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commit/galaxy-central: 9 new changesets
by commits-noreply＠bitbucket.org 11 Aug '14

11 Aug '14

9 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f58a9199e992/ Changeset: f58a9199e992 User: jmchilton Date: 2014-08-10 20:05:31 Summary: Fix failing test test/unit/workflows/test_extract_summary.py. Affected #: 1 file diff -r de2e33813275b89a04e7de4e95b21f6d2e100d4e -r f58a9199e9922c3bef27240aa613a9a3c5bae67e test/unit/workflows/test_extract_summary.py --- a/test/unit/workflows/test_extract_summary.py +++ b/test/unit/workflows/test_extract_summary.py @@ -71,6 +71,10 @@ def __init__( self ): self.active_datasets = [] + @property + def active_contents( self ): + return self.active_datasets + class MockTrans( object ): @@ -87,6 +91,7 @@ self.id = 123 self.state = state self.copied_from_history_dataset_association = None + self.history_content_type = "dataset" if job is not UNDEFINED_JOB: if not job: job = model.Job() https://bitbucket.org/galaxy/galaxy-central/commits/f1a1c52f8495/ Changeset: f1a1c52f8495 User: jmchilton Date: 2014-08-10 20:05:31 Summary: Move galaxy.dataset_collections.util to galaxy.managers.collections_util to prevent circular dependency error. Still some problems with histories and hda managers when loading from unit tests: ====================================================================== ERROR: Failure: ImportError (cannot import name histories) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/john/workspace/lwr/.venv/local/lib/python2.7/site-packages/nose/loader.py", line 414, in loadTestsFromName addr.filename, addr.module) File "/home/john/workspace/lwr/.venv/local/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "/home/john/workspace/lwr/.venv/local/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/home/john/workspace/galaxy-central/test/unit/workflows/test_workflow_run_request.py", line 4, in <module> from galaxy.workflow import run_request File "/home/john/workspace/galaxy-central/lib/galaxy/workflow/run_request.py", line 4, in <module> import galaxy.managers.histories File "/home/john/workspace/galaxy-central/lib/galaxy/managers/histories.py", line 12, in <module> import galaxy.managers.hdas File "/home/john/workspace/galaxy-central/lib/galaxy/managers/hdas.py", line 11, in <module> from galaxy.managers import histories as history_manager ImportError: cannot import name histories Affected #: 9 files diff -r f58a9199e9922c3bef27240aa613a9a3c5bae67e -r f1a1c52f8495d1035d1c0a5e21b710974db0908e lib/galaxy/dataset_collections/__init__.py --- a/lib/galaxy/dataset_collections/__init__.py +++ b/lib/galaxy/dataset_collections/__init__.py @@ -1,7 +1,6 @@ from .registry import DatasetCollectionTypesRegistry from .matching import MatchingCollections from .type_description import CollectionTypeDescriptionFactory -from .util import validate_input_element_identifiers from galaxy import model @@ -14,7 +13,7 @@ UsesTagsMixin, ) from galaxy.managers import hdas # TODO: Refactor all mixin use into managers. - +from galaxy.managers.collections_util import validate_input_element_identifiers from galaxy.util import validation from galaxy.util import odict diff -r f58a9199e9922c3bef27240aa613a9a3c5bae67e -r f1a1c52f8495d1035d1c0a5e21b710974db0908e lib/galaxy/dataset_collections/util.py --- a/lib/galaxy/dataset_collections/util.py +++ /dev/null @@ -1,95 +0,0 @@ -from galaxy import exceptions -from galaxy import web -from galaxy import model - -import logging -log = logging.getLogger( __name__ ) - -ERROR_MESSAGE_UNKNOWN_SRC = "Unknown dataset source (src) %s." -ERROR_MESSAGE_NO_NESTED_IDENTIFIERS = "Dataset source new_collection requires nested element_identifiers for new collection." -ERROR_MESSAGE_NO_NAME = "Cannot load invalid dataset identifier - missing name - %s" -ERROR_MESSAGE_NO_COLLECTION_TYPE = "No collection_type define for nested collection %s." -ERROR_MESSAGE_INVALID_PARAMETER_FOUND = "Found invalid parameter %s in element identifier description %s." -ERROR_MESSAGE_DUPLICATED_IDENTIFIER_FOUND = "Found duplicated element identifier name %s." - - -def api_payload_to_create_params( payload ): - """ - Cleanup API payload to pass into dataset_collections. - """ - required_parameters = [ "collection_type", "element_identifiers" ] - missing_parameters = [ p for p in required_parameters if p not in payload ] - if missing_parameters: - message = "Missing required parameters %s" % missing_parameters - raise exceptions.ObjectAttributeMissingException( message ) - - params = dict( - collection_type=payload.get( "collection_type" ), - element_identifiers=payload.get( "element_identifiers" ), - name=payload.get( "name", None ), - ) - - return params - - -def validate_input_element_identifiers( element_identifiers ): - """ Scan through the list of element identifiers supplied by the API consumer - and verify the structure is valid. - """ - log.debug( "Validating %d element identifiers for collection creation." % len( element_identifiers ) ) - identifier_names = set() - for element_identifier in element_identifiers: - if "__object__" in element_identifier: - message = ERROR_MESSAGE_INVALID_PARAMETER_FOUND % ( "__model_object__", element_identifier ) - raise exceptions.RequestParameterInvalidException( message ) - if "name" not in element_identifier: - message = ERROR_MESSAGE_NO_NAME % element_identifier - raise exceptions.RequestParameterInvalidException( message ) - name = element_identifier[ "name" ] - if name in identifier_names: - message = ERROR_MESSAGE_DUPLICATED_IDENTIFIER_FOUND % name - raise exceptions.RequestParameterInvalidException( message ) - else: - identifier_names.add( name ) - src = element_identifier.get( "src", "hda" ) - if src not in [ "hda", "hdca", "ldda", "new_collection" ]: - message = ERROR_MESSAGE_UNKNOWN_SRC % src - raise exceptions.RequestParameterInvalidException( message ) - if src == "new_collection": - if "element_identifiers" not in element_identifier: - message = ERROR_MESSAGE_NO_NESTED_IDENTIFIERS - raise exceptions.RequestParameterInvalidException( ERROR_MESSAGE_NO_NESTED_IDENTIFIERS ) - if "collection_type" not in element_identifier: - message = ERROR_MESSAGE_NO_COLLECTION_TYPE % element_identifier - raise exceptions.RequestParameterInvalidException( message ) - validate_input_element_identifiers( element_identifier[ "element_identifiers" ] ) - - -def dictify_dataset_collection_instance( dataset_colleciton_instance, parent, security, view="element" ): - dict_value = dataset_colleciton_instance.to_dict( view=view ) - encoded_id = security.encode_id( dataset_colleciton_instance.id ) - if isinstance( parent, model.History ): - encoded_history_id = security.encode_id( parent.id ) - dict_value[ 'url' ] = web.url_for( 'history_content_typed', history_id=encoded_history_id, id=encoded_id, type="dataset_collection" ) - elif isinstance( parent, model.LibraryFolder ): - encoded_library_id = security.encode_id( parent.library.id ) - encoded_folder_id = security.encode_id( parent.id ) - # TODO: Work in progress - this end-point is not right yet... - dict_value[ 'url' ] = web.url_for( 'library_content', library_id=encoded_library_id, id=encoded_id, folder_id=encoded_folder_id ) - if view == "element": - dict_value[ 'elements' ] = map( dictify_element, dataset_colleciton_instance.collection.elements ) - security.encode_all_ids( dict_value, recursive=True ) # TODO: Use Kyle's recusrive formulation of this. - return dict_value - - -def dictify_element( element ): - dictified = element.to_dict( view="element" ) - object_detials = element.element_object.to_dict() - if element.child_collection: - # Recursively yield elements for each nested collection... - object_detials[ "elements" ] = map( dictify_element, element.child_collection.elements ) - - dictified[ "object" ] = object_detials - return dictified - -__all__ = [ api_payload_to_create_params, dictify_dataset_collection_instance ] diff -r f58a9199e9922c3bef27240aa613a9a3c5bae67e -r f1a1c52f8495d1035d1c0a5e21b710974db0908e lib/galaxy/managers/collections.py --- /dev/null +++ b/lib/galaxy/managers/collections.py @@ -0,0 +1,1 @@ +""" Future home of dataset collections managers. """ diff -r f58a9199e9922c3bef27240aa613a9a3c5bae67e -r f1a1c52f8495d1035d1c0a5e21b710974db0908e lib/galaxy/managers/collections_util.py --- /dev/null +++ b/lib/galaxy/managers/collections_util.py @@ -0,0 +1,95 @@ +from galaxy import exceptions +from galaxy import web +from galaxy import model + +import logging +log = logging.getLogger( __name__ ) + +ERROR_MESSAGE_UNKNOWN_SRC = "Unknown dataset source (src) %s." +ERROR_MESSAGE_NO_NESTED_IDENTIFIERS = "Dataset source new_collection requires nested element_identifiers for new collection." +ERROR_MESSAGE_NO_NAME = "Cannot load invalid dataset identifier - missing name - %s" +ERROR_MESSAGE_NO_COLLECTION_TYPE = "No collection_type define for nested collection %s." +ERROR_MESSAGE_INVALID_PARAMETER_FOUND = "Found invalid parameter %s in element identifier description %s." +ERROR_MESSAGE_DUPLICATED_IDENTIFIER_FOUND = "Found duplicated element identifier name %s." + + +def api_payload_to_create_params( payload ): + """ + Cleanup API payload to pass into dataset_collections. + """ + required_parameters = [ "collection_type", "element_identifiers" ] + missing_parameters = [ p for p in required_parameters if p not in payload ] + if missing_parameters: + message = "Missing required parameters %s" % missing_parameters + raise exceptions.ObjectAttributeMissingException( message ) + + params = dict( + collection_type=payload.get( "collection_type" ), + element_identifiers=payload.get( "element_identifiers" ), + name=payload.get( "name", None ), + ) + + return params + + +def validate_input_element_identifiers( element_identifiers ): + """ Scan through the list of element identifiers supplied by the API consumer + and verify the structure is valid. + """ + log.debug( "Validating %d element identifiers for collection creation." % len( element_identifiers ) ) + identifier_names = set() + for element_identifier in element_identifiers: + if "__object__" in element_identifier: + message = ERROR_MESSAGE_INVALID_PARAMETER_FOUND % ( "__model_object__", element_identifier ) + raise exceptions.RequestParameterInvalidException( message ) + if "name" not in element_identifier: + message = ERROR_MESSAGE_NO_NAME % element_identifier + raise exceptions.RequestParameterInvalidException( message ) + name = element_identifier[ "name" ] + if name in identifier_names: + message = ERROR_MESSAGE_DUPLICATED_IDENTIFIER_FOUND % name + raise exceptions.RequestParameterInvalidException( message ) + else: + identifier_names.add( name ) + src = element_identifier.get( "src", "hda" ) + if src not in [ "hda", "hdca", "ldda", "new_collection" ]: + message = ERROR_MESSAGE_UNKNOWN_SRC % src + raise exceptions.RequestParameterInvalidException( message ) + if src == "new_collection": + if "element_identifiers" not in element_identifier: + message = ERROR_MESSAGE_NO_NESTED_IDENTIFIERS + raise exceptions.RequestParameterInvalidException( ERROR_MESSAGE_NO_NESTED_IDENTIFIERS ) + if "collection_type" not in element_identifier: + message = ERROR_MESSAGE_NO_COLLECTION_TYPE % element_identifier + raise exceptions.RequestParameterInvalidException( message ) + validate_input_element_identifiers( element_identifier[ "element_identifiers" ] ) + + +def dictify_dataset_collection_instance( dataset_colleciton_instance, parent, security, view="element" ): + dict_value = dataset_colleciton_instance.to_dict( view=view ) + encoded_id = security.encode_id( dataset_colleciton_instance.id ) + if isinstance( parent, model.History ): + encoded_history_id = security.encode_id( parent.id ) + dict_value[ 'url' ] = web.url_for( 'history_content_typed', history_id=encoded_history_id, id=encoded_id, type="dataset_collection" ) + elif isinstance( parent, model.LibraryFolder ): + encoded_library_id = security.encode_id( parent.library.id ) + encoded_folder_id = security.encode_id( parent.id ) + # TODO: Work in progress - this end-point is not right yet... + dict_value[ 'url' ] = web.url_for( 'library_content', library_id=encoded_library_id, id=encoded_id, folder_id=encoded_folder_id ) + if view == "element": + dict_value[ 'elements' ] = map( dictify_element, dataset_colleciton_instance.collection.elements ) + security.encode_all_ids( dict_value, recursive=True ) # TODO: Use Kyle's recusrive formulation of this. + return dict_value + + +def dictify_element( element ): + dictified = element.to_dict( view="element" ) + object_detials = element.element_object.to_dict() + if element.child_collection: + # Recursively yield elements for each nested collection... + object_detials[ "elements" ] = map( dictify_element, element.child_collection.elements ) + + dictified[ "object" ] = object_detials + return dictified + +__all__ = [ api_payload_to_create_params, dictify_dataset_collection_instance ] diff -r f58a9199e9922c3bef27240aa613a9a3c5bae67e -r f1a1c52f8495d1035d1c0a5e21b710974db0908e lib/galaxy/managers/histories.py --- a/lib/galaxy/managers/histories.py +++ b/lib/galaxy/managers/histories.py @@ -10,9 +10,9 @@ from galaxy.managers import base as manager_base import galaxy.managers.hdas +import galaxy.managers.collections_util import galaxy.web -import galaxy.dataset_collections.util import logging log = logging.getLogger( __name__ ) @@ -141,7 +141,7 @@ history and an array of serialized history contents respectively. """ hda_mgr = galaxy.managers.hdas.HDAManager() - collection_dictifier = galaxy.dataset_collections.util.dictify_dataset_collection_instance + collection_dictifier = galaxy.managers.collections_util.dictify_dataset_collection_instance history_dictionary = {} contents_dictionaries = [] diff -r f58a9199e9922c3bef27240aa613a9a3c5bae67e -r f1a1c52f8495d1035d1c0a5e21b710974db0908e lib/galaxy/webapps/galaxy/api/dataset_collections.py --- a/lib/galaxy/webapps/galaxy/api/dataset_collections.py +++ b/lib/galaxy/webapps/galaxy/api/dataset_collections.py @@ -4,8 +4,7 @@ from galaxy.web.base.controller import UsesHistoryMixin from galaxy.web.base.controller import UsesLibraryMixinItems -from galaxy.dataset_collections.util import api_payload_to_create_params -from galaxy.dataset_collections.util import dictify_dataset_collection_instance +from galaxy.managers.collections_util import api_payload_to_create_params, dictify_dataset_collection_instance from logging import getLogger log = getLogger( __name__ ) diff -r f58a9199e9922c3bef27240aa613a9a3c5bae67e -r f1a1c52f8495d1035d1c0a5e21b710974db0908e lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -16,12 +16,9 @@ from galaxy.web.base.controller import UsesLibraryMixinItems from galaxy.web.base.controller import UsesTagsMixin -from galaxy.dataset_collections.util import api_payload_to_create_params -from galaxy.dataset_collections.util import dictify_dataset_collection_instance - - from galaxy.managers import histories from galaxy.managers import hdas +from galaxy.managers.collections_util import api_payload_to_create_params, dictify_dataset_collection_instance import logging log = logging.getLogger( __name__ ) diff -r f58a9199e9922c3bef27240aa613a9a3c5bae67e -r f1a1c52f8495d1035d1c0a5e21b710974db0908e lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -5,11 +5,10 @@ from galaxy import web from galaxy import exceptions from galaxy.web import _future_expose_api as expose_api -from galaxy.dataset_collections.util import api_payload_to_create_params -from galaxy.dataset_collections.util import dictify_dataset_collection_instance from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems from galaxy.web.base.controller import UsesHistoryDatasetAssociationMixin from galaxy.web.base.controller import HTTPBadRequest, url_for +from galaxy.managers.collections_util import api_payload_to_create_params, dictify_dataset_collection_instance from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex from sqlalchemy.orm.exc import MultipleResultsFound from sqlalchemy.orm.exc import NoResultFound diff -r f58a9199e9922c3bef27240aa613a9a3c5bae67e -r f1a1c52f8495d1035d1c0a5e21b710974db0908e lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -9,7 +9,8 @@ from galaxy.visualization.genomes import GenomeRegion from galaxy.util.json import to_json_string from galaxy.visualization.data_providers.genome import * -from galaxy.dataset_collections.util import dictify_dataset_collection_instance + +from galaxy.managers.collections_util import dictify_dataset_collection_instance import logging log = logging.getLogger( __name__ ) https://bitbucket.org/galaxy/galaxy-central/commits/b17747153f1a/ Changeset: b17747153f1a User: jmchilton Date: 2014-08-10 20:05:31 Summary: Extract all the workflow run API param handling out... This should allow for the reuse of all of this in asynchronous workflow running and make unit testing of all the different paths easier (though that is not included in this commit - the API functional test coverage for this code is pretty decent at this point). Affected #: 2 files diff -r f1a1c52f8495d1035d1c0a5e21b710974db0908e -r b17747153f1a55292a03392cf2c9f5a6c69c5460 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -15,7 +15,7 @@ from galaxy.web.base.controller import SharableMixin from galaxy.workflow.extract import extract_workflow from galaxy.workflow.run import invoke -from galaxy.workflow.run import WorkflowRunConfig +from galaxy.workflow.run_request import build_workflow_run_config log = logging.getLogger(__name__) @@ -212,105 +212,12 @@ message = "Invalid workflow_id specified." raise exceptions.RequestParameterInvalidException( message ) - # Pull other parameters out of payload. - param_map = payload.get( 'parameters', {} ) - inputs = payload.get( 'inputs', None ) - inputs_by = payload.get( 'inputs_by', None ) - if inputs is None: - # 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' - 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' - - valid_inputs_by = [ 'step_id', 'step_index', 'name' ] - if inputs_by not in valid_inputs_by: - trans.response.status = 403 - error_message_template = "Invalid inputs_by specified '%s' must be one of %s" - error_message = error_message_template % ( inputs_by, valid_inputs_by ) - raise ValueError( error_message ) - - add_to_history = 'no_add_to_history' not in payload - history_param = payload.get('history', '') - # Get workflow + accessibility check. stored_workflow = self.__get_stored_accessible_workflow( trans, workflow_id ) workflow = stored_workflow.latest_workflow - # Sanity checks. - if len( workflow.steps ) == 0: - raise exceptions.MessageException( "Workflow cannot be run because it does not have any steps" ) - if workflow.has_cycles: - raise exceptions.MessageException( "Workflow cannot be run because it contains cycles" ) - if workflow.has_errors: - message = "Workflow cannot be run because of validation errors in some steps" - raise exceptions.MessageException( message ) - - # Get target history. - if history_param.startswith('hist_id='): - # Passing an existing history to use. - encoded_history_id = history_param[ 8: ] - history_id = self.__decode_id( trans, encoded_history_id, model_type="history" ) - history = self.history_manager.get( trans, history_id, check_ownership=True ) - else: - # Send workflow outputs to new history. - history = self.app.model.History(name=history_param, user=trans.user) - trans.sa_session.add(history) - trans.sa_session.flush() - - # Set workflow inputs. - for k in inputs: - try: - if inputs[k]['src'] == 'ldda': - ldda = trans.sa_session.query(self.app.model.LibraryDatasetDatasetAssociation).get( - trans.security.decode_id(inputs[k]['id'])) - assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), ldda.dataset ) - content = ldda.to_history_dataset_association(history, add_to_history=add_to_history) - elif inputs[k]['src'] == 'ld': - ldda = trans.sa_session.query(self.app.model.LibraryDataset).get( - trans.security.decode_id(inputs[k]['id'])).library_dataset_dataset_association - assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), ldda.dataset ) - content = ldda.to_history_dataset_association(history, add_to_history=add_to_history) - elif inputs[k]['src'] == 'hda': - # Get dataset handle, add to dict and history if necessary - content = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get( - trans.security.decode_id(inputs[k]['id'])) - assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), content.dataset ) - elif inputs[k]['src'] == 'hdca': - content = self.app.dataset_collections_service.get_dataset_collection_instance( - trans, - 'history', - inputs[k]['id'] - ) - else: - message = "Unknown workflow input source '%s' specified." % inputs[k]['src'] - raise exceptions.RequestParameterInvalidException( message ) - if add_to_history and content.history != history: - content = content.copy() - if isinstance( content, self.app.model.HistoryDatasetAssociation ): - history.add_dataset( content ) - else: - history.add_dataset_collection( content ) - inputs[k]['hda'] = content # TODO: rename key to 'content', prescreen input ensure not populated explicitly - except AssertionError: - message = "Invalid workflow input '%s' specified" % inputs[k]['id'] - raise exceptions.ItemAccessibilityException( message ) - - # Run each step, connecting outputs to inputs - replacement_dict = payload.get('replacement_params', {}) - - run_config = WorkflowRunConfig( - target_history=history, - replacement_dict=replacement_dict, - inputs=inputs, - inputs_by=inputs_by, - param_map=param_map, - ) + run_config = build_workflow_run_config( trans, workflow, payload ) + history = run_config.target_history # invoke may throw MessageExceptions on tool erors, failure # to match up inputs, etc... @@ -525,8 +432,8 @@ return stored_workflow def __get_stored_workflow( self, trans, workflow_id ): + workflow_id = self.__decode_id( trans, workflow_id ) try: - workflow_id = self.__decode_id( trans, workflow_id ) query = trans.sa_session.query( trans.app.model.StoredWorkflow ) stored_workflow = query.get( workflow_id ) except Exception: diff -r f1a1c52f8495d1035d1c0a5e21b710974db0908e -r b17747153f1a55292a03392cf2c9f5a6c69c5460 lib/galaxy/workflow/run_request.py --- /dev/null +++ b/lib/galaxy/workflow/run_request.py @@ -0,0 +1,114 @@ +from galaxy import exceptions + +from galaxy.managers import histories +from galaxy.workflow.run import WorkflowRunConfig + + +def build_workflow_run_config( trans, workflow, payload ): + app = trans.app + history_manager = histories.HistoryManager() + + # Pull other parameters out of payload. + param_map = payload.get( 'parameters', {} ) + inputs = payload.get( 'inputs', None ) + inputs_by = payload.get( 'inputs_by', None ) + if inputs is None: + # 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' + 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' + + valid_inputs_by = [ 'step_id', 'step_index', 'name' ] + if inputs_by not in valid_inputs_by: + trans.response.status = 403 + error_message_template = "Invalid inputs_by specified '%s' must be one of %s" + error_message = error_message_template % ( inputs_by, valid_inputs_by ) + raise ValueError( error_message ) + + add_to_history = 'no_add_to_history' not in payload + history_param = payload.get('history', '') + + # Sanity checks. + if len( workflow.steps ) == 0: + raise exceptions.MessageException( "Workflow cannot be run because it does not have any steps" ) + if workflow.has_cycles: + raise exceptions.MessageException( "Workflow cannot be run because it contains cycles" ) + if workflow.has_errors: + message = "Workflow cannot be run because of validation errors in some steps" + raise exceptions.MessageException( message ) + + # Get target history. + if history_param.startswith('hist_id='): + # Passing an existing history to use. + encoded_history_id = history_param[ 8: ] + history_id = __decode_id( trans, encoded_history_id, model_type="history" ) + history = history_manager.get( trans, history_id, check_ownership=True ) + else: + # Send workflow outputs to new history. + history = app.model.History(name=history_param, user=trans.user) + trans.sa_session.add(history) + trans.sa_session.flush() + + # Set workflow inputs. + for k in inputs: + try: + if inputs[k]['src'] == 'ldda': + ldda = trans.sa_session.query(app.model.LibraryDatasetDatasetAssociation).get( + trans.security.decode_id(inputs[k]['id'])) + assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), ldda.dataset ) + content = ldda.to_history_dataset_association(history, add_to_history=add_to_history) + elif inputs[k]['src'] == 'ld': + ldda = trans.sa_session.query(app.model.LibraryDataset).get( + trans.security.decode_id(inputs[k]['id'])).library_dataset_dataset_association + assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), ldda.dataset ) + content = ldda.to_history_dataset_association(history, add_to_history=add_to_history) + elif inputs[k]['src'] == 'hda': + # Get dataset handle, add to dict and history if necessary + content = trans.sa_session.query(app.model.HistoryDatasetAssociation).get( + trans.security.decode_id(inputs[k]['id'])) + assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), content.dataset ) + elif inputs[k]['src'] == 'hdca': + content = app.dataset_collections_service.get_dataset_collection_instance( + trans, + 'history', + inputs[k]['id'] + ) + else: + message = "Unknown workflow input source '%s' specified." % inputs[k]['src'] + raise exceptions.RequestParameterInvalidException( message ) + if add_to_history and content.history != history: + content = content.copy() + if isinstance( content, app.model.HistoryDatasetAssociation ): + history.add_dataset( content ) + else: + history.add_dataset_collection( content ) + inputs[k]['hda'] = content # TODO: rename key to 'content', prescreen input ensure not populated explicitly + except AssertionError: + message = "Invalid workflow input '%s' specified" % inputs[k]['id'] + raise exceptions.ItemAccessibilityException( message ) + + # Run each step, connecting outputs to inputs + replacement_dict = payload.get('replacement_params', {}) + + run_config = WorkflowRunConfig( + target_history=history, + replacement_dict=replacement_dict, + inputs=inputs, + inputs_by=inputs_by, + param_map=param_map, + ) + return run_config + + +def __decode_id( trans, workflow_id, model_type="workflow" ): + try: + return trans.security.decode_id( workflow_id ) + except Exception: + message = "Malformed %s id ( %s ) specified, unable to decode" % ( model_type, workflow_id ) + raise exceptions.MalformedId( message ) https://bitbucket.org/galaxy/galaxy-central/commits/041779f857a1/ Changeset: 041779f857a1 User: jmchilton Date: 2014-08-10 20:05:31 Summary: Hack to get around circular dependency by histories and hdas manager modules. ====================================================================== ERROR: Failure: ImportError (cannot import name histories) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/john/workspace/lwr/.venv/local/lib/python2.7/site-packages/nose/loader.py", line 414, in loadTestsFromName addr.filename, addr.module) File "/home/john/workspace/lwr/.venv/local/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "/home/john/workspace/lwr/.venv/local/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/home/john/workspace/galaxy-central/test/unit/workflows/test_workflow_run_request.py", line 4, in <module> from galaxy.workflow import run_request File "/home/john/workspace/galaxy-central/lib/galaxy/workflow/run_request.py", line 4, in <module> import galaxy.managers.histories File "/home/john/workspace/galaxy-central/lib/galaxy/managers/histories.py", line 12, in <module> import galaxy.managers.hdas File "/home/john/workspace/galaxy-central/lib/galaxy/managers/hdas.py", line 11, in <module> from galaxy.managers import histories as history_manager ImportError: cannot import name histories Affected #: 1 file diff -r b17747153f1a55292a03392cf2c9f5a6c69c5460 -r 041779f857a178092e216a628b62d3c04a4c8977 lib/galaxy/managers/histories.py --- a/lib/galaxy/managers/histories.py +++ b/lib/galaxy/managers/histories.py @@ -9,7 +9,6 @@ from galaxy.model import orm from galaxy.managers import base as manager_base -import galaxy.managers.hdas import galaxy.managers.collections_util import galaxy.web @@ -140,6 +139,8 @@ Returns a dictionary containing ``history`` and ``contents``, serialized history and an array of serialized history contents respectively. """ + # import here prevents problems related to circular dependecy between histories and hdas managers. + import galaxy.managers.hdas hda_mgr = galaxy.managers.hdas.HDAManager() collection_dictifier = galaxy.managers.collections_util.dictify_dataset_collection_instance https://bitbucket.org/galaxy/galaxy-central/commits/7772ff282e95/ Changeset: 7772ff282e95 User: jmchilton Date: 2014-08-10 20:05:31 Summary: Cleanup repeated dictionary access in build_workflow_run_config, better error handling. Affected #: 1 file diff -r 041779f857a178092e216a628b62d3c04a4c8977 -r 7772ff282e95516a4d39ef0a87afeabb8b123d23 lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -56,31 +56,39 @@ trans.sa_session.flush() # Set workflow inputs. - for k in inputs: + for input_dict in inputs.itervalues(): + if 'src' not in input_dict: + message = "Not input source type defined for input '%s'." % input_dict + raise exceptions.RequestParameterInvalidException( message ) + if 'id' not in input_dict: + message = "Not input id defined for input '%s'." % input_dict + raise exceptions.RequestParameterInvalidException( message ) + input_source = input_dict['src'] + input_id = input_dict['id'] try: - if inputs[k]['src'] == 'ldda': + if input_source == 'ldda': ldda = trans.sa_session.query(app.model.LibraryDatasetDatasetAssociation).get( - trans.security.decode_id(inputs[k]['id'])) + trans.security.decode_id(input_id)) assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), ldda.dataset ) content = ldda.to_history_dataset_association(history, add_to_history=add_to_history) - elif inputs[k]['src'] == 'ld': + elif input_source == 'ld': ldda = trans.sa_session.query(app.model.LibraryDataset).get( - trans.security.decode_id(inputs[k]['id'])).library_dataset_dataset_association + trans.security.decode_id(input_id)).library_dataset_dataset_association assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), ldda.dataset ) content = ldda.to_history_dataset_association(history, add_to_history=add_to_history) - elif inputs[k]['src'] == 'hda': + elif input_source == 'hda': # Get dataset handle, add to dict and history if necessary content = trans.sa_session.query(app.model.HistoryDatasetAssociation).get( - trans.security.decode_id(inputs[k]['id'])) + trans.security.decode_id(input_id)) assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), content.dataset ) - elif inputs[k]['src'] == 'hdca': + elif input_source == 'hdca': content = app.dataset_collections_service.get_dataset_collection_instance( trans, 'history', - inputs[k]['id'] + input_id ) else: - message = "Unknown workflow input source '%s' specified." % inputs[k]['src'] + message = "Unknown workflow input source '%s' specified." % input_source raise exceptions.RequestParameterInvalidException( message ) if add_to_history and content.history != history: content = content.copy() @@ -88,9 +96,9 @@ history.add_dataset( content ) else: history.add_dataset_collection( content ) - inputs[k]['hda'] = content # TODO: rename key to 'content', prescreen input ensure not populated explicitly + input_dict['hda'] = content # TODO: rename key to 'content', prescreen input ensure not populated explicitly except AssertionError: - message = "Invalid workflow input '%s' specified" % inputs[k]['id'] + message = "Invalid workflow input '%s' specified" % input_id raise exceptions.ItemAccessibilityException( message ) # Run each step, connecting outputs to inputs https://bitbucket.org/galaxy/galaxy-central/commits/84caa9526b5f/ Changeset: 84caa9526b5f User: jmchilton Date: 2014-08-10 20:05:31 Summary: Change 'hda' input name in workflow inputs dict to 'content'... ... 'content' better reflects that this can be either an HDA or an HDCA. Affected #: 2 files diff -r 7772ff282e95516a4d39ef0a87afeabb8b123d23 -r 84caa9526b5fe407718082dcdd7c8b65cb210175 lib/galaxy/workflow/run.py --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -224,7 +224,7 @@ else: raise Exception("Unknown history content encountered") if self.inputs: - outputs[ step.id ][ 'output' ] = self.inputs_by_step_id[ step.id ][ 'hda' ] + outputs[ step.id ][ 'output' ] = self.inputs_by_step_id[ step.id ][ 'content' ] return job diff -r 7772ff282e95516a4d39ef0a87afeabb8b123d23 -r 84caa9526b5fe407718082dcdd7c8b65cb210175 lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -63,6 +63,9 @@ if 'id' not in input_dict: message = "Not input id defined for input '%s'." % input_dict raise exceptions.RequestParameterInvalidException( message ) + if 'content' in input_dict: + message = "Input cannot specify explicit 'content' attribute %s'." % input_dict + raise exceptions.RequestParameterInvalidException( message ) input_source = input_dict['src'] input_id = input_dict['id'] try: @@ -96,7 +99,7 @@ history.add_dataset( content ) else: history.add_dataset_collection( content ) - input_dict['hda'] = content # TODO: rename key to 'content', prescreen input ensure not populated explicitly + input_dict['content'] = content except AssertionError: message = "Invalid workflow input '%s' specified" % input_id raise exceptions.ItemAccessibilityException( message ) https://bitbucket.org/galaxy/galaxy-central/commits/483ceff2d2b6/ Changeset: 483ceff2d2b6 User: jmchilton Date: 2014-08-10 20:05:31 Summary: Normalize workflow step parameters earlier... ... this will allow linking to actual steps (referential integrity) if/when we store workflow requests in the database. Also unit tests. Affected #: 4 files diff -r 84caa9526b5fe407718082dcdd7c8b65cb210175 -r 483ceff2d2b6f41432cd16f4dbf539355c3f4dde lib/galaxy/workflow/run.py --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -41,9 +41,9 @@ that step ('name'). :type inputs_by: str - :param param_map: Override tool and/or step parameters (see documentation on - _update_step_parameters below). - :type param_map: + :param param_map: Override step parameters - should be dict with step id keys and + tool param name-value dicts as values. + :type param_map: dict """ def __init__( self, target_history, replacement_dict, copy_inputs_to_history=False, inputs={}, inputs_by='step_id', param_map={} ): @@ -304,36 +304,9 @@ self.inputs_by_step_id[ step.id ] = self.inputs[ key ] -def _update_step_parameters(step, param_map): - """ - Update ``step`` parameters based on the user-provided ``param_map`` dict. - - ``param_map`` should be structured as follows:: - - PARAM_MAP = {STEP_ID: PARAM_DICT, ...} - PARAM_DICT = {NAME: VALUE, ...} - - For backwards compatibility, the following (deprecated) format is - also supported for ``param_map``:: - - PARAM_MAP = {TOOL_ID: PARAM_DICT, ...} - - in which case PARAM_DICT affects all steps with the given tool id. - If both by-tool-id and by-step-id specifications are used, the - latter takes precedence. - - Finally (again, for backwards compatibility), PARAM_DICT can also - be specified as:: - - PARAM_DICT = {'param': NAME, 'value': VALUE} - - Note that this format allows only one parameter to be set per step. - """ - param_dict = param_map.get(step.tool_id, {}).copy() - param_dict.update(param_map.get(str(step.id), {})) +def _update_step_parameters(step, normalized_param_map): + param_dict = normalized_param_map.get(step.id, {}) if param_dict: - if 'param' in param_dict and 'value' in param_dict: - param_dict[param_dict['param']] = param_dict['value'] step.state.inputs.update(param_dict) diff -r 84caa9526b5fe407718082dcdd7c8b65cb210175 -r 483ceff2d2b6f41432cd16f4dbf539355c3f4dde lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -4,12 +4,62 @@ from galaxy.workflow.run import WorkflowRunConfig +def normalize_step_parameters(steps, param_map): + """ Take a complex param_map that can reference parameters by + step_id in the new flexible way or in the old one-parameter + per tep fashion or by tool id and normalize the parameters so + everything is referenced by a numeric step id. + """ + normalized_param_map = {} + for step in steps: + param_dict = _step_parameters(step, param_map) + if param_dict: + normalized_param_map[step.id] = param_dict + return normalized_param_map + + +def _step_parameters(step, param_map): + """ + Update ``step`` parameters based on the user-provided ``param_map`` dict. + + ``param_map`` should be structured as follows:: + + PARAM_MAP = {STEP_ID: PARAM_DICT, ...} + PARAM_DICT = {NAME: VALUE, ...} + + For backwards compatibility, the following (deprecated) format is + also supported for ``param_map``:: + + PARAM_MAP = {TOOL_ID: PARAM_DICT, ...