._assert_status_code_is( upload_response, 200 ) - self._assert_user_has_workflow_with_name( "test_import (imported from API)" ) + self._assert_user_has_workflow_with_name( "%s (imported from API)" % name ) + return upload_response + + def test_update( self ): + original_workflow = self.workflow_populator.load_workflow( name="test_import" ) + + upload_response = self.__test_upload( ) + workflow_id = upload_response.json()["id"] + + def update(workflow_object): + data = dict( + workflow=workflow_object + ) + raw_url = 'workflows/%s' % workflow_id + url = self._api_url( raw_url, use_key=True ) + put_response = put( url, data=dumps(data) ) + self._assert_status_code_is( put_response, 200 ) + return put_response + + workflow_content = self._download_workflow(workflow_id) + steps = workflow_content["steps"] + + def tweak_step(step): + assert step['position']['top'] != 1 + assert step['position']['left'] != 1 + step['position'] = {'top': 1, 'left': 1} + + map(tweak_step, steps.values()) + + update(workflow_content) + + def check_step(step): + assert step['position']['top'] == 1 + assert step['position']['left'] == 1 + + updated_workflow_content = self._download_workflow(workflow_id) + map(check_step, updated_workflow_content['steps'].values()) + + # Re-update against original worklfow... + update(original_workflow) + + updated_workflow_content = self._download_workflow(workflow_id) + + # Make sure the positions have been updated. + map(tweak_step, updated_workflow_content['steps'].values()) def test_import_deprecated( self ): workflow_id = self.workflow_populator.simple_workflow( "test_import_published_deprecated", publish=True ) https://bitbucket.org/galaxy/galaxy-central/commits/2647ac82f98d/ Changeset: 2647ac82f98d User: jmchilton Date: 2014-12-16 03:20:11+00:00 Summary: Move body of _workflow_to_dict to new WorkflowContentsManager. Getting closer to killing UsesStoredWorkflowMixin. Affected #: 2 files diff -r a81fd56c879dc517dd61e6bcd9bae0b9dd5bca7b -r 2647ac82f98dcd90a133be765122f97d6dede45e lib/galaxy/managers/workflows.py --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -11,7 +11,9 @@ # For WorkflowContentManager from galaxy.util.sanitize_html import sanitize_html from galaxy.workflow.steps import attach_ordered_steps -from galaxy.workflow.modules import module_factory, is_tool_module_type +from galaxy.workflow.modules import module_factory, is_tool_module_type, ToolModule +from galaxy.tools.parameters.basic import DataToolParameter, DataCollectionToolParameter +from galaxy.tools.parameters import visit_input_values class WorkflowsManager( object ): @@ -312,6 +314,108 @@ errors.append( "This workflow contains cycles" ) return workflow, errors + def workflow_to_dict(self, trans, stored, style="export" ): + """ + """ + workflow = stored.latest_workflow + workflow_annotation = self.get_item_annotation_obj( trans.sa_session, trans.user, stored ) + annotation_str = "" + if workflow_annotation: + annotation_str = workflow_annotation.annotation + # Pack workflow data into a dictionary and return + data = {} + data['a_galaxy_workflow'] = 'true' # Placeholder for identifying galaxy workflow + data['format-version'] = "0.1" + data['name'] = workflow.name + data['annotation'] = annotation_str + if workflow.uuid is not None: + data['uuid'] = str(workflow.uuid) + data['steps'] = {} + # For each step, rebuild the form and encode the state + for step in workflow.steps: + # Load from database representation + module = module_factory.from_workflow_step( trans, step ) + if not module: + return None + # Get user annotation. + step_annotation = self.get_item_annotation_obj(trans.sa_session, trans.user, step ) + annotation_str = "" + if step_annotation: + annotation_str = step_annotation.annotation + # Step info + step_dict = { + 'id': step.order_index, + 'type': module.type, + 'tool_id': module.get_tool_id(), + 'tool_version': step.tool_version, + 'name': module.get_name(), + 'tool_state': module.get_state( secure=False ), + 'tool_errors': module.get_errors(), + ## 'data_inputs': module.get_data_inputs(), + ## 'data_outputs': module.get_data_outputs(), + 'annotation': annotation_str + } + # Add post-job actions to step dict. + if module.type == 'tool': + pja_dict = {} + for pja in step.post_job_actions: + pja_dict[pja.action_type + pja.output_name] = dict( action_type=pja.action_type, + output_name=pja.output_name, + action_arguments=pja.action_arguments ) + step_dict[ 'post_job_actions' ] = pja_dict + # Data inputs + step_dict['inputs'] = module.get_runtime_input_dicts( annotation_str ) + # User outputs + step_dict['user_outputs'] = [] + + # All step outputs + step_dict['outputs'] = [] + if type( module ) is ToolModule: + for output in module.get_data_outputs(): + step_dict['outputs'].append( { 'name': output['name'], 'type': output['extensions'][0] } ) + + # Connections + input_connections = step.input_connections + if step.type is None or step.type == 'tool': + # Determine full (prefixed) names of valid input datasets + data_input_names = {} + + def callback( input, value, prefixed_name, prefixed_label ): + if isinstance( input, DataToolParameter ) or isinstance( input, DataCollectionToolParameter ): + data_input_names[ prefixed_name ] = True + # FIXME: this updates modules silently right now; messages from updates should be provided. + module.check_and_update_state() + visit_input_values( module.tool.inputs, module.state.inputs, callback ) + # Filter + # FIXME: this removes connection without displaying a message currently! + input_connections = [ conn for conn in input_connections if conn.input_name in data_input_names ] + + # Encode input connections as dictionary + input_conn_dict = {} + unique_input_names = set( [conn.input_name for conn in input_connections] ) + for input_name in unique_input_names: + input_conn_dict[ input_name ] = \ + [ dict( id=conn.output_step.order_index, output_name=conn.output_name ) for conn in input_connections if conn.input_name == input_name ] + + # Preserve backward compatability. Previously Galaxy + # assumed input connections would be dictionaries not + # lists of dictionaries, so replace any singleton list + # with just the dictionary so that workflows exported from + # newer Galaxy instances can be used with older Galaxy + # instances if they do no include multiple input + # tools. This should be removed at some point. Mirrored + # hack in _workflow_from_dict should never be removed so + # existing workflow exports continue to function. + for input_name, input_conn in dict(input_conn_dict).iteritems(): + if len(input_conn) == 1: + input_conn_dict[input_name] = input_conn[0] + step_dict['input_connections'] = input_conn_dict + # Position + step_dict['position'] = step.position + # Add to return value + data['steps'][step.order_index] = step_dict + return data + class MissingToolsException(object): diff -r a81fd56c879dc517dd61e6bcd9bae0b9dd5bca7b -r 2647ac82f98dcd90a133be765122f97d6dede45e lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1590,111 +1590,11 @@ """ Converts a workflow to a dict of attributes suitable for exporting. """ - workflow = stored.latest_workflow - workflow_annotation = self.get_item_annotation_obj( trans.sa_session, trans.user, stored ) - annotation_str = "" - if workflow_annotation: - annotation_str = workflow_annotation.annotation - # Pack workflow data into a dictionary and return - data = {} - data['a_galaxy_workflow'] = 'true' # Placeholder for identifying galaxy workflow - data['format-version'] = "0.1" - data['name'] = workflow.name - data['annotation'] = annotation_str - if workflow.uuid is not None: - data['uuid'] = str(workflow.uuid) - data['steps'] = {} - # For each step, rebuild the form and encode the state - for step in workflow.steps: - # Load from database representation - module = module_factory.from_workflow_step( trans, step ) - if not module: - return None - # Get user annotation. - step_annotation = self.get_item_annotation_obj(trans.sa_session, trans.user, step ) - annotation_str = "" - if step_annotation: - annotation_str = step_annotation.annotation - # Step info - step_dict = { - 'id': step.order_index, - 'type': module.type, - 'tool_id': module.get_tool_id(), - 'tool_version' : step.tool_version, - 'name': module.get_name(), - 'tool_state': module.get_state( secure=False ), - 'tool_errors': module.get_errors(), - ## 'data_inputs': module.get_data_inputs(), - ## 'data_outputs': module.get_data_outputs(), - 'annotation' : annotation_str - } - # Add post-job actions to step dict. - if module.type == 'tool': - pja_dict = {} - for pja in step.post_job_actions: - pja_dict[pja.action_type+pja.output_name] = dict( action_type = pja.action_type, - output_name = pja.output_name, - action_arguments = pja.action_arguments ) - step_dict[ 'post_job_actions' ] = pja_dict - # Data inputs - step_dict['inputs'] = module.get_runtime_input_dicts( annotation_str ) - # User outputs - step_dict['user_outputs'] = [] -# module_outputs = module.get_data_outputs() -# step_outputs = trans.sa_session.query( WorkflowOutput ).filter( step=step ) -# for output in step_outputs: -# name = output.output_name -# annotation = "" -# for module_output in module_outputs: -# if module_output.get( 'name', None ) == name: -# output_type = module_output.get( 'extension', '' ) -# break -# data['outputs'][name] = { 'name' : name, 'annotation' : annotation, 'type' : output_type } - - # All step outputs - step_dict['outputs'] = [] - if type( module ) is ToolModule: - for output in module.get_data_outputs(): - step_dict['outputs'].append( { 'name' : output['name'], 'type' : output['extensions'][0] } ) - # Connections - input_connections = step.input_connections - if step.type is None or step.type == 'tool': - # Determine full (prefixed) names of valid input datasets - data_input_names = {} - - def callback( input, value, prefixed_name, prefixed_label ): - if isinstance( input, DataToolParameter ) or isinstance( input, DataCollectionToolParameter ): - data_input_names[ prefixed_name ] = True - # FIXME: this updates modules silently right now; messages from updates should be provided. - module.check_and_update_state() - visit_input_values( module.tool.inputs, module.state.inputs, callback ) - # Filter - # FIXME: this removes connection without displaying a message currently! - input_connections = [ conn for conn in input_connections if conn.input_name in data_input_names ] - # Encode input connections as dictionary - input_conn_dict = {} - unique_input_names = set( [conn.input_name for conn in input_connections] ) - for input_name in unique_input_names: - input_conn_dict[ input_name ] = \ - [ dict( id=conn.output_step.order_index, output_name=conn.output_name ) for conn in input_connections if conn.input_name == input_name ] - # Preserve backward compatability. Previously Galaxy - # assumed input connections would be dictionaries not - # lists of dictionaries, so replace any singleton list - # with just the dictionary so that workflows exported from - # newer Galaxy instances can be used with older Galaxy - # instances if they do no include multiple input - # tools. This should be removed at some point. Mirrored - # hack in _workflow_from_dict should never be removed so - # existing workflow exports continue to function. - for input_name, input_conn in dict(input_conn_dict).iteritems(): - if len(input_conn) == 1: - input_conn_dict[input_name] = input_conn[0] - step_dict['input_connections'] = input_conn_dict - # Position - step_dict['position'] = step.position - # Add to return value - data['steps'][step.order_index] = step_dict - return data + workflow_contents_manager = workflows.WorkflowContentsManager() + return workflow_contents_manager.workflow_to_dict( + trans, + stored, + ) class UsesFormDefinitionsMixin: https://bitbucket.org/galaxy/galaxy-central/commits/b05becef6c64/ Changeset: b05becef6c64 User: jmchilton Date: 2014-12-16 03:20:11+00:00 Summary: Move more workflow logic out of controller into manager. This logic for building up editor representation of the workflow. Introduce concept of a workflow to dict style - with 'export' and 'editor' as first cracks. Affected #: 4 files diff -r 2647ac82f98dcd90a133be765122f97d6dede45e -r b05becef6c64a4eb63bdc814a21243f2f5af799c lib/galaxy/managers/workflows.py --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -14,6 +14,7 @@ from galaxy.workflow.modules import module_factory, is_tool_module_type, ToolModule from galaxy.tools.parameters.basic import DataToolParameter, DataCollectionToolParameter from galaxy.tools.parameters import visit_input_values +from galaxy.web import url_for class WorkflowsManager( object ): @@ -314,8 +315,143 @@ errors.append( "This workflow contains cycles" ) return workflow, errors - def workflow_to_dict(self, trans, stored, style="export" ): + def workflow_to_dict( self, trans, stored, style="export" ): + """ Export the workflow contents to a dictionary ready for JSON-ification and to be + sent out via API for instance. There are two styles of export allowed 'editor' and 'export'. + The Galaxy team will do it best to preserve the backward compatibility of the 'export' stye - + but the 'editor' style is subject to rapid and unannounced changes. """ + if style == "editor": + return self._workflow_to_dict_editor( trans, stored ) + else: + return self._workflow_to_dict_export( trans, stored ) + + def _workflow_to_dict_editor(self, trans, stored): + """ + """ + workflow = stored.latest_workflow + # Pack workflow data into a dictionary and return + data = {} + data['name'] = workflow.name + data['steps'] = {} + data['upgrade_messages'] = {} + # For each step, rebuild the form and encode the state + for step in workflow.steps: + # Load from database representation + module = module_factory.from_workflow_step( trans, step ) + if not module: + step_annotation = self.get_item_annotation_obj( trans.sa_session, trans.user, step ) + annotation_str = "" + if step_annotation: + annotation_str = step_annotation.annotation + invalid_tool_form_html = """<div class="toolForm tool-node-error"><div class="toolFormTitle form-row-error">Unrecognized Tool: %s</div><div class="toolFormBody"><div class="form-row"> + The tool id '%s' for this tool is unrecognized.<br/><br/>To save this workflow, you will need to delete this step or enable the tool. + </div></div></div>""" % (step.tool_id, step.tool_id) + step_dict = { + 'id': step.order_index, + 'type': 'invalid', + 'tool_id': step.tool_id, + 'name': 'Unrecognized Tool: %s' % step.tool_id, + 'tool_state': None, + 'tooltip': None, + 'tool_errors': ["Unrecognized Tool Id: %s" % step.tool_id], + 'data_inputs': [], + 'data_outputs': [], + 'form_html': invalid_tool_form_html, + 'annotation': annotation_str, + 'input_connections': {}, + 'post_job_actions': {}, + 'workflow_outputs': [] + } + # Position + step_dict['position'] = step.position + # Add to return value + data['steps'][step.order_index] = step_dict + continue + # Fix any missing parameters + upgrade_message = module.check_and_update_state() + if upgrade_message: + # FIXME: Frontend should be able to handle workflow messages + # as a dictionary not just the values + data['upgrade_messages'][step.order_index] = upgrade_message.values() + # Get user annotation. + step_annotation = self.get_item_annotation_obj( trans.sa_session, trans.user, step ) + annotation_str = "" + if step_annotation: + annotation_str = step_annotation.annotation + # Pack attributes into plain dictionary + step_dict = { + 'id': step.order_index, + 'type': module.type, + 'tool_id': module.get_tool_id(), + 'name': module.get_name(), + 'tool_state': module.get_state(), + 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ), + 'tool_errors': module.get_errors(), + 'data_inputs': module.get_data_inputs(), + 'data_outputs': module.get_data_outputs(), + 'form_html': module.get_config_form(), + 'annotation': annotation_str, + 'post_job_actions': {}, + 'workflow_outputs': [] + } + # Connections + input_connections = step.input_connections + input_connections_type = {} + multiple_input = {} # Boolean value indicating if this can be mutliple + if step.type is None or step.type == 'tool': + # Determine full (prefixed) names of valid input datasets + data_input_names = {} + + def callback( input, value, prefixed_name, prefixed_label ): + if isinstance( input, DataToolParameter ) or isinstance( input, DataCollectionToolParameter ): + data_input_names[ prefixed_name ] = True + multiple_input[ prefixed_name ] = input.multiple + if isinstance( input, DataToolParameter ): + input_connections_type[ input.name ] = "dataset" + if isinstance( input, DataCollectionToolParameter ): + input_connections_type[ input.name ] = "dataset_collection" + visit_input_values( module.tool.inputs, module.state.inputs, callback ) + # Filter + # FIXME: this removes connection without displaying a message currently! + input_connections = [ conn for conn in input_connections if conn.input_name in data_input_names ] + # post_job_actions + pja_dict = {} + for pja in step.post_job_actions: + pja_dict[pja.action_type + pja.output_name] = dict( + action_type=pja.action_type, + output_name=pja.output_name, + action_arguments=pja.action_arguments + ) + step_dict['post_job_actions'] = pja_dict + #workflow outputs + outputs = [] + for output in step.workflow_outputs: + outputs.append(output.output_name) + step_dict['workflow_outputs'] = outputs + # Encode input connections as dictionary + input_conn_dict = {} + for conn in input_connections: + input_type = "dataset" + if conn.input_name in input_connections_type: + input_type = input_connections_type[ conn.input_name ] + conn_dict = dict( id=conn.output_step.order_index, output_name=conn.output_name, input_type=input_type ) + if conn.input_name in multiple_input: + if conn.input_name in input_conn_dict: + input_conn_dict[ conn.input_name ].append( conn_dict ) + else: + input_conn_dict[ conn.input_name ] = [ conn_dict ] + else: + input_conn_dict[ conn.input_name ] = conn_dict + step_dict['input_connections'] = input_conn_dict + # Position + step_dict['position'] = step.position + # Add to return value + data['steps'][step.order_index] = step_dict + return data + + def _workflow_to_dict_export( self, trans, stored ): + """ Export the workflow contents to a dictionary ready for JSON-ification and export. """ workflow = stored.latest_workflow workflow_annotation = self.get_item_annotation_obj( trans.sa_session, trans.user, stored ) diff -r 2647ac82f98dcd90a133be765122f97d6dede45e -r b05becef6c64a4eb63bdc814a21243f2f5af799c lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -28,6 +28,7 @@ super( BaseAPIController, self ).__init__( app ) self.history_manager = histories.HistoryManager() self.workflow_manager = workflows.WorkflowsManager( app ) + self.workflow_contents_manager = workflows.WorkflowContentsManager() @expose_api def index(self, trans, **kwd): @@ -221,7 +222,8 @@ """ stored_workflow = self.__get_stored_accessible_workflow( trans, workflow_id ) - ret_dict = self._workflow_to_dict( trans, stored_workflow ) + style = kwd.get("style", "export") + ret_dict = self.workflow_contents_manager.workflow_to_dict( trans, stored_workflow, style=style ) if not ret_dict: # This workflow has a tool that's missing from the distribution message = "Workflow cannot be exported due to missing tools." diff -r 2647ac82f98dcd90a133be765122f97d6dede45e -r b05becef6c64a4eb63bdc814a21243f2f5af799c lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -669,126 +669,8 @@ """ trans.workflow_building_mode = True stored = self.get_stored_workflow( trans, id, check_ownership=True, check_accessible=False ) - workflow = stored.latest_workflow - # Pack workflow data into a dictionary and return - data = {} - data['name'] = workflow.name - data['steps'] = {} - data['upgrade_messages'] = {} - # For each step, rebuild the form and encode the state - for step in workflow.steps: - # Load from database representation - module = module_factory.from_workflow_step( trans, step ) - if not module: - step_annotation = self.get_item_annotation_obj( trans.sa_session, trans.user, step ) - annotation_str = "" - if step_annotation: - annotation_str = step_annotation.annotation - invalid_tool_form_html = """<div class="toolForm tool-node-error"><div class="toolFormTitle form-row-error">Unrecognized Tool: %s</div><div class="toolFormBody"><div class="form-row"> - The tool id '%s' for this tool is unrecognized.<br/><br/>To save this workflow, you will need to delete this step or enable the tool. - </div></div></div>""" % (step.tool_id, step.tool_id) - step_dict = { - 'id': step.order_index, - 'type': 'invalid', - 'tool_id': step.tool_id, - 'name': 'Unrecognized Tool: %s' % step.tool_id, - 'tool_state': None, - 'tooltip': None, - 'tool_errors': ["Unrecognized Tool Id: %s" % step.tool_id], - 'data_inputs': [], - 'data_outputs': [], - 'form_html': invalid_tool_form_html, - 'annotation': annotation_str, - 'input_connections': {}, - 'post_job_actions': {}, - 'workflow_outputs': [] - } - # Position - step_dict['position'] = step.position - # Add to return value - data['steps'][step.order_index] = step_dict - continue - # Fix any missing parameters - upgrade_message = module.check_and_update_state() - if upgrade_message: - # FIXME: Frontend should be able to handle workflow messages - # as a dictionary not just the values - data['upgrade_messages'][step.order_index] = upgrade_message.values() - # Get user annotation. - step_annotation = self.get_item_annotation_obj( trans.sa_session, trans.user, step ) - annotation_str = "" - if step_annotation: - annotation_str = step_annotation.annotation - # Pack attributes into plain dictionary - step_dict = { - 'id': step.order_index, - 'type': module.type, - 'tool_id': module.get_tool_id(), - 'name': module.get_name(), - 'tool_state': module.get_state(), - 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ), - 'tool_errors': module.get_errors(), - 'data_inputs': module.get_data_inputs(), - 'data_outputs': module.get_data_outputs(), - 'form_html': module.get_config_form(), - 'annotation': annotation_str, - 'post_job_actions': {}, - 'workflow_outputs': [] - } - # Connections - input_connections = step.input_connections - input_connections_type = {} - multiple_input = {} # Boolean value indicating if this can be mutliple - if step.type is None or step.type == 'tool': - # Determine full (prefixed) names of valid input datasets - data_input_names = {} - - def callback( input, value, prefixed_name, prefixed_label ): - if isinstance( input, DataToolParameter ) or isinstance( input, DataCollectionToolParameter ): - data_input_names[ prefixed_name ] = True - multiple_input[ prefixed_name ] = input.multiple - if isinstance( input, DataToolParameter ): - input_connections_type[ input.name ] = "dataset" - if isinstance( input, DataCollectionToolParameter ): - input_connections_type[ input.name ] = "dataset_collection" - visit_input_values( module.tool.inputs, module.state.inputs, callback ) - # Filter - # FIXME: this removes connection without displaying a message currently! - input_connections = [ conn for conn in input_connections if conn.input_name in data_input_names ] - # post_job_actions - pja_dict = {} - for pja in step.post_job_actions: - pja_dict[pja.action_type + pja.output_name] = dict( - action_type=pja.action_type, - output_name=pja.output_name, - action_arguments=pja.action_arguments - ) - step_dict['post_job_actions'] = pja_dict - #workflow outputs - outputs = [] - for output in step.workflow_outputs: - outputs.append(output.output_name) - step_dict['workflow_outputs'] = outputs - # Encode input connections as dictionary - input_conn_dict = {} - for conn in input_connections: - input_type = "dataset" - if conn.input_name in input_connections_type: - input_type = input_connections_type[ conn.input_name ] - conn_dict = dict( id=conn.output_step.order_index, output_name=conn.output_name, input_type=input_type ) - if conn.input_name in multiple_input: - if conn.input_name in input_conn_dict: - input_conn_dict[ conn.input_name ].append( conn_dict ) - else: - input_conn_dict[ conn.input_name ] = [ conn_dict ] - else: - input_conn_dict[ conn.input_name ] = conn_dict - step_dict['input_connections'] = input_conn_dict - # Position - step_dict['position'] = step.position - # Add to return value - data['steps'][step.order_index] = step_dict - return data + workflow_contents_manager = workflows.WorkflowContentsManager() + return workflow_contents_manager.workflow_to_dict( trans, stored, style="editor" ) @web.json def save_workflow( self, trans, id, workflow_data ): diff -r 2647ac82f98dcd90a133be765122f97d6dede45e -r b05becef6c64a4eb63bdc814a21243f2f5af799c test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -324,6 +324,46 @@ first_input = downloaded_workflow[ "steps" ][ "0" ][ "inputs" ][ 0 ] assert first_input[ "name" ] == "WorkflowInput1" assert first_input[ "description" ] == "input1 description" + self._assert_has_keys( downloaded_workflow, "a_galaxy_workflow", "format-version", "annotation", "uuid", "steps" ) + for step in downloaded_workflow["steps"].values(): + self._assert_has_keys( + step, + 'id', + 'type', + 'tool_id', + 'tool_version', + 'name', + 'tool_state', + 'tool_errors', + 'annotation', + 'inputs', + 'user_outputs', + 'outputs' + ) + if step['type'] == "tool": + self._assert_has_keys( step, "post_job_actions" ) + + def test_export_editor( self ): + uploaded_workflow_id = self.workflow_populator.simple_workflow( "test_for_export" ) + downloaded_workflow = self._download_workflow( uploaded_workflow_id, style="editor" ) + self._assert_has_keys( downloaded_workflow, "name", "steps", "upgrade_messages" ) + for step in downloaded_workflow["steps"].values(): + self._assert_has_keys( + step, + 'id', + 'type', + 'tool_id', + 'name', + 'tool_state', + 'tooltip', + 'tool_errors', + 'data_inputs', + 'data_outputs', + 'form_html', + 'annotation', + 'post_job_actions', + 'workflow_outputs', + ) def test_import_export_with_runtime_inputs( self ): workflow = self.workflow_populator.load_workflow_from_resource( name="test_workflow_with_runtime_input" ) @@ -771,8 +811,11 @@ ) return self._post( route, import_data ) - def _download_workflow(self, workflow_id): - download_response = self._get( "workflows/%s/download" % workflow_id ) + def _download_workflow(self, workflow_id, style=None): + params = {} + if style: + params = {"style": style} + download_response = self._get( "workflows/%s/download" % workflow_id, params ) self._assert_status_code_is( download_response, 200 ) downloaded_workflow = download_response.json() return downloaded_workflow https://bitbucket.org/galaxy/galaxy-central/commits/3e807234d175/ Changeset: 3e807234d175 User: jmchilton Date: 2014-12-16 03:20:11+00:00 Summary: Introduce yet another workflow to_dict style - 'instance'. This is the style used by workflow 'show' - this consolidates all step handling to_dict style-logic from controller/base.py, controller/workflow.py, and api/workflows.py into the new WorkflowContentsManager - with API test cases for everything. Affected #: 2 files diff -r b05becef6c64a4eb63bdc814a21243f2f5af799c -r 3e807234d17565ef13a6ade7157af87c690c630b lib/galaxy/managers/workflows.py --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -317,12 +317,17 @@ def workflow_to_dict( self, trans, stored, style="export" ): """ Export the workflow contents to a dictionary ready for JSON-ification and to be - sent out via API for instance. There are two styles of export allowed 'editor' and 'export'. - The Galaxy team will do it best to preserve the backward compatibility of the 'export' stye - - but the 'editor' style is subject to rapid and unannounced changes. + sent out via API for instance. There are three styles of export allowed 'export', 'instance', and + 'editor'. The Galaxy team will do it best to preserve the backward compatibility of the + 'export' stye - this is the export method meant to be portable across Galaxy instances and over + time. The 'editor' style is subject to rapid and unannounced changes. The 'instance' export + option describes the workflow in a context more tied to the current Galaxy instance and includes + fields like 'url' and 'url' and actual unencoded step ids instead of 'order_index'. """ if style == "editor": return self._workflow_to_dict_editor( trans, stored ) + elif style == "instance": + return self._workflow_to_dict_instance( trans, stored ) else: return self._workflow_to_dict_export( trans, stored ) @@ -552,6 +557,45 @@ data['steps'][step.order_index] = step_dict return data + def _workflow_to_dict_instance(self, trans, stored): + item = stored.