} + + in which case PARAM_DICT affects all steps with the given tool id. + If both by-tool-id and by-step-id specifications are used, the + latter takes precedence. + + Finally (again, for backwards compatibility), PARAM_DICT can also + be specified as:: + + PARAM_DICT = {'param': NAME, 'value': VALUE} + + Note that this format allows only one parameter to be set per step. + """ + param_dict = param_map.get(step.tool_id, {}).copy() + param_dict.update(param_map.get(str(step.id), {})) + if param_dict: + if 'param' in param_dict and 'value' in param_dict: + param_dict[param_dict['param']] = param_dict['value'] + del param_dict[ 'param' ] + del param_dict[ 'value' ] + return param_dict + + def build_workflow_run_config( trans, workflow, payload ): app = trans.app history_manager = histories.HistoryManager() # Pull other parameters out of payload. param_map = payload.get( 'parameters', {} ) + param_map = normalize_step_parameters( workflow.steps, param_map ) inputs = payload.get( 'inputs', None ) inputs_by = payload.get( 'inputs_by', None ) if inputs is None: diff -r 84caa9526b5fe407718082dcdd7c8b65cb210175 -r 483ceff2d2b6f41432cd16f4dbf539355c3f4dde test/unit/workflows/test_run_parameters.py --- /dev/null +++ b/test/unit/workflows/test_run_parameters.py @@ -0,0 +1,84 @@ +from .workflow_support import MockTrans + +from galaxy import model +from galaxy.workflow.run_request import normalize_step_parameters + + +def test_normalize_parameters_empty(): + normalized_params = __normalize_parameters_against_fixture( {} ) + assert normalized_params == {} + + +def test_normalize_parameters_by_tool(): + normalized_params = __normalize_parameters_against_fixture( { + 'cat1': { 'foo': 'bar' } + } ) + # Tool specified parameters are expanded out. + assert normalized_params[ 3 ] == { 'foo': 'bar' } + assert normalized_params[ 4 ] == { 'foo': 'bar' } + assert len( normalized_params.keys() ) == 2 + + +def test_step_parameters(): + normalized_params = __normalize_parameters_against_fixture( { + '1': { 'foo': 'bar' } + } ) + assert normalized_params[ 1 ] == { 'foo': 'bar' } + assert len( normalized_params.keys() ) == 1 + + +def test_step_parameters_legacy(): + normalized_params = __normalize_parameters_against_fixture( { + '1': { 'param': 'foo', 'value': 'bar' } + } ) + assert normalized_params[ 1 ] == { 'foo': 'bar' }, normalized_params + assert len( normalized_params.keys() ) == 1 + + +def __normalize_parameters_against_fixture( params ): + trans = MockTrans() + workflow = __workflow_fixure( trans ) + normalized_params = normalize_step_parameters( workflow.steps, params ) + return normalized_params + + +def __workflow_fixure( trans ): + user = model.User( + email="testworkflow_params(a)bx.psu.edu", + password="pass" + ) + stored_workflow = model.StoredWorkflow() + stored_workflow.user = user + workflow = model.Workflow() + workflow.stored_workflow = stored_workflow + + def add_step( **kwds ): + workflow_step = model.WorkflowStep() + for key, value in kwds.iteritems(): + setattr(workflow_step, key, value) + workflow.steps.append( workflow_step ) + + trans.app.model.context.add( + workflow, + ) + + add_step( + type="input", + order_index=0, + ) + add_step( + type="input", + order_index=1, + ) + add_step( + type="tool", + tool_id="cat1", + order_index=2, + ) + add_step( + type="tool", + tool_id="cat1", + order_index=4, + ) + trans.app.model.context.flush() + return workflow diff -r 84caa9526b5fe407718082dcdd7c8b65cb210175 -r 483ceff2d2b6f41432cd16f4dbf539355c3f4dde test/unit/workflows/workflow_support.py --- /dev/null +++ b/test/unit/workflows/workflow_support.py @@ -0,0 +1,19 @@ +from galaxy.util import bunch +from galaxy.model import mapping + + +class MockTrans( object ): + + def __init__( self ): + self.app = TestApp() + + +class TestApp( object ): + + def __init__( self ): + self.config = bunch.Bunch( ) + self.model = mapping.init( + "/tmp", + "sqlite:///:memory:", + create_tables=True + ) https://bitbucket.org/galaxy/galaxy-central/commits/9664ed5cbb9f/ Changeset: 9664ed5cbb9f User: jmchilton Date: 2014-08-10 20:05:31 Summary: Normalize workflow input dataset dict earlier... ... this will allow linking to actual steps (referential integrity) if/when we store workflow requests in the database and failing faster. Also more unit tests. Affected #: 3 files diff -r 483ceff2d2b6f41432cd16f4dbf539355c3f4dde -r 9664ed5cbb9fa654da1972772b5a3065450d2a15 lib/galaxy/workflow/run.py --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -46,12 +46,11 @@ :type param_map: dict """ - def __init__( self, target_history, replacement_dict, copy_inputs_to_history=False, inputs={}, inputs_by='step_id', param_map={} ): + def __init__( self, target_history, replacement_dict, copy_inputs_to_history=False, inputs={}, param_map={} ): self.target_history = target_history self.replacement_dict = replacement_dict self.copy_inputs_to_history = copy_inputs_to_history self.inputs = inputs - self.inputs_by = inputs_by self.param_map = param_map @@ -73,9 +72,7 @@ self.target_history = workflow_run_config.target_history self.replacement_dict = workflow_run_config.replacement_dict self.copy_inputs_to_history = workflow_run_config.copy_inputs_to_history - self.inputs = workflow_run_config.inputs - self.inputs_by = workflow_run_config.inputs_by - self.inputs_by_step_id = {} + self.inputs_by_step_id = workflow_run_config.inputs self.param_map = workflow_run_config.param_map self.outputs = odict() @@ -223,8 +220,8 @@ outputs[ step.id ][ 'input_ds_copy' ] = new_hdca else: raise Exception("Unknown history content encountered") - if self.inputs: - outputs[ step.id ][ 'output' ] = self.inputs_by_step_id[ step.id ][ 'content' ] + if self.inputs_by_step_id: + outputs[ step.id ][ 'output' ] = self.inputs_by_step_id[ step.id ] return job @@ -289,20 +286,6 @@ step.module = modules.module_factory.from_workflow_step( self.trans, step ) step.state = step.module.get_runtime_state() - # This is an input step. Make sure we have an available input. - if step.type in [ 'data_input', 'data_collection_input' ]: - if self.inputs_by == "step_id": - key = str( step.id ) - elif self.inputs_by == "name": - key = step.tool_inputs.get( 'name', None ) - else: - key = str( step.order_index ) - if key not in self.inputs: - message = "Workflow cannot be run because an expected input step '%s' has no input dataset." % step.id - raise exceptions.MessageException( message ) - else: - self.inputs_by_step_id[ step.id ] = self.inputs[ key ] - def _update_step_parameters(step, normalized_param_map): param_dict = normalized_param_map.get(step.id, {}) diff -r 483ceff2d2b6f41432cd16f4dbf539355c3f4dde -r 9664ed5cbb9fa654da1972772b5a3065450d2a15 lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -3,6 +3,32 @@ from galaxy.managers import histories from galaxy.workflow.run import WorkflowRunConfig +INPUT_STEP_TYPES = [ 'data_input', 'data_collection_input' ] + + +def normalize_inputs(steps, inputs, inputs_by): + normalized_inputs = {} + for step in steps: + 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 == "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: + message = "Workflow cannot be run because an expected input step '%s' has no input dataset." % step.id + raise exceptions.MessageException( message ) + + normalized_inputs[ step.id ] = inputs[ inputs_key ][ 'content' ] + + return normalized_inputs + def normalize_step_parameters(steps, param_map): """ Take a complex param_map that can reference parameters by @@ -74,13 +100,6 @@ # of Galaxy at the time of workflow import. inputs_by = inputs_by or 'step_index' - valid_inputs_by = [ 'step_id', 'step_index', 'name' ] - if inputs_by not in valid_inputs_by: - trans.response.status = 403 - error_message_template = "Invalid inputs_by specified '%s' must be one of %s" - error_message = error_message_template % ( inputs_by, valid_inputs_by ) - raise ValueError( error_message ) - add_to_history = 'no_add_to_history' not in payload history_param = payload.get('history', '') @@ -154,14 +173,15 @@ message = "Invalid workflow input '%s' specified" % input_id raise exceptions.ItemAccessibilityException( message ) + normalized_inputs = normalize_inputs( workflow.steps, inputs, inputs_by ) + # Run each step, connecting outputs to inputs replacement_dict = payload.get('replacement_params', {}) run_config = WorkflowRunConfig( target_history=history, replacement_dict=replacement_dict, - inputs=inputs, - inputs_by=inputs_by, + inputs=normalized_inputs, param_map=param_map, ) return run_config diff -r 483ceff2d2b6f41432cd16f4dbf539355c3f4dde -r 9664ed5cbb9fa654da1972772b5a3065450d2a15 test/unit/workflows/test_run_parameters.py --- a/test/unit/workflows/test_run_parameters.py +++ b/test/unit/workflows/test_run_parameters.py @@ -2,6 +2,9 @@ from galaxy import model from galaxy.workflow.run_request import normalize_step_parameters +from galaxy.workflow.run_request import normalize_inputs + +STEP_ID_OFFSET = 4 # Offset a little so ids and order index are different. def test_normalize_parameters_empty(): @@ -14,34 +17,87 @@ 'cat1': { 'foo': 'bar' } } ) # Tool specified parameters are expanded out. - assert normalized_params[ 3 ] == { 'foo': 'bar' } - assert normalized_params[ 4 ] == { 'foo': 'bar' } + assert normalized_params[ STEP_ID_OFFSET + 3 ] == { 'foo': 'bar' } + assert normalized_params[ STEP_ID_OFFSET + 4 ] == { 'foo': 'bar' } assert len( normalized_params.keys() ) == 2 def test_step_parameters(): normalized_params = __normalize_parameters_against_fixture( { - '1': { 'foo': 'bar' } + str( STEP_ID_OFFSET + 1 ): { 'foo': 'bar' } } ) - assert normalized_params[ 1 ] == { 'foo': 'bar' } + assert normalized_params[ STEP_ID_OFFSET + 1 ] == { 'foo': 'bar' } assert len( normalized_params.keys() ) == 1 def test_step_parameters_legacy(): normalized_params = __normalize_parameters_against_fixture( { - '1': { 'param': 'foo', 'value': 'bar' } + str( STEP_ID_OFFSET + 1 ): { 'param': 'foo', 'value': 'bar' } } ) - assert normalized_params[ 1 ] == { 'foo': 'bar' }, normalized_params + assert normalized_params[ STEP_ID_OFFSET + 1 ] == { 'foo': 'bar' }, normalized_params assert len( normalized_params.keys() ) == 1 +def test_inputs_by_step_id(): + input1 = __new_input() + input2 = __new_input() + normalized_inputs = __normalize_inputs_against_fixture( { + str( STEP_ID_OFFSET + 1 ): input1, + str( STEP_ID_OFFSET + 2 ): input2 + }, inputs_by="step_id" ) + assert normalized_inputs[ STEP_ID_OFFSET + 1 ] == input1[ 'content' ] + assert normalized_inputs[ STEP_ID_OFFSET + 2 ] == input2[ 'content' ] + + +def test_inputs_by_step_index(): + input1 = __new_input() + input2 = __new_input() + normalized_inputs = __normalize_inputs_against_fixture( { + str( 0 ): input1, + str( 1 ): input2 + }, inputs_by="step_index" ) + assert normalized_inputs[ STEP_ID_OFFSET + 1 ] == input1[ 'content' ] + assert normalized_inputs[ STEP_ID_OFFSET + 2 ] == input2[ 'content' ] + + +def test_inputs_by_name(): + input1 = __new_input() + input2 = __new_input() + normalized_inputs = __normalize_inputs_against_fixture( { + "input1": input1, + "input2": input2 + }, inputs_by="name" ) + print normalized_inputs + assert normalized_inputs[ STEP_ID_OFFSET + 1 ] == input1[ 'content' ] + assert normalized_inputs[ STEP_ID_OFFSET + 2 ] == input2[ 'content' ] + + def __normalize_parameters_against_fixture( params ): trans = MockTrans() + # Create a throw away workflow so step ids and order_index + # are different for actual fixture. + __workflow_fixure( trans ) + workflow = __workflow_fixure( trans ) normalized_params = normalize_step_parameters( workflow.steps, params ) return normalized_params +def __normalize_inputs_against_fixture( inputs, inputs_by ): + trans = MockTrans() + # Create a throw away workflow so step ids and order_index + # are different for actual fixture. + __workflow_fixure( trans ) + + workflow = __workflow_fixure( trans ) + normalized_inputs = normalize_inputs( workflow.steps, inputs, inputs_by ) + return normalized_inputs + + +def __new_input( ): + return dict( content=model.HistoryDatasetAssociation() ) + + def __workflow_fixure( trans ): user = model.User( email="testworkflow_params(a)bx.psu.edu", @@ -63,12 +119,14 @@ ) add_step( - type="input", + type="data_input", order_index=0, + tool_inputs={"name": "input1"} ) add_step( - type="input", + type="data_input", order_index=1, + tool_inputs={"name": "input2"} ) add_step( type="tool", @@ -81,4 +139,8 @@ order_index=4, ) trans.app.model.context.flush() - return workflow + # Expunge and reload to ensure step state is as expected from database. + workflow_id = workflow.id + trans.app.model.context.expunge_all() + + return trans.app.model.context.query( model.Workflow ).get( workflow_id ) https://bitbucket.org/galaxy/galaxy-central/commits/bdc4017c2e7e/ Changeset: bdc4017c2e7e User: jmchilton Date: 2014-08-10 20:05:31 Summary: Move WorkflowConfig so run_request doesn't need to import run. This is a more logical organization of these modules. Affected #: 2 files diff -r 9664ed5cbb9fa654da1972772b5a3065450d2a15 -r bdc4017c2e7e9ecb5dfa3d36798f535402ec80aa lib/galaxy/workflow/run.py --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -13,47 +13,12 @@ from galaxy.tools.execute import execute from galaxy.util.odict import odict from galaxy.workflow import modules +from galaxy.workflow.run_request import WorkflowRunConfig import logging log = logging.getLogger( __name__ ) -class WorkflowRunConfig( object ): - """ Wrapper around all the ways a workflow execution can be parameterized. - - :param target_history: History to execute workflow in. - :type target_history: galaxy.model.History. - - :param replacement_dict: Workflow level parameters used for renaming post - job actions. - :type replacement_dict: dict - - :param copy_inputs_to_history: Should input data parameters be copied to - target_history. (Defaults to False) - :type copy_inputs_to_history: bool - - :param inputs: Map from step ids to dict's containing HDA for these steps. - :type inputs: dict - - :param inputs_by: How inputs maps to inputs (datasets/collections) to workflows - steps - by unencoded database id ('step_id'), index in workflow - 'step_index' (independent of database), or by input name for - that step ('name'). - :type inputs_by: str - - :param param_map: Override step parameters - should be dict with step id keys and - tool param name-value dicts as values. - :type param_map: dict - """ - - def __init__( self, target_history, replacement_dict, copy_inputs_to_history=False, inputs={}, param_map={} ): - self.target_history = target_history - self.replacement_dict = replacement_dict - self.copy_inputs_to_history = copy_inputs_to_history - self.inputs = inputs - self.param_map = param_map - - def invoke( trans, workflow, workflow_run_config ): """ Run the supplied workflow in the supplied target_history. """ diff -r 9664ed5cbb9fa654da1972772b5a3065450d2a15 -r bdc4017c2e7e9ecb5dfa3d36798f535402ec80aa lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -1,11 +1,46 @@ from galaxy import exceptions from galaxy.managers import histories -from galaxy.workflow.run import WorkflowRunConfig INPUT_STEP_TYPES = [ 'data_input', 'data_collection_input' ] +class WorkflowRunConfig( object ): + """ Wrapper around all the ways a workflow execution can be parameterized. + + :param target_history: History to execute workflow in. + :type target_history: galaxy.model.History. + + :param replacement_dict: Workflow level parameters used for renaming post + job actions. + :type replacement_dict: dict + + :param copy_inputs_to_history: Should input data parameters be copied to + target_history. (Defaults to False) + :type copy_inputs_to_history: bool + + :param inputs: Map from step ids to dict's containing HDA for these steps. + :type inputs: dict + + :param inputs_by: How inputs maps to inputs (datasets/collections) to workflows + steps - by unencoded database id ('step_id'), index in workflow + 'step_index' (independent of database), or by input name for + that step ('name'). + :type inputs_by: str + + :param param_map: Override step parameters - should be dict with step id keys and + tool param name-value dicts as values. + :type param_map: dict + """ + + def __init__( self, target_history, replacement_dict, copy_inputs_to_history=False, inputs={}, param_map={} ): + self.target_history = target_history + self.replacement_dict = replacement_dict + self.copy_inputs_to_history = copy_inputs_to_history + self.inputs = inputs + self.param_map = param_map + + def normalize_inputs(steps, inputs, inputs_by): normalized_inputs = {} for step in steps: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: refine label track position calculation.
by commits-noreply＠bitbucket.org 10 Aug '14

10 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d85ae37476a1/ Changeset: d85ae37476a1 Branch: next-stable User: jgoecks Date: 2014-08-09 21:38:33 Summary: Trackster: refine label track position calculation. Affected #: 2 files diff -r 990bc0688199410ab08d5e8a418770b516c6f4e2 -r d85ae37476a17205c9869d633f3aafd104b48a98 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/viz_views","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(ab,w,V,j,s,J,h,X,P,R){var o=ab.extend;var l={};var i=function(ac,ad){l[ac.attr("id")]=ad};var k=function(ac,ad,af,ae){af=".group";l[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=l[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=l[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}l[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);l[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));l[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. 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Y=Backbone.View.extend({initialize:function(ac){o(ac,{obj_type:"View"});y.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ac.name})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container);var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(n(ah,ac,ac))})})});this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})},minLength:2})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get_value(ac.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){this.intro_div.toggle(this.drawables.length===0)},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=v;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new B(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-v});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+v});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad===undefined&&aj===undefined){ae.low=0;ae.high=ae.max_high}else{ae.low=(ad!==undefined?Math.max(ad,0):0);if(aj===undefined){ae.low=Math.max(ae.low-15,0);ae.high=ae.low+30}else{ae.high=Math.min(aj,ae.max_high)}}ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):undefined),ac=(ad[2]?parseInt(ad[2],10):undefined);this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div();var ac=this;ad.config.on("change",function(){ac.changed()})},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){y.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport();this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ac){P.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new t({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new w.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new N(view,view,{name:ad.config.get_value("name")});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(x+ag.message)}else{af(ag)}}})}});var C=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ac,af,ag,ad,ae){b.call(this,ac,af,ag,ad,ae)};K.prototype.predisplay_actions=function(){};var M=function(ae,aj,al,ad,ag,ah,am,ac,ai,af,ak){b.call(this,ae,aj,al,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ai;this.has_icons=false;this.incomplete_features=af;this.other_tiles_features_drawn={};this.seq_data=ak};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){};var f=function(ad,ac,ae){o(ae,{drag_handle_class:"draghandle"});p.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.data_manager=("data_manager" in ae?ae.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.config.get_value("name")+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new w.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.config.get_value("content_visible")){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.set_value("height",ac.visible_height_px);ac.changed()}).appendTo(ac.container_div)},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(m);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(H)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(u);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(T);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_default_value("min_value",ae);ac.config.set_default_value("max_value",ag);ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},get_drawables:function(){return this}});var L=function(ae,ad,ag){f.call(this,ae,ad,ag);var ac=this;k(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new h.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new q(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();o(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.config.get_value("min_value")))||isNaN(parseFloat(ac.config.get_value("max_value")))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.set_value("mode",ad);if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;ac.action_icons.filters_icon.toggle(ac.filters_available);ac.action_icons.tools_icon.toggle(ac.tool!==null);ac.action_icons.param_space_viz_icon.toggle(ac.tool!==null)},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ak=Math.floor(Q*af),ac=Math.floor(al/ak),am,ah,ai=[],ao=[];while((ac*ak)<ag){am=new w.GenomeRegion({chrom:this.view.chrom,start:ac*ak,end:Math.min((ac+1)*ak,this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.config.get_value(ac))}else{ae=$("<div/>").text(ad.config.get_value(ac)).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.config.get_value("label_color"));this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof K)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof K)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",D)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(A,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(ab.find(ap,function(aD){return j.is_deferred(aD)})){ae.tile_cache.set_elt(am,undefined);$.when(ae.draw_helper(al,an,ao)).then(function(aD){ac.resolve(aD)});return}if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new K(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=Math.round((ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah);if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){f.call(this,ad,ac,{resize:false,header:false});this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var e=function(ad,ac,ag){L.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=n(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof c||ah instanceof S){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ac=this.visible_height_px;ab.each(this.drawables,function(ad){ad.visible_height_px=ac});f.prototype.on_resize.call(this)},change_mode:function(ac){L.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new N(this.view,this.container,{name:this.config.get_value("name")}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){var ad=ab.min(ab.map(this.drawables,function(ae){return ae.config.get_value("min_value")})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.config.get_value("max_value")}));this.config.set_value("min_value",ad);this.config.set_value("max_value",ac);ab.each(this.drawables,function(ae){ae.config.set_value("min_value",ad);ae.config.set_value("max_value",ac)})},update_all_min_max:function(){var ad=this,ac=this.config.get_value("min_value"),ae=this.config.get_value("max_value");ab.each(this.drawables,function(af){af.config.set_value("min_value",ac);af.config.set_value("max_value",ae)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var B=function(ac){L.call(this,ac,{content_div:ac.top_labeltrack},{resize:false,header:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ah,ad){var ac=this.tiles_div.is(":visible"),ag,ae=null;if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();ag=true;ae=L.prototype.draw_helper.call(this,af,ah,ad)}else{ag=false;this.tiles_div.hide()}if(ac!==ag){this.view.resize_viewport()}return ae},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new b(this,ah,al,ac,ad)}});var g=function(ad,ac,ae){this.mode="Histogram";L.call(this,ad,ac,ae)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ad,ac,ae){this.mode="Heatmap";L.call(this,ad,ac,ae)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:ab.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new b(this,ag,ai,af,ac.data)}});var c=function(ad,ac,ae){L.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(ao,af,aq,an){L.prototype.postdraw_actions.call(this,ao,af,aq,an);var ah=this,ai,am=ab.filter(ao,function(ar){return(ar instanceof K)});if(am.length===0){var ac={};ab.each(ab.pluck(ao,"incomplete_features"),function(ar){ab.each(ar,function(at){ac[at[0]]=at})});var ap=this;ab.each(ao,function(av){var aw=ab.omit(ac,ab.map(av.incomplete_features,function(ay){return ay[0]}));aw=ab.omit(aw,ab.keys(av.other_tiles_features_drawn));if(ab.size(aw)!==0){var at={data:ab.values(aw)},au=ap.view.canvas_manager.new_canvas(),ar=au.getContext("2d");au.height=Math.max(av.canvas.height,ap.get_canvas_height(at,av.mode,av.w_scale,100));au.width=av.canvas.width;ar.drawImage(av.canvas,0,0);ar.translate(ah.left_offset,0);var ax=ap.draw_tile(at,ar,av.mode,av.region,av.w_scale,av.seq_data);$(av.canvas).replaceWith($(ax.canvas));av.canvas=au;ab.extend(av.other_tiles_features_drawn,ac)}})}if(ah.filters_manager){var ag=ah.filters_manager.filters,ak;for(ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<ao.length;ai++){if(ao[ai].data.length){al=ao[ai].data[0];for(ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(ao[0] instanceof M){var ad=true;for(ai=0;ai<ao.length;ai++){if(!ao[ai].all_slotted){ad=false;break}}this.action_icons.show_more_rows_icon.toggle(!ad)}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,z,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(an,at,aq,ag,ak,af,ao){var ar=this,ae=at.