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } ) + workflow = stored.latest_workflow + item['url'] = url_for('workflow', id=item['id']) + item['owner'] = stored.user.username + inputs = {} + for step in workflow.steps: + step_type = step.type + if step_type in ['data_input', 'data_collection_input']: + if step.tool_inputs and "name" in step.tool_inputs: + label = step.tool_inputs['name'] + elif step_type == "data_input": + label = "Input Dataset" + elif step_type == "data_collection_input": + label = "Input Dataset Collection" + else: + raise ValueError("Invalid step_type %s" % step_type) + inputs[step.id] = {'label': label, 'value': ""} + else: + pass + # Eventually, allow regular tool parameters to be inserted and modified at runtime. + # p = step.get_required_parameters() + item['inputs'] = inputs + item['annotation'] = self.get_item_annotation_str( trans.sa_session, stored.user, stored ) + steps = {} + for step in workflow.steps: + steps[step.id] = {'id': step.id, + 'type': step.type, + 'tool_id': step.tool_id, + 'tool_version': step.tool_version, + 'annotation': self.get_item_annotation_str( trans.sa_session, stored.user, step ), + 'tool_inputs': step.tool_inputs, + 'input_steps': {}} + for conn in step.input_connections: + steps[step.id]['input_steps'][conn.input_name] = {'source_step': conn.output_step_id, + 'step_output': conn.output_name} + item['steps'] = steps + return item + class MissingToolsException(object): diff -r b05becef6c64a4eb63bdc814a21243f2f5af799c -r 3e807234d17565ef13a6ade7157af87c690c630b lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -76,8 +76,7 @@ if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: message = "Workflow is neither importable, nor owned by or shared with current user" raise exceptions.ItemAccessibilityException( message ) - latest_workflow = stored_workflow.latest_workflow - return self.__encode_workflow( trans, stored_workflow, latest_workflow ) + return self.workflow_contents_manager.workflow_to_dict( trans, stored_workflow, style="instance" ) @expose_api def create(self, trans, payload, **kwd): @@ -303,7 +302,7 @@ else: message = "Updating workflow requires dictionary containing 'workflow' attribute with new JSON description." raise exceptions.RequestParameterInvalidException( message ) - return self.__encode_workflow( trans, stored_workflow, workflow ) + return self.workflow_contents_manager.workflow_to_dict( trans, stored_workflow, style="instance" ) def __api_import_new_workflow( self, trans, payload, **kwd ): data = payload['workflow'] @@ -510,44 +509,6 @@ ) return self.__encode_invocation_step( trans, invocation_step ) - def __encode_workflow( self, trans, stored_workflow, workflow ): - item = stored_workflow.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } ) - item['url'] = url_for('workflow', id=item['id']) - item['owner'] = stored_workflow.user.username - inputs = {} - for step in workflow.steps: - step_type = step.type - if step_type in ['data_input', 'data_collection_input']: - if step.tool_inputs and "name" in step.tool_inputs: - label = step.tool_inputs['name'] - elif step_type == "data_input": - label = "Input Dataset" - elif step_type == "data_collection_input": - label = "Input Dataset Collection" - else: - raise ValueError("Invalid step_type %s" % step_type) - inputs[step.id] = {'label': label, 'value': ""} - else: - pass - # Eventually, allow regular tool parameters to be inserted and modified at runtime. - # p = step.get_required_parameters() - item['inputs'] = inputs - item['annotation'] = self.get_item_annotation_str( trans.sa_session, stored_workflow.user, stored_workflow ) - steps = {} - for step in workflow.steps: - steps[step.id] = {'id': step.id, - 'type': step.type, - 'tool_id': step.tool_id, - 'tool_version': step.tool_version, - 'annotation': self.get_item_annotation_str( trans.sa_session, stored_workflow.user, step ), - 'tool_inputs': step.tool_inputs, - 'input_steps': {}} - for conn in step.input_connections: - steps[step.id]['input_steps'][conn.input_name] = {'source_step': conn.output_step_id, - 'step_output': conn.output_name} - item['steps'] = steps - return item - def __encode_invocation_step( self, trans, invocation_step ): return self.encode_all_ids( trans, https://bitbucket.org/galaxy/galaxy-central/commits/4b542b64f6b2/ Changeset: 4b542b64f6b2 User: jmchilton Date: 2014-12-16 03:20:11+00:00 Summary: Allow implicit connections between workflow steps (no editor GUI yet). This means steps that are not connecting an output of one step to the input of another. This could potentially address all sorts of untraditional (in a Galaxy sense) workflows where some sort of data is managed externally. The most important use I think I have heard discussed is that of data managers - this can be used in cases where data managers depend on one another (grab the fasta files in one step, index them in another) or workflows where a downstream analysis depends on index data populated via data managers in earlier steps. Not really sure how to represent these in the workflow editor - but this is a power user feature anyway so hopefully that is not super pressing. The YAML to workflow DSL supports the operation (see test cases) so these power users (a euphemism for Dan I guess) can just use that for now. Affected #: 6 files diff -r 3e807234d17565ef13a6ade7157af87c690c630b -r 4b542b64f6b2add47fd55d535f06d026f26f7e3c lib/galaxy/managers/workflows.py --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -529,7 +529,7 @@ visit_input_values( module.tool.inputs, module.state.inputs, callback ) # Filter # FIXME: this removes connection without displaying a message currently! - input_connections = [ conn for conn in input_connections if conn.input_name in data_input_names ] + input_connections = [ conn for conn in input_connections if (conn.input_name in data_input_names or conn.non_data_connection) ] # Encode input connections as dictionary input_conn_dict = {} diff -r 3e807234d17565ef13a6ade7157af87c690c630b -r 4b542b64f6b2add47fd55d535f06d026f26f7e3c lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3077,6 +3077,12 @@ class WorkflowStepConnection( object ): + # Constant used in lieu of output_name and input_name to indicate an + # implicit connection between two steps that is not dependent on a dataset + # or a dataset collection. Allowing for instance data manager steps to setup + # index data before a normal tool runs or for workflows that manage data + # outside of Galaxy. + NON_DATA_CONNECTION = "__NO_INPUT_OUTPUT_NAME__" def __init__( self ): self.output_step_id = None @@ -3084,6 +3090,15 @@ self.input_step_id = None self.input_name = None + def set_non_data_connection(self): + self.output_name = WorkflowStepConnection.NON_DATA_CONNECTION + self.input_name = WorkflowStepConnection.NON_DATA_CONNECTION + + @property + def non_data_connection(self): + return (self.output_name == WorkflowStepConnection.NON_DATA_CONNECTION and + self.input_name == WorkflowStepConnection.NON_DATA_CONNECTION) + class WorkflowOutput(object): @@ -3153,6 +3168,13 @@ step_invocations[ step_id ].append( invocation_step ) return step_invocations + def step_invocations_for_step_id( self, step_id ): + step_invocations = [] + for invocation_step in self.steps: + if step_id == invocation_step.workflow_step_id: + step_invocations.append( invocation_step ) + return step_invocations + @staticmethod def poll_active_workflow_ids( sa_session, diff -r 3e807234d17565ef13a6ade7157af87c690c630b -r 4b542b64f6b2add47fd55d535f06d026f26f7e3c lib/galaxy/workflow/run.py --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -136,6 +136,8 @@ for step in remaining_steps: jobs = None try: + self.__check_implicitly_dependent_steps(step) + jobs = self._invoke_step( step ) for job in (util.listify( jobs ) or [None]): # Record invocation @@ -160,6 +162,38 @@ # invocations. return self.progress.outputs + def __check_implicitly_dependent_steps( self, step ): + """ Method will delay the workflow evaluation if implicitly dependent + steps (steps dependent but not through an input->output way) are not + yet complete. + """ + for input_connection in step.input_connections: + if input_connection.non_data_connection: + output_id = input_connection.output_step.id + self.__check_implicitly_dependent_step( output_id ) + + def __check_implicitly_dependent_step( self, output_id ): + step_invocations = self.workflow_invocation.step_invocations_for_step_id( output_id ) + + # No steps created yet - have to delay evaluation. + if not step_invocations: + raise modules.DelayedWorkflowEvaluation() + + for step_invocation in step_invocations: + job = step_invocation.job + if job: + # At least one job in incomplete. + if not job.finished: + raise modules.DelayedWorkflowEvaluation() + + if job.state != job.states.OK: + raise modules.CancelWorkflowEvaluation() + + else: + # TODO: Handle implicit dependency on stuff like + # pause steps. + pass + def _invoke_step( self, step ): jobs = step.module.execute( self.trans, self.progress, self.workflow_invocation, step ) return jobs diff -r 3e807234d17565ef13a6ade7157af87c690c630b -r 4b542b64f6b2add47fd55d535f06d026f26f7e3c test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -107,7 +107,7 @@ invocation_details = invocation_details_response.json() return invocation_details - def _run_jobs( self, jobs_yaml, history_id=None ): + def _run_jobs( self, jobs_yaml, history_id=None, wait=True ): if history_id is None: history_id = self.history_id workflow_id = self._upload_yaml_workflow( @@ -153,8 +153,9 @@ invocation_id = invocation[ "id" ] # Wait for workflow to become fully scheduled and then for all jobs # complete. - self.wait_for_invocation( workflow_id, invocation_id ) - self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + if wait: + self.wait_for_invocation( workflow_id, invocation_id ) + self.dataset_populator.wait_for_history( history_id, assert_ok=True ) jobs = self._history_jobs( history_id ) return RunJobsSummary( history_id=history_id, @@ -516,6 +517,60 @@ invocation = self._invocation_details( uploaded_workflow_id, invocation_id ) assert invocation[ 'state' ] == 'cancelled' + def test_run_with_implicit_connection( self ): + history_id = self.dataset_populator.new_history() + run_summary = self._run_jobs(""" +steps: +- label: test_input + type: input +- label: first_cat + tool_id: cat1 + state: + input1: + $link: test_input +- label: the_pause + type: pause + connect: + input: + - first_cat#out_file1 +- label: second_cat + tool_id: cat1 + state: + input1: + $link: the_pause +- label: third_cat + tool_id: random_lines1 + connect: + $step: second_cat + state: + num_lines: 1 + input: + $link: test_input + seed_source: + seed_source_selector: set_seed + seed: asdf + __current_case__: 1 +test_data: + test_input: "hello world" +""", history_id=history_id, wait=False) + time.sleep( 2 ) + history_id = run_summary.history_id + workflow_id = run_summary.workflow_id + invocation_id = run_summary.workflow_id + self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + invocation = self._invocation_details( workflow_id, invocation_id ) + assert invocation[ 'state' ] != 'scheduled' + # Expect two jobs - the upload and first cat. randomlines shouldn't run + # it is implicitly dependent on second cat. + assert len( self._history_jobs( history_id ) ) == 2 + + self.__review_paused_steps( workflow_id, invocation_id, order_index=2, action=True ) + self.wait_for_invocation( workflow_id, invocation_id ) + time.sleep(1) + self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + time.sleep(1) + assert len( self._history_jobs( history_id ) ) == 4 + def test_cannot_run_inaccessible_workflow( self ): workflow = self.workflow_populator.load_workflow( name="test_for_run_cannot_access" ) workflow_request, history_id = self._setup_workflow_run( workflow ) diff -r 3e807234d17565ef13a6ade7157af87c690c630b -r 4b542b64f6b2add47fd55d535f06d026f26f7e3c test/api/test_workflows_from_yaml.py --- a/test/api/test_workflows_from_yaml.py +++ b/test/api/test_workflows_from_yaml.py @@ -102,3 +102,34 @@ print self._get("workflows/%s/download" % workflow_id).json() assert False # TODO: fill out test... + + def test_implicit_connections( self ): + workflow_id = self._upload_yaml_workflow(""" +- label: test_input + type: input +- label: first_cat + tool_id: cat1 + state: + input1: + $link: test_input +- label: the_pause + type: pause + connect: + input: + - first_cat#out_file1 +- label: second_cat + tool_id: cat1 + state: + input1: + $link: the_pause +- label: third_cat + tool_id: cat1 + connect: + $step: second_cat + state: + input1: + $link: test_input +""") + workflow = self._get("workflows/%s/download" % workflow_id).json() + print workflow + assert False diff -r 3e807234d17565ef13a6ade7157af87c690c630b -r 4b542b64f6b2add47fd55d535f06d026f26f7e3c test/api/yaml_to_workflow.py --- a/test/api/yaml_to_workflow.py +++ b/test/api/yaml_to_workflow.py @@ -262,6 +262,8 @@ values = [ values ] for value in values: if not isinstance(value, dict): + if key == "$step": + value += "#__NO_INPUT_OUTPUT_NAME__" value_parts = str(value).split("#") if len(value_parts) == 1: value_parts.append("output") @@ -270,6 +272,8 @@ id = context.labels[id] value = {"id": int(id), "output_name": value_parts[1]} input_connection_value.append(value) + if key == "$step": + key = "__NO_INPUT_OUTPUT_NAME__" input_connections[key] = input_connection_value https://bitbucket.org/galaxy/galaxy-central/commits/10d20731e6cc/ Changeset: 10d20731e6cc User: jmchilton Date: 2014-12-16 03:20:12+00:00 Summary: Slightly improved error message for incorrect workflow connection uploads. Affected #: 1 file diff -r 4b542b64f6b2add47fd55d535f06d026f26f7e3c -r 10d20731e6ccbe4a48a110d95ffe02a0e04ffcd3 lib/galaxy/managers/workflows.py --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -201,6 +201,10 @@ if not isinstance(conn_list, list): # Older style singleton connection conn_list = [conn_list] for conn_dict in conn_list: + if 'output_name' not in conn_dict or 'id' not in conn_dict: + template = "Invalid connection [%s] - must be dict with output_name and id fields." + message = template % conn_dict + raise exceptions.MessageException(message) conn = model.WorkflowStepConnection() conn.input_step = step conn.input_name = input_name https://bitbucket.org/galaxy/galaxy-central/commits/afed68c51bc2/ Changeset: afed68c51bc2 User: jmchilton Date: 2014-12-16 03:20:12+00:00 Summary: De-duplication of step creation across update and create worklfows. Affected #: 1 file diff -r 10d20731e6ccbe4a48a110d95ffe02a0e04ffcd3 -r afed68c51bc23c80aa99c9379649476ffba4f796 lib/galaxy/managers/workflows.py --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -167,14 +167,11 @@ # First pass to build step objects and populate basic values for step_index in step_indices: step_dict = supplied_steps[ step_index ] - # Create the model class for the step - step = model.WorkflowStep() + + module, step = self.__module_from_dict( trans, step_dict, secure=False ) steps.append( step ) steps_by_external_id[ step_dict['id' ] ] = step - # FIXME: Position should be handled inside module - step.position = step_dict['position'] - module = module_factory.from_dict( trans, step_dict, secure=False ) - module.save_to_step( step ) + if module.type == 'tool' and module.tool is None: # A required tool is not available in the local Galaxy instance. missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) @@ -185,13 +182,7 @@ step.config = json.dumps(step_dict) if step.tool_errors: workflow.has_errors = True - # Stick this in the step temporarily - step.temp_input_connections = step_dict['input_connections'] - # Save step annotation. - annotation = step_dict[ 'annotation' ] - if annotation: - annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) - self.add_item_annotation( trans.sa_session, trans.get_user(), step, annotation ) + # Second pass to deal with connections between steps for step in steps: # Input connections @@ -269,14 +260,10 @@ # First pass to build step objects and populate basic values for key, step_dict in data['steps'].iteritems(): + module, step = self.__module_from_dict( trans, step_dict, secure=from_editor ) # Create the model class for the step - step = model.WorkflowStep() steps.append( step ) steps_by_external_id[ step_dict['id' ] ] = step - # FIXME: Position should be handled inside module - step.position = step_dict['position'] - module = module_factory.from_dict( trans, step_dict, secure=from_editor ) - module.save_to_step( step ) if 'workflow_outputs' in step_dict: for output_name in step_dict['workflow_outputs']: m = model.WorkflowOutput(workflow_step=step, output_name=output_name) @@ -284,13 +271,7 @@ if step.tool_errors: # DBTODO Check for conditional inputs here. workflow.has_errors = True - # Stick this in the step temporarily - step.temp_input_connections = step_dict['input_connections'] - # Save step annotation. - annotation = step_dict[ 'annotation' ] - if annotation: - annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) - self.add_item_annotation( trans.sa_session, trans.get_user(), step, annotation ) + # Second pass to deal with connections between steps for step in steps: # Input connections @@ -600,6 +581,28 @@ item['steps'] = steps return item + def __module_from_dict( self, trans, step_dict, secure ): + """ Create a WorkflowStep model object and corrsponding module representing + type-specific functionality from the incoming dicitionary. + """ + step = model.WorkflowStep() + + # TODO: Consider handling position inside module. + step.position = step_dict['position'] + + module = module_factory.from_dict( trans, step_dict, secure=secure ) + module.save_to_step( step ) + + annotation = step_dict[ 'annotation' ] + if annotation: + annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) + self.add_item_annotation( trans.sa_session, trans.get_user(), step, annotation ) + + # Stick this in the step temporarily + step.temp_input_connections = step_dict['input_connections'] + + return module, step + class MissingToolsException(object): https://bitbucket.org/galaxy/galaxy-central/commits/f7a77c6b57c7/ Changeset: f7a77c6b57c7 User: jmchilton Date: 2014-12-16 03:20:12+00:00 Summary: De-duplicatation for setting up workflow connections during creation/update. Affected #: 1 file diff -r afed68c51bc23c80aa99c9379649476ffba4f796 -r f7a77c6b57c74750097c3802185716ebd4e912b1 lib/galaxy/managers/workflows.py --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -184,24 +184,7 @@ workflow.has_errors = True # Second pass to deal with connections between steps - for step in steps: - # Input connections - for input_name, conn_list in step.temp_input_connections.iteritems(): - if not conn_list: - continue - if not isinstance(conn_list, list): # Older style singleton connection - conn_list = [conn_list] - for conn_dict in conn_list: - if 'output_name' not in conn_dict or 'id' not in conn_dict: - template = "Invalid connection [%s] - must be dict with output_name and id fields." - message = template % conn_dict - raise exceptions.MessageException(message) - conn = model.WorkflowStepConnection() - conn.input_step = step - conn.input_name = input_name - conn.output_name = conn_dict['output_name'] - conn.output_step = steps_by_external_id[ conn_dict['id'] ] - del step.temp_input_connections + self.__connect_workflow_steps( steps, steps_by_external_id ) # Order the steps if possible attach_ordered_steps( workflow, steps ) @@ -273,18 +256,8 @@ workflow.has_errors = True # Second pass to deal with connections between steps - for step in steps: - # Input connections - for input_name, conns in step.temp_input_connections.iteritems(): - if conns: - conn_dicts = conns if isinstance(conns, list) else [ conns ] - for conn_dict in conn_dicts: - conn = model.WorkflowStepConnection() - conn.input_step = step - conn.input_name = input_name - conn.output_name = conn_dict['output_name'] - conn.output_step = steps_by_external_id[ conn_dict['id'] ] - del step.temp_input_connections + self.__connect_workflow_steps( steps, steps_by_external_id ) + # Order the steps if possible attach_ordered_steps( workflow, steps ) # Connect up @@ -603,6 +576,31 @@ return module, step + def __connect_workflow_steps( self, steps, steps_by_external_id ): + """ Second pass to deal with connections between steps. + + Create workflow connection objects using externally specified ids + using during creation or update. + """ + for step in steps: + # Input connections + for input_name, conn_list in step.temp_input_connections.iteritems(): + if not conn_list: + continue + if not isinstance(conn_list, list): # Older style singleton connection + conn_list = [conn_list] + for conn_dict in conn_list: + if 'output_name' not in conn_dict or 'id' not in conn_dict: + template = "Invalid connection [%s] - must be dict with output_name and id fields." + message = template % conn_dict + raise exceptions.MessageException(message) + conn = model.WorkflowStepConnection() + conn.input_step = step + conn.input_name = input_name + conn.output_name = conn_dict['output_name'] + conn.output_step = steps_by_external_id[ conn_dict['id'] ] + del step.temp_input_connections + class MissingToolsException(object): https://bitbucket.org/galaxy/galaxy-central/commits/f9595a9840c1/ Changeset: f9595a9840c1 User: jmchilton Date: 2014-12-16 03:20:12+00:00 Summary: Create abstraction for walking over step dicts to share between create/update methods. Affected #: 1 file diff -r f7a77c6b57c74750097c3802185716ebd4e912b1 -r f9595a9840c172a85fd8a5335688afb924afaa97 lib/galaxy/managers/workflows.py --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -155,19 +155,7 @@ # the local Galaxy instance. Each tuple in the list of missing_tool_tups # will be ( tool_id, tool_name, tool_version ). missing_tool_tups = [] - supplied_steps = data[ 'steps' ] - # Try to iterate through imported workflow in such a way as to - # preserve step order. - step_indices = supplied_steps.keys() - try: - step_indices = sorted( step_indices, key=int ) - except ValueError: - # to defensive, were these ever or will they ever not be integers? - pass - # First pass to build step objects and populate basic values - for step_index in step_indices: - step_dict = supplied_steps[ step_index ] - + for step_dict in self.__walk_step_dicts( data ): module, step = self.__module_from_dict( trans, step_dict, secure=False ) steps.append( step ) steps_by_external_id[ step_dict['id' ] ] = step @@ -242,7 +230,7 @@ raise MissingToolsException(workflow, errors) # First pass to build step objects and populate basic values - for key, step_dict in data['steps'].iteritems(): + for step_dict in self.__walk_step_dicts( data ): module, step = self.__module_from_dict( trans, step_dict, secure=from_editor ) # Create the model class for the step steps.append( step ) @@ -554,6 +542,24 @@ item['steps'] = steps return item + def __walk_step_dicts( self, data ): + """ Walk over the supplid step dictionaries and return them in a way designed + to preserve step order when possible. + """ + supplied_steps = data[ 'steps' ] + # Try to iterate through imported workflow in such a way as to + # preserve step order. + step_indices = supplied_steps.keys() + try: + step_indices = sorted( step_indices, key=int ) + except ValueError: + # to defensive, were these ever or will they ever not be integers? + pass + # First pass to build step objects and populate basic values + for step_index in step_indices: + step_dict = supplied_steps[ step_index ] + yield step_dict + def __module_from_dict( self, trans, step_dict, secure ): """ Create a WorkflowStep model object and corrsponding module representing type-specific functionality from the incoming dicitionary. https://bitbucket.org/galaxy/galaxy-central/commits/10696df64a3a/ Changeset: 10696df64a3a User: jmchilton Date: 2014-12-16 03:20:12+00:00 Summary: Augment workflow step model for improved tracking. Give every step a UUID that can be preserved across edit to the workflow. Likewise - allow every step to be given a label (a unique short name for that workflow) - that allows for a human consumable way to reference steps for use in tests and when driving workflows via the API. Workflow editor doesn't yet (and might never) display these attributes but it does preserve them across workflow saves. Implement automated testing that uploading workflows, updating workflows, and exporting them handle UUID and labels. Manually tested workflow editor preserves labels and UUID across changes. Affected #: 6 files diff -r f9595a9840c172a85fd8a5335688afb924afaa97 -r 10696df64a3a439ba87f0e3b6089ddd924c37f45 client/galaxy/scripts/galaxy.workflow_editor.canvas.js --- a/client/galaxy/scripts/galaxy.workflow_editor.canvas.js +++ b/client/galaxy/scripts/galaxy.workflow_editor.canvas.js @@ -784,6 +784,8 @@ this.tooltip = data.tooltip ? data.tooltip : ""; this.annotation = data.annotation; this.post_job_actions = data.post_job_actions ? data.post_job_actions : {}; + this.label = data.label; + this.uuid = data.uuid; this.workflow_outputs = data.workflow_outputs ? data.workflow_outputs : []; var node = this; @@ -991,6 +993,8 @@ position : $(node.element).position(), annotation: node.annotation, post_job_actions: node.post_job_actions, + uuid: node.uuid, + label: node.label, workflow_outputs: node.workflow_outputs }; nodes[ node.id ] = node_data; diff -r f9595a9840c172a85fd8a5335688afb924afaa97 -r 10696df64a3a439ba87f0e3b6089ddd924c37f45 lib/galaxy/managers/workflows.py --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -312,6 +312,8 @@ 'annotation': annotation_str, 'input_connections': {}, 'post_job_actions': {}, + 'uuid': str(step.uuid), + 'label': step.label or None, 'workflow_outputs': [] } # Position @@ -344,6 +346,8 @@ 'form_html': module.get_config_form(), 'annotation': annotation_str, 'post_job_actions': {}, + 'uuid': str(step.uuid), + 'label': step.label or None, 'workflow_outputs': [] } # Connections @@ -438,6 +442,8 @@ 'name': module.get_name(), 'tool_state': module.get_state( secure=False ), 'tool_errors': module.get_errors(), + 'uuid': str(step.uuid), + 'label': step.label or None, ## 'data_inputs': module.get_data_inputs(), ## 'data_outputs': module.get_data_outputs(), 'annotation': annotation_str @@ -568,7 +574,10 @@ # TODO: Consider handling position inside module. step.position = step_dict['position'] - + if "uuid" in step_dict: + step.uuid = step_dict["uuid"] + if "label" in step_dict: + step.label = step_dict["label"] module = module_factory.from_dict( trans, step_dict, secure=secure ) module.save_to_step( step ) diff -r f9595a9840c172a85fd8a5335688afb924afaa97 -r 10696df64a3a439ba87f0e3b6089ddd924c37f45 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3074,6 +3074,7 @@ self.position = None self.input_connections = [] self.config = None + self.uuid = uuid4() class WorkflowStepConnection( object ): diff -r f9595a9840c172a85fd8a5335688afb924afaa97 -r 10696df64a3a439ba87f0e3b6089ddd924c37f45 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -715,6 +715,8 @@ Column( "position", JSONType ), Column( "config", JSONType ), Column( "order_index", Integer ), + Column( "uuid", UUIDType ), + Column( "label", Unicode(255) ), ## Column( "input_connections", JSONType ) ) diff -r f9595a9840c172a85fd8a5335688afb924afaa97 -r 10696df64a3a439ba87f0e3b6089ddd924c37f45 lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py @@ -0,0 +1,56 @@ +""" +Migration script to enhance workflow step usability by adding labels and UUIDs. +""" +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +from galaxy.model.custom_types import * + +import datetime +now = datetime.datetime.utcnow + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData() + + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + metadata.reflect() + + StepLabel_column = Column( "label", TrimmedString(255) ) + StepUUID_column = Column( "uuid", UUIDType, nullable=True ) + __add_column( StepLabel_column, "workflow_step", metadata ) + __add_column( StepUUID_column, "workflow_step", metadata ) + + +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + + for table in TABLES: + __drop(table) + + __drop_column( "label", "workflow_step", metadata ) + __drop_column( "uuid", "workflow_step", metadata ) + + +def __add_column(column, table_name, metadata, **kwds): + try: + table = Table( table_name, metadata, autoload=True ) + column.create( table, **kwds ) + except Exception as e: + print str(e) + log.exception( "Adding column %s column failed." % column) + + +def __drop_column( column_name, table_name, metadata ): + try: + table = Table( table_name, metadata, autoload=True ) + getattr( table.c, column_name ).drop() + except Exception as e: + print str(e) + log.exception( "Dropping column %s failed." % column_name ) diff -r f9595a9840c172a85fd8a5335688afb924afaa97 -r 10696df64a3a439ba87f0e3b6089ddd924c37f45 test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -3,6 +3,7 @@ from base import api from json import dumps from collections import namedtuple +from uuid import uuid4 import time @@ -227,9 +228,11 @@ def test_upload_deprecated( self ): self.__test_upload( use_deprecated_route=True ) - def __test_upload( self, use_deprecated_route=False, name="test_import" ): + def __test_upload( self, use_deprecated_route=False, name="test_import", workflow=None ): + if workflow is None: + workflow = self.workflow_populator.load_workflow( name=name ) data = dict( - workflow=dumps( self.workflow_populator.load_workflow( name=name ) ), + workflow=dumps( workflow ), ) if use_deprecated_route: route = "workflows/upload" @@ -242,8 +245,25 @@ def test_update( self ): original_workflow = self.workflow_populator.load_workflow( name="test_import" ) + uuids = {} + labels = {} - upload_response = self.__test_upload( ) + for order_index, step_dict in original_workflow["steps"].iteritems(): + uuid = str(uuid4()) + step_dict["uuid"] = uuid + uuids[order_index] = uuid + label = "label_%s" % order_index + step_dict["label"] = label + labels[order_index] = label + + def check_label_and_uuid(order_index, step_dict): + assert order_index in uuids + assert order_index in labels + + self.assertEquals(uuids[order_index], step_dict["uuid"]) + self.assertEquals(labels[order_index], step_dict["label"]) + + upload_response = self.__test_upload( workflow=original_workflow ) workflow_id = upload_response.json()["id"] def update(workflow_object): @@ -260,20 +280,24 @@ steps = workflow_content["steps"] def tweak_step(step): - assert step['position']['top'] != 1 - assert step['position']['left'] != 1 - step['position'] = {'top': 1, 'left': 1} + order_index, step_dict = step + check_label_and_uuid( order_index, step_dict) + assert step_dict['position']['top'] != 1 + assert step_dict['position']['left'] != 1 + step_dict['position'] = {'top': 1, 'left': 1} - map(tweak_step, steps.values()) + map(tweak_step, steps.iteritems()) update(workflow_content) def check_step(step): - assert step['position']['top'] == 1 - assert step['position']['left'] == 1 + order_index, step_dict = step + check_label_and_uuid(order_index, step_dict) + assert step_dict['position']['top'] == 1 + assert step_dict['position']['left'] == 1 updated_workflow_content = self._download_workflow(workflow_id) - map(check_step, updated_workflow_content['steps'].values()) + map(check_step, updated_workflow_content['steps'].iteritems()) # Re-update against original worklfow... update(original_workflow) @@ -281,7 +305,7 @@ updated_workflow_content = self._download_workflow(workflow_id) # Make sure the positions have been updated. - map(tweak_step, updated_workflow_content['steps'].values()) + map(tweak_step, updated_workflow_content['steps'].iteritems()) def test_import_deprecated( self ): workflow_id = self.workflow_populator.simple_workflow( "test_import_published_deprecated", publish=True ) @@ -364,6 +388,8 @@ 'annotation', 'post_job_actions', 'workflow_outputs', + 'uuid', + 'label', ) def test_import_export_with_runtime_inputs( self ): https://bitbucket.org/galaxy/galaxy-central/commits/b6f28aec47bd/ Changeset: b6f28aec47bd User: jmchilton Date: 2014-12-16 03:20:12+00:00 Summary: Pack scripts (for workflow step tracking changes). Affected #: 1 file diff -r 10696df64a3a439ba87f0e3b6089ddd924c37f45 -r b6f28aec47bd4fd6294a5aa5d1ea19fafcdb4f7e static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js +++ b/static/scripts/galaxy.workflow_editor.canvas.js @@ -784,6 +784,8 @@ this.tooltip = data.tooltip ? data.tooltip : ""; this.annotation = data.annotation; this.post_job_actions = data.post_job_actions ? data.post_job_actions : {}; + this.label = data.label; + this.uuid = data.uuid; this.workflow_outputs = data.workflow_outputs ? data.workflow_outputs : []; var node = this; @@ -991,6 +993,8 @@ position : $(node.element).position(), annotation: node.annotation, post_job_actions: node.post_job_actions, + uuid: node.uuid, + label: node.label, workflow_outputs: node.workflow_outputs }; nodes[ node.id ] = node_data; https://bitbucket.org/galaxy/galaxy-central/commits/2543786e0614/ Changeset: 2543786e0614 User: jmchilton Date: 2014-12-16 03:20:12+00:00 Summary: Ensure unique step label and UUIDs across workflows during create/update. Affected #: 5 files diff -r b6f28aec47bd4fd6294a5aa5d1ea19fafcdb4f7e -r 2543786e06148d5ceabc603553828e4040882c7b lib/galaxy/exceptions/__init__.py --- a/lib/galaxy/exceptions/__init__.py +++ b/lib/galaxy/exceptions/__init__.py @@ -51,6 +51,11 @@ err_code = error_codes.USER_SLUG_DUPLICATE +class DuplicatedIdentifierException( MessageException ): + status_code = 400 + err_code = error_codes.USER_IDENTIFIER_DUPLICATE + + class ObjectAttributeInvalidException( MessageException ): status_code = 400 err_code = error_codes.USER_OBJECT_ATTRIBUTE_INVALID diff -r b6f28aec47bd4fd6294a5aa5d1ea19fafcdb4f7e -r 2543786e06148d5ceabc603553828e4040882c7b lib/galaxy/exceptions/error_codes.json --- a/lib/galaxy/exceptions/error_codes.json +++ b/lib/galaxy/exceptions/error_codes.json @@ -55,6 +55,11 @@ "message": "The request contains unknown type of contents." }, { + "name": "USER_IDENTIFIER_DUPLICATE", + "code": 400011, + "message": "Request contained a duplicated identifier that must be unique." + }, + { "name": "USER_TOOL_META_PARAMETER_PROBLEM", "code": 400011, "message": "Supplied incorrect or incompatible tool meta parameters." diff -r b6f28aec47bd4fd6294a5aa5d1ea19fafcdb4f7e -r 2543786e06148d5ceabc603553828e4040882c7b lib/galaxy/managers/workflows.py --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -561,9 +561,24 @@ except ValueError: # to defensive, were these ever or will they ever not be integers? pass + + discovered_labels = set() + discovered_uuids = set() + # First pass to build step objects and populate basic values for step_index in step_indices: step_dict = supplied_steps[ step_index ] + uuid = step_dict.get("uuid", None) + if uuid: + if uuid in discovered_uuids: + raise exceptions.DuplicatedIdentifierException("Duplicate step UUID in request.") + discovered_uuids.add(uuid) + label = step_dict.get("label", None) + if label: + if label in discovered_labels: + raise exceptions.DuplicatedIdentifierException("Duplicated step label in request.") + discovered_labels.add(label) + yield step_dict def __module_from_dict( self, trans, step_dict, secure ): diff -r b6f28aec47bd4fd6294a5aa5d1ea19fafcdb4f7e -r 2543786e06148d5ceabc603553828e4040882c7b test/api/helpers.py --- a/test/api/helpers.py +++ b/test/api/helpers.py @@ -198,13 +198,17 @@ return self.create_workflow( workflow, **create_kwds ) def create_workflow( self, workflow, **create_kwds ): + upload_response = self.create_workflow_response( workflow, **create_kwds ) + uploaded_workflow_id = upload_response.json()[ "id" ] + return uploaded_workflow_id + + def create_workflow_response( self, workflow, **create_kwds ): data = dict( workflow=json.dumps( workflow ), **create_kwds ) upload_response = self.galaxy_interactor.post( "workflows/upload", data=data ) - uploaded_workflow_id = upload_response.json()[ "id" ] - return uploaded_workflow_id + return upload_response class LibraryPopulator( object ): diff -r b6f28aec47bd4fd6294a5aa5d1ea19fafcdb4f7e -r 2543786e06148d5ceabc603553828e4040882c7b test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -307,6 +307,21 @@ # Make sure the positions have been updated. map(tweak_step, updated_workflow_content['steps'].iteritems()) + def test_require_unique_step_uuids( self ): + workflow_dup_uuids = self.workflow_populator.load_workflow( name="test_import" ) + uuid0 = str(uuid4()) + for step_dict in workflow_dup_uuids["steps"].values(): + step_dict["uuid"] = uuid0 + response = self.workflow_populator.create_workflow_response( workflow_dup_uuids ) + self._assert_status_code_is( response, 400 ) + + def test_require_unique_step_labels( self ): + workflow_dup_label = self.workflow_populator.load_workflow( name="test_import" ) + for step_dict in workflow_dup_label["steps"].values(): + step_dict["label"] = "my duplicated label" + response = self.workflow_populator.create_workflow_response( workflow_dup_label ) + self._assert_status_code_is( response, 400 ) + def test_import_deprecated( self ): workflow_id = self.workflow_populator.simple_workflow( "test_import_published_deprecated", publish=True ) with self._different_user(): https://bitbucket.org/galaxy/galaxy-central/commits/52f58efee2dc/ Changeset: 52f58efee2dc User: jmchilton Date: 2014-12-16 03:20:12+00:00 Summary: Allow specifing workflow parameter replacements by step UUID. Affected #: 3 files diff -r 2543786e06148d5ceabc603553828e4040882c7b -r 52f58efee2dce225f5aeac7a382896eaad80baa8 lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -112,6 +112,10 @@ """ param_dict = param_map.get(step.tool_id, {}).copy() param_dict.update(param_map.get(str(step.id), {})) + step_uuid = step.uuid + if step_uuid: + uuid_params = param_map.get(str(step_uuid), {}) + param_dict.update(uuid_params) if param_dict: if 'param' in param_dict and 'value' in param_dict: param_dict[param_dict['param']] = param_dict['value'] diff -r 2543786e06148d5ceabc603553828e4040882c7b -r 52f58efee2dce225f5aeac7a382896eaad80baa8 test/api/test_workflow_2.ga --- a/test/api/test_workflow_2.ga +++ b/test/api/test_workflow_2.ga @@ -25,6 +25,7 @@ "tool_state": "{\"name\": \"Input Dataset\"}", "tool_version": null, "type": "data_input", + "uuid": "58dffcc9-bcb7-4117-a0e1-61513524b3b0", "user_outputs": [] }, "1": { @@ -54,6 +55,7 @@ "tool_state": "{\"__page__\": 0, \"num_lines\": \"\\\"8\\\"\", \"seed_source\": \"{\\\"__current_case__\\\": 0, \\\"seed_source_selector\\\": \\\"no_seed\\\"}\", \"input\": \"null\", \"chromInfo\": \"\\\"/home/john/workspace/galaxy-central-workflows-params/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", "tool_version": null, "type": "tool", + "uuid": "58dffcc9-bcb7-4117-a0e1-61513524b3b1", "user_outputs": [] }, "2": { @@ -83,6 +85,7 @@ "tool_state": "{\"__page__\": 0, \"num_lines\": \"\\\"6\\\"\", \"seed_source\": \"{\\\"__current_case__\\\": 0, \\\"seed_source_selector\\\": \\\"no_seed\\\"}\", \"input\": \"null\", \"chromInfo\": \"\\\"/home/john/workspace/galaxy-central-workflows-params/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", "tool_version": null, "type": "tool", + "uuid": "58dffcc9-bcb7-4117-a0e1-61513524b3b2", "user_outputs": [] } } diff -r 2543786e06148d5ceabc603553828e4040882c7b -r 52f58efee2dce225f5aeac7a382896eaad80baa8 test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -714,6 +714,20 @@ self.__assert_lines_hid_line_count_is( history_id, 2, 5 ) self.__assert_lines_hid_line_count_is( history_id, 3, 5 ) + @skip_without_tool( "random_lines1" ) + def test_run_replace_params_by_uuid( self ): + workflow_request, history_id = self._setup_random_x2_workflow( "test_for_replace_tool_params" ) + workflow_request[ "parameters" ] = dumps( { + "58dffcc9-bcb7-4117-a0e1-61513524b3b1": dict( num_lines=4 ), + "58dffcc9-bcb7-4117-a0e1-61513524b3b2": dict( num_lines=3 ), + } ) + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 200 ) + self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + # Would be 8 and 6 without modification + self.__assert_lines_hid_line_count_is( history_id, 2, 4 ) + self.__assert_lines_hid_line_count_is( history_id, 3, 3 ) + @skip_without_tool( "validation_default" ) def test_parameter_substitution_validation( self ): substitions = dict( input1="\" ; echo \"moo" ) https://bitbucket.org/galaxy/galaxy-central/commits/7ee34c597572/ Changeset: 7ee34c597572 User: jmchilton Date: 2014-12-16 03:20:12+00:00 Summary: Allow specifing workflow inputs by step UUID. Pass in the parameter 'inputs_by' as 'step_uuid' to the workflow run command to use this. Specifing inputs by UUID has the nice advantage that it survives workflows saves - so if one sets up an API script or something to target a workflow - saving the workflow in the editor doesn't need to break the script as long as inputs were not added or deleted. The UUID (like the order_index) has the advantage of the step id that it is predeterminable - so one can set it up a workflow script against any Galaxy and the script doesn't need to be adapted to raw ids the steps get assigned in that instance. Affected #: 2 files diff -r 52f58efee2dce225f5aeac7a382896eaad80baa8 -r 7ee34c5975728c0f508a4283ef2f1ee35672ab0e lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -57,6 +57,8 @@ inputs_key = str( step.id ) elif inputs_by == "step_index": inputs_key = str( step.order_index ) + elif inputs_by == "step_uuid": + inputs_key = str( step.uuid ) elif inputs_by == "name": inputs_key = step.tool_inputs.get( 'name', None ) else: @@ -170,6 +172,11 @@ # of Galaxy at the time of workflow import. inputs_by = inputs_by or 'step_index' + # TODO: with a little reworking this default could be + # step_index or step_uuid depending on what is inputs - + # unlike step_id and step_index there is not chance of + # conflicts. + add_to_history = 'no_add_to_history' not in payload history_param = payload.get('history', '') diff -r 52f58efee2dce225f5aeac7a382896eaad80baa8 -r 7ee34c5975728c0f508a4283ef2f1ee35672ab0e test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -78,6 +78,13 @@ elif inputs_by == "name": workflow_request[ "inputs" ] = dumps( label_map ) workflow_request[ "inputs_by" ] = 'name' + elif inputs_by == "step_uuid": + uuid_map = { + workflow["steps"]["0"]["uuid"]: self._ds_entry(hda1), + workflow["steps"]["1"]["uuid"]: self._ds_entry(hda2), + } + workflow_request[ "inputs" ] = dumps( uuid_map ) + workflow_request[ "inputs_by" ] = "step_uuid" return workflow_request, history_id @@ -421,6 +428,10 @@ self.__run_cat_workflow( inputs_by='step_index' ) @skip_without_tool( "cat1" ) + def test_run_workflow_by_uuid( self ): + self.__run_cat_workflow( inputs_by='step_uuid' ) + + @skip_without_tool( "cat1" ) def test_run_workflow_by_name( self ): self.__run_cat_workflow( inputs_by='name' ) @@ -430,11 +441,13 @@ def __run_cat_workflow( self, inputs_by ): workflow = self.workflow_populator.load_workflow( name="test_for_run" ) + workflow["steps"]["0"]["uuid"] = str(uuid4()) + workflow["steps"]["1"]["uuid"] = str(uuid4()) workflow_request, history_id = self._setup_workflow_run( workflow, inputs_by=inputs_by ) # TODO: This should really be a post to workflows/<workflow_id>/run or # something like that. run_workflow_response = self._post( "workflows", data=workflow_request ) - + self._assert_status_code_is( run_workflow_response, 200 ) invocation_id = run_workflow_response.json()[ "id" ] invocation = self._invocation_details( workflow_request[ "workflow_id" ], invocation_id ) assert invocation[ "state" ] == "scheduled", invocation https://bitbucket.org/galaxy/galaxy-central/commits/8d5089f2ba81/ Changeset: 8d5089f2ba81 User: jmchilton Date: 2014-12-16 03:20:12+00:00 Summary: Allow workflow inputs to be specifiable by UUID without explicit inputs_by. Since there is no chance of conflict with step.id or step.order_index, just allow inputs or ds_map respectively to be indexed by UUID. Affected #: 2 files diff -r 7ee34c5975728c0f508a4283ef2f1ee35672ab0e -r 8d5089f2ba8183439a866026f3583c377f8bfa74 lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -53,18 +53,25 @@ if step.type not in INPUT_STEP_TYPES: continue - if inputs_by == "step_id": - inputs_key = str( step.id ) - elif inputs_by == "step_index": - inputs_key = str( step.order_index ) - elif inputs_by == "step_uuid": - inputs_key = str( step.uuid ) - elif inputs_by == "name": - inputs_key = step.tool_inputs.get( 'name', None ) - else: - message = "Workflow cannot be run because unexpected inputs_by value specified." - raise exceptions.MessageException( message ) - if inputs_key not in inputs: + possible_input_keys = [] + for inputs_by_el in inputs_by.split("|"): + if inputs_by_el == "step_id": + possible_input_keys = [str( step.id )] + elif inputs_by_el == "step_index": + possible_input_keys = [str( step.order_index )] + elif inputs_by_el == "step_uuid": + possible_input_keys = [str( step.uuid )] + elif inputs_by_el == "name": + possible_input_keys = [step.tool_inputs.get( 'name', None )] + else: + message = "Workflow cannot be run because unexpected inputs_by value specified." + raise exceptions.MessageException( message ) + inputs_key = None + for possible_input_key in possible_input_keys: + if possible_input_key in inputs: + inputs_key = possible_input_key + + if not inputs_key: message = "Workflow cannot be run because an expected input step '%s' has no input dataset." % step.id raise exceptions.MessageException( message ) @@ -164,18 +171,13 @@ # Default to legacy behavior - read ds_map and reference steps # by unencoded step id (a raw database id). inputs = payload.get( 'ds_map', {} ) - inputs_by = inputs_by or 'step_id' + inputs_by = inputs_by or 'step_id|step_uuid' else: inputs = inputs or {} # New default is to reference steps by index of workflow step # which is intrinsic to the workflow and independent of the state # of Galaxy at the time of workflow import. - inputs_by = inputs_by or 'step_index' - - # TODO: with a little reworking this default could be - # step_index or step_uuid depending on what is inputs - - # unlike step_id and step_index there is not chance of - # conflicts. + inputs_by = inputs_by or 'step_index|step_uuid' add_to_history = 'no_add_to_history' not in payload history_param = payload.get('history', '') diff -r 7ee34c5975728c0f508a4283ef2f1ee35672ab0e -r 8d5089f2ba8183439a866026f3583c377f8bfa74 test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -78,13 +78,14 @@ elif inputs_by == "name": workflow_request[ "inputs" ] = dumps( label_map ) workflow_request[ "inputs_by" ] = 'name' - elif inputs_by == "step_uuid": + elif inputs_by in [ "step_uuid", "uuid_implicitly" ]: uuid_map = { workflow["steps"]["0"]["uuid"]: self._ds_entry(hda1), workflow["steps"]["1"]["uuid"]: self._ds_entry(hda2), } workflow_request[ "inputs" ] = dumps( uuid_map ) - workflow_request[ "inputs_by" ] = "step_uuid" + if inputs_by == "step_uuid": + workflow_request[ "inputs_by" ] = "step_uuid" return workflow_request, history_id @@ -432,6 +433,10 @@ self.__run_cat_workflow( inputs_by='step_uuid' ) @skip_without_tool( "cat1" ) + def test_run_workflow_by_uuid_implicitly( self ): + self.__run_cat_workflow( inputs_by='uuid_implicitly' ) + + @skip_without_tool( "cat1" ) def test_run_workflow_by_name( self ): self.__run_cat_workflow( inputs_by='name' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/45b206f6ab8f/ Changeset: 45b206f6ab8f User: dannon Date: 2014-12-16 00:38:00+00:00 Summary: Provide both user email and preferred contact email (if different) in error report form. Affected #: 1 file diff -r f06ac1a9f76efef1eb1cc174979184a73a01711d -r 45b206f6ab8fc8bf319766368d128f9b0fc6b4d1 lib/galaxy/tools/errors.py --- a/lib/galaxy/tools/errors.py +++ b/lib/galaxy/tools/errors.py @@ -22,7 +22,7 @@ ${history_view_link} ----------------------------------------------------------------------------- -The user '${email}' provided the following information: +The user ${email_str} provided the following information: ${message} ----------------------------------------------------------------------------- @@ -74,12 +74,16 @@ else: roles = [] return self.app.security_agent.can_access_dataset( roles, self.hda.dataset ) - def create_report( self, email='', message='', **kwd ): + def create_report( self, user, email='', message='', **kwd ): hda = self.hda job = self.job host = web.url_for( '/', qualified=True ) history_view_link = web.url_for( controller="history", action="view", id=self.app.security.encode_id( hda.history_id ), qualified=True ) # Build the email message + if user and user.email != email: + email_str = "'%s' (providing preferred contact email '%s')" % (user.email, email) + else: + email_str = "'%s'" % email self.report = string.Template( error_report_template ) \ .safe_substitute( host=host, dataset_id=hda.dataset_id, @@ -97,22 +101,22 @@ job_stdout=util.unicodify( job.stdout ), job_info=util.unicodify( job.info ), job_traceback=util.unicodify( job.traceback ), - email=email, + email_str=email_str, message=util.unicodify( message ) ) def _send_report( self, user, email=None, message=None, **kwd ): return self.report def send_report( self, user, email=None, message=None, **kwd ): if self.report is None: - self.create_report( email=email, message=message, **kwd ) + self.create_report( user, email=email, message=message, **kwd ) return self._send_report( user, email=email, message=message, **kwd ) - + class EmailErrorReporter( ErrorReporter ): def _send_report( self, user, email=None, message=None, **kwd ): smtp_server = self.app.config.smtp_server assert smtp_server, ValueError( "Mail is not configured for this galaxy instance" ) to_address = self.app.config.error_email_to assert to_address, ValueError( "Error reporting has been disabled for this galaxy instance" ) - + frm = to_address # Check email a bit email = email or '' https://bitbucket.org/galaxy/galaxy-central/commits/4f767bb3989f/ Changeset: 4f767bb3989f User: dannon Date: 2014-12-16 00:40:28+00:00 Summary: Pep8 standardized method spacing in lib/galaxy/tools/errors.py Affected #: 1 file diff -r 45b206f6ab8fc8bf319766368d128f9b0fc6b4d1 -r 4f767bb3989f2ee9b7e3fdb47fa4cdf716205fc6 lib/galaxy/tools/errors.py --- a/lib/galaxy/tools/errors.py +++ b/lib/galaxy/tools/errors.py @@ -50,9 +50,10 @@ (This is an automated message). """ + class ErrorReporter( object ): def __init__( self, hda, app ): - # Get the dataset + # Get the dataset sa_session = app.model.context if not isinstance( hda, model.HistoryDatasetAssociation ): hda_id = hda @@ -68,12 +69,14 @@ self.app = app self.tool_id = self.job.tool_id self.report = None + def _can_access_dataset( self, user ): if user: roles = user.all_roles() else: roles = [] return self.app.security_agent.can_access_dataset( roles, self.hda.dataset ) + def create_report( self, user, email='', message='', **kwd ): hda = self.hda job = self.job @@ -103,13 +106,16 @@ job_traceback=util.unicodify( job.traceback ), email_str=email_str, message=util.unicodify( message ) ) + def _send_report( self, user, email=None, message=None, **kwd ): return self.report + def send_report( self, user, email=None, message=None, **kwd ): if self.report is None: self.create_report( user, email=email, message=message, **kwd ) return self._send_report( user, email=email, message=message, **kwd ) + class EmailErrorReporter( ErrorReporter ): def _send_report( self, user, email=None, message=None, **kwd ): smtp_server = self.app.config.smtp_server Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3351ffb48668/ Changeset: 3351ffb48668 User: dannon Date: 2014-12-15 19:01:47+00:00 Summary: Slightly more specific error message (and removal of the useless stack dump) for IOError when loading a tool. Affected #: 1 file diff -r 6d85572398e770efcd0fbf46cf9d7655795dd3e1 -r 3351ffb48668c9bb3076c2cfb6645e179b722535 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -629,7 +629,9 @@ integrated_panel_dict[ key ] = tool else: integrated_panel_dict.insert( index, key, tool ) - except: + except IOError: + log.error( "Error reading tool configuration file from path: %s." % path ) + except Exception: log.exception( "Error reading tool from path: %s" % path ) def __add_tool( self, tool, load_panel_dict, panel_dict ): https://bitbucket.org/galaxy/galaxy-central/commits/f06ac1a9f76e/ Changeset: f06ac1a9f76e User: dannon Date: 2014-12-15 22:26:32+00:00 Summary: Merge. Affected #: 4 files diff -r 3351ffb48668c9bb3076c2cfb6645e179b722535 -r f06ac1a9f76efef1eb1cc174979184a73a01711d templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako --- a/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako +++ b/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako @@ -57,7 +57,7 @@ <td>${tool_dependency.version|h}</td><td>${tool_dependency.type|h}</td><td>${tool_dependency.status|h}</td> - <td>${error_message|h}</td> + <td>${error_message}</td></tr> %endfor </table> diff -r 3351ffb48668c9bb3076c2cfb6645e179b722535 -r f06ac1a9f76efef1eb1cc174979184a73a01711d test/functional/tools/code_file.py --- /dev/null +++ b/test/functional/tools/code_file.py @@ -0,0 +1,14 @@ + + +from galaxy.tools.parameters import DataToolParameter + + + +def validate_input( trans, error_map, param_values, page_param_map ): + """ + Validates the user input, before execution. + """ + first = param_values['name1'] + second = param_values['name2'] + if first == second: + error_map['name1'] = "The value names should be different." diff -r 3351ffb48668c9bb3076c2cfb6645e179b722535 -r f06ac1a9f76efef1eb1cc174979184a73a01711d test/functional/tools/code_file.xml --- /dev/null +++ b/test/functional/tools/code_file.xml @@ -0,0 +1,15 @@ +<tool id="code_file" name="code_file" version="1.0.0"> + <description>code_file</description> + <code file="code_file.py" /> + <command>cat $input1 > $output</command> + <inputs> + <param name="input1" type="data" label="Concatenate Dataset" /> + <param name="name1" type="text" value="FactorName" label="value one should be different than value two" /> + <param name="name2" type="text" value="FactorName" label="value one should be different than value two" /> + </inputs> + <outputs> + <data format="txt" name="output" /> + </outputs> + <tests> + </tests> +</tool> diff -r 3351ffb48668c9bb3076c2cfb6645e179b722535 -r f06ac1a9f76efef1eb1cc174979184a73a01711d test/functional/tools/samples_tool_conf.xml --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -3,6 +3,7 @@ <tool file="upload.xml"/><tool file="simple_constructs.xml" /><tool file="composite.xml" /> + <tool file="code_file.xml" /><tool file="disambiguate_cond.xml" /><tool file="multi_repeats.xml"/><tool file="multi_page.xml"/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ae59198cc9b9/ Changeset: ae59198cc9b9 User: dan Date: 2014-12-15 22:01:07+00:00 Summary: Do not |h escape tool dependency error message, as it is escaped and formated by tool_shed.util.basic_util.to_html_string Affected #: 1 file diff -r b89b8f8e57615b2a480d5abe13a111df159981e5 -r ae59198cc9b9ba4459881025f746bfda59fa98cd templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako --- a/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako +++ b/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako @@ -57,7 +57,7 @@ <td>${tool_dependency.version|h}</td><td>${tool_dependency.type|h}</td><td>${tool_dependency.status|h}</td> - <td>${error_message|h}</td> + <td>${error_message}</td></tr> %endfor </table> https://bitbucket.org/galaxy/galaxy-central/commits/d8b93cd3b491/ Changeset: d8b93cd3b491 Branch: next-stable User: dan Date: 2014-12-15 22:01:07+00:00 Summary: Do not |h escape tool dependency error message, as it is escaped and formated by tool_shed.util.basic_util.to_html_string Affected #: 1 file diff -r fc799502f7a6310f19230f58f11ab1fbe82b09ba -r d8b93cd3b491946703f52f74bf231c2aee339373 templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako --- a/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako +++ b/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako @@ -57,7 +57,7 @@ <td>${tool_dependency.version|h}</td><td>${tool_dependency.type|h}</td><td>${tool_dependency.status|h}</td> - <td>${error_message|h}</td> + <td>${error_message}</td></tr> %endfor </table> https://bitbucket.org/galaxy/galaxy-central/commits/c3d0d6202179/ Changeset: c3d0d6202179 User: dan Date: 2014-12-15 22:02:44+00:00 Summary: merge Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

[galaxyproject/usegalaxy-playbook] e8119d: Banner for tomorrow's Corral downtime.
by GitHub 15 Dec '14

15 Dec '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e8119d8b39f7a631419a373386608b0e5f27cc4b https://github.com/galaxyproject/usegalaxy-playbook/commit/e8119d8b39f7a631… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-12-15 (Mon, 15 Dec 2014) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M production/group_vars/galaxyservers.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- Banner for tomorrow's Corral downtime.

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commit/galaxy-central: jmchilton: Add code_file example tool from Bjoern.
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b89b8f8e5761/ Changeset: b89b8f8e5761 User: jmchilton Date: 2014-12-15 19:37:22+00:00 Summary: Add code_file example tool from Bjoern. Affected #: 3 files diff -r 6d85572398e770efcd0fbf46cf9d7655795dd3e1 -r b89b8f8e57615b2a480d5abe13a111df159981e5 test/functional/tools/code_file.py --- /dev/null +++ b/test/functional/tools/code_file.py @@ -0,0 +1,14 @@ + + +from galaxy.tools.parameters import DataToolParameter + + + +def validate_input( trans, error_map, param_values, page_param_map ): + """ + Validates the user input, before execution. + """ + first = param_values['name1'] + second = param_values['name2'] + if first == second: + error_map['name1'] = "The value names should be different." diff -r 6d85572398e770efcd0fbf46cf9d7655795dd3e1 -r b89b8f8e57615b2a480d5abe13a111df159981e5 test/functional/tools/code_file.xml --- /dev/null +++ b/test/functional/tools/code_file.xml @@ -0,0 +1,15 @@ +<tool id="code_file" name="code_file" version="1.0.0"> + <description>code_file</description> + <code file="code_file.py" /> + <command>cat $input1 > $output</command> + <inputs> + <param name="input1" type="data" label="Concatenate Dataset" /> + <param name="name1" type="text" value="FactorName" label="value one should be different than value two" /> + <param name="name2" type="text" value="FactorName" label="value one should be different than value two" /> + </inputs> + <outputs> + <data format="txt" name="output" /> + </outputs> + <tests> + </tests> +</tool> diff -r 6d85572398e770efcd0fbf46cf9d7655795dd3e1 -r b89b8f8e57615b2a480d5abe13a111df159981e5 test/functional/tools/samples_tool_conf.xml --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -3,6 +3,7 @@ <tool file="upload.xml"/><tool file="simple_constructs.xml" /><tool file="composite.xml" /> + <tool file="code_file.xml" /><tool file="disambiguate_cond.xml" /><tool file="multi_repeats.xml"/><tool file="multi_page.xml"/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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[galaxyproject/usegalaxy-playbook] dee3d7: Update Test admin users and pull mutable configs.
by GitHub 15 Dec '14

15 Dec '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dee3d7903023d5acc86c937d1faadbf908bcb651 https://github.com/galaxyproject/usegalaxy-playbook/commit/dee3d7903023d5ac… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-12-15 (Mon, 15 Dec 2014) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml M stage/secret_vars/galaxyservers.yml Log Message: ----------- Update Test admin users and pull mutable configs.