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,at,aq,ag,ak)}var aj=[],ap=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ap)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.config.to_key_value_dict(),aq,aC,aA,af,function(aE){return ar.view.get_base_color(aE)});var ax=null;at.fillStyle=this.config.get_value("block_color");at.font=at.canvas.manager.default_font;at.textAlign="right";if(an.data){var ac=aB.draw(at,ae.width,ae.height,ak,ap);ax=ac.feature_mapper;incomplete_features=ac.incomplete_features;ax.translation=-ah}if(!ao){return new M(ar,ag,ak,ae,an.data,aq,an.message,all_slotted,ax,incomplete_features,af)}}});var Z=function(ad,ac,ae){L.call(this,ad,ac,ae);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new b(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){L.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof K)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.config.get_value("show_labels")&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.config.get_value("summary_height")-ac)/2+"px"}));if(this.config.get_value("show_sample_data")){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ad,ac,ae){c.call(this,ad,ac,ae);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Z,VcfTrack:Z};var n=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/viz_views","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(ab,w,V,j,s,J,h,X,P,R){var o=ab.extend;var l={};var i=function(ac,ad){l[ac.attr("id")]=ad};var k=function(ac,ad,af,ae){af=".group";l[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=l[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=l[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}l[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);l[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));l[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var p=function(ad,ac,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ag.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ag.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=null;if(ag.header!==false){var ae=new V.TrackHeaderView({model:this,id:this.id});this.header_div=ae.$el;this.container_div.append(this.header_div);var af=ae.icons_div;this.action_icons=ae.action_icons;this.container_div.hover(function(){af.show()},function(){af.hide()})}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.config.get_value("content_visible")){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.config.set_value("content_visible",false)}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.config.set_value("content_visible",true);ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ad){var ac=new R.ConfigSettingCollectionView({collection:ad.config});ac.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.config.get_value("name");this.config.set_value("name",ac)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ad,ac,ae){p.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=n(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var N=function(ad,ac,af){o(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.filters_manager.parent_div.after($("<div style='clear: both'/>"));this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new h.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){this.action_icons.composite_icon.toggle(this.drawables[0] instanceof e);this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new h.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){y.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){o(ac,{obj_type:"View"});y.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ac.name})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container);var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(n(ah,ac,ac))})})});this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})},minLength:2})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get_value(ac.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){this.intro_div.toggle(this.drawables.length===0)},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=v;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new B(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-v});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+v});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad===undefined&&aj===undefined){ae.low=0;ae.high=ae.max_high}else{ae.low=(ad!==undefined?Math.max(ad,0):0);if(aj===undefined){ae.low=Math.max(ae.low-15,0);ae.high=ae.low+30}else{ae.high=Math.min(aj,ae.max_high)}}ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):undefined),ac=(ad[2]?parseInt(ad[2],10):undefined);this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div();var ac=this;ad.config.on("change",function(){ac.changed()})},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){y.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport();this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ac){P.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new t({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new w.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new N(view,view,{name:ad.config.get_value("name")});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(x+ag.message)}else{af(ag)}}})}});var C=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ac,af,ag,ad,ae){b.call(this,ac,af,ag,ad,ae)};K.prototype.predisplay_actions=function(){};var M=function(ae,aj,al,ad,ag,ah,am,ac,ai,af,ak){b.call(this,ae,aj,al,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ai;this.has_icons=false;this.incomplete_features=af;this.other_tiles_features_drawn={};this.seq_data=ak};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){};var f=function(ad,ac,ae){o(ae,{drag_handle_class:"draghandle"});p.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.data_manager=("data_manager" in ae?ae.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.config.get_value("name")+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new w.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.config.get_value("content_visible")){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.set_value("height",ac.visible_height_px);ac.changed()}).appendTo(ac.container_div)},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(m);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(H)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(u);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(T);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_default_value("min_value",ae);ac.config.set_default_value("max_value",ag);ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},get_drawables:function(){return this}});var L=function(ae,ad,ag){f.call(this,ae,ad,ag);var ac=this;k(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new h.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new q(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();o(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.config.get_value("min_value")))||isNaN(parseFloat(ac.config.get_value("max_value")))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.set_value("mode",ad);if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;ac.action_icons.filters_icon.toggle(ac.filters_available);ac.action_icons.tools_icon.toggle(ac.tool!==null);ac.action_icons.param_space_viz_icon.toggle(ac.tool!==null)},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ak=Math.floor(Q*af),ac=Math.floor(al/ak),am,ah,ai=[],ao=[];while((ac*ak)<ag){am=new w.GenomeRegion({chrom:this.view.chrom,start:ac*ak,end:Math.min((ac+1)*ak,this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.config.get_value(ac))}else{ae=$("<div/>").text(ad.config.get_value(ac)).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.config.get_value("label_color"));this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof K)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof K)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",D)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(A,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(ab.find(ap,function(aD){return j.is_deferred(aD)})){ae.tile_cache.set_elt(am,undefined);$.when(ae.draw_helper(al,an,ao)).then(function(aD){ac.resolve(aD)});return}if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new K(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=Math.round((ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah);if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){f.call(this,ad,ac,{resize:false,header:false});this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=Math.floor((ac-ae.low)/af*ah);ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var e=function(ad,ac,ag){L.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=n(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof c||ah instanceof S){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ac=this.visible_height_px;ab.each(this.drawables,function(ad){ad.visible_height_px=ac});f.prototype.on_resize.call(this)},change_mode:function(ac){L.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new N(this.view,this.container,{name:this.config.get_value("name")}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){var ad=ab.min(ab.map(this.drawables,function(ae){return ae.config.get_value("min_value")})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.config.get_value("max_value")}));this.config.set_value("min_value",ad);this.config.set_value("max_value",ac);ab.each(this.drawables,function(ae){ae.config.set_value("min_value",ad);ae.config.set_value("max_value",ac)})},update_all_min_max:function(){var ad=this,ac=this.config.get_value("min_value"),ae=this.config.get_value("max_value");ab.each(this.drawables,function(af){af.config.set_value("min_value",ac);af.config.set_value("max_value",ae)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var B=function(ac){L.call(this,ac,{content_div:ac.top_labeltrack},{resize:false,header:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ah,ad){var ac=this.tiles_div.is(":visible"),ag,ae=null;if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();ag=true;ae=L.prototype.draw_helper.call(this,af,ah,ad)}else{ag=false;this.tiles_div.hide()}if(ac!==ag){this.view.resize_viewport()}return ae},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new b(this,ah,al,ac,ad)}});var g=function(ad,ac,ae){this.mode="Histogram";L.call(this,ad,ac,ae)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ad,ac,ae){this.mode="Heatmap";L.call(this,ad,ac,ae)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:ab.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new b(this,ag,ai,af,ac.data)}});var c=function(ad,ac,ae){L.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with 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ad=true;for(ai=0;ai<ao.length;ai++){if(!ao[ai].all_slotted){ad=false;break}}this.action_icons.show_more_rows_icon.toggle(!ad)}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,z,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new 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ax=null;at.fillStyle=this.config.get_value("block_color");at.font=at.canvas.manager.default_font;at.textAlign="right";if(an.data){var ac=aB.draw(at,ae.width,ae.height,ak,ap);ax=ac.feature_mapper;incomplete_features=ac.incomplete_features;ax.translation=-ah}if(!ao){return new M(ar,ag,ak,ae,an.data,aq,an.message,all_slotted,ax,incomplete_features,af)}}});var Z=function(ad,ac,ae){L.call(this,ad,ac,ae);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary 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(this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){L.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof K)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.config.get_value("show_labels")&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.config.get_value("summary_height")-ac)/2+"px"}));if(this.config.get_value("show_sample_data")){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top 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only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Z,VcfTrack:Z};var n=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file diff -r 990bc0688199410ab08d5e8a418770b516c6f4e2 -r d85ae37476a17205c9869d633f3aafd104b48a98 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3242,7 +3242,7 @@ width = this.view.container.width(), new_div = $("<div/>").addClass('label-container'); while ( position < view.high ) { - var screenPosition = ( position - view.low ) / range * width; + var screenPosition = Math.floor( ( position - view.low ) / range * width ); new_div.append( $("<div/>").addClass('label').text(commatize( position )).css( { left: screenPosition })); 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 jmchilton/galaxy-central-fork-1 (pull request #452)