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commit/galaxy-central: dannon: Merge next-stable.
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6d85572398e7/ Changeset: 6d85572398e7 User: dannon Date: 2014-12-15 16:18:20+00:00 Summary: Merge next-stable. Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: nsoranzo: Fix variable name causing a NameError.
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fc799502f7a6/ Changeset: fc799502f7a6 Branch: next-stable User: nsoranzo Date: 2014-12-15 15:43:16+00:00 Summary: Fix variable name causing a NameError. Affected #: 1 file diff -r 6704c0ee9fec6b0624d739669cb7c66ea08d480a -r fc799502f7a6310f19230f58f11ab1fbe82b09ba lib/galaxy/managers/folders.py --- a/lib/galaxy/managers/folders.py +++ b/lib/galaxy/managers/folders.py @@ -195,7 +195,7 @@ if ( ( len( encoded_folder_id ) % 16 == 1 ) and encoded_folder_id.startswith( 'F' ) ): cut_id = encoded_folder_id[ 1: ] else: - raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( encoded_id ) ) + raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( encoded_folder_id ) ) return cut_id def decode_folder_id( self, trans, encoded_folder_id ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: nsoranzo: Fix variable name causing a NameError.
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/733696644b89/ Changeset: 733696644b89 User: nsoranzo Date: 2014-12-15 15:43:16+00:00 Summary: Fix variable name causing a NameError. Affected #: 1 file diff -r 3c0acd32969bc282603607037522a2e16d70d074 -r 733696644b89ba39bbeeaf5908b97f4698d6868c lib/galaxy/managers/folders.py --- a/lib/galaxy/managers/folders.py +++ b/lib/galaxy/managers/folders.py @@ -195,7 +195,7 @@ if ( ( len( encoded_folder_id ) % 16 == 1 ) and encoded_folder_id.startswith( 'F' ) ): cut_id = encoded_folder_id[ 1: ] else: - raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( encoded_id ) ) + raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( encoded_folder_id ) ) return cut_id def decode_folder_id( self, trans, encoded_folder_id ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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[galaxyproject/usegalaxy-playbook] fdfbf4: added ga_code for google analytics purposes
by GitHub 15 Dec '14

15 Dec '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fdfbf4b48b6f86f9a524772c11a0f41a95fdad76 https://github.com/galaxyproject/usegalaxy-playbook/commit/fdfbf4b48b6f86f9… Author: Marten <emulatorer(a)gmail.com> Date: 2014-12-12 (Fri, 12 Dec 2014) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- added ga_code for google analytics purposes Commit: 9485f82f52b57445b6e45d63845bc162c7ab155b https://github.com/galaxyproject/usegalaxy-playbook/commit/9485f82f52b57445… Author: Marten <emulatorer(a)gmail.com> Date: 2014-12-12 (Fri, 12 Dec 2014) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- add ga_code for google analytics purposes Commit: 8f1785c81d7ee068b564f079dd02f4eaa33c49de https://github.com/galaxyproject/usegalaxy-playbook/commit/8f1785c81d7ee068… Author: Marten <emulatorer(a)gmail.com> Date: 2014-12-12 (Fri, 12 Dec 2014) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- add ga script and onclick event sending to track whether the cycle thing is used Commit: 33e106b5e2f13eeb88b5c5356b4c49a87a615c62 https://github.com/galaxyproject/usegalaxy-playbook/commit/33e106b5e2f13eeb… Author: Marten <emulatorer(a)gmail.com> Date: 2014-12-12 (Fri, 12 Dec 2014) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- do not init ga twice use the one in top.window instead Commit: 1bbaae7a09fa230a97337d42d5b4cd754d377ba1 https://github.com/galaxyproject/usegalaxy-playbook/commit/1bbaae7a09fa230a… Author: Marten <emulatorer(a)gmail.com> Date: 2014-12-15 (Mon, 15 Dec 2014) Changed paths: M production/group_vars/galaxyservers.yml M stage/group_vars/galaxyservers.yml M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Merge pull request #2 from martenson/master track how people click on the carousel links Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/15b2fa183d58...…

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commit/galaxy-central: dannon: Retab, whitespace in base.less
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3c0acd32969b/ Changeset: 3c0acd32969b User: dannon Date: 2014-12-15 14:56:25+00:00 Summary: Retab, whitespace in base.less Affected #: 1 file diff -r 36457cc1ec26c440e7a996ce51eb87ed7c58cc4d -r 3c0acd32969bc282603607037522a2e16d70d074 static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -1,7 +1,7 @@ // bootstrap.less modified for Galaxy @import "bootstrap.less"; -// Galaxy specific variables +// Galaxy specific variables @import "galaxy_variables.less"; @white: #fff; @@ -92,23 +92,23 @@ } #messagebox { - position:absolute; + position:absolute; top: @navbar-height + @layout_top_padding + 1; - left:0; - width:100%; + left:0; + width:100%; height: @panel-message-height !important; - overflow: hidden; + overflow: hidden; border-bottom: solid #999 1px; font-size: 90%; } #inactivebox { - position:absolute; + position:absolute; top: @navbar-height + @layout_top_padding + 1; - left:0; - width:100%; + left:0; + width:100%; height: @panel-message-height !important; - overflow: hidden; + overflow: hidden; border-bottom: solid #999 1px; font-size: 90%; } @@ -116,10 +116,10 @@ // Panels #left, #left-border, #center, #right-border, #right { - position: absolute; + position: absolute; top: @navbar-height + @layout_top_padding + 1; bottom: 0px; - overflow: hidden; + overflow: hidden; background: #fff; } #left, #center, #right, #left-border, #right-border { @@ -145,7 +145,7 @@ } #right { width: 250px; - right: 0px; + right: 0px; z-index: 200; border-left: solid @layout-border-color 1px; } @@ -277,11 +277,11 @@ } } } - + .menu-bg { background: whiteSmoke top repeat-x; } - + div.unified-panel-body { position: absolute; top: @panel_header_height; @@ -326,10 +326,10 @@ z-index: 900; // Bootstrap elements start at 1000 position: absolute; top: 0; - left: 0; + left: 0; width: 100%; height: 100%; -} +} // Messages for message box, slightly different style @@ -345,19 +345,19 @@ background-position: 6px 50%; } -.panel-warning-message +.panel-warning-message { background-image: url(warn_small.png); background-color: @state-warning-bg; } -.panel-done-message +.panel-done-message { background-image: url(ok_small.png); background-color: @state-success-bg; } -.panel-info-message +.panel-info-message { background-image: url(info_small.png); background-color: @state-info-bg; @@ -367,9 +367,9 @@ #masthead { - position:absolute; - top:0; - left:0; + position:absolute; + top:0; + left:0; width:100%; min-width:990px; padding: 0; @@ -385,7 +385,7 @@ color: gold; } } - + //.dropdown-menu { // z-index: 15002; //} @@ -412,8 +412,8 @@ z-index: 2000; img { - display: inline; - width: 26px; + display: inline; + width: 26px; vertical-align: top; } a { @@ -421,7 +421,7 @@ text-decoration: none; } } - + .iconbar { position : absolute; @@ -448,7 +448,7 @@ left : 23px; top : -12px; } - + .toggle { color : gold; @@ -542,7 +542,7 @@ border-color:#999; } -div.metadataHelpBody { +div.metadataHelpBody { width:100%;overflow:auto; } @@ -553,7 +553,7 @@ padding-bottom: 0.25em; } -// Forms +// Forms div.toolFormBody div.toolFormTitle { background: transparent; @@ -602,7 +602,7 @@ .border-radius(@panel-border-radius); } -div.form-title, div.toolFormTitle { +div.form-title, div.toolFormTitle { // font-size: @font-size-base * 1.25; // line-height: @line-height-base * 1.5; padding: 5px 10px; @@ -610,7 +610,7 @@ border-bottom: solid @form-border 1px; } -div.form-body { +div.form-body { padding: 5px 0; } @@ -687,7 +687,7 @@ font: inherit; } -.form-row { +.form-row { select, textarea, input[type="text"], input[type="file"], input[type="password"] { // -webkit-box-sizing: border-box; max-width: 90%; @@ -733,15 +733,15 @@ } .search-spinner { - position: absolute; - display: none; - right: 6px; + position: absolute; + display: none; + right: 6px; top: 9px; } #search-clear-btn { - position: absolute; - right: 6px; + position: absolute; + right: 6px; top: 9px; display: block; font-size: 1.4em !important; @@ -753,7 +753,7 @@ } } -// Messages +// Messages .errormessagelarge, .warningmessagelarge, .donemessagelarge, .infomessagelarge { .alert(); @@ -786,7 +786,7 @@ background-image: url(info_large.png); } -.screencastBox { +.screencastBox { padding-left: 10px; border-color: #AAAA66; background-color: #FFFFCC; @@ -891,7 +891,7 @@ line-height: @line-height-base; } -table.colored tr.header { +table.colored tr.header { background: @table-heading-bg; color: contrast(@complement-color-3); background-repeat: repeat-x; @@ -900,11 +900,11 @@ font-weight: bold; } -table.colored tr { +table.colored tr { background: @white; } -table.colored tr.odd_row { +table.colored tr.odd_row { background: @table-bg-accent; } @@ -1018,7 +1018,7 @@ height: 18px; vertical-align: middle; margin-left: 2px; - + } .search-box-input { border: 0; @@ -1051,7 +1051,7 @@ div.odd_row { background: @table-bg-accent; } - + #footer { display: none; } @@ -1199,15 +1199,15 @@ cursor: pointer; position: relative; .unselectable; - + // border: solid transparent 1px; // -moz-border-radius: 0.25em; // -webkit-border-radius: 0.25em; // border-radius: 0.25em; - + // padding: 1px 0.25em; // margin: -1px -0.25em; - + a { text-decoration: none; } @@ -1335,28 +1335,28 @@ background:#aaa; color:#aaa; } - + table { border-collapse:collapse; border-top:1px solid #ccc; border-left:1px solid #ccc; } - + blockquote { color:#666; } - + fieldset { border-color:#ccc; border:1px solid #ccc; } - + th,td { border-bottom:1px solid #ddd; border-right:1px solid #ccc; } - + th,td { padding:.8em; } @@ -1438,7 +1438,7 @@ margin:10px 0; padding-left:5px; } - + // ============================================================================ History @import "sprite-history-states.less"; @import "sprite-history-buttons.less"; @@ -1457,7 +1457,7 @@ @import "ui/pagination.less"; -// ==== Tool menu styles +// ==== Tool menu styles .toolMenuContainer { @@ -1480,7 +1480,7 @@ } div.toolSectionDetailsInner -{ +{ margin-left: 5px; margin-right: 5px; } @@ -1565,9 +1565,9 @@ .toolMenuAndView .toolForm { - float: left; - background-color: white; - margin: 10px; + float: left; + background-color: white; + margin: 10px; } // @import "base_sprites"; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

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commit/galaxy-central: dannon: Organize and deduplicate imports, pep8 in lib/galaxy/config.py
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7e68aa3d8d16/ Changeset: 7e68aa3d8d16 User: dannon Date: 2014-12-15 13:28:21+00:00 Summary: Organize and deduplicate imports, pep8 in lib/galaxy/config.py Affected #: 1 file diff -r 5223de4eacea84dc2f39ec1ecec33ce45fa84739 -r 7e68aa3d8d161ff2a0526101aedebc026b4d71cc lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -4,23 +4,22 @@ # absolute_import needed for tool_shed package. from __future__ import absolute_import +import ConfigParser +import logging +import logging.config import os import re import socket import string import sys import tempfile -import logging -import logging.config -import ConfigParser from datetime import timedelta +from galaxy import eggs +from galaxy.util import listify +from galaxy.util import string_as_bool +from galaxy.util.dbkeys import GenomeBuilds from galaxy.web.formatting import expand_pretty_datetime_format -from galaxy.util import string_as_bool -from galaxy.util import listify -from galaxy.util.dbkeys import GenomeBuilds -from galaxy import eggs -import ConfigParser log = logging.getLogger( __name__ ) @@ -442,23 +441,23 @@ Backwards compatibility for config files moved to the config/ dir. """ defaults = dict( - data_manager_config_file = [ 'config/data_manager_conf.xml', 'data_manager_conf.xml', 'config/data_manager_conf.xml.sample' ], - datatypes_config_file = [ 'config/datatypes_conf.xml', 'datatypes_conf.xml', 'config/datatypes_conf.xml.sample' ], - external_service_type_config_file = [ 'config/external_service_types_conf.xml', 'external_service_types_conf.xml', 'config/external_service_types_conf.xml.sample' ], - job_config_file = [ 'config/job_conf.xml', 'job_conf.xml' ], - job_metrics_config_file = [ 'config/job_metrics_conf.xml', 'job_metrics_conf.xml' ], - dependency_resolvers_config_file = [ 'config/dependency_resolvers_conf.xml', 'dependency_resolvers_conf.xml' ], - job_resource_params_file = [ 'config/job_resource_params_conf.xml', 'job_resource_params_conf.xml' ], - migrated_tools_config = [ 'migrated_tools_conf.xml', 'config/migrated_tools_conf.xml' ], - object_store_config_file = [ 'config/object_store_conf.xml', 'object_store_conf.xml' ], - openid_config_file = [ 'config/openid_conf.xml', 'openid_conf.xml', 'config/openid_conf.xml.sample' ], - shed_data_manager_config_file = [ 'shed_data_manager_conf.xml', 'config/shed_data_manager_conf.xml' ], - shed_tool_data_table_config = [ 'shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml' ], - tool_sheds_config_file = [ 'config/tool_sheds_conf.xml', 'tool_sheds_conf.xml', 'config/tool_sheds_conf.xml.sample' ], + data_manager_config_file=[ 'config/data_manager_conf.xml', 'data_manager_conf.xml', 'config/data_manager_conf.xml.sample' ], + datatypes_config_file=[ 'config/datatypes_conf.xml', 'datatypes_conf.xml', 'config/datatypes_conf.xml.sample' ], + external_service_type_config_file=[ 'config/external_service_types_conf.xml', 'external_service_types_conf.xml', 'config/external_service_types_conf.xml.sample' ], + job_config_file=[ 'config/job_conf.xml', 'job_conf.xml' ], + job_metrics_config_file=[ 'config/job_metrics_conf.xml', 'job_metrics_conf.xml' ], + dependency_resolvers_config_file=[ 'config/dependency_resolvers_conf.xml', 'dependency_resolvers_conf.xml' ], + job_resource_params_file=[ 'config/job_resource_params_conf.xml', 'job_resource_params_conf.xml' ], + migrated_tools_config=[ 'migrated_tools_conf.xml', 'config/migrated_tools_conf.xml' ], + object_store_config_file=[ 'config/object_store_conf.xml', 'object_store_conf.xml' ], + openid_config_file=[ 'config/openid_conf.xml', 'openid_conf.xml', 'config/openid_conf.xml.sample' ], + shed_data_manager_config_file=[ 'shed_data_manager_conf.xml', 'config/shed_data_manager_conf.xml' ], + shed_tool_data_table_config=[ 'shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml' ], + tool_sheds_config_file=[ 'config/tool_sheds_conf.xml', 'tool_sheds_conf.xml', 'config/tool_sheds_conf.xml.sample' ], ) listify_defaults = dict( - tool_data_table_config_path = [ 'config/tool_data_table_conf.xml', 'tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ], + tool_data_table_config_path=[ 'config/tool_data_table_conf.xml', 'tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ], # rationale: # [0]: user has explicitly created config/tool_conf.xml but did not # move their existing shed_tool_conf.xml, don't use @@ -469,7 +468,7 @@ # [0], probably moved their shed_tool_conf.xml as well # [2]: user has done nothing, use the old files # [3]: fresh install - tool_config_file = [ 'config/tool_conf.xml,shed_tool_conf.xml', 'config/tool_conf.xml,config/shed_tool_conf.xml', 'tool_conf.xml,shed_tool_conf.xml', 'config/tool_conf.xml.sample,config/shed_tool_conf.xml' ] + tool_config_file=[ 'config/tool_conf.xml,shed_tool_conf.xml', 'config/tool_conf.xml,config/shed_tool_conf.xml', 'tool_conf.xml,shed_tool_conf.xml', 'config/tool_conf.xml.sample,config/shed_tool_conf.xml' ] ) for var, defaults in defaults.items(): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Merge.
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5223de4eacea/ Changeset: 5223de4eacea User: dannon Date: 2014-12-15 13:25:15+00:00 Summary: Merge. Affected #: 1 file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6704c0ee9fec/ Changeset: 6704c0ee9fec Branch: next-stable User: dannon Date: 2014-12-15 13:23:47+00:00 Summary: Bugfix for openid configuration locations, pointed out by Jelle in https://trello.com/c/AwZwAx4l/2289-lib-galaxy-config-py-missing-comma-on-op… Affected #: 1 file diff -r 7a027f285f3b441f8ff1fe48dfc5841d8bc41bfa -r 6704c0ee9fec6b0624d739669cb7c66ea08d480a lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -445,7 +445,7 @@ job_resource_params_file = [ 'config/job_resource_params_conf.xml', 'job_resource_params_conf.xml' ], migrated_tools_config = [ 'migrated_tools_conf.xml', 'config/migrated_tools_conf.xml' ], object_store_config_file = [ 'config/object_store_conf.xml', 'object_store_conf.xml' ], - openid_config_file = [ 'config/openid_conf.xml', 'openid_conf.xml' 'config/openid_conf.xml.sample' ], + openid_config_file = [ 'config/openid_conf.xml', 'openid_conf.xml', 'config/openid_conf.xml.sample' ], shed_data_manager_config_file = [ 'shed_data_manager_conf.xml', 'config/shed_data_manager_conf.xml' ], shed_tool_data_table_config = [ 'shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml' ], tool_sheds_config_file = [ 'config/tool_sheds_conf.xml', 'tool_sheds_conf.xml', 'config/tool_sheds_conf.xml.sample' ], https://bitbucket.org/galaxy/galaxy-central/commits/6fee59d63b7e/ Changeset: 6fee59d63b7e User: dannon Date: 2014-12-15 13:23:47+00:00 Summary: Bugfix for openid configuration locations, pointed out by Jelle in https://trello.com/c/AwZwAx4l/2289-lib-galaxy-config-py-missing-comma-on-op… Affected #: 1 file diff -r ad28e42a8af34c81f0ebcbe6f3baef9bdcf80ae8 -r 6fee59d63b7e042851b2a63e4d66ad6dde630e3b lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -451,7 +451,7 @@ job_resource_params_file = [ 'config/job_resource_params_conf.xml', 'job_resource_params_conf.xml' ], migrated_tools_config = [ 'migrated_tools_conf.xml', 'config/migrated_tools_conf.xml' ], object_store_config_file = [ 'config/object_store_conf.xml', 'object_store_conf.xml' ], - openid_config_file = [ 'config/openid_conf.xml', 'openid_conf.xml' 'config/openid_conf.xml.sample' ], + openid_config_file = [ 'config/openid_conf.xml', 'openid_conf.xml', 'config/openid_conf.xml.sample' ], shed_data_manager_config_file = [ 'shed_data_manager_conf.xml', 'config/shed_data_manager_conf.xml' ], shed_tool_data_table_config = [ 'shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml' ], tool_sheds_config_file = [ 'config/tool_sheds_conf.xml', 'tool_sheds_conf.xml', 'config/tool_sheds_conf.xml.sample' ], Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Merged in jjohnson/galaxy-central-7 (pull request #609)
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ad28e42a8af3/ Changeset: ad28e42a8af3 User: dannon Date: 2014-12-15 12:43:42+00:00 Summary: Merged in jjohnson/galaxy-central-7 (pull request #609) Add dataproviders for SQlite datatype Affected #: 2 files diff -r ecac8a8679612d419347dcbedc398319418b077e -r ad28e42a8af34c81f0ebcbe6f3baef9bdcf80ae8 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -620,6 +620,16 @@ dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.dataset.SQliteDataProvider( dataset_source, **settings ) + @dataproviders.decorators.dataprovider_factory( 'sqlite-table', dataproviders.dataset.SQliteDataTableProvider.settings ) + def sqlite_datatableprovider( self, dataset, **settings ): + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return dataproviders.dataset.SQliteDataTableProvider( dataset_source, **settings ) + + @dataproviders.decorators.dataprovider_factory( 'sqlite-dict', dataproviders.dataset.SQliteDataDictProvider.settings ) + def sqlite_datadictprovider( self, dataset, **settings ): + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return dataproviders.dataset.SQliteDataDictProvider( dataset_source, **settings ) + Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite) diff -r ecac8a8679612d419347dcbedc398319418b077e -r ad28e42a8af34c81f0ebcbe6f3baef9bdcf80ae8 lib/galaxy/datatypes/dataproviders/dataset.py --- a/lib/galaxy/datatypes/dataproviders/dataset.py +++ b/lib/galaxy/datatypes/dataproviders/dataset.py @@ -13,6 +13,7 @@ import external from galaxy.util import sqlite import re +import sys from galaxy import eggs eggs.require( 'bx-python' ) @@ -726,3 +727,55 @@ else: yield +class SQliteDataTableProvider( base.DataProvider ): + """ + Data provider that uses a sqlite database file as its source. + Allows any query to be run and returns the resulting rows as arrays of arrays + """ + settings = { + 'query': 'str', + 'headers': 'bool', + 'limit': 'int' + } + + def __init__( self, source, query=None, headers=False, limit=sys.maxint, **kwargs ): + self.query = query + self.headers = headers + self.limit = limit + self.connection = sqlite.connect(source.dataset.file_name) + super( SQliteDataTableProvider, self ).__init__( source, **kwargs ) + + def __iter__( self ): + if (self.query is not None) and sqlite.is_read_only_query(self.query): + cur = self.connection.cursor() + results = cur.execute(self.query) + if self.headers: + yield [col[0] for col in cur.description] + for i,row in enumerate(results): + if i >= self.limit: + break + yield [val for val in row] + else: + yield + +class SQliteDataDictProvider( base.DataProvider ): + """ + Data provider that uses a sqlite database file as its source. + Allows any query to be run and returns the resulting rows as arrays of dicts + """ + settings = { + 'query': 'str' + } + + def __init__( self, source, query=None, **kwargs ): + self.query = query + self.connection = sqlite.connect(source.dataset.file_name) + super( SQliteDataDictProvider, self ).__init__( source, **kwargs ) + + def __iter__( self ): + if (self.query is not None) and sqlite.is_read_only_query(self.query): + cur = self.connection.cursor() + for row in cur.execute(self.query): + yield [dict((cur.description[i][0], value) for i, value in enumerate(row))] + else: + yield Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1e6035e53de5/ Changeset: 1e6035e53de5 User: jjohnson Date: 2014-12-12 19:35:40+00:00 Summary: Add SQlite dataproviders: SQliteDataTableProvider - Allows any query to be run and returns the resulting rows as arrays of arrays, SQliteDataDictProvider - Allows any query to be run and returns the resulting rows as arrays of dicts Affected #: 1 file diff -r efd0286e7629289c4c583898ebecb32646834c64 -r 1e6035e53de58ce4fe1687ab74512da711d99989 lib/galaxy/datatypes/dataproviders/dataset.py --- a/lib/galaxy/datatypes/dataproviders/dataset.py +++ b/lib/galaxy/datatypes/dataproviders/dataset.py @@ -13,6 +13,7 @@ import external from galaxy.util import sqlite import re +import sys from galaxy import eggs eggs.require( 'bx-python' ) @@ -726,3 +727,55 @@ else: yield +class SQliteDataTableProvider( base.DataProvider ): + """ + Data provider that uses a sqlite database file as its source. + Allows any query to be run and returns the resulting rows as arrays of arrays + """ + settings = { + 'query': 'str', + 'headers': 'bool', + 'limit': 'int' + } + + def __init__( self, source, query=None, headers=False, limit=sys.maxint, **kwargs ): + self.query = query + self.headers = headers + self.limit = limit + self.connection = sqlite.connect(source.dataset.file_name) + super( SQliteDataTableProvider, self ).__init__( source, **kwargs ) + + def __iter__( self ): + if (self.query is not None) and sqlite.is_read_only_query(self.query): + cur = self.connection.cursor() + results = cur.execute(self.query) + if self.headers: + yield [col[0] for col in cur.description] + for i,row in enumerate(results): + if i >= self.limit: + break + yield [val for val in row] + else: + yield + +class SQliteDataDictProvider( base.DataProvider ): + """ + Data provider that uses a sqlite database file as its source. + Allows any query to be run and returns the resulting rows as arrays of dicts + """ + settings = { + 'query': 'str' + } + + def __init__( self, source, query=None, **kwargs ): + self.query = query + self.connection = sqlite.connect(source.dataset.file_name) + super( SQliteDataDictProvider, self ).__init__( source, **kwargs ) + + def __iter__( self ): + if (self.query is not None) and sqlite.is_read_only_query(self.query): + cur = self.connection.cursor() + for row in cur.execute(self.query): + yield [dict((cur.description[i][0], value) for i, value in enumerate(row))] + else: + yield https://bitbucket.org/galaxy/galaxy-central/commits/c207054ea196/ Changeset: c207054ea196 User: jjohnson Date: 2014-12-12 19:41:35+00:00 Summary: Add dataproviders to the SQlite dataype Affected #: 1 file diff -r 1e6035e53de58ce4fe1687ab74512da711d99989 -r c207054ea1966bc9d4640a6215192414e8071739 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -620,6 +620,16 @@ dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.dataset.SQliteDataProvider( dataset_source, **settings ) + @dataproviders.decorators.dataprovider_factory( 'sqlite-table', dataproviders.dataset.SQliteDataTableProvider.settings ) + def sqlite_datatableprovider( self, dataset, **settings ): + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return dataproviders.dataset.SQliteDataTableProvider( dataset_source, **settings ) + + @dataproviders.decorators.dataprovider_factory( 'sqlite-dict', dataproviders.dataset.SQliteDataDictProvider.settings ) + def sqlite_datadictprovider( self, dataset, **settings ): + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return dataproviders.dataset.SQliteDataDictProvider( dataset_source, **settings ) + Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite) https://bitbucket.org/galaxy/galaxy-central/commits/ad28e42a8af3/ Changeset: ad28e42a8af3 User: dannon Date: 2014-12-15 12:43:42+00:00 Summary: Merged in jjohnson/galaxy-central-7 (pull request #609) Add dataproviders for SQlite datatype Affected #: 2 files diff -r ecac8a8679612d419347dcbedc398319418b077e -r ad28e42a8af34c81f0ebcbe6f3baef9bdcf80ae8 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -620,6 +620,16 @@ dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.dataset.SQliteDataProvider( dataset_source, **settings ) + @dataproviders.decorators.dataprovider_factory( 'sqlite-table', dataproviders.dataset.SQliteDataTableProvider.settings ) + def sqlite_datatableprovider( self, dataset, **settings ): + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return dataproviders.dataset.SQliteDataTableProvider( dataset_source, **settings ) + + @dataproviders.decorators.dataprovider_factory( 'sqlite-dict', dataproviders.dataset.SQliteDataDictProvider.settings ) + def sqlite_datadictprovider( self, dataset, **settings ): + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return dataproviders.dataset.SQliteDataDictProvider( dataset_source, **settings ) + Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite) diff -r ecac8a8679612d419347dcbedc398319418b077e -r ad28e42a8af34c81f0ebcbe6f3baef9bdcf80ae8 lib/galaxy/datatypes/dataproviders/dataset.py --- a/lib/galaxy/datatypes/dataproviders/dataset.py +++ b/lib/galaxy/datatypes/dataproviders/dataset.py @@ -13,6 +13,7 @@ import external from galaxy.util import sqlite import re +import sys from galaxy import eggs eggs.require( 'bx-python' ) @@ -726,3 +727,55 @@ else: yield +class SQliteDataTableProvider( base.DataProvider ): + """ + Data provider that uses a sqlite database file as its source. + Allows any query to be run and returns the resulting rows as arrays of arrays + """ + settings = { + 'query': 'str', + 'headers': 'bool', + 'limit': 'int' + } + + def __init__( self, source, query=None, headers=False, limit=sys.maxint, **kwargs ): + self.query = query + self.headers = headers + self.limit = limit + self.connection = sqlite.connect(source.dataset.file_name) + super( SQliteDataTableProvider, self ).__init__( source, **kwargs ) + + def __iter__( self ): + if (self.query is not None) and sqlite.is_read_only_query(self.query): + cur = self.connection.cursor() + results = cur.execute(self.query) + if self.headers: + yield [col[0] for col in cur.description] + for i,row in enumerate(results): + if i >= self.limit: + break + yield [val for val in row] + else: + yield + +class SQliteDataDictProvider( base.DataProvider ): + """ + Data provider that uses a sqlite database file as its source. + Allows any query to be run and returns the resulting rows as arrays of dicts + """ + settings = { + 'query': 'str' + } + + def __init__( self, source, query=None, **kwargs ): + self.query = query + self.connection = sqlite.connect(source.dataset.file_name) + super( SQliteDataDictProvider, self ).__init__( source, **kwargs ) + + def __iter__( self ): + if (self.query is not None) and sqlite.is_read_only_query(self.query): + cur = self.connection.cursor() + for row in cur.execute(self.query): + yield [dict((cur.description[i][0], value) for i, value in enumerate(row))] + else: + yield Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 7 new changesets
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