by commits-noreply＠bitbucket.org 09 Aug '14

09 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/de2e33813275/ Changeset: de2e33813275 User: jmchilton Date: 2014-08-09 15:15:11 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #452) More RESTful workflow API (attempt 3) Affected #: 4 files diff -r fcbd2849ebd17a80e66e0fbdac9df7bb37f88fa2 -r de2e33813275b89a04e7de4e95b21f6d2e100d4e lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1664,7 +1664,7 @@ session.flush() return imported_stored - def _workflow_from_dict( self, trans, data, source=None, add_to_menu=False ): + def _workflow_from_dict( self, trans, data, source=None, add_to_menu=False, publish=False ): """ Creates a workflow from a dict. Created workflow is stored in the database and returned. """ @@ -1752,6 +1752,7 @@ workflow.stored_workflow = stored stored.latest_workflow = workflow stored.user = trans.user + stored.published = publish if data[ 'annotation' ]: self.add_item_annotation( trans.sa_session, stored.user, stored, data[ 'annotation' ] ) diff -r fcbd2849ebd17a80e66e0fbdac9df7bb37f88fa2 -r de2e33813275b89a04e7de4e95b21f6d2e100d4e lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -6,11 +6,13 @@ import logging from sqlalchemy import desc, or_ -from galaxy import exceptions, util, web +from galaxy import exceptions, util from galaxy.model.item_attrs import UsesAnnotations +from galaxy.managers import histories from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin from galaxy.web.base.controller import UsesHistoryMixin +from galaxy.web.base.controller import SharableMixin from galaxy.workflow.extract import extract_workflow from galaxy.workflow.run import invoke from galaxy.workflow.run import WorkflowRunConfig @@ -18,9 +20,13 @@ log = logging.getLogger(__name__) -class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin, UsesAnnotations): +class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin, UsesAnnotations, SharableMixin): - @web.expose_api + def __init__( self, app ): + super( BaseAPIController, self ).__init__( app ) + self.history_manager = histories.HistoryManager() + + @expose_api def index(self, trans, **kwd): """ GET /api/workflows @@ -54,30 +60,21 @@ rval.append(item) return rval - @web.expose_api + @expose_api def show(self, trans, id, **kwd): """ GET /api/workflows/{encoded_workflow_id} Displays information needed to run a workflow from the command line. """ - workflow_id = id - try: - decoded_workflow_id = trans.security.decode_id(workflow_id) - except TypeError: - trans.response.status = 400 - return "Malformed workflow id ( %s ) specified, unable to decode." % str(workflow_id) - try: - stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).get(decoded_workflow_id) - if stored_workflow.importable is False and stored_workflow.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: - trans.response.status = 400 - return("Workflow is neither importable, nor owned by or shared with current user") - except: - trans.response.status = 400 - return "That workflow does not exist." + stored_workflow = self.__get_stored_workflow( trans, id ) + if stored_workflow.importable is False and stored_workflow.user != trans.user and not trans.user_is_admin(): + 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=workflow_id) + item['url'] = url_for('workflow', id=id) item['owner'] = stored_workflow.user.username latest_workflow = stored_workflow.latest_workflow inputs = {} @@ -114,7 +111,7 @@ item['steps'] = steps return item - @web.expose_api + @expose_api def create(self, trans, payload, **kwd): """ POST /api/workflows @@ -161,10 +158,20 @@ :param workflow_name: If from_history_id is set - name of the workflow to create when extracting a workflow from history :type workflow_name: str """ + ways_to_create = set( [ + 'workflow_id', + 'installed_repository_file', + 'from_history_id', + 'shared_workflow_id', + 'workflow', + ] ).intersection( payload ) + if len( ways_to_create ) == 0: + message = "One parameter among - %s - must be specified" % ", ".join( ways_to_create ) + raise exceptions.RequestParameterMissingException( message ) - if len( set( ['workflow_id', 'installed_repository_file', 'from_history_id'] ).intersection( payload ) ) > 1: - trans.response.status = 403 - return "Only one among 'workflow_id', 'installed_repository_file', 'from_history_id' must be specified" + if len( ways_to_create ) > 1: + message = "Only one parameter among - %s - must be specified" % ", ".join( ways_to_create ) + raise exceptions.RequestParameterInvalidException( message ) if 'installed_repository_file' in payload: workflow_controller = trans.webapp.controllers[ 'workflow' ] @@ -193,10 +200,17 @@ item[ 'url' ] = url_for( 'workflow', id=item[ 'id' ] ) return item + if 'shared_workflow_id' in payload: + workflow_id = payload[ 'shared_workflow_id' ] + return self.__api_import_shared_workflow( trans, workflow_id, payload ) + + if 'workflow' in payload: + return self.__api_import_new_workflow( trans, payload, **kwd ) + workflow_id = payload.get( 'workflow_id', None ) if not workflow_id: - trans.response.status = 403 - return "Either workflow_id, installed_repository_file or from_history_id must be specified" + message = "Invalid workflow_id specified." + raise exceptions.RequestParameterInvalidException( message ) # Pull other parameters out of payload. param_map = payload.get( 'parameters', {} ) @@ -225,34 +239,24 @@ history_param = payload.get('history', '') # Get workflow + accessibility check. - stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id)) - if stored_workflow.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: - trans.response.status = 400 - return("Workflow is not owned by or shared with current user") + stored_workflow = self.__get_stored_accessible_workflow( trans, workflow_id ) workflow = stored_workflow.latest_workflow # Sanity checks. - if not workflow: - trans.response.status = 400 - return "Workflow not found." if len( workflow.steps ) == 0: - trans.response.status = 400 - return "Workflow cannot be run because it does not have any steps" + raise exceptions.MessageException( "Workflow cannot be run because it does not have any steps" ) if workflow.has_cycles: - trans.response.status = 400 - return "Workflow cannot be run because it contains cycles" + raise exceptions.MessageException( "Workflow cannot be run because it contains cycles" ) if workflow.has_errors: - trans.response.status = 400 - return "Workflow cannot be run because of validation errors in some steps" + message = "Workflow cannot be run because of validation errors in some steps" + raise exceptions.MessageException( message ) # Get target history. if history_param.startswith('hist_id='): # Passing an existing history to use. - history = trans.sa_session.query(self.app.model.History).get(trans.security.decode_id(history_param[8:])) - if history.user != trans.user and not trans.user_is_admin(): - trans.response.status = 400 - return "Invalid History specified." + encoded_history_id = history_param[ 8: ] + history_id = self.__decode_id( trans, encoded_history_id, model_type="history" ) + history = self.history_manager.get( trans, history_id, check_ownership=True ) else: # Send workflow outputs to new history. history = self.app.model.History(name=history_param, user=trans.user) @@ -284,8 +288,8 @@ inputs[k]['id'] ) else: - trans.response.status = 400 - return "Unknown dataset source '%s' specified." % inputs[k]['src'] + message = "Unknown workflow input source '%s' specified." % inputs[k]['src'] + raise exceptions.RequestParameterInvalidException( message ) if add_to_history and content.history != history: content = content.copy() if isinstance( content, self.app.model.HistoryDatasetAssociation ): @@ -294,8 +298,8 @@ history.add_dataset_collection( content ) inputs[k]['hda'] = content # TODO: rename key to 'content', prescreen input ensure not populated explicitly except AssertionError: - trans.response.status = 400 - return "Invalid Dataset '%s' Specified" % inputs[k]['id'] + message = "Invalid workflow input '%s' specified" % inputs[k]['id'] + raise exceptions.ItemAccessibilityException( message ) # Run each step, connecting outputs to inputs replacement_dict = payload.get('replacement_params', {}) @@ -308,6 +312,8 @@ param_map=param_map, ) + # invoke may throw MessageExceptions on tool erors, failure + # to match up inputs, etc... outputs = invoke( trans=trans, workflow=workflow, @@ -327,30 +333,22 @@ return rval - @web.expose_api + @expose_api def workflow_dict( self, trans, workflow_id, **kwd ): """ GET /api/workflows/{encoded_workflow_id}/download Returns a selected workflow as a json dictionary. """ - try: - stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id)) - except Exception, e: - return ("Workflow with ID='%s' can not be found\n Exception: %s") % (workflow_id, str( e )) - # check to see if user has permissions to selected workflow - if stored_workflow.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: - trans.response.status = 400 - return("Workflow is not owned by or shared with current user") + stored_workflow = self.__get_stored_accessible_workflow( trans, workflow_id ) ret_dict = self._workflow_to_dict( trans, stored_workflow ) if not ret_dict: # This workflow has a tool that's missing from the distribution - trans.response.status = 400 - return "Workflow cannot be exported due to missing tools." + message = "Workflow cannot be exported due to missing tools." + raise exceptions.MessageException( message ) return ret_dict - @web.expose_api + @expose_api def delete( self, trans, id, **kwd ): """ DELETE /api/workflows/{encoded_workflow_id} @@ -379,19 +377,39 @@ # TODO: Unsure of response message to let api know that a workflow was successfully deleted return ( "Workflow '%s' successfully deleted" % stored_workflow.name ) - @web.expose_api - def import_new_workflow(self, trans, payload, **kwd): + @expose_api + def import_new_workflow_deprecated(self, trans, payload, **kwd): """ POST /api/workflows/upload Importing dynamic workflows from the api. Return newly generated workflow id. Author: rpark # currently assumes payload['workflow'] is a json representation of a workflow to be inserted into the database + + Deprecated in favor to POST /api/workflows with encoded 'workflow' in + payload the same way. """ + return self.__api_import_new_workflow( trans, payload, **kwd ) + def __api_import_new_workflow( self, trans, payload, **kwd ): data = payload['workflow'] - workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source="API" ) + publish = util.string_as_bool( payload.get( "publish", False ) ) + # If 'publish' set, default to importable. + importable = util.string_as_bool( payload.get( "importable", publish ) ) + + if publish and not importable: + raise exceptions.RequestParameterInvalidException( "Published workflow must be importable." ) + + from_dict_kwds = dict( + source="API", + publish=publish, + ) + workflow, missing_tool_tups = self._workflow_from_dict( trans, data, **from_dict_kwds ) + + if importable: + self._make_item_accessible( trans.sa_session, workflow ) + trans.sa_session.flush() # galaxy workflow newly created id workflow_id = workflow.id @@ -409,7 +427,7 @@ return item @expose_api - def import_shared_workflow(self, trans, payload, **kwd): + def import_shared_workflow_deprecated(self, trans, payload, **kwd): """ POST /api/workflows/import Import a workflow shared by other users. @@ -423,14 +441,17 @@ workflow_id = payload.get('workflow_id', None) if workflow_id is None: raise exceptions.ObjectAttributeMissingException( "Missing required parameter 'workflow_id'." ) + self.