7 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/563a28409672/ Changeset: 563a28409672 User: jmchilton Date: 2014-12-15 05:20:35+00:00 Summary: Allow multiple tool data table config files... ... use this functionality to implement tests for tool data API. Affected #: 5 files diff -r 6363c839528ca8bbbbc60c1b3784c788468d9445 -r 563a28409672988f6b30545ba987017e7da2e14c lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -31,8 +31,10 @@ # at server startup. If tool shed repositories are installed that contain a valid file named tool_data_table_conf.xml.sample, entries # from that file are inserted into this dict at the time of installation. self.data_tables = {} - if config_filename: - self.load_from_config_file( config_filename, self.tool_data_path, from_shed_config=False ) + for single_config_filename in util.listify( config_filename ): + if not single_config_filename: + continue + self.load_from_config_file( single_config_filename, self.tool_data_path, from_shed_config=False ) def __getitem__( self, key ): return self.data_tables.__getitem__( key ) diff -r 6363c839528ca8bbbbc60c1b3784c788468d9445 -r 563a28409672988f6b30545ba987017e7da2e14c scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -231,7 +231,16 @@ start_server = 'GALAXY_TEST_EXTERNAL' not in os.environ tool_data_table_config_path = None if os.path.exists( 'tool_data_table_conf.test.xml' ): + # If explicitly defined tables for test, use those. tool_data_table_config_path = 'tool_data_table_conf.test.xml' + else: + # ... otherise find whatever Galaxy would use as the default and + # the sample data for fucntional tests to that. + default_tool_data_config = 'config/tool_data_table_conf.xml.sample' + for tool_data_config in ['config/tool_data_table_conf.xml', 'tool_data_table_conf.xml' ]: + if os.path.exists( tool_data_config ): + default_tool_data_config = tool_data_config + tool_data_table_config_path = '%s,test/functional/tool-data/sample_tool_data_tables.xml' % default_tool_data_config shed_tool_data_table_config = 'config/shed_tool_data_table_conf.xml' tool_dependency_dir = os.environ.get( 'GALAXY_TOOL_DEPENDENCY_DIR', None ) use_distributed_object_store = os.environ.get( 'GALAXY_USE_DISTRIBUTED_OBJECT_STORE', False ) diff -r 6363c839528ca8bbbbc60c1b3784c788468d9445 -r 563a28409672988f6b30545ba987017e7da2e14c test/api/test_tool_data.py --- /dev/null +++ b/test/api/test_tool_data.py @@ -0,0 +1,30 @@ +""" Tests for the tool data API. +""" +from base import api + +import operator + + +class ToolDataApiTestCase( api.ApiTestCase ): + + def test_admin_only( self ): + index_response = self._get( "tool_data", admin=False ) + self._assert_status_code_is( index_response, 403 ) + + def test_list(self): + index_response = self._get( "tool_data", admin=True ) + self._assert_status_code_is( index_response, 200 ) + print index_response.content + index = index_response.json() + assert "testalpha" in map(operator.itemgetter("name"), index) + + def test_show(self): + show_response = self._get( "tool_data/testalpha", admin=True ) + self._assert_status_code_is( show_response, 200 ) + print show_response.content + data_table = show_response.json() + assert data_table["columns"] == ["value", "name", "path"] + first_entry = data_table["fields"][0] + assert first_entry[0] == "data1" + assert first_entry[1] == "data1name" + assert first_entry[2].endswith("test/functional/tool-data/data1/entry.txt") diff -r 6363c839528ca8bbbbc60c1b3784c788468d9445 -r 563a28409672988f6b30545ba987017e7da2e14c test/functional/tool-data/sample_tool_data_tables.xml --- /dev/null +++ b/test/functional/tool-data/sample_tool_data_tables.xml @@ -0,0 +1,12 @@ +<tables> + <table name="testalpha" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/testalpha.loc" /> + </table> +  +</tables> diff -r 6363c839528ca8bbbbc60c1b3784c788468d9445 -r 563a28409672988f6b30545ba987017e7da2e14c test/functional/tool-data/testalpha.loc --- /dev/null +++ b/test/functional/tool-data/testalpha.loc @@ -0,0 +1,2 @@ +data1 data1name ${__HERE__}/data1/entry.txt +data2 data2name ${__HERE__}/data2/entry.txt https://bitbucket.org/galaxy/galaxy-central/commits/8795d0fe13c4/ Changeset: 8795d0fe13c4 User: jmchilton Date: 2014-12-15 05:20:35+00:00 Summary: PEP-8 fixes for lib/galaxy/tools/data/__init__.py. Affected #: 1 file diff -r 563a28409672988f6b30545ba987017e7da2e14c -r 8795d0fe13c45804ea53f4543c71ee7ca6f41a0c lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -9,9 +9,7 @@ import logging import os import os.path -import shutil import string -import tempfile from galaxy import util from galaxy.util.odict import odict @@ -22,6 +20,7 @@ DEFAULT_TABLE_TYPE = 'tabular' + class ToolDataTableManager( object ): """Manages a collection of tool data tables""" @@ -81,7 +80,7 @@ log.debug( "Loaded tool data table '%s'", table.name ) else: log.debug( "Loading another instance of data table '%s', attempting to merge content.", table.name ) - self.data_tables[ table.name ].merge_tool_data_table( table, allow_duplicates=False ) #only merge content, do not persist to disk, do not allow duplicate rows when merging + self.data_tables[ table.name ].merge_tool_data_table( table, allow_duplicates=False ) # only merge content, do not persist to disk, do not allow duplicate rows when merging # FIXME: This does not account for an entry with the same unique build ID, but a different path. return table_elems @@ -128,7 +127,7 @@ """ if not ( new_elems or remove_elems ): log.debug( 'ToolDataTableManager.to_xml_file called without any elements to add or remove.' ) - return #no changes provided, no need to persist any changes + return # no changes provided, no need to persist any changes if not new_elems: new_elems = [] if not remove_elems: @@ -175,7 +174,7 @@ assert table_type in tool_data_table_types, "Unknown data table type '%s'" % type return tool_data_table_types[ table_type ]( table_elem, tool_data_path, from_shed_config=from_shed_config, filename=filename ) - def __init__( self, config_element, tool_data_path, from_shed_config = False, filename=None ): + def __init__( self, config_element, tool_data_path, from_shed_config=False, filename=None ): self.name = config_element.get( 'name' ) self.comment_char = config_element.get( 'comment_char' ) self.empty_field_value = config_element.get( 'empty_field_value', '' ) @@ -187,7 +186,7 @@ # increment this variable any time a new entry is added, or when the table is totally reloaded # This value has no external meaning, and does not represent an abstract version of the underlying data self._loaded_content_version = 1 - self._load_info = ( [ config_element, tool_data_path ], { 'from_shed_config':from_shed_config } ) + self._load_info = ( [ config_element, tool_data_path ], { 'from_shed_config': from_shed_config } ) self._merged_load_info = [] def _update_version( self, version=None ): @@ -252,13 +251,13 @@ type_key = 'tabular' - def __init__( self, config_element, tool_data_path, from_shed_config = False, filename=None ): + def __init__( self, config_element, tool_data_path, from_shed_config=False, filename=None ): super( TabularToolDataTable, self ).__init__( config_element, tool_data_path, from_shed_config, filename) self.config_element = config_element self.data = [] self.configure_and_load( config_element, tool_data_path, from_shed_config) - def configure_and_load( self, config_element, tool_data_path, from_shed_config = False): + def configure_and_load( self, config_element, tool_data_path, from_shed_config=False): """ Configure and load table from an XML element. """ @@ -323,7 +322,6 @@ else: log.debug( "Filename '%s' already exists in filenames (%s), not adding", filename, self.filenames.keys() ) - def merge_tool_data_table( self, other_table, allow_duplicates=True, persist=False, persist_on_error=False, entry_source=None, **kwd ): assert self.columns == other_table.columns, "Merging tabular data tables with non matching columns is not allowed: %s:%s != %s:%s" % ( self.name, self.columns, other_table.name, other_table.columns ) #merge filename info @@ -350,7 +348,7 @@ for i, field in enumerate( fields ): field_name = named_colums[i] if field_name is None: - field_name = i #check that this is supposed to be 0 based. + field_name = i # check that this is supposed to be 0 based. field_dict[ field_name ] = field rval.append( field_dict ) return rval @@ -508,7 +506,7 @@ data_table_fh = open( filename, 'wb' ) if os.stat( filename )[6] != 0: # ensure last existing line ends with new line - data_table_fh.seek( -1, 2 ) #last char in file + data_table_fh.seek( -1, 2 ) # last char in file last_char = data_table_fh.read( 1 ) if last_char not in [ '\n', '\r' ]: data_table_fh.write( '\n' ) @@ -577,7 +575,7 @@ def to_dict(self, view='collection'): rval = super(TabularToolDataTable, self).to_dict() if view == 'element': - rval['columns'] = sorted(self.columns.keys(), key=lambda x:self.columns[x]) + rval['columns'] = sorted(self.columns.keys(), key=lambda x: self.columns[x]) rval['fields'] = self.get_fields() return rval https://bitbucket.org/galaxy/galaxy-central/commits/6d54a7fd1fe9/ Changeset: 6d54a7fd1fe9 User: jmchilton Date: 2014-12-15 05:20:35+00:00 Summary: Small improvements to tool data API. Update tool data API to use newer API decorator for better error handling, create some abstractions for reuse down stream, etc... Affected #: 1 file diff -r 8795d0fe13c45804ea53f4543c71ee7ca6f41a0c -r 6d54a7fd1fe9edfdf2f5c2fdb1b5ddb7eebdf59a lib/galaxy/webapps/galaxy/api/tool_data.py --- a/lib/galaxy/webapps/galaxy/api/tool_data.py +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -1,4 +1,6 @@ +from galaxy import exceptions from galaxy import web +from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController @@ -8,21 +10,21 @@ """ @web.require_admin - @web.expose_api + @expose_api def index( self, trans, **kwds ): """ GET /api/tool_data: returns a list tool_data tables:: """ - return list( a.to_dict() for a in trans.app.tool_data_tables.data_tables.values() ) + return list( a.to_dict() for a in self._data_tables.values() ) @web.require_admin - @web.expose_api + @expose_api def show( self, trans, id, **kwds ): - return trans.app.tool_data_tables.data_tables[id].to_dict(view='element') + return self._data_table(id).to_dict(view='element') @web.require_admin - @web.expose_api + @expose_api def delete( self, trans, id, **kwd ): """ DELETE /api/tool_data/{id} @@ -61,3 +63,13 @@ return "Invalid data table item ( %s ) specified. Wrong number of columns (%s given, %s required)." % ( str( values ), str(len(split_values)), str(len(data_table.get_column_name_list()))) return data_table.remove_entry(split_values) + + def _data_table( self, id ): + try: + return self._data_tables[id] + except IndexError: + raise exceptions.ObjectNotFound("No such data table %s" % id) + + @property + def _data_tables( self ): + return self.app.tool_data_tables.data_tables https://bitbucket.org/galaxy/galaxy-central/commits/edbe286564de/ Changeset: edbe286564de User: jmchilton Date: 2014-12-15 05:20:35+00:00 Summary: Implement a detailed break down of data table fields via API. Originally this approach was laid out by Kyle Ellrott in this pull request (https://bitbucket.org/galaxy/galaxy-central/pull-request/531/add-downloads-…) The changes to galaxy.tools.data are entirely his contribution, I only reworked the API and endpoint slightly and did some stylistic fixes and refactoring. Affected #: 4 files diff -r 6d54a7fd1fe9edfdf2f5c2fdb1b5ddb7eebdf59a -r edbe286564de14b2d51656c03443b3e4aa99e3ab lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -9,7 +9,11 @@ import logging import os import os.path +import re import string +import hashlib + +from glob import glob from galaxy import util from galaxy.util.odict import odict @@ -340,6 +344,13 @@ def get_fields( self ): return self.data + def get_field(self, value): + rval = None + for i in self.get_named_fields_list(): + if i['value'] == value: + rval = TabularToolDataField(i) + return rval + def get_named_fields_list( self ): rval = [] named_colums = self.get_column_name_list() @@ -580,6 +591,58 @@ return rval +class TabularToolDataField(Dictifiable, object): + + dict_collection_visible_keys = [] + + def __init__(self, data): + self.data = data + + def __getitem__(self, key): + return self.data[key] + + def get_base_path(self): + return os.path.normpath(os.path.abspath( self.data['path'] )) + + def get_base_dir(self): + path = self.get_base_path() + if not os.path.isdir(path): + path = os.path.dirname(path) + return path + + def clean_base_dir(self, path): + return re.sub( "^" + self.get_base_dir() + r"/*", "", path ) + + def get_files(self): + return glob( self.get_base_path() + "*" ) + + def get_filesize_map(self, rm_base_dir=False): + out = {} + for path in self.get_files(): + if rm_base_dir: + out[self.clean_base_dir(path)] = os.path.getsize(path) + else: + out[path] = os.path.getsize(path) + return out + + def get_fingerprint(self): + sha1 = hashlib.sha1() + fmap = self.get_filesize_map(True) + for k in sorted(fmap.keys()): + sha1.update(k) + sha1.update(str(fmap[k])) + return sha1.hexdigest() + + def to_dict(self): + rval = super(TabularToolDataField, self).to_dict() + rval['name'] = self.data['value'] + rval['fields'] = self.data + rval['base_dir'] = self.get_base_dir(), + rval['files'] = self.get_filesize_map(True) + rval['fingerprint'] = self.get_fingerprint() + return rval + + def expand_here_template(content, here=None): if here and content: content = string.Template(content).safe_substitute( { "__HERE__": here }) diff -r 6d54a7fd1fe9edfdf2f5c2fdb1b5ddb7eebdf59a -r edbe286564de14b2d51656c03443b3e4aa99e3ab lib/galaxy/webapps/galaxy/api/tool_data.py --- a/lib/galaxy/webapps/galaxy/api/tool_data.py +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -64,6 +64,22 @@ return data_table.remove_entry(split_values) + @web.require_admin + @expose_api + def show_field( self, trans, id, value, **kwds ): + """ + GET /api/tool_data/<id>/fields/<value> + + Get information about a partiular field in a tool_data table + """ + return self._data_table_field( id, value ).to_dict() + + def _data_table_field( self, id, value ): + out = self._data_table(id).get_field(value) + if out is None: + raise exceptions.ObjectNotFound("No such field %s in data table %s." % (value, id)) + return out + def _data_table( self, id ): try: return self._data_tables[id] diff -r 6d54a7fd1fe9edfdf2f5c2fdb1b5ddb7eebdf59a -r edbe286564de14b2d51656c03443b3e4aa99e3ab lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -171,6 +171,7 @@ webapp.mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) webapp.mapper.resource( 'tool_data', 'tool_data', path_prefix='/api' ) + webapp.mapper.connect( '/api/tool_data/{id:.+?}/fields/{value:.+?}', action='show_field', controller="tool_data" ) webapp.mapper.resource( 'dataset_collection', 'dataset_collections', path_prefix='/api/') webapp.mapper.resource( 'sample', 'samples', path_prefix='/api' ) webapp.mapper.resource( 'request', 'requests', path_prefix='/api' ) diff -r 6d54a7fd1fe9edfdf2f5c2fdb1b5ddb7eebdf59a -r edbe286564de14b2d51656c03443b3e4aa99e3ab test/api/test_tool_data.py --- a/test/api/test_tool_data.py +++ b/test/api/test_tool_data.py @@ -28,3 +28,11 @@ assert first_entry[0] == "data1" assert first_entry[1] == "data1name" assert first_entry[2].endswith("test/functional/tool-data/data1/entry.txt") + + def test_show_field(self): + show_field_response = self._get( "tool_data/testalpha/fields/data1", admin=True ) + self._assert_status_code_is( show_field_response, 200 ) + field = show_field_response.json() + self._assert_has_keys( field, "files", "name", "fields", "fingerprint", "base_dir" ) + files = field[ "files" ] + assert len( files ) == 2 https://bitbucket.org/galaxy/galaxy-central/commits/e416c3a2f956/ Changeset: e416c3a2f956 User: jmchilton Date: 2014-12-15 05:20:35+00:00 Summary: Allow downloading index files via tool data API. This provides direct access to the files to admins - probably still wise to provide some mechanism to download a copressed archive of these files. Affected #: 3 files diff -r edbe286564de14b2d51656c03443b3e4aa99e3ab -r e416c3a2f956a28127eb730076f37ad6ee4b1d8b lib/galaxy/webapps/galaxy/api/tool_data.py --- a/lib/galaxy/webapps/galaxy/api/tool_data.py +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -1,6 +1,9 @@ +import os + from galaxy import exceptions from galaxy import web from galaxy.web import _future_expose_api as expose_api +from galaxy.web import _future_expose_api_raw as expose_api_raw from galaxy.web.base.controller import BaseAPIController @@ -74,6 +77,16 @@ """ return self._data_table_field( id, value ).to_dict() + @web.require_admin + @expose_api_raw + def download_field_file( self, trans, id, value, path, **kwds ): + field_value = self._data_table_field( id, value ) + base_dir = field_value.get_base_dir() + full_path = os.path.join( base_dir, path ) + if full_path not in field_value.get_files(): + raise exceptions.ObjectNotFound("No such path in data table field.") + return open(full_path, "r") + def _data_table_field( self, id, value ): out = self._data_table(id).get_field(value) if out is None: diff -r edbe286564de14b2d51656c03443b3e4aa99e3ab -r e416c3a2f956a28127eb730076f37ad6ee4b1d8b lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -171,6 +171,7 @@ webapp.mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) webapp.mapper.resource( 'tool_data', 'tool_data', path_prefix='/api' ) + webapp.mapper.connect( '/api/tool_data/{id:.+?}/fields/{value:.+?}/files/{path:.+?}', action='download_field_file', controller="tool_data" ) webapp.mapper.connect( '/api/tool_data/{id:.+?}/fields/{value:.+?}', action='show_field', controller="tool_data" ) webapp.mapper.resource( 'dataset_collection', 'dataset_collections', path_prefix='/api/') webapp.mapper.resource( 'sample', 'samples', path_prefix='/api' ) diff -r edbe286564de14b2d51656c03443b3e4aa99e3ab -r e416c3a2f956a28127eb730076f37ad6ee4b1d8b test/api/test_tool_data.py --- a/test/api/test_tool_data.py +++ b/test/api/test_tool_data.py @@ -36,3 +36,9 @@ self._assert_has_keys( field, "files", "name", "fields", "fingerprint", "base_dir" ) files = field[ "files" ] assert len( files ) == 2 + + def test_download_field_file(self): + show_field_response = self._get( "tool_data/testalpha/fields/data1/files/entry.txt", admin=True ) + self._assert_status_code_is( show_field_response, 200 ) + content = show_field_response.content + assert content == "This is data 1.", content https://bitbucket.org/galaxy/galaxy-central/commits/66fbbbd58209/ Changeset: 66fbbbd58209 User: jmchilton Date: 2014-12-15 05:20:35+00:00 Summary: Allow specification of multiple data manager configuration files... ... use this to create API functional tests for data managers. Affected #: 7 files diff -r e416c3a2f956a28127eb730076f37ad6ee4b1d8b -r 66fbbbd58209dba224f95c2aaf973ec7c64b7c11 lib/galaxy/tools/data_manager/manager.py --- a/lib/galaxy/tools/data_manager/manager.py +++ b/lib/galaxy/tools/data_manager/manager.py @@ -25,7 +25,10 @@ self.managed_data_tables = odict() self.tool_path = None self.filename = xml_filename or self.app.config.data_manager_config_file - self.load_from_xml( self.filename ) + for filename in util.listify( self.filename ): + if not filename: + continue + self.load_from_xml( filename ) if self.app.config.shed_data_manager_config_file: self.load_from_xml( self.app.config.shed_data_manager_config_file, store_tool_path=False, replace_existing=True ) diff -r e416c3a2f956a28127eb730076f37ad6ee4b1d8b -r 66fbbbd58209dba224f95c2aaf973ec7c64b7c11 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -241,6 +241,12 @@ if os.path.exists( tool_data_config ): default_tool_data_config = tool_data_config tool_data_table_config_path = '%s,test/functional/tool-data/sample_tool_data_tables.xml' % default_tool_data_config + + default_data_manager_config = 'config/data_manager_conf.xml.sample' + for data_manager_config in ['config/data_manager_conf.xml', 'data_manager_conf.xml' ]: + if os.path.exists( data_manager_config ): + default_data_manager_config = data_manager_config + data_manager_config_file = "%s,test/functional/tools/sample_data_manager_conf.xml" % default_data_manager_config shed_tool_data_table_config = 'config/shed_tool_data_table_conf.xml' tool_dependency_dir = os.environ.get( 'GALAXY_TOOL_DEPENDENCY_DIR', None ) use_distributed_object_store = os.environ.get( 'GALAXY_USE_DISTRIBUTED_OBJECT_STORE', False ) @@ -329,6 +335,7 @@ master_api_key=master_api_key, use_tasked_jobs=True, enable_beta_tool_formats=True, + data_manager_config_file=data_manager_config_file, ) if install_database_connection is not None: kwargs[ 'install_database_connection' ] = install_database_connection diff -r e416c3a2f956a28127eb730076f37ad6ee4b1d8b -r 66fbbbd58209dba224f95c2aaf973ec7c64b7c11 test/api/test_tool_data.py --- a/test/api/test_tool_data.py +++ b/test/api/test_tool_data.py @@ -1,6 +1,9 @@ """ Tests for the tool data API. """ +import json + from base import api +from .helpers import DatasetPopulator import operator @@ -42,3 +45,19 @@ self._assert_status_code_is( show_field_response, 200 ) content = show_field_response.content assert content == "This is data 1.", content + + def test_create_data_with_manager(self): + dataset_populator = DatasetPopulator( self.galaxy_interactor ) + history_id = dataset_populator.new_history() + payload = dataset_populator.run_tool_payload( + tool_id="data_manager", + inputs={"ignored_value": "moo"}, + history_id=history_id, + ) + create_response = self._post( "tools", data=payload ) + self._assert_status_code_is( create_response, 200 ) + dataset_populator.wait_for_history( history_id, assert_ok=True ) + show_response = self._get( "tool_data/testbeta", admin=True ) + print show_response.content + assert False + diff -r e416c3a2f956a28127eb730076f37ad6ee4b1d8b -r 66fbbbd58209dba224f95c2aaf973ec7c64b7c11 test/functional/tool-data/sample_tool_data_tables.xml --- a/test/functional/tool-data/sample_tool_data_tables.xml +++ b/test/functional/tool-data/sample_tool_data_tables.xml @@ -3,10 +3,8 @@ <columns>value, name, path</columns><file path="${__HERE__}/testalpha.loc" /></table> - </tables> diff -r e416c3a2f956a28127eb730076f37ad6ee4b1d8b -r 66fbbbd58209dba224f95c2aaf973ec7c64b7c11 test/functional/tools/data_manager.xml --- /dev/null +++ b/test/functional/tools/data_manager.xml @@ -0,0 +1,16 @@ +<tool id="data_manager" name="Test Data Manager" tool_type="manage_data" version="0.0.1"> + <configfiles> + <configfile name="static_test_data">{"data_tables": {"testbeta": [{"value": "newvalue", "path": "newvalue.txt"}]}}</configfile> + </configfiles> + <command> + mkdir $out_file.files_path ; + echo "A new value" > $out_file.files_path/newvalue.txt; + cp $static_test_data $out_file + </command> + <inputs> + <param type="text" name="ignored_value" value="" label="Ignored" /> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json"/> + </outputs> +</tool> diff -r e416c3a2f956a28127eb730076f37ad6ee4b1d8b -r 66fbbbd58209dba224f95c2aaf973ec7c64b7c11 test/functional/tools/sample_data_manager_conf.xml --- /dev/null +++ b/test/functional/tools/sample_data_manager_conf.xml @@ -0,0 +1,16 @@ +<data_managers tool_path="test/functional/tools"> + <data_manager tool_file="data_manager.xml" id="test_data_manager" version="1.0"> + <data_table name="testbeta"> + <output> + <column name="value" /> + <column name="path" output_ref="out_file" > + <move type="directory" relativize_symlinks="True"> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">testbeta/${value}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/testbeta/${value}/${path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers> https://bitbucket.org/galaxy/galaxy-central/commits/ecac8a867961/ Changeset: ecac8a867961 User: jmchilton Date: 2014-12-15 05:20:35+00:00 Summary: Implement test case for Pull Request #577. Affected #: 1 file diff -r 66fbbbd58209dba224f95c2aaf973ec7c64b7c11 -r ecac8a8679612d419347dcbedc398319418b077e test/api/test_tool_data.py --- a/test/api/test_tool_data.py +++ b/test/api/test_tool_data.py @@ -5,6 +5,8 @@ from base import api from .helpers import DatasetPopulator +from requests import delete + import operator @@ -46,7 +48,10 @@ content = show_field_response.content assert content == "This is data 1.", content - def test_create_data_with_manager(self): + def test_delete_entry(self): + show_response = self._get( "tool_data/testbeta", admin=True ) + original_count = len(show_response.json()["fields"]) + dataset_populator = DatasetPopulator( self.galaxy_interactor ) history_id = dataset_populator.new_history() payload = dataset_populator.run_tool_payload( @@ -58,6 +63,12 @@ self._assert_status_code_is( create_response, 200 ) dataset_populator.wait_for_history( history_id, assert_ok=True ) show_response = self._get( "tool_data/testbeta", admin=True ) - print show_response.content - assert False + updated_fields = show_response.json()["fields"] + assert len(updated_fields) == original_count + 1 + field0 = updated_fields[0] + url = self._api_url( "tool_data/testbeta?key=%s" % self.galaxy_interactor.master_api_key ) + delete( url, data=json.dumps({"values": "\t".join(field0)}) ) + show_response = self._get( "tool_data/testbeta", admin=True ) + updated_fields = show_response.json()["fields"] + assert len(updated_fields) == original_count Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Merged in abretaud/galaxy-central (pull request #577)