__api_import_shared_workflow( trans, workflow_id, payload ) + + def __api_import_shared_workflow( self, trans, workflow_id, payload, **kwd ): try: stored_workflow = self.get_stored_workflow( trans, workflow_id, check_ownership=False ) except: raise exceptions.ObjectNotFound( "Malformed workflow id ( %s ) specified." % workflow_id ) if stored_workflow.importable is False: - raise exceptions.MessageException( 'The owner of this workflow has disabled imports via this link.' ) + raise exceptions.ItemAccessibilityException( 'The owner of this workflow has disabled imports via this link.' ) elif stored_workflow.deleted: - raise exceptions.MessageException( "You can't import this workflow because it has been deleted." ) + raise exceptions.ItemDeletionException( "You can't import this workflow because it has been deleted." ) imported_workflow = self._import_shared_workflow( trans, stored_workflow ) item = imported_workflow.to_dict( value_mapper={ 'id': trans.security.encode_id } ) encoded_id = trans.security.encode_id(imported_workflow.id) @@ -491,3 +512,32 @@ if out is not None: return self.encode_all_ids( trans, out.to_dict('element'), True) return None + + def __get_stored_accessible_workflow( self, trans, workflow_id ): + stored_workflow = self.__get_stored_workflow( trans, workflow_id ) + + # check to see if user has permissions to selected workflow + if stored_workflow.user != trans.user and not trans.user_is_admin(): + if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: + message = "Workflow is not owned by or shared with current user" + raise exceptions.ItemAccessibilityException( message ) + + return stored_workflow + + def __get_stored_workflow( self, trans, workflow_id ): + try: + workflow_id = self.__decode_id( trans, workflow_id ) + query = trans.sa_session.query( trans.app.model.StoredWorkflow ) + stored_workflow = query.get( workflow_id ) + except Exception: + raise exceptions.ObjectNotFound( "No such workflow found - invalid workflow identifier." ) + if stored_workflow is None: + raise exceptions.ObjectNotFound( "No such workflow found." ) + return stored_workflow + + def __decode_id( self, trans, workflow_id, model_type="workflow" ): + try: + return trans.security.decode_id( workflow_id ) + except Exception: + message = "Malformed %s id ( %s ) specified, unable to decode" % ( model_type, workflow_id ) + raise exceptions.MalformedId( message ) diff -r fcbd2849ebd17a80e66e0fbdac9df7bb37f88fa2 -r de2e33813275b89a04e7de4e95b21f6d2e100d4e lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -213,13 +213,13 @@ webapp.add_route( '/visualization/show/:visualization_name', controller='visualization', action='render', visualization_name=None ) - # "POST /api/workflows/import" => ``workflows.import_workflow()``. - # Defines a named route "import_workflow". - webapp.mapper.connect( 'import_workflow', '/api/workflows/upload', controller='workflows', action='import_new_workflow', conditions=dict( method=['POST'] ) ) + # Deprecated in favor of POST /api/workflows with 'workflow' in payload. + webapp.mapper.connect( 'import_workflow_deprecated', '/api/workflows/upload', controller='workflows', action='import_new_workflow_deprecated', conditions=dict( method=['POST'] ) ) webapp.mapper.connect( 'workflow_dict', '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) # Preserve the following download route for now for dependent applications -- deprecate at some point webapp.mapper.connect( 'workflow_dict', '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) - webapp.mapper.connect( 'import_shared_workflow', '/api/workflows/import', controller='workflows', action='import_shared_workflow', conditions=dict( method=['POST'] ) ) + # Deprecated in favor of POST /api/workflows with shared_workflow_id in payload. + webapp.mapper.connect( 'import_shared_workflow_deprecated', '/api/workflows/import', controller='workflows', action='import_shared_workflow_deprecated', conditions=dict( method=['POST'] ) ) webapp.mapper.connect( 'workflow_usage', '/api/workflows/{workflow_id}/usage', controller='workflows', action='workflow_usage', conditions=dict(method=['GET'])) webapp.mapper.connect( 'workflow_usage_contents', '/api/workflows/{workflow_id}/usage/{usage_id}', controller='workflows', action='workflow_usage_contents', conditions=dict(method=['GET'])) diff -r fcbd2849ebd17a80e66e0fbdac9df7bb37f88fa2 -r de2e33813275b89a04e7de4e95b21f6d2e100d4e test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -9,6 +9,7 @@ from .helpers import skip_without_tool from base.interactor import delete_request # requests like delete +from galaxy.exceptions import error_codes # Workflow API TODO: @@ -24,6 +25,16 @@ self.dataset_populator = DatasetPopulator( self.galaxy_interactor ) self.dataset_collection_populator = DatasetCollectionPopulator( self.galaxy_interactor ) + def test_show_invalid_is_404( self ): + show_response = self._get( "workflow/%s" % self._random_key() ) + self._assert_status_code_is( show_response, 404 ) + + def test_cannot_show_private_workflow( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_not_importportable" ) + with self._different_user(): + show_response = self._get( "workflows/%s" % workflow_id ) + self._assert_status_code_is( show_response, 403 ) + def test_delete( self ): workflow_id = self.workflow_populator.simple_workflow( "test_delete" ) workflow_name = "test_delete (imported from API)" @@ -46,14 +57,44 @@ self._assert_status_code_is( index_response, 200 ) assert isinstance( index_response.json(), list ) - def test_import( self ): + def test_upload( self ): + self.__test_upload( use_deprecated_route=False ) + + def test_upload_deprecated( self ): + self.__test_upload( use_deprecated_route=True ) + + def __test_upload( self, use_deprecated_route ): data = dict( workflow=dumps( self.workflow_populator.load_workflow( name="test_import" ) ), ) - upload_response = self._post( "workflows/upload", data=data ) + if use_deprecated_route: + route = "workflows/upload" + else: + 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)" ) + def test_import_deprecated( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_import_published_deprecated", publish=True ) + with self._different_user(): + other_import_response = self.__import_workflow( workflow_id ) + self._assert_status_code_is( other_import_response, 200 ) + self._assert_user_has_workflow_with_name( "imported: test_import_published_deprecated (imported from API)") + + def test_not_importable_prevents_import( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_not_importportable" ) + with self._different_user(): + other_import_response = self.__import_workflow( workflow_id ) + self._assert_status_code_is( other_import_response, 403 ) + + def test_import_published( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_import_published", publish=True ) + with self._different_user(): + other_import_response = self.__import_workflow( workflow_id, deprecated_route=True ) + self._assert_status_code_is( other_import_response, 200 ) + self._assert_user_has_workflow_with_name( "imported: test_import_published (imported from API)") + def test_export( self ): uploaded_workflow_id = self.workflow_populator.simple_workflow( "test_for_export" ) download_response = self._get( "workflows/%s/download" % uploaded_workflow_id ) @@ -85,6 +126,29 @@ self._assert_status_code_is( run_workflow_response, 200 ) self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + 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 ) + with self._different_user(): + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 403 ) + + def test_404_on_invalid_workflow( self ): + workflow = self.workflow_populator.load_workflow( name="test_for_run_does_not_exist" ) + workflow_request, history_id = self._setup_workflow_run( workflow ) + workflow_request[ "workflow_id" ] = self._random_key() + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 404 ) + + def test_cannot_run_against_other_users_history( self ): + workflow = self.workflow_populator.load_workflow( name="test_for_run_does_not_exist" ) + workflow_request, history_id = self._setup_workflow_run( workflow ) + with self._different_user(): + other_history_id = self.dataset_populator.new_history() + workflow_request[ "history" ] = "hist_id=%s" % other_history_id + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 403 ) + @skip_without_tool( "cat1" ) @skip_without_tool( "collection_two_paired" ) def test_run_workflow_collection_params( self ): @@ -233,6 +297,20 @@ collection_step_state = loads( collection_step[ "tool_state" ] ) self.assertEquals( collection_step_state[ "collection_type" ], u"paired" ) + def test_empty_create( self ): + response = self._post( "workflows" ) + self._assert_status_code_is( response, 400 ) + self._assert_error_code_is( response, error_codes.USER_REQUEST_MISSING_PARAMETER ) + + def test_invalid_create_multiple_types( self ): + data = { + 'shared_workflow_id': '1234567890abcdef', + 'from_history_id': '1234567890abcdef' + } + response = self._post( "workflows", data ) + self._assert_status_code_is( response, 400 ) + self._assert_error_code_is( response, error_codes.USER_REQUEST_INVALID_PARAMETER ) + @skip_without_tool( "random_lines1" ) def test_extract_mapping_workflow_from_history( self ): history_id = self.dataset_populator.new_history() @@ -551,3 +629,16 @@ self._assert_status_code_is( index_response, 200 ) names = map( lambda w: w[ "name" ], index_response.json() ) return names + + def __import_workflow( self, workflow_id, deprecated_route=False ): + if deprecated_route: + route = "workflows/import" + import_data = dict( + workflow_id=workflow_id, + ) + else: + route = "workflows" + import_data = dict( + shared_workflow_id=workflow_id, + ) + return self._post( route, import_data ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 5 new changesets
by commits-noreply＠bitbucket.org 09 Aug '14

09 Aug '14

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d7ebdeca53d2/ Changeset: d7ebdeca53d2 User: jmchilton Date: 2014-08-08 15:16:55 Summary: More RESTful shared workflow import. Previous route was "POST /api/workflows/shared", this still works but should be condisdered deprecated in favor of POSTing to /api/workflows with shared_workflow_id in the payload. Affected #: 2 files diff -r 5f663734a26e8e2d1c462320741c86c9b5d9aef6 -r d7ebdeca53d28ac3d21e7e242629811a81f68082 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -161,8 +161,13 @@ :param workflow_name: If from_history_id is set - name of the workflow to create when extracting a workflow from history :type workflow_name: str """ - - if len( set( ['workflow_id', 'installed_repository_file', 'from_history_id'] ).intersection( payload ) ) > 1: + ways_to_create = set( [ + 'workflow_id', + 'installed_repository_file', + 'from_history_id', + 'shared_workflow_id', + ] ) + if len( ways_to_create.intersection( payload ) ) > 1: trans.response.status = 403 return "Only one among 'workflow_id', 'installed_repository_file', 'from_history_id' must be specified" @@ -193,6 +198,10 @@ item[ 'url' ] = url_for( 'workflow', id=item[ 'id' ] ) return item + if 'shared_workflow_id' in payload: + workflow_id = payload[ 'shared_workflow_id' ] + return self.__api_import_shared_workflow( trans, workflow_id, payload ) + workflow_id = payload.get( 'workflow_id', None ) if not workflow_id: trans.response.status = 403 @@ -409,7 +418,7 @@ return item @expose_api - def import_shared_workflow(self, trans, payload, **kwd): + def import_shared_workflow_deprecated(self, trans, payload, **kwd): """ POST /api/workflows/import Import a workflow shared by other users. @@ -423,6 +432,9 @@ workflow_id = payload.get('workflow_id', None) if workflow_id is None: raise exceptions.ObjectAttributeMissingException( "Missing required parameter 'workflow_id'." ) + self.__api_import_shared_workflow( trans, workflow_id, payload ) + + def __api_import_shared_workflow( self, trans, workflow_id, payload, **kwd ): try: stored_workflow = self.get_stored_workflow( trans, workflow_id, check_ownership=False ) except: diff -r 5f663734a26e8e2d1c462320741c86c9b5d9aef6 -r d7ebdeca53d28ac3d21e7e242629811a81f68082 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -219,7 +219,8 @@ webapp.mapper.connect( 'workflow_dict', '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) # Preserve the following download route for now for dependent applications -- deprecate at some point webapp.mapper.connect( 'workflow_dict', '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) - webapp.mapper.connect( 'import_shared_workflow', '/api/workflows/import', controller='workflows', action='import_shared_workflow', conditions=dict( method=['POST'] ) ) + # Deprecated in favor of POST /api/workflows with shared_workflow_id in payload. + webapp.mapper.connect( 'import_shared_workflow_deprecated', '/api/workflows/import', controller='workflows', action='import_shared_workflow_deprecated', conditions=dict( method=['POST'] ) ) webapp.mapper.connect( 'workflow_usage', '/api/workflows/{workflow_id}/usage', controller='workflows', action='workflow_usage', conditions=dict(method=