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6363c839528c/ Changeset: 6363c839528c User: jmchilton Date: 2014-12-15 05:17:31+00:00 Summary: Merged in abretaud/galaxy-central (pull request #577) Add an API to remove items from tool data tables Affected #: 2 files diff -r ac537b0a4167cbd14e0cb93175cc85c096275697 -r 6363c839528ca8bbbbc60c1b3784c788468d9445 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -211,6 +211,13 @@ self.add_entry( entry, allow_duplicates=allow_duplicates, persist=persist, persist_on_error=persist_on_error, entry_source=entry_source, **kwd ) return self._loaded_content_version + def _remove_entry(self, values): + raise NotImplementedError( "Abstract method" ) + + def remove_entry(self, values): + self._remove_entry( values ) + return self._update_version() + def is_current_version( self, other_version ): return self._loaded_content_version == other_version @@ -506,6 +513,42 @@ data_table_fh.write( "%s\n" % ( self.separator.join( fields ) ) ) return not is_error + def _remove_entry( self, values): + + # update every file + for filename in self.filenames: + + if os.path.exists( filename ): + values = self._replace_field_separators( values ) + self.filter_file_fields( filename, values ) + else: + log.warn( "Cannot find index file '%s' for tool data table '%s'" % ( filename, self.name ) ) + + self.reload_from_files() + + def filter_file_fields( self, loc_file, values ): + """ + Reads separated lines from file and print back only the lines that pass a filter. + """ + separator_char = (lambda c: '<TAB>' if c == '\t' else c)(self.separator) + + with open(loc_file) as reader: + rval = "" + for i, line in enumerate( reader ): + if line.lstrip().startswith( self.comment_char ): + rval += line + else: + line_s = line.rstrip( "\n\r" ) + if line_s: + fields = line_s.split( self.separator ) + if fields != values: + rval += line + + with open(loc_file, 'wb') as writer: + writer.write(rval) + + return rval + def _replace_field_separators( self, fields, separator=None, replace=None, comment_char=None ): #make sure none of the fields contain separator #make sure separator replace is different from comment_char, diff -r ac537b0a4167cbd14e0cb93175cc85c096275697 -r 6363c839528ca8bbbbc60c1b3784c788468d9445 lib/galaxy/webapps/galaxy/api/tool_data.py --- a/lib/galaxy/webapps/galaxy/api/tool_data.py +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -20,3 +20,44 @@ @web.expose_api def show( self, trans, id, **kwds ): return trans.app.tool_data_tables.data_tables[id].to_dict(view='element') + + @web.require_admin + @web.expose_api + def delete( self, trans, id, **kwd ): + """ + DELETE /api/tool_data/{id} + Removes an item from a data table + + :type id: str + :param id: the id of the data table containing the item to delete + :type kwd: dict + :param kwd: (required) dictionary structure containing: + + * payload: a dictionary itself containing: + * values: <TAB> separated list of column contents, there must be a value for all the columns of the data table + """ + decoded_tool_data_id = id + + try: + data_table = trans.app.tool_data_tables.data_tables.get(decoded_tool_data_id) + except: + data_table = None + if not data_table: + trans.response.status = 400 + return "Invalid data table id ( %s ) specified." % str( decoded_tool_data_id ) + + values = None + if kwd.get( 'payload', None ): + values = kwd['payload'].get( 'values', '' ) + + if not values: + trans.response.status = 400 + return "Invalid data table item ( %s ) specified." % str( values ) + + split_values = values.split("\t") + + if len(split_values) != len(data_table.get_column_name_list()): + trans.response.status = 400 + return "Invalid data table item ( %s ) specified. Wrong number of columns (%s given, %s required)." % ( str( values ), str(len(split_values)), str(len(data_table.get_column_name_list()))) + + return data_table.remove_entry(split_values) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5edaafeecfed/ Changeset: 5edaafeecfed User: abretaud Date: 2014-11-27 13:18:18+00:00 Summary: Add an API to remove items from tool data tables Affected #: 2 files diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -211,6 +211,13 @@ self.add_entry( entry, allow_duplicates=allow_duplicates, persist=persist, persist_on_error=persist_on_error, entry_source=entry_source, **kwd ) return self._loaded_content_version + def _remove_entry(self, values, **kwd): + raise NotImplementedError( "Abstract method" ) + + def remove_entry(self, values, **kwd): + self._remove_entry_and_reload( values,**kwd ) + return self._update_version() + def is_current_version( self, other_version ): return self._loaded_content_version == other_version @@ -506,6 +513,42 @@ data_table_fh.write( "%s\n" % ( self.separator.join( fields ) ) ) return not is_error + def _remove_entry_and_reload( self, values): + + # update every file + for filename in self.filenames: + + if os.path.exists( filename ): + values = self._replace_field_separators( values ) + self.filter_file_fields( filename, values ) + else: + log.warn( "Cannot find index file '%s' for tool data table '%s'" % ( filename, self.name ) ) + + self.reload_from_files() + + def filter_file_fields( self, loc_file, values ): + """ + Reads separated lines from file and print back only the lines that pass a filter. + """ + separator_char = (lambda c: '<TAB>' if c == '\t' else c)(self.separator) + + with open(loc_file) as reader: + rval = "" + for i, line in enumerate( reader ): + if line.lstrip().startswith( self.comment_char ): + rval += line + else: + line_s = line.rstrip( "\n\r" ) + if line_s: + fields = line_s.split( self.separator ) + if fields != values: + rval += line + + with open(loc_file, 'wb') as writer: + writer.write(rval) + + return rval + def _replace_field_separators( self, fields, separator=None, replace=None, comment_char=None ): #make sure none of the fields contain separator #make sure separator replace is different from comment_char, diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 lib/galaxy/webapps/galaxy/api/tool_data.py --- a/lib/galaxy/webapps/galaxy/api/tool_data.py +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -20,3 +20,44 @@ @web.expose_api def show( self, trans, id, **kwds ): return trans.app.tool_data_tables.data_tables[id].to_dict(view='element') + + @web.require_admin + @web.expose_api + def delete( self, trans, id, **kwd ): + """ + DELETE /api/tool_data/{id} + Removes a role from a group + + :type id: str + :param id: the encoded id of the history to delete + :type kwd: dict + :param kwd: (required) dictionary structure containing: + + * payload: a dictionary itself containing: + * values: <TAB> separated list of column contents, there must be a value for all the columns of the data table + """ + decoded_tool_data_id = id + + try: + data_table = trans.app.tool_data_tables.data_tables.get(decoded_tool_data_id) + except: + data_table = None + if not data_table: + trans.response.status = 400 + return "Invalid data table id ( %s ) specified." % str( decoded_tool_data_id ) + + values = None + if kwd.get( 'payload', None ): + values = kwd['payload'].get( 'values', '' ) + + if not values: + trans.response.status = 400 + return "Invalid data table item ( %s ) specified." % str( values ) + + split_values = values.split("\t") + + if len(split_values) != len(data_table.get_column_name_list()): + trans.response.status = 400 + return "Invalid data table item ( %s ) specified. Wrong number of columns (%s given, %s required)." % ( str( values ), str(len(split_values)), str(len(data_table.get_column_name_list()))) + + return data_table.remove_entry(split_values) https://bitbucket.org/galaxy/galaxy-central/commits/d76253bb22c4/ Changeset: d76253bb22c4 User: abretaud Date: 2014-12-09 14:01:47+00:00 Summary: Merged galaxy/galaxy-central into default Affected #: 184 files diff -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 -r d76253bb22c4f64c73523956d119c0c5ab0a357b .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -acc8d1e2bc88530aa8d8651cf5f88649f6769304 latest_2014.10.06 +acb2548443ae42d39ef200d035ccc0481d6b930c latest_2014.10.06 diff -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 -r d76253bb22c4f64c73523956d119c0c5ab0a357b client/galaxy/scripts/galaxy.library.js --- a/client/galaxy/scripts/galaxy.library.js +++ b/client/galaxy/scripts/galaxy.library.js @@ -36,7 +36,7 @@ initialize: function() { this.routesHit = 0; //keep count of number of routes handled by the application - Backbone.history.on('route', function() { this.routesHit++; }, this); + Backbone.history.on( 'route', function() { this.routesHit++; }, this ); }, routes: { @@ -45,6 +45,7 @@ "library/:library_id/permissions" : "library_permissions", "folders/:folder_id/permissions" : "folder_permissions", "folders/:id" : "folder_content", + "folders/:id/page/:show_page" : "folder_page", "folders/:folder_id/datasets/:dataset_id" : "dataset_detail", "folders/:folder_id/datasets/:dataset_id/permissions" : "dataset_permissions", "folders/:folder_id/datasets/:dataset_id/versions/:ldda_id" : "dataset_version", @@ -53,13 +54,13 @@ }, back: function() { - if(this.routesHit > 1) { + if( this.routesHit > 1 ) { //more than one route hit -> user did not land to current page directly window.history.back(); } else { //otherwise go to the home page. Use replaceState if available so //the navigation doesn't create an extra history entry - this.navigate('#', {trigger:true, replace:true}); + this.navigate( '#', { trigger:true, replace:true } ); } } }); @@ -71,7 +72,8 @@ with_deleted : false, sort_order : 'asc', sort_by : 'name', - library_page_size : 20 + library_page_size : 20, + folder_page_size : 15 } }); @@ -94,10 +96,10 @@ this.library_router = new LibraryRouter(); - this.library_router.on('route:libraries', function() { - Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView(); - Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView(); - }); + this.library_router.on( 'route:libraries', function() { + Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView(); + Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView(); + }); this.library_router.on('route:libraries_page', function( show_page ) { if ( Galaxy.libraries.libraryToolbarView === null ){ @@ -108,66 +110,77 @@ } }); - this.library_router.on('route:folder_content', function(id) { + this.library_router.on( 'route:folder_content', function( id ) { if (Galaxy.libraries.folderToolbarView){ - Galaxy.libraries.folderToolbarView.$el.unbind('click'); - } - Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: id}); - Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: id}); - }); + Galaxy.libraries.folderToolbarView.$el.unbind( 'click' ); + } + Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView( { id: id } ); + Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView( { id: id } ); + }); - this.library_router.on('route:download', function(folder_id, format) { - if ($('#folder_list_body').find(':checked').length === 0) { - mod_toastr.info( 'You must select at least one dataset to download' ); - Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); - } else { - Galaxy.libraries.folderToolbarView.download(folder_id, format); - Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: false, replace: true}); - } - }); + this.library_router.on( 'route:folder_page', function( id, show_page ) { + if ( Galaxy.libraries.folderToolbarView === null ){ + Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView( {id: id} ); + Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView( { id: id, show_page: show_page } ); + } else { + Galaxy.libraries.folderListView.render( { id: id, show_page: parseInt( show_page ) } ) + } + }); - this.library_router.on('route:dataset_detail', function(folder_id, dataset_id){ - if (Galaxy.libraries.datasetView){ - Galaxy.libraries.datasetView.$el.unbind('click'); - } - Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id}); - }); - this.library_router.on('route:dataset_version', function(folder_id, dataset_id, ldda_id){ - if (Galaxy.libraries.datasetView){ - Galaxy.libraries.datasetView.$el.unbind('click'); - } - Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, ldda_id: ldda_id, show_version: true}); - }); + this.library_router.on( 'route:download', function( folder_id, format ) { + if ( $( '#folder_list_body' ).find( ':checked' ).length === 0 ) { + mod_toastr.info( 'You must select at least one dataset to download' ); + Galaxy.libraries.library_router.navigate( 'folders/' + folder_id, { trigger: true, replace: true } ); + } else { + Galaxy.libraries.folderToolbarView.download( folder_id, format ); + Galaxy.libraries.library_router.navigate( 'folders/' + folder_id, { trigger: false, replace: true } ); + } + }); - this.library_router.on('route:dataset_permissions', function(folder_id, dataset_id){ - if (Galaxy.libraries.datasetView){ - Galaxy.libraries.datasetView.$el.unbind('click'); - } - Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true}); - }); + this.library_router.on( 'route:dataset_detail', function(folder_id, dataset_id){ + if (Galaxy.libraries.datasetView){ + Galaxy.libraries.datasetView.$el.unbind('click'); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id}); + }); - this.library_router.on('route:library_permissions', function(library_id){ - if (Galaxy.libraries.libraryView){ - Galaxy.libraries.libraryView.$el.unbind('click'); - } - Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({id: library_id, show_permissions: true}); - }); + this.library_router.on( 'route:dataset_version', function(folder_id, dataset_id, ldda_id){ + if (Galaxy.libraries.datasetView){ + Galaxy.libraries.datasetView.$el.unbind('click'); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, ldda_id: ldda_id, show_version: true}); + }); - this.library_router.on('route:folder_permissions', function(folder_id){ - if (Galaxy.libraries.folderView){ - Galaxy.libraries.folderView.$el.unbind('click'); - } - Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true}); - }); - this.library_router.on('route:import_datasets', function(folder_id, source){ - if (Galaxy.libraries.folderToolbarView && Galaxy.libraries.folderListView){ - Galaxy.libraries.folderToolbarView.showImportModal({source:source}); - } else { - Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: folder_id}); - Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: folder_id}); - Galaxy.libraries.folderToolbarView.showImportModal({source: source}); - } - }); + this.library_router.on( 'route:dataset_permissions', function(folder_id, dataset_id){ + if (Galaxy.libraries.datasetView){ + Galaxy.libraries.datasetView.$el.unbind('click'); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true}); + }); + + this.library_router.on( 'route:library_permissions', function(library_id){ + if (Galaxy.libraries.libraryView){ + Galaxy.libraries.libraryView.$el.unbind('click'); + } + Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({id: library_id, show_permissions: true}); + }); + + this.library_router.on( 'route:folder_permissions', function(folder_id){ + if (Galaxy.libraries.folderView){ + Galaxy.libraries.folderView.$el.unbind('click'); + } + Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true}); + }); + + this.library_router.on( 'route:import_datasets', function( folder_id, source ){ + if ( Galaxy.libraries.folderToolbarView && Galaxy.libraries.folderListView ){ + Galaxy.libraries.folderToolbarView.showImportModal( { source:source } ); + } else { + Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView( { id: folder_id } ); + Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView( { id: folder_id } ); + Galaxy.libraries.folderToolbarView.showImportModal( { source: source } ); + } + }); Backbone.history.start({pushState: false}); } diff -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 -r d76253bb22c4f64c73523956d119c0c5ab0a357b client/galaxy/scripts/jq-plugins/ui/filter-control.js --- /dev/null +++ b/client/galaxy/scripts/jq-plugins/ui/filter-control.js @@ -0,0 +1,204 @@ +// from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js +// Uses AMD or browser globals to create a jQuery plugin. +(function (factory) { + if (typeof define === 'function' && define.amd) { + // AMD. Register as an anonymous module. + define(['jquery'], factory); + } else { + // Browser globals + factory(jQuery); + } + +}(function ($) { + //============================================================================== + /** + * Template function that produces a bootstrap dropdown to replace the + * vanilla HTML select input. Pass in an array of options and an initial selection: + * $( '.my-div' ).append( dropDownSelect( [ 'option1', 'option2' ], 'option2' ); + * + * When the user changes the selected option a 'change.dropdown-select' event will + * fire with both the jq event and the new selection text as arguments. + * + * Get the currently selected choice using: + * var userChoice = $( '.my-div .dropdown-select .dropdown-select-selected' ).text(); + * + */ + function dropDownSelect( options, selected ){ + // replacement for vanilla select element using bootstrap dropdowns instead + selected = selected || (( !_.isEmpty( options ) )?( options[0] ):( '' )); + var $select = $([ + '<div class="dropdown-select btn-group">', + '<button type="button" class="btn btn-default">', + '<span class="dropdown-select-selected">' + selected + '</span>', + '</button>', + '</div>' + ].join( '\n' )); + + // if there's only one option, do not style/create as buttons, dropdown - use simple span + // otherwise, a dropdown displaying the current selection + if( options && options.length > 1 ){ + $select.find( 'button' ) + .addClass( 'dropdown-toggle' ).attr( 'data-toggle', 'dropdown' ) + .append( ' <span class="caret"></span>' ); + $select.append([ + '<ul class="dropdown-menu" role="menu">', + _.map( options, function( option ){ + return [ + '<li><a href="javascript:void(0)">', option, '</a></li>' + ].join( '' ); + }).join( '\n' ), + '</ul>' + ].join( '\n' )); + } + + // trigger 'change.dropdown-select' when a new selection is made using the dropdown + function selectThis( event ){ + var $this = $( this ), + $select = $this.parents( '.dropdown-select' ), + newSelection = $this.text(); + $select.find( '.dropdown-select-selected' ).text( newSelection ); + $select.trigger( 'change.dropdown-select', newSelection ); + } + + $select.find( 'a' ).click( selectThis ); + return $select; + } + + //============================================================================== + /** + * Creates a three part bootstrap button group (key, op, value) meant to + * allow the user control of filters (e.g. { key: 'name', op: 'contains', value: 'my_history' }) + * + * Each field uses a dropDownSelect (from ui.js) to allow selection + * (with the 'value' field appearing as an input when set to do so). + * + * Any change or update in any of the fields will trigger a 'change.filter-control' + * event which will be passed an object containing those fields (as the example above). + * + * Pass in an array of possible filter objects to control what the user can select. + * Each filter object should have: + * key : generally the attribute name on which to filter something + * ops : an array of 1 or more filter operations (e.g. [ 'is', '<', 'contains', '!=' ]) + * values (optional) : an array of possible values for the filter (e.g. [ 'true', 'false' ]) + * @example: + * $( '.my-div' ).filterControl({ + * filters : [ + * { key: 'name', ops: [ 'is exactly', 'contains' ] } + * { key: 'deleted', ops: [ 'is' ], values: [ 'true', 'false' ] } + * ] + * }); + * // after initialization, you can prog. get the current value using: + * $( '.my-div' ).filterControl( 'val' ) + * + */ + function FilterControl( element, options ){ + return this.init( element, options ); + } + /** the data key that this object will be stored under in the DOM element */ + FilterControl.prototype.DATA_KEY = 'filter-control'; + + /** parses options, sets up instance vars, and does initial render */ + FilterControl.prototype.init = function _init( element, options ){ + options = options || { filters: [] }; + this.$element = $( element ).addClass( 'filter-control btn-group' ); + this.options = jQuery.extend( true, {}, this.defaults, options ); + + this.currFilter = this.options.filters[0]; + return this.render(); + }; + + /** render (or re-render) the controls on the element */ + FilterControl.prototype.render = function _render(){ + this.$element.empty() + .append([ this._renderKeySelect(), this._renderOpSelect(), this._renderValueInput() ]); + return this; + }; + + /** render the key dropDownSelect, bind a change event to it, and return it */ + FilterControl.prototype._renderKeySelect = function __renderKeySelect(){ + var filterControl = this; + var keys = this.options.filters.map( function( filter ){ + return filter.key; + }); + this.$keySelect = dropDownSelect( keys, this.currFilter.key ) + .addClass( 'filter-control-key' ) + .on( 'change.dropdown-select', function( event, selection ){ + filterControl.currFilter = _.findWhere( filterControl.options.filters, { key: selection }); + // when the filter/key changes, re-render the control entirely + filterControl.render()._triggerChange(); + }); + return this.$keySelect; + }; + + /** render the op dropDownSelect, bind a change event to it, and return it */ + FilterControl.prototype._renderOpSelect = function __renderOpSelect(){ + var filterControl = this, + ops = this.currFilter.ops; + //TODO: search for currOp in avail. ops: use that for selected if there; otherwise: first op + this.$opSelect = dropDownSelect( ops, ops[0] ) + .addClass( 'filter-control-op' ) + .on( 'change.dropdown-select', function( event, selection ){ + filterControl._triggerChange(); + }); + return this.$opSelect; + }; + + /** render the value control, bind a change event to it, and return it */ + FilterControl.prototype._renderValueInput = function __renderValueInput(){ + var filterControl = this; + // if a values attribute is prov. on the filter - make this a dropdown; otherwise, use an input + if( this.currFilter.values ){ + this.$valueSelect = dropDownSelect( this.currFilter.values, this.currFilter.values[0] ) + .on( 'change.dropdown-select', function( event, selection ){ + filterControl._triggerChange(); + }); + } else { + //TODO: allow setting a value type (mainly for which html5 input to use: range, number, etc.) + this.$valueSelect = $( '<input/>' ).addClass( 'form-control' ) + .on( 'change', function( event, value ){ + filterControl._triggerChange(); + }); + } + this.$valueSelect.addClass( 'filter-control-value' ); + return this.$valueSelect; + }; + + /** return the current state/setting for the filter as a three key object: key, op, value */ + FilterControl.prototype.val = function _val(){ + var key = this.$element.find( '.filter-control-key .dropdown-select-selected' ).text(), + op = this.$element.find( '.filter-control-op .dropdown-select-selected' ).text(), + // handle either a dropdown or plain input + $value = this.$element.find( '.filter-control-value' ), + value = ( $value.hasClass( 'dropdown-select' ) )?( $value.find( '.dropdown-select-selected' ).text() ) + :( $value.val() ); + return { key: key, op: op, value: value }; + }; + + // single point of change for change event + FilterControl.prototype._triggerChange = function __triggerChange(){ + this.$element.trigger( 'change.filter-control', this.val() ); + }; + + // as jq plugin + jQuery.fn.extend({ + filterControl : function $filterControl( options ){ + var nonOptionsArgs = jQuery.makeArray( arguments ).slice( 1 ); + return this.map( function(){ + var $this = $( this ), + data = $this.data( FilterControl.prototype.DATA_KEY ); + + if( jQuery.type( options ) === 'object' ){ + data = new FilterControl( $this, options ); + $this.data( FilterControl.prototype.DATA_KEY, data ); + } + if( data && jQuery.type( options ) === 'string' ){ + var fn = data[ options ]; + if( jQuery.type( fn ) === 'function' ){ + return fn.apply( data, nonOptionsArgs ); + } + } + return this; + }); + } + }); +})); diff -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 -r d76253bb22c4f64c73523956d119c0c5ab0a357b client/galaxy/scripts/jq-plugins/ui/mode-button.js --- /dev/null +++ b/client/galaxy/scripts/jq-plugins/ui/mode-button.js @@ -0,0 +1,191 @@ +// from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js +// Uses AMD or browser globals to create a jQuery plugin. +(function (factory) { + if (typeof define === 'function' && define.amd) { + //TODO: So...this turns out to be an all or nothing thing. If I load jQuery in the define below, it will + // (of course) wipe the old jquery *and all the plugins loaded into it*. So the define below *is still + // relying on jquery being loaded globally* in order to preserve plugins. + define([], factory); + } else { + // Browser globals + factory(jQuery); + } + +}(function () { + + /** Multi 'mode' button (or any element really) that changes the html + * contents of itself when clicked. Pass in an ordered list of + * objects with 'html' and (optional) onclick functions. + * + * When clicked in a particular node, the onclick function will + * be called (with the element as this) and the element will + * switch to the next mode, replacing its html content with + * that mode's html. + * + * If there is no next mode, the element will switch back to + * the first mode. + * @example: + * $( '.myElement' ).modeButton({ + * modes : [ + * { + * mode: 'bler', + * html: '<h5>Bler</h5>', + * onclick : function(){ + * $( 'body' ).css( 'background-color', 'red' ); + * } + * }, + * { + * mode: 'bloo', + * html: '<h4>Bloo</h4>', + * onclick : function(){ + * $( 'body' ).css( 'background-color', 'blue' ); + * } + * }, + * { + * mode: 'blah', + * html: '<h3>Blah</h3>', + * onclick : function(){ + * $( 'body' ).css( 'background-color', 'grey' ); + * } + * }, + * ] + * }); + * $( '.myElement' ).modeButton( 'callModeFn', 'bler' ); + */ + /** constructor */ + function ModeButton( element, options ){ + this.currModeIndex = 0; + return this._init( element, options ); + } + + /** html5 data key to store this object inside an element */ + ModeButton.prototype.DATA_KEY = 'mode-button'; + /** default options */ + ModeButton.prototype.defaults = { + switchModesOnClick : true + }; + + // ---- private interface + /** set up options, intial mode, and the click handler */ + ModeButton.prototype._init = function _init( element, options ){ + //console.debug( 'ModeButton._init:', element, options ); + options = options || {}; + this.$element = $( element ); + this.options = $.extend( true, {}, this.defaults, options ); + if( !options.modes ){ + throw new Error( 'ModeButton requires a "modes" array' ); + } + + var modeButton = this; + this.$element.click( function _ModeButtonClick( event ){ + // call the curr mode fn + modeButton.callModeFn(); + // inc the curr mode index + if( modeButton.options.switchModesOnClick ){ modeButton._incModeIndex(); } + // set the element html + $( this ).html( modeButton.options.modes[ modeButton.currModeIndex ].html ); + }); + return this.reset(); + }; + /** increment the mode index to the next in the array, looping back to zero if at the last */ + ModeButton.prototype._incModeIndex = function _incModeIndex(){ + this.currModeIndex += 1; + if( this.currModeIndex >= this.options.modes.length ){ + this.currModeIndex = 0; + } + return this; + }; + /** get the mode index in the modes array for the given key (mode name) */ + ModeButton.prototype._getModeIndex = function _getModeIndex( modeKey ){ + for( var i=0; i<this.options.modes.length; i+=1 ){ + if( this.options.modes[ i ].mode === modeKey ){ return i; } + } + throw new Error( 'mode not found: ' + modeKey ); + }; + /** set the current mode to the one with the given index and set button html */ + ModeButton.prototype._setModeByIndex = function _setModeByIndex( index ){ + var newMode = this.options.modes[ index ]; + if( !newMode ){ + throw new Error( 'mode index not found: ' + index ); + } + this.currModeIndex = index; + if( newMode.html ){ + this.$element.html( newMode.html ); + } + return this; + }; + + // ---- public interface + /** get the current mode object (not just the mode name) */ + ModeButton.prototype.currentMode = function currentMode(){ + return this.options.modes[ this.currModeIndex ]; + }; + /** return the mode key of the current mode */ + ModeButton.prototype.current = function current(){ + // sugar for returning mode name + return this.currentMode().mode; + }; + /** get the mode with the given modeKey or the current mode if modeKey is undefined */ + ModeButton.prototype.getMode = function getMode( modeKey ){ + if( !modeKey ){ return this.currentMode(); } + return this.options.modes[( this._getModeIndex( modeKey ) )]; + }; + /** T/F if the button has the given mode */ + ModeButton.prototype.hasMode = function hasMode( modeKey ){ + try { + return !!this.getMode( modeKey ); + } catch( err ){} + return false; + }; + /** set the current mode to the mode with the given name */ + ModeButton.prototype.setMode = function setMode( modeKey ){ + return this._setModeByIndex( this._getModeIndex( modeKey ) ); + }; + /** reset to the initial mode */ + ModeButton.prototype.reset = function reset(){ + this.currModeIndex = 0; + if( this.options.initialMode ){ + this.currModeIndex = this._getModeIndex( this.options.initialMode ); + } + return this._setModeByIndex( this.currModeIndex ); + }; + /** manually call the click handler of the given mode */ + ModeButton.prototype.callModeFn = function callModeFn( modeKey ){ + var modeFn = this.getMode( modeKey ).onclick; + if( modeFn && $.type( modeFn === 'function' ) ){ + // call with the element as context (std jquery pattern) + return modeFn.call( this.$element.get(0) ); + } + return undefined; + }; + + // as jq plugin + $.fn.modeButton = function $modeButton( options ){ + if( !this.size() ){ return this; } + + //TODO: does map still work with jq multi selection (i.e. $( '.class-for-many-btns' ).modeButton)? + if( $.type( options ) === 'object' ){ + return this.map( function(){ + var $this = $( this ); + $this.data( 'mode-button', new ModeButton( $this, options ) ); + return this; + }); + } + + var $first = $( this[0] ), + button = $first.data( 'mode-button' ); + + if( !button ){ + throw new Error( 'modeButton needs an options object or string name of a function' ); + } + + if( button && $.type( options ) === 'string' ){ + var fnName = options; + if( button && $.type( button[ fnName ] ) === 'function' ){ + return button[ fnName ].apply( button, $.makeArray( arguments ).slice( 1 ) ); + } + } + return button; + }; + +})); diff -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 -r d76253bb22c4f64c73523956d119c0c5ab0a357b client/galaxy/scripts/jq-plugins/ui/pagination.js --- /dev/null +++ b/client/galaxy/scripts/jq-plugins/ui/pagination.js @@ -0,0 +1,226 @@ +// from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js +// Uses AMD or browser globals to create a jQuery plugin. +(function (factory) { + if (typeof define === 'function' && define.amd) { + // AMD. Register as an anonymous module. + define(['jquery'], factory); + } else { + // Browser globals + factory(jQuery); + } + +}(function ($) { + + /** Builds (twitter bootstrap styled) pagination controls. + * If the totalDataSize is not null, a horizontal list of page buttons is displayed. + * If totalDataSize is null, two links ('Prev' and 'Next) are displayed. + * When pages are changed, a 'pagination.page-change' event is fired + * sending the event and the (0-based) page requested. + */ + function Pagination( element, options ){ + /** the total number of pages */ + this.numPages = null; + /** the current, active page */ + this.currPage = 0; + return this.init( element, options ); + } + + /** data key under which this object will be stored in the element */ + Pagination.prototype.DATA_KEY = 'pagination'; + /** default options */ + Pagination.prototype.defaults = { + /** which page to begin at */ + startingPage : 0, + /** number of data per page */ + perPage : 20, + /** the total number of data (null == unknown) */ + totalDataSize : null, + /** size of current data on current page */ + currDataSize : null + }; + + /** init the control, calc numPages if possible, and render + * @param {jQuery} the element that will contain the pagination control + * @param {Object} options a map containing overrides to the pagination default options + */ + Pagination.prototype.init = function _init( $element, options ){ + options = options || {}; + this.$element = $element; + this.options = jQuery.extend( true, {}, this.defaults, options ); + + this.currPage = this.options.startingPage; + if( this.options.totalDataSize !== null ){ + this.numPages = Math.ceil( this.options.totalDataSize / this.options.perPage ); + // limit currPage by numPages + if( this.currPage >= this.numPages ){ + this.currPage = this.numPages - 1; + } + } + //console.debug( 'Pagination.prototype.init:', this.$element, this.currPage ); + //console.debug( JSON.stringify( this.options ) ); + + // bind to data of element + this.$element.data( Pagination.prototype.DATA_KEY, this ); + + this._render(); + return this; + }; + + /** helper to create a simple li + a combo */ + function _make$Li( contents ){ + return $([ + '<li><a href="javascript:void(0);">', contents, '</a></li>' + ].join( '' )); + } + + /** render previous and next pagination buttons */ + Pagination.prototype._render = function __render(){ + // no data - no pagination + if( this.options.totalDataSize === 0 ){ return this; } + // only one page + if( this.numPages === 1 ){ return this; } + + // when the number of pages are known, render each page as a link + if( this.numPages > 0 ){ + this._renderPages(); + this._scrollToActivePage(); + + // when the number of pages is not known, render previous or next + } else { + this._renderPrevNext(); + } + return this; + }; + + /** render previous and next pagination buttons */ + Pagination.prototype._renderPrevNext = function __renderPrevNext(){ + var pagination = this, + $prev = _make$Li( 'Prev' ), + $next = _make$Li( 'Next' ), + $paginationContainer = $( '<ul/>' ).addClass( 'pagination pagination-prev-next' ); + + // disable if it either end + if( this.currPage === 0 ){ + $prev.addClass( 'disabled' ); + } else { + $prev.click( function(){ pagination.prevPage(); }); + } + if( ( this.numPages && this.currPage === ( this.numPages - 1 ) ) + || ( this.options.currDataSize && this.options.currDataSize < this.options.perPage ) ){ + $next.addClass( 'disabled' ); + } else { + $next.click( function(){ pagination.nextPage(); }); + } + + this.$element.html( $paginationContainer.append([ $prev, $next ]) ); + //console.debug( this.$element, this.$element.html() ); + return this.$element; + }; + + /** render page links for each possible page (if we can) */ + Pagination.prototype._renderPages = function __renderPages(){ + // it's better to scroll the control and let the user see all pages + // than to force her/him to change pages in order to find the one they want (as traditional << >> does) + var pagination = this, + $scrollingContainer = $( '<div>' ).addClass( 'pagination-scroll-container' ), + $paginationContainer = $( '<ul/>' ).addClass( 'pagination pagination-page-list' ), + page$LiClick = function( ev ){ + pagination.goToPage( $( this ).data( 'page' ) ); + }; + + for( var i=0; i<this.numPages; i+=1 ){ + // add html5 data tag 'page' for later click event handler use + var $pageLi = _make$Li( i + 1 ).attr( 'data-page', i ).click( page$LiClick ); + // highlight the current page + if( i === this.currPage ){ + $pageLi.addClass( 'active' ); + } + //console.debug( '\t', $pageLi ); + $paginationContainer.append( $pageLi ); + } + return this.$element.html( $scrollingContainer.html( $paginationContainer ) ); + }; + + /** scroll scroll-container (if any) to show the active page */ + Pagination.prototype._scrollToActivePage = function __scrollToActivePage(){ + // scroll to show active page in center of scrollable area + var $container = this.$element.find( '.pagination-scroll-container' ); + // no scroll container : don't scroll + if( !$container.size() ){ return this; } + + var $activePage = this.$element.find( 'li.active' ), + midpoint = $container.width() / 2; + //console.debug( $container, $activePage, midpoint ); + $container.scrollLeft( $container.scrollLeft() + $activePage.position().left - midpoint ); + return this; + }; + + /** go to a certain page */ + Pagination.prototype.goToPage = function goToPage( page ){ + if( page <= 0 ){ page = 0; } + if( this.numPages && page >= this.numPages ){ page = this.numPages - 1; } + if( page === this.currPage ){ return this; } + + //console.debug( '\t going to page ' + page ) + this.currPage = page; + this.$element.trigger( 'pagination.page-change', this.currPage ); + //console.info( 'pagination:page-change', this.currPage ); + this._render(); + return this; + }; + + /** go to the previous page */ + Pagination.prototype.prevPage = function prevPage(){ + return this.goToPage( this.currPage - 1 ); + }; + + /** go to the next page */ + Pagination.prototype.nextPage = function nextPage(){ + return this.goToPage( this.currPage + 1 ); + }; + + /** return the current page */ + Pagination.prototype.page = function page(){ + return this.currPage; + }; + + // alternate constructor invocation + Pagination.create = function _create( $element, options ){ + return new Pagination( $element, options ); + }; + + // as jq plugin + jQuery.fn.extend({ + pagination : function $pagination( options ){ + var nonOptionsArgs = jQuery.makeArray( arguments ).slice( 1 ); + + // if passed an object - use that as an options map to create pagination for each selected + if( jQuery.type( options ) === 'object' ){ + return this.map( function(){ + Pagination.create( $( this ), options ); + return this; + }); + } + + // (other invocations only work on the first element in selected) + var $firstElement = $( this[0] ), + previousControl = $firstElement.data( Pagination.prototype.DATA_KEY ); + // if a pagination control was found for this element, either... + if( previousControl ){ + // invoke a function on the pagination object if passed a string (the function name) + if( jQuery.type( options ) === 'string' ){ + var fn = previousControl[ options ]; + if( jQuery.type( fn ) === 'function' ){ + return fn.apply( previousControl, nonOptionsArgs ); + } + + // if passed nothing, return the previously set control + } else { + return previousControl; + } + } + // if there is no control already set, return undefined + return undefined; + } + }); +})); diff -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 -r d76253bb22c4f64c73523956d119c0c5ab0a357b client/galaxy/scripts/jq-plugins/ui/peek-column-selector.js --- /dev/null +++ b/client/galaxy/scripts/jq-plugins/ui/peek-column-selector.js @@ -0,0 +1,317 @@ +// from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js +// Uses AMD or browser globals to create a jQuery plugin. +(function (factory) { + if (typeof define === 'function' && define.amd) { + // AMD. Register as an anonymous module. + define(['jquery'], factory); + } else { + // Browser globals + factory(jQuery); + } + +}(function ($) { + //============================================================================== + /** Column selection using the peek display as the control. + * Adds rows to the bottom of the peek with clickable areas in each cell + * to allow the user to select columns. + * Column selection can be limited to a single column or multiple. + * (Optionally) adds a left hand column of column selection prompts. + * (Optionally) allows the column headers to be clicked/renamed + * and set to some initial value. + * (Optionally) hides comment rows. + * (Optionally) allows pre-selecting and disabling certain columns for + * each row control. + * + * Construct by selecting a peek table to be used with jQuery and + * calling 'peekColumnSelector' with options. + * Options must include a 'controls' array and can include other options + * listed below. + * @example: + * $( 'pre.peek' ).peekColumnSelector({ + * columnNames : ["Chromosome", "Start", "Base", "", "", "Qual" ], + * controls : [ + * { label: 'X Column', id: 'xColumn' }, + * { label: 'Y Column', id: 'yColumn', selected: 2 }, + * { label: 'ID Column', id: 'idColumn', selected: 4, disabled: [ 1, 5 ] }, + * { label: 'Heatmap', id: 'heatmap', selected: [ 2, 4 ], disabled: [ 0, 1 ], multiselect: true, + * selectedText: 'Included', unselectedText: 'Excluded' } + * ], + * renameColumns : true, + * hideCommentRows : true, + * includePrompts : true, + * topLeftContent : 'Data sample:' + * }).on( 'peek-column-selector.change', function( ev, selection ){ + * console.info( 'new selection:', selection ); + * //{ yColumn: 2 } + * }).on( 'peek-column-selector.rename', function( ev, names ){ + * console.info( 'column names', names ); + * //[ 'Bler', 'Start', 'Base', '', '', 'Qual' ] + * }); + * + * An event is fired when column selection is changed and the event + * is passed an object in the form: { the row id : the new selection value }. + * An event is also fired when the table headers are re-named and + * is passed the new array of column names. + */ + + /** option defaults */ + var defaults = { + /** does this control allow renaming headers? */ + renameColumns : false, + /** does this control allow renaming headers? */ + columnNames : [], + /** the comment character used by the peek's datatype */ + commentChar : '#', + /** should comment rows be shown or hidden in the peek */ + hideCommentRows : false, + /** should a column of row control prompts be used */ + includePrompts : true, + /** what is the content of the top left cell (often a title) */ + topLeftContent : 'Columns:' + }, + /** class added to the pre.peek element (to allow css on just the control) */ + PEEKCONTROL_CLASS = 'peek-column-selector', + /** the string of the event fired when a control row changes */ + CHANGE_EVENT = 'peek-column-selector.change', + /** the string of the event fired when a column is renamed */ + RENAME_EVENT = 'peek-column-selector.rename', + /** class added to the control rows */ + ROW_CLASS = 'control', + /** class added to the left-hand cells that serve as row prompts */ + PROMPT_CLASS = 'control-prompt', + /** class added to selected _cells_/tds */ + SELECTED_CLASS = 'selected', + /** class added to disabled/un-clickable cells/tds */ + DISABLED_CLASS = 'disabled', + /** class added to the clickable surface within a cell to select it */ + BUTTON_CLASS = 'button', + /** class added to peek table header (th) cells to indicate they can be clicked and are renamable */ + RENAMABLE_HEADER_CLASS = 'renamable-header', + /** the data key used for each cell to store the column index ('data-...') */ + COLUMN_INDEX_DATA_KEY = 'column-index', + /** renamable header data key used to store the column name (w/o the number and dot: '1.Bler') */ + COLUMN_NAME_DATA_KEY = 'column-name'; + + //TODO: not happy with pure functional here - rows should polymorph (multi, single, etc.) + //TODO: needs clean up, move handlers to outer scope + + // ........................................................................ + /** validate the control data sent in for each row */ + function validateControl( control ){ + if( control.disabled && jQuery.type( control.disabled ) !== 'array' ){ + throw new Error( '"disabled" must be defined as an array of indeces: ' + JSON.stringify( control ) ); + } + if( control.multiselect && control.selected && jQuery.type( control.selected ) !== 'array' ){ + throw new Error( 'Mulitselect rows need an array for "selected": ' + JSON.stringify( control ) ); + } + if( !control.label || !control.id ){ + throw new Error( 'Peek controls need a label and id for each control row: ' + JSON.stringify( control ) ); + } + if( control.disabled && control.disabled.indexOf( control.selected ) !== -1 ){ + throw new Error( 'Selected column is in the list of disabled columns: ' + JSON.stringify( control ) ); + } + return control; + } + + /** build the inner control surface (i.e. button-like) */ + function buildButton( control, columnIndex ){ + return $( '<div/>' ).addClass( BUTTON_CLASS ).text( control.label ); + } + + /** build the basic (shared) cell structure */ + function buildControlCell( control, columnIndex ){ + var $td = $( '<td/>' ) + .html( buildButton( control, columnIndex ) ) + .attr( 'data-' + COLUMN_INDEX_DATA_KEY, columnIndex ); + + // disable if index in disabled array + if( control.disabled && control.disabled.indexOf( columnIndex ) !== -1 ){ + $td.addClass( DISABLED_CLASS ); + } + return $td; + } + + /** set the text of the control based on selected/un */ + function setSelectedText( $cell, control, columnIndex ){ + var $button = $cell.children( '.' + BUTTON_CLASS ); + if( $cell.hasClass( SELECTED_CLASS ) ){ + $button.html( ( control.selectedText !== undefined )?( control.selectedText ):( control.label ) ); + } else { + $button.html( ( control.unselectedText !== undefined )?( control.unselectedText ):( control.label ) ); + } + } + + /** build a cell for a row that only allows one selection */ + function buildSingleSelectCell( control, columnIndex ){ + // only one selection - selected is single index + var $cell = buildControlCell( control, columnIndex ); + if( control.selected === columnIndex ){ + $cell.addClass( SELECTED_CLASS ); + } + setSelectedText( $cell, control, columnIndex ); + + // only add the handler to non-disabled controls + if( !$cell.hasClass( DISABLED_CLASS ) ){ + $cell.click( function selectClick( ev ){ + var $cell = $( this ); + // don't re-select or fire event if already selected + if( !$cell.hasClass( SELECTED_CLASS ) ){ + // only one can be selected - remove selected on all others, add it here + var $otherSelected = $cell.parent().children( '.' + SELECTED_CLASS ).removeClass( SELECTED_CLASS ); + $otherSelected.each( function(){ + setSelectedText( $( this ), control, columnIndex ); + }); + + $cell.addClass( SELECTED_CLASS ); + setSelectedText( $cell, control, columnIndex ); + + // fire the event from the table itself, passing the id and index of selected + var eventData = {}, + key = $cell.parent().attr( 'id' ), + val = $cell.data( COLUMN_INDEX_DATA_KEY ); + eventData[ key ] = val; + $cell.parents( '.peek' ).trigger( CHANGE_EVENT, eventData ); + } + }); + } + return $cell; + } + + /** build a cell for a row that allows multiple selections */ + function buildMultiSelectCell( control, columnIndex ){ + var $cell = buildControlCell( control, columnIndex ); + // multiple selection - selected is an array + if( control.selected && control.selected.indexOf( columnIndex ) !== -1 ){ + $cell.addClass( SELECTED_CLASS ); + } + setSelectedText( $cell, control, columnIndex ); + + // only add the handler to non-disabled controls + if( !$cell.hasClass( DISABLED_CLASS ) ){ + $cell.click( function multiselectClick( ev ){ + var $cell = $( this ); + // can be more than one selected - toggle selected on this cell + $cell.toggleClass( SELECTED_CLASS ); + setSelectedText( $cell, control, columnIndex ); + var selectedColumnIndeces = $cell.parent().find( '.' + SELECTED_CLASS ).map( function( i, e ){ + return $( e ).data( COLUMN_INDEX_DATA_KEY ); + }); + // fire the event from the table itself, passing the id and index of selected + var eventData = {}, + key = $cell.parent().attr( 'id' ), + val = jQuery.makeArray( selectedColumnIndeces ); + eventData[ key ] = val; + $cell.parents( '.peek' ).trigger( CHANGE_EVENT, eventData ); + }); + } + return $cell; + } + + /** iterate over columns in peek and create a control for each */ + function buildControlCells( count, control ){ + var $cells = []; + // build a control for each column - using a build fn based on control + for( var columnIndex=0; columnIndex<count; columnIndex+=1 ){ + $cells.push( control.multiselect? buildMultiSelectCell( control, columnIndex ) + : buildSingleSelectCell( control, columnIndex ) ); + } + return $cells; + } + + /** build a row of controls for the peek */ + function buildControlRow( cellCount, control, includePrompts ){ + var $controlRow = $( '<tr/>' ).attr( 'id', control.id ).addClass( ROW_CLASS ); + if( includePrompts ){ + var $promptCell = $( '<td/>' ).addClass( PROMPT_CLASS ).text( control.label + ':' ); + $controlRow.append( $promptCell ); + } + $controlRow.append( buildControlCells( cellCount, control ) ); + return $controlRow; + } + + // ........................................................................ + /** add to the peek, using options for configuration, return the peek */ + function peekColumnSelector( options ){ + options = jQuery.extend( true, {}, defaults, options ); + + var $peek = $( this ).addClass( PEEKCONTROL_CLASS ), + $peektable = $peek.find( 'table' ), + // get the size of the tables - width and height, number of comment rows + columnCount = $peektable.find( 'th' ).size(), + rowCount = $peektable.find( 'tr' ).size(), + // get the rows containing text starting with the comment char (also make them grey) + $commentRows = $peektable.find( 'td[colspan]' ).map( function( e, i ){ + var $this = $( this ); + if( $this.text() && $this.text().match( new RegExp( '^' + options.commentChar ) ) ){ + return $( this ).css( 'color', 'grey' ).parent().get(0); + } + return null; + }); + + // should comment rows in the peek be hidden? + if( options.hideCommentRows ){ + $commentRows.hide(); + rowCount -= $commentRows.size(); + } + //console.debug( 'rowCount:', rowCount, 'columnCount:', columnCount, '$commentRows:', $commentRows ); + + // should a first column of control prompts be added? + if( options.includePrompts ){ + var $topLeft = $( '<th/>' ).addClass( 'top-left' ).text( options.topLeftContent ) + .attr( 'rowspan', rowCount ); + $peektable.find( 'tr' ).first().prepend( $topLeft ); + } + + // save either the options column name or the parsed text of each column header in html5 data attr and text + var $headers = $peektable.find( 'th:not(.top-left)' ).each( function( i, e ){ + var $this = $( this ), + // can be '1.name' or '1' + text = $this.text().replace( /^\d+\.*/, '' ), + name = options.columnNames[ i ] || text; + $this.attr( 'data-' + COLUMN_NAME_DATA_KEY, name ) + .text( ( i + 1 ) + (( name )?( '.' + name ):( '' )) ); + }); + + // allow renaming of columns when the header is clicked + if( options.renameColumns ){ + $headers.addClass( RENAMABLE_HEADER_CLASS ) + .click( function renameColumn(){ + // prompt for new name + var $this = $( this ), + index = $this.index() + ( options.includePrompts? 0: 1 ), + prevName = $this.data( COLUMN_NAME_DATA_KEY ), + newColumnName = prompt( 'New column name:', prevName ); + if( newColumnName !== null && newColumnName !== prevName ){ + // set the new text and data + $this.text( index + ( newColumnName?( '.' + newColumnName ):'' ) ) + .data( COLUMN_NAME_DATA_KEY, newColumnName ) + .attr( 'data-', COLUMN_NAME_DATA_KEY, newColumnName ); + // fire event for new column names + var columnNames = jQuery.makeArray( + $this.parent().children( 'th:not(.top-left)' ).map( function(){ + return $( this ).data( COLUMN_NAME_DATA_KEY ); + })); + $this.parents( '.peek' ).trigger( RENAME_EVENT, columnNames ); + } + }); + } + + // build a row for each control + options.controls.forEach( function( control, i ){ + validateControl( control ); + var $controlRow = buildControlRow( columnCount, control, options.includePrompts ); + $peektable.find( 'tbody' ).append( $controlRow ); + }); + return this; + } + + // ........................................................................ + // as jq plugin + jQuery.fn.extend({ + peekColumnSelector : function $peekColumnSelector( options ){ + return this.map( function(){ + return peekColumnSelector.call( this, options ); + }); + } + }); +})); diff -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 -r d76253bb22c4f64c73523956d119c0c5ab0a357b client/galaxy/scripts/mvc/history/multi-panel.js --- a/client/galaxy/scripts/mvc/history/multi-panel.js +++ b/client/galaxy/scripts/mvc/history/multi-panel.js @@ -2,7 +2,8 @@ "mvc/history/history-model", "mvc/history/history-panel-edit", "mvc/base-mvc", - "utils/ajax-queue" + "utils/ajax-queue", + "jq-plugins/ui/mode-button" ], function( HISTORY_MODEL, HPANEL_EDIT, baseMVC, ajaxQueue ){ window.HISTORY_MODEL = HISTORY_MODEL; //============================================================================== diff -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 -r d76253bb22c4f64c73523956d119c0c5ab0a357b client/galaxy/scripts/mvc/library/library-folderlist-view.js --- a/client/galaxy/scripts/mvc/library/library-folderlist-view.js +++ b/client/galaxy/scripts/mvc/library/library-folderlist-view.js @@ -15,322 +15,359 @@ ) { var FolderListView = Backbone.View.extend({ - el : '#folder_items_element', - defaults: { - 'include_deleted' : false - }, - // progress percentage - progress: 0, - // progress rate per one item - progressStep: 1, - // self modal - modal : null, + el : '#folder_items_element', + // progress percentage + progress: 0, + // progress rate per one item + progressStep: 1, - folderContainer: null, + folderContainer: null, - sort: 'asc', + sort: 'asc', - events: { - 'click #select-all-checkboxes' : 'selectAll', - 'click .dataset_row' : 'selectClickedRow', - 'click .sort-folder-link' : 'sortColumnClicked' - }, + events: { + 'click #select-all-checkboxes' : 'selectAll', + 'click .dataset_row' : 'selectClickedRow', + 'click .sort-folder-link' : 'sortColumnClicked' + }, - // cache of rendered views - rowViews: {}, - - initialize : function(options){ - this.options = _.defaults(this.options || {}, options); - this.fetchFolder(); - }, + collection: null, - fetchFolder: function(options){ - var options = options || {}; - this.options.include_deleted = options.include_deleted; - var that = this; + defaults: { + include_deleted: false, + page_count: null, + show_page: null + }, - this.collection = new mod_library_model.Folder(); + /** + * Initialize and fetch the folder from the server. + * @param {object} options an object with options + */ + initialize : function( options ){ + this.options = _.defaults( this.options || {}, this.defaults, options ); + this.modal = null; + // map of folder item ids to item views = cache + this.rowViews = {}; - // start to listen if someone modifies collection - this.listenTo(this.collection, 'add', this.renderOne); - this.listenTo(this.collection, 'remove', this.removeOne); + // create a collection of folder items for this view + this.collection = new mod_library_model.Folder(); - this.folderContainer = new mod_library_model.FolderContainer({id: this.options.id}); - this.folderContainer.url = this.folderContainer.attributes.urlRoot + this.options.id + '/contents'; - if (this.options.include_deleted){ - this.folderContainer.url = this.folderContainer.url + '?include_deleted=true'; - } - this.folderContainer.fetch({ - success: function(folder_container) { - that.folder_container = folder_container; - that.render(); - that.addAll(folder_container.get('folder').models); - if (that.options.dataset_id){ - row = _.findWhere(that.rowViews, {id: that.options.dataset_id}); - if (row) { + // start to listen if someone modifies the collection + this.listenTo( this.collection, 'add', this.renderOne ); + this.listenTo( this.collection, 'remove', this.removeOne ); + + this.fetchFolder(); + }, + + fetchFolder: function( options ){ + var options = options || {}; + this.options.include_deleted = options.include_deleted; + var that = this; + + this.folderContainer = new mod_library_model.FolderContainer( { id: this.options.id } ); + this.folderContainer.url = this.folderContainer.attributes.urlRoot + this.options.id + '/contents'; + + if ( this.options.include_deleted ){ + this.folderContainer.url = this.folderContainer.url + '?include_deleted=true'; + } + this.folderContainer.fetch({ + success: function( folder_container ) { + that.folder_container = folder_container; + that.render(); + }, + error: function( model, response ){ + if ( typeof response.responseJSON !== "undefined" ){ + mod_toastr.error( response.responseJSON.err_msg + ' Click this to go back.', '', { onclick: function() { Galaxy.libraries.library_router.back(); } } ); + } else { + mod_toastr.error( 'An error ocurred. Click this to go back.', '', { onclick: function() { Galaxy.libraries.library_router.back(); } } ); + } + } + }); + }, + + render: function ( options ){ + this.options = _.extend( this.options, options ); + var template = this.templateFolder(); + $(".tooltip").hide(); + + // find the upper id in the full path + var path = this.folderContainer.attributes.metadata.full_path; + var upper_folder_id; + if ( path.length === 1 ){ // the library is above us + upper_folder_id = 0; + } else { + upper_folder_id = path[ path.length-2 ][ 0 ]; + } + + this.$el.html( template( { + path: this.folderContainer.attributes.metadata.full_path, + parent_library_id: this.folderContainer.attributes.metadata.parent_library_id, + id: this.options.id, + upper_folder_id: upper_folder_id, + order: this.sort + } ) ); + + // when dataset_id is present render its details too + if ( this.options.dataset_id ){ + row = _.findWhere( that.rowViews, { id: this.options.dataset_id } ); + if ( row ) { row.showDatasetDetails(); } else { - mod_toastr.error('Dataset not found. Showing folder instead.'); + mod_toastr.error( 'Requested dataset not found. Showing folder instead.' ); } + } else { + if ( this.options.show_page === null || this.options.show_page < 1 ){ + this.options.show_page = 1; + } + this.paginate(); + } + $("#center [data-toggle]").tooltip(); + $("#center").css('overflow','auto'); + }, + + paginate: function( options ){ + this.options = _.extend( this.options, options ); + + if ( this.options.show_page === null || this.options.show_page < 1 ){ + this.options.show_page = 1; + } + this.options.total_items_count = this.folder_container.get( 'folder' ).models.length; + this.options.page_count = Math.ceil( this.options.total_items_count / Galaxy.libraries.preferences.get( 'folder_page_size' ) ); + var page_start = ( Galaxy.libraries.preferences.get( 'folder_page_size' ) * ( this.options.show_page - 1 ) ); + var items_to_render = null; + items_to_render = this.folder_container.get( 'folder' ).models.slice( page_start, page_start + Galaxy.libraries.preferences.get( 'folder_page_size' ) ); + this.options.items_shown = items_to_render.length; + // User requests page with no items + if ( Galaxy.libraries.preferences.get( 'folder_page_size' ) * this.options.show_page > ( this.options.total_items_count + Galaxy.libraries.preferences.get( 'folder_page_size' ) ) ){ + items_to_render = []; + } + Galaxy.libraries.folderToolbarView.renderPaginator( this.options ); + this.collection.reset(); + this.addAll( items_to_render ) + }, + + /** + * Adds all given models to the collection. + * @param {array of Item or FolderAsModel} array of models that should + * be added to the view's collection. + */ + addAll: function( models ){ + _.each(models, function( model ) { + Galaxy.libraries.folderListView.collection.add( model ); + }); + $( "#center [data-toggle]" ).tooltip(); + this.checkEmptiness(); + this.postRender(); + }, + + /** + * Call this after all models are added to the collection + * to ensure that the folder toolbar will show proper options + * and that event will be bound on all subviews. + */ + postRender: function(){ + var fetched_metadata = this.folderContainer.attributes.metadata; + fetched_metadata.contains_file = typeof this.collection.findWhere({type: 'file'}) !== 'undefined'; + Galaxy.libraries.folderToolbarView.configureElements(fetched_metadata); + $('.library-row').hover(function() { + $(this).find('.show_on_hover').show(); + }, function () { + $(this).find('.show_on_hover').hide(); + }); + }, + + /** + * Iterates this view's collection and calls the render + * function for each. Also binds the hover behavior. + */ + renderAll: function(){ + var that = this; + _.each( this.collection.models.reverse(), function( model ) { + that.renderOne( model ); + }); + this.postRender(); + }, + + /** + * Creates a view for the given model and adds it to the folder view. + * @param {Item or FolderAsModel} model of the view that will be rendered + */ + renderOne: function(model){ + if (model.get('type') !== 'folder'){ + this.options.contains_file = true; + // model.set('readable_size', this.size_to_string(model.get('file_size'))); } - }, - error: function(model, response){ - if (typeof response.responseJSON !== "undefined"){ - mod_toastr.error(response.responseJSON.err_msg + ' Click this to go back.', '', {onclick: function() {Galaxy.libraries.library_router.back();}}); - } else { - mod_toastr.error('An error ocurred. Click this to go back.', '', {onclick: function() {Galaxy.libraries.library_router.back();}}); - } + model.set('folder_id', this.id); + var rowView = new mod_library_folderrow_view.FolderRowView(model); + + // save new rowView to cache + this.rowViews[model.get('id')] = rowView; + + this.$el.find('#first_folder_item').after(rowView.el); + + $('.library-row').hover(function() { + $(this).find('.show_on_hover').show(); + }, function () { + $(this).find('.show_on_hover').hide(); + }); + }, + + /** + * removes the view of the given model from the DOM + * @param {Item or FolderAsModel} model of the view that will be removed + */ + removeOne: function( model ){ + this.$el.find( '#' + model.id ).remove(); + }, + + /** Checks whether the list is empty and adds/removes the message */ + checkEmptiness : function(){ + if ((this.$el.find('.dataset_row').length === 0) && (this.$el.find('.folder_row').length === 0)){ + this.$el.find('.empty-folder-message').show(); + } else { + this.$el.find('.empty-folder-message').hide(); } - }); - }, + }, - render: function (options) { - this.options = _.defaults(this.options, options); - var template = this.templateFolder(); - $(".tooltip").hide(); + /** User clicked the table heading = he wants to sort stuff */ + sortColumnClicked : function(event){ + event.preventDefault(); + if (this.sort === 'asc'){ + this.sortFolder('name','desc'); + this.sort = 'desc'; + } else { + this.sortFolder('name','asc'); + this.sort = 'asc'; + } + this.render(); + this.renderAll(); + this.checkEmptiness(); + }, - // TODO move to server - // find the upper id in the full path - var path = this.folderContainer.attributes.metadata.full_path; - var upper_folder_id; - if (path.length === 1){ // the library is above us - upper_folder_id = 0; - } else { - upper_folder_id = path[path.length-2][0]; + /** + * Sorts the underlying collection according to the parameters received. + * Currently supports only sorting by name. + */ + sortFolder: function(sort_by, order){ + if (sort_by === 'name'){ + if (order === 'asc'){ + return this.collection.sortByNameAsc(); + } else if (order === 'desc'){ + return this.collection.sortByNameDesc(); + } + } + }, + + /** + * User clicked the checkbox in the table heading + * @param {context} event + */ + selectAll : function (event) { + var selected = event.target.checked; + that = this; + // Iterate each checkbox + $(':checkbox', '#folder_list_body').each(function() { + this.checked = selected; + $row = $(this.parentElement.parentElement); + // Change color of selected/unselected + if (selected) { + that.makeDarkRow($row); + } else { + that.makeWhiteRow($row); + } + }); + }, + + /** + * Check checkbox if user clicks on the whole row or + * on the checkbox itself + */ + selectClickedRow : function (event) { + var checkbox = ''; + var $row; + var source; + if (event.target.localName === 'input'){ + checkbox = event.target; + $row = $(event.target.parentElement.parentElement); + source = 'input'; + } else if (event.target.localName === 'td') { + checkbox = $("#" + event.target.parentElement.id).find(':checkbox')[0]; + $row = $(event.target.parentElement); + source = 'td'; + } + if (checkbox.checked){ + if (source==='td'){ + checkbox.checked = ''; + this.makeWhiteRow($row); + } else if (source==='input') { + this.makeDarkRow($row); + } + } else { + if (source==='td'){ + checkbox.checked = 'selected'; + this.makeDarkRow($row); + } else if (source==='input') { + this.makeWhiteRow($row); + } + } + }, + + makeDarkRow: function($row){ + $row.removeClass('light').addClass('dark'); + $row.find('a').removeClass('light').addClass('dark'); + $row.find('.fa-file-o').removeClass('fa-file-o').addClass('fa-file'); + }, + + makeWhiteRow: function($row){ + $row.removeClass('dark').addClass('light'); + $row.find('a').removeClass('dark').addClass('light'); + $row.find('.fa-file').removeClass('fa-file').addClass('fa-file-o'); + }, + + templateFolder : function (){ + var tmpl_array = []; + + // BREADCRUMBS + tmpl_array.push('<ol class="breadcrumb">'); + tmpl_array.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>'); + tmpl_array.push(' <% _.each(path, function(path_item) { %>'); + tmpl_array.push(' <% if (path_item[0] != id) { %>'); + tmpl_array.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> '); + tmpl_array.push( '<% } else { %>'); + tmpl_array.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</ol>'); + + // FOLDER CONTENT + tmpl_array.push('<table data-library-id="<%- parent_library_id %>" id="folder_table" class="grid table table-condensed">'); + tmpl_array.push(' <thead>'); + tmpl_array.push(' <th class="button_heading"></th>'); + tmpl_array.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); + tmpl_array.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>'); + tmpl_array.push(' <th style="width:5%;">data type</th>'); + tmpl_array.push(' <th style="width:10%;">size</th>'); + tmpl_array.push(' <th style="width:160px;">time updated (UTC)</th>'); + tmpl_array.push(' <th style="width:10%;"></th> '); + tmpl_array.push(' </thead>'); + tmpl_array.push(' <tbody id="folder_list_body">'); + tmpl_array.push(' <tr id="first_folder_item">'); + tmpl_array.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' </tr>'); + + tmpl_array.push(' </tbody>'); + tmpl_array.push('</table>'); + tmpl_array.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>'); + + return _.template(tmpl_array.join('')); } - - this.$el.html(template({ path: this.folderContainer.attributes.metadata.full_path, parent_library_id: this.folderContainer.attributes.metadata.parent_library_id, id: this.options.id, upper_folder_id: upper_folder_id, order: this.sort})); - - // initialize the library tooltips - $("#center [data-toggle]").tooltip(); - //hack to show scrollbars - $("#center").css('overflow','auto'); - }, - - /** - * Call this after all models are added to the collection - * to ensure that the folder toolbar will show proper options - * and that event will be bound on all subviews. - */ - postRender: function(){ - var fetched_metadata = this.folderContainer.attributes.metadata; - fetched_metadata.contains_file = typeof this.collection.findWhere({type: 'file'}) !== 'undefined'; - Galaxy.libraries.folderToolbarView.configureElements(fetched_metadata); - $('.library-row').hover(function() { - $(this).find('.show_on_hover').show(); - }, function () { - $(this).find('.show_on_hover').hide(); - }); - }, - - /** - * Adds all given models to the collection. - * @param {array of Item or FolderAsModel} array of models that should - * be added to the view's collection. - */ - addAll: function(models){ - _.each(models.reverse(), function(model) { - Galaxy.libraries.folderListView.collection.add(model); - }); - - $("#center [data-toggle]").tooltip(); - this.checkEmptiness(); - - this.postRender(); - }, - - /** - * Iterates this view's collection and calls the render - * function for each. Also binds the hover behavior. - */ - renderAll: function(){ - var that = this; - _.each(this.collection.models.reverse(), function(model) { - that.renderOne(model); - }); - this.postRender(); - }, - - /** - * Creates a view for the given model and adds it to the folder view. - * @param {Item or FolderAsModel} model of the view that will be rendered - */ - renderOne: function(model){ - if (model.get('type') !== 'folder'){ - this.options.contains_file = true; - // model.set('readable_size', this.size_to_string(model.get('file_size'))); - } - model.set('folder_id', this.id); - var rowView = new mod_library_folderrow_view.FolderRowView(model); - - // save new rowView to cache - this.rowViews[model.get('id')] = rowView; - - this.$el.find('#first_folder_item').after(rowView.el); - - $('.library-row').hover(function() { - $(this).find('.show_on_hover').show(); - }, function () { - $(this).find('.show_on_hover').hide(); - }); - }, - - /** - * removes the view of the given model from the DOM - * @param {Item or FolderAsModel} model of the view that will be removed - */ - removeOne: function(model){ - this.$el.find('#' + model.id).remove(); - }, - - /** Checks whether the list is empty and adds/removes the message */ - checkEmptiness : function(){ - if ((this.$el.find('.dataset_row').length === 0) && (this.$el.find('.folder_row').length === 0)){ - this.$el.find('.empty-folder-message').show(); - } else { - this.$el.find('.empty-folder-message').hide(); - } - }, - - /** User clicked the table heading = he wants to sort stuff */ - sortColumnClicked : function(event){ - event.preventDefault(); - if (this.sort === 'asc'){ - this.sortFolder('name','desc'); - this.sort = 'desc'; - } else { - this.sortFolder('name','asc'); - this.sort = 'asc'; - } - this.render(); - this.renderAll(); - this.checkEmptiness(); - }, - - /** - * Sorts the underlying collection according to the parameters received. - * Currently supports only sorting by name. - */ - sortFolder: function(sort_by, order){ - if (sort_by === 'name'){ - if (order === 'asc'){ - return this.collection.sortByNameAsc(); - } else if (order === 'desc'){ - return this.collection.sortByNameDesc(); - } - } - }, - - /** - * User clicked the checkbox in the table heading - * @param {context} event - */ - selectAll : function (event) { - var selected = event.target.checked; - that = this; - // Iterate each checkbox - $(':checkbox', '#folder_list_body').each(function() { - this.checked = selected; - $row = $(this.parentElement.parentElement); - // Change color of selected/unselected - if (selected) { - that.makeDarkRow($row); - } else { - that.makeWhiteRow($row); - } - }); - }, - - /** - * Check checkbox if user clicks on the whole row or - * on the checkbox itself - */ - selectClickedRow : function (event) { - var checkbox = ''; - var $row; - var source; - if (event.target.localName === 'input'){ - checkbox = event.target; - $row = $(event.target.parentElement.parentElement); - source = 'input'; - } else if (event.target.localName === 'td') { - checkbox = $("#" + event.target.parentElement.id).find(':checkbox')[0]; - $row = $(event.target.parentElement); - source = 'td'; - } - if (checkbox.checked){ - if (source==='td'){ - checkbox.checked = ''; - this.makeWhiteRow($row); - } else if (source==='input') { - this.makeDarkRow($row); - } - } else { - if (source==='td'){ - checkbox.checked = 'selected'; - this.makeDarkRow($row); - } else if (source==='input') { - this.makeWhiteRow($row); - } - } - }, - - makeDarkRow: function($row){ - $row.removeClass('light').addClass('dark'); - $row.find('a').removeClass('light').addClass('dark'); - $row.find('.fa-file-o').removeClass('fa-file-o').addClass('fa-file'); - }, - - makeWhiteRow: function($row){ - $row.removeClass('dark').addClass('light'); - $row.find('a').removeClass('dark').addClass('light'); - $row.find('.fa-file').removeClass('fa-file').addClass('fa-file-o'); - }, - - templateFolder : function (){ - var tmpl_array = []; - - // BREADCRUMBS - tmpl_array.push('<ol class="breadcrumb">'); - tmpl_array.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>'); - tmpl_array.push(' <% _.each(path, function(path_item) { %>'); - tmpl_array.push(' <% if (path_item[0] != id) { %>'); - tmpl_array.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> '); - tmpl_array.push( '<% } else { %>'); - tmpl_array.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>'); - tmpl_array.push(' <% } %>'); - tmpl_array.push(' <% }); %>'); - tmpl_array.push('</ol>'); - - // FOLDER CONTENT - tmpl_array.push('<table data-library-id="<%- parent_library_id %>" id="folder_table" class="grid table table-condensed">'); - tmpl_array.push(' <thead>'); - tmpl_array.push(' <th class="button_heading"></th>'); - tmpl_array.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); - tmpl_array.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>'); - tmpl_array.push(' <th style="width:5%;">data type</th>'); - tmpl_array.push(' <th style="width:10%;">size</th>'); - tmpl_array.push(' <th style="width:160px;">time updated (UTC)</th>'); - tmpl_array.push(' <th style="width:10%;"></th> '); - tmpl_array.push(' </thead>'); - tmpl_array.push(' <tbody id="folder_list_body">'); - tmpl_array.push(' <tr id="first_folder_item">'); - tmpl_array.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' </tr>'); - - tmpl_array.push(' </tbody>'); - tmpl_array.push('</table>'); - tmpl_array.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>'); - - return _.template(tmpl_array.join('')); - } - + }); return { diff -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 -r d76253bb22c4f64c73523956d119c0c5ab0a357b client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js --- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js @@ -20,7 +20,9 @@ 'click #toolbtn_bulk_import' : 'modalBulkImport', 'click #include_deleted_datasets_chk' : 'checkIncludeDeleted', 'click #toolbtn_show_libinfo' : 'showLibInfo', - 'click #toolbtn_bulk_delete' : 'deleteSelectedDatasets' + 'click #toolbtn_bulk_delete' : 'deleteSelectedDatasets', + 'click #page_size_prompt' : 'showPageSizePrompt' + }, defaults: { @@ -90,6 +92,22 @@ this.$el.html(toolbar_template(template_defaults)); }, + /** + * Called from FolderListView when needed. + * @param {object} options common options + */ + renderPaginator: function( options ){ + this.options = _.extend( this.options, options ); + var paginator_template = this.templatePaginator(); + this.$el.find( '#folder_paginator' ).html( paginator_template({ + id: this.options.id, + show_page: parseInt( this.options.show_page ), + page_count: parseInt( this.options.page_count ), + total_items_count: this.options.total_items_count, + items_shown: this.options.items_shown + })); + }, + configureElements: function(options){ this.options = _.extend(this.options, options); @@ -833,11 +851,11 @@ var popped_item = lddas_set.pop(); if ( typeof popped_item === "undefined" ) { if ( this.options.chain_call_control.failed_number === 0 ){ - mod_toastr.success( 'Selected datasets deleted' ); + mod_toastr.success( 'Selected datasets were deleted.' ); } else if ( this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number ){ - mod_toastr.error( 'There was an error and no datasets were deleted.' ); + mod_toastr.error( 'There was an error and no datasets were deleted. Please make sure you have sufficient permissions.' ); } else if ( this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number ){ - mod_toastr.warning( 'Some of the datasets could not be deleted' ); + mod_toastr.warning( 'Some of the datasets could not be deleted. Please make sure you have sufficient permissions.' ); } Galaxy.modal.hide(); return this.deleted_lddas; @@ -976,6 +994,14 @@ } }, + showPageSizePrompt: function(){ + var folder_page_size = prompt( 'How many items per page do you want to see?', Galaxy.libraries.preferences.get( 'folder_page_size' ) ); + if ( ( folder_page_size != null ) && ( folder_page_size == parseInt( folder_page_size ) ) ) { + Galaxy.libraries.preferences.set( { 'folder_page_size': parseInt( folder_page_size ) } ); + Galaxy.libraries.folderListView.render( { id: this.options.id, show_page: 1 } ); + } + }, + templateToolBar: function(){ tmpl_array = []; @@ -1016,7 +1042,6 @@ tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>'); tmpl_array.push('<% } %>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>'); tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">'); tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">'); @@ -1032,6 +1057,10 @@ tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>'); tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>'); + tmpl_array.push(' <span id="folder_paginator" class="library-paginator">'); + // paginator will append here + tmpl_array.push(' </span>'); + tmpl_array.push(' </div>'); // TOOLBAR END tmpl_array.push(' <div id="folder_items_element">'); @@ -1239,7 +1268,41 @@ tmpl_array.push('</ul>'); return _.template(tmpl_array.join('')); - } + }, + + templatePaginator: function(){ + tmpl_array = []; + + tmpl_array.push(' <ul class="pagination pagination-sm">'); + tmpl_array.push(' <% if ( ( show_page - 1 ) > 0 ) { %>'); + tmpl_array.push(' <% if ( ( show_page - 1 ) > page_count ) { %>'); // we are on higher page than total page count + tmpl_array.push(' <li><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>'); + tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <li><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>'); + tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' <% } else { %>'); // we are on the first page + tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>'); + tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' <li class="active">'); + tmpl_array.push(' <a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page ) %></a>'); + tmpl_array.push(' </li>'); + tmpl_array.push(' <% if ( ( show_page ) < page_count ) { %>'); + tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>'); + tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page + 1 ) %></a></li>'); + tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </ul>'); + tmpl_array.push(' <span>'); + tmpl_array.push(' showing <a data-toggle="tooltip" data-placement="top" title="Click to change the number of items on page" id="page_size_prompt"><%- items_shown %></a> of <%- total_items_count %> items'); + tmpl_array.push(' </span>'); + + return _.template(tmpl_array.join('')); + }, }); This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/a0bbd59cb420/ Changeset: a0bbd59cb420 User: abretaud Date: 2014-12-11 16:02:05+00:00 Summary: fix method names and api doc Affected #: 2 files diff -r d76253bb22c4f64c73523956d119c0c5ab0a357b -r a0bbd59cb420442c2fb518540fd2fdfbb2b2da0a lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -211,11 +211,11 @@ self.add_entry( entry, allow_duplicates=allow_duplicates, persist=persist, persist_on_error=persist_on_error, entry_source=entry_source, **kwd ) return self._loaded_content_version - def _remove_entry(self, values, **kwd): + def _remove_entry(self, values): raise NotImplementedError( "Abstract method" ) - def remove_entry(self, values, **kwd): - self._remove_entry_and_reload( values,**kwd ) + def remove_entry(self, values): + self._remove_entry( values ) return self._update_version() def is_current_version( self, other_version ): @@ -513,7 +513,7 @@ data_table_fh.write( "%s\n" % ( self.separator.join( fields ) ) ) return not is_error - def _remove_entry_and_reload( self, values): + def _remove_entry( self, values): # update every file for filename in self.filenames: diff -r d76253bb22c4f64c73523956d119c0c5ab0a357b -r a0bbd59cb420442c2fb518540fd2fdfbb2b2da0a lib/galaxy/webapps/galaxy/api/tool_data.py --- a/lib/galaxy/webapps/galaxy/api/tool_data.py +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -26,10 +26,10 @@ def delete( self, trans, id, **kwd ): """ DELETE /api/tool_data/{id} - Removes a role from a group + Removes an item from a data table :type id: str - :param id: the encoded id of the history to delete + :param id: the id of the data table containing the item to delete :type kwd: dict :param kwd: (required) dictionary structure containing: https://bitbucket.org/galaxy/galaxy-central/commits/6363c839528c/ Changeset: 6363c839528c User: jmchilton Date: 2014-12-15 05:17:31+00:00 Summary: Merged in abretaud/galaxy-central (pull request #577) Add an API to remove items from tool data tables Affected #: 2 files diff -r ac537b0a4167cbd14e0cb93175cc85c096275697 -r 6363c839528ca8bbbbc60c1b3784c788468d9445 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -211,6 +211,13 @@ self.add_entry( entry, allow_duplicates=allow_duplicates, persist=persist, persist_on_error=persist_on_error, entry_source=entry_source, **kwd ) return self._loaded_content_version + def _remove_entry(self, values): + raise NotImplementedError( "Abstract method" ) + + def remove_entry(self, values): + self._remove_entry( values ) + return self._update_version() + def is_current_version( self, other_version ): return self._loaded_content_version == other_version @@ -506,6 +513,42 @@ data_table_fh.write( "%s\n" % ( self.separator.join( fields ) ) ) return not is_error + def _remove_entry( self, values): + + # update every file + for filename in self.filenames: + + if os.path.exists( filename ): + values = self._replace_field_separators( values ) + self.filter_file_fields( filename, values ) + else: + log.warn( "Cannot find index file '%s' for tool data table '%s'" % ( filename, self.name ) ) + + self.reload_from_files() + + def filter_file_fields( self, loc_file, values ): + """ + Reads separated lines from file and print back only the lines that pass a filter. + """ + separator_char = (lambda c: '<TAB>' if c == '\t' else c)(self.separator) + + with open(loc_file) as reader: + rval = "" + for i, line in enumerate( reader ): + if line.lstrip().startswith( self.comment_char ): + rval += line + else: + line_s = line.rstrip( "\n\r" ) + if line_s: + fields = line_s.split( self.separator ) + if fields != values: + rval += line + + with open(loc_file, 'wb') as writer: + writer.write(rval) + + return rval + def _replace_field_separators( self, fields, separator=None, replace=None, comment_char=None ): #make sure none of the fields contain separator #make sure separator replace is different from comment_char, diff -r ac537b0a4167cbd14e0cb93175cc85c096275697 -r 6363c839528ca8bbbbc60c1b3784c788468d9445 lib/galaxy/webapps/galaxy/api/tool_data.py --- a/lib/galaxy/webapps/galaxy/api/tool_data.py +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -20,3 +20,44 @@ @web.expose_api def show( self, trans, id, **kwds ): return trans.app.tool_data_tables.data_tables[id].to_dict(view='element') + + @web.require_admin + @web.expose_api + def delete( self, trans, id, **kwd ): + """ + DELETE /api/tool_data/{id} + Removes an item from a data table + + :type id: str + :param id: the id of the data table containing the item to delete + :type kwd: dict + :param kwd: (required) dictionary structure containing: + + * payload: a dictionary itself containing: + * values: <TAB> separated list of column contents, there must be a value for all the columns of the data table + """ + decoded_tool_data_id = id + + try: + data_table = trans.app.tool_data_tables.data_tables.get(decoded_tool_data_id) + except: + data_table = None + if not data_table: + trans.response.status = 400 + return "Invalid data table id ( %s ) specified." % str( decoded_tool_data_id ) + + values = None + if kwd.get( 'payload', None ): + values = kwd['payload'].get( 'values', '' ) + + if not values: + trans.response.status = 400 + return "Invalid data table item ( %s ) specified." % str( values ) + + split_values = values.split("\t") + + if len(split_values) != len(data_table.get_column_name_list()): + trans.response.status = 400 + return "Invalid data table item ( %s ) specified. Wrong number of columns (%s given, %s required)." % ( str( values ), str(len(split_values)), str(len(data_table.get_column_name_list()))) + + return data_table.remove_entry(split_values) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Merged in lance_parsons/galaxy-central-pull-requests/blastdb_p.loc.sample (pull request #605)
by commits-noreply＠bitbucket.org 14 Dec '14

14 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ac537b0a4167/ Changeset: ac537b0a4167 User: jmchilton Date: 2014-12-14 23:08:48+00:00 Summary: Merged in lance_parsons/galaxy-central-pull-requests/blastdb_p.loc.sample (pull request #605) Removed blastdb_p.loc.sample, moved to tool-shed repo Affected #: 1 file diff -r 16e4b33e850e1a644624d97ecf676bbaaf1aabf9 -r ac537b0a4167cbd14e0cb93175cc85c096275697 tool-data/blastdb_p.loc.sample --- a/tool-data/blastdb_p.loc.sample +++ /dev/null @@ -1,27 +0,0 @@ -#This is a sample file distributed with Galaxy that is used to define a -#list of protein BLAST databases, using three columns tab separated -#(longer whitespace are TAB characters): -# -#<unique_id><database_caption><base_name_path> -# -#The captions typically contain spaces and might end with the build date. -#It is important that the actual database name does not have a space in it, -#and that the first tab that appears in the line is right before the path. -# -#So, for example, if your database is NR and the path to your base name -#is /data/blastdb/nr, then the blastdb_p.loc entry would look like this: -# -#nr NCBI NR (non redundant) /data/blastdb/nr -# -#and your /data/blastdb directory would contain all of the files associated -#with the database, /data/blastdb/nr.*. -# -#Your blastdb_p.loc file should include an entry per line for each "base name" -#you have stored. For example: -# -#nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr -#nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr -#...etc... -# -#See also blastdb.loc which is for any nucleotide BLAST database. -# Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 14 Dec '14

14 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6d6757abda20/ Changeset: 6d6757abda20 Branch: blastdb_p.loc.sample User: lance_parsons Date: 2014-12-10 17:43:33+00:00 Summary: Removed blastdb_p.loc.sample, moved to tool-shed repo Affected #: 1 file diff -r d66ad58a40e31defb6de0eb8b8b543b7e0f26ae5 -r 6d6757abda20cd49d85d8b59d382de9e69bf1588 tool-data/blastdb_p.loc.sample --- a/tool-data/blastdb_p.loc.sample +++ /dev/null @@ -1,27 +0,0 @@ -#This is a sample file distributed with Galaxy that is used to define a -#list of protein BLAST databases, using three columns tab separated -#(longer whitespace are TAB characters): -# -#<unique_id><database_caption><base_name_path> -# -#The captions typically contain spaces and might end with the build date. -#It is important that the actual database name does not have a space in it, -#and that the first tab that appears in the line is right before the path. -# -#So, for example, if your database is NR and the path to your base name -#is /data/blastdb/nr, then the blastdb_p.loc entry would look like this: -# -#nr NCBI NR (non redundant) /data/blastdb/nr -# -#and your /data/blastdb directory would contain all of the files associated -#with the database, /data/blastdb/nr.*. -# -#Your blastdb_p.loc file should include an entry per line for each "base name" -#you have stored. For example: -# -#nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr -#nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr -#...etc... -# -#See also blastdb.loc which is for any nucleotide BLAST database. -# https://bitbucket.org/galaxy/galaxy-central/commits/ac537b0a4167/ Changeset: ac537b0a4167 User: jmchilton Date: 2014-12-14 23:08:48+00:00 Summary: Merged in lance_parsons/galaxy-central-pull-requests/blastdb_p.loc.sample (pull request #605) Removed blastdb_p.loc.sample, moved to tool-shed repo Affected #: 1 file diff -r 16e4b33e850e1a644624d97ecf676bbaaf1aabf9 -r ac537b0a4167cbd14e0cb93175cc85c096275697 tool-data/blastdb_p.loc.sample --- a/tool-data/blastdb_p.loc.sample +++ /dev/null @@ -1,27 +0,0 @@ -#This is a sample file distributed with Galaxy that is used to define a -#list of protein BLAST databases, using three columns tab separated -#(longer whitespace are TAB characters): -# -#<unique_id><database_caption><base_name_path> -# -#The captions typically contain spaces and might end with the build date. -#It is important that the actual database name does not have a space in it, -#and that the first tab that appears in the line is right before the path. -# -#So, for example, if your database is NR and the path to your base name -#is /data/blastdb/nr, then the blastdb_p.loc entry would look like this: -# -#nr NCBI NR (non redundant) /data/blastdb/nr -# -#and your /data/blastdb directory would contain all of the files associated -#with the database, /data/blastdb/nr.*. -# -#Your blastdb_p.loc file should include an entry per line for each "base name" -#you have stored. For example: -# -#nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr -#nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr -#...etc... -# -#See also blastdb.loc which is for any nucleotide BLAST database. -# Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Allow specification of multiple datatypes_conf.xml files.
by commits-noreply＠bitbucket.org 14 Dec '14

14 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/16e4b33e850e/ Changeset: 16e4b33e850e User: jmchilton Date: 2014-12-14 18:16:11+00:00 Summary: Allow specification of multiple datatypes_conf.xml files. If there are conflicting datatype registrations - the registration that appears last in these files will be used. There is an open issue here regarding order of sniffers. This is going to just piggy back on whatever the tool shed would do - so however we decide for instance to resolve sniffer orders in that respect will work with this mechanism as well. For now though - lets just specify that the best practice should be to just place all non-shed sniffers in one file if specifing multiple datatypes configurations manually like this. Affected #: 2 files diff -r 1422966f1ca88472b8685015f5a8cdd3dd0f1db9 -r 16e4b33e850e1a644624d97ecf676bbaaf1aabf9 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -212,8 +212,10 @@ # Directory where chrom len files are kept, currently mainly used by trackster #len_file_path = tool-data/shared/ucsc/chrom -# Datatypes config file, defines what data (file) types are available in -# Galaxy (.sample is used if default does not exist). +# Datatypes config file(s), defines what data (file) types are available in +# Galaxy (.sample is used if default does not exist). If a datatype appears in +# multiple files - the last definition is used (though the first sniffer is used +# so limit sniffer definitions to one file). #datatypes_config_file = config/datatypes_conf.xml # Disable the 'Auto-detect' option for file uploads diff -r 1422966f1ca88472b8685015f5a8cdd3dd0f1db9 -r 16e4b33e850e1a644624d97ecf676bbaaf1aabf9 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -583,8 +583,9 @@ for path in tool_configs: if not os.path.exists( path ): raise ConfigurationError("Tool config file not found: %s" % path ) - if not os.path.isfile( self.datatypes_config ): - raise ConfigurationError("Datatypes config file not found: %s" % self.datatypes_config ) + for datatypes_config in listify( self.datatypes_config ): + if not os.path.isfile( datatypes_config ): + raise ConfigurationError("Datatypes config file not found: %s" % datatypes_config ) # Check for deprecated options. for key in self.config_dict.keys(): if key in self.deprecated_options: @@ -746,7 +747,12 @@ # between 2 proprietary datatypes, the datatype from the repository that was installed earliest will take precedence. installed_repository_manager.load_proprietary_datatypes() # Load the data types in the Galaxy distribution, which are defined in self.config.datatypes_config. - self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) + datatypes_configs = self.config.datatypes_config + for datatypes_config in listify( datatypes_configs ): + # Setting override=False would make earlier files would take + # precedence - but then they wouldn't override tool shed + # datatypes. + self.datatypes_registry.load_datatypes( self.config.root, datatypes_config, override=True ) def _configure_object_store( self, **kwds ): from galaxy.objectstore import build_object_store_from_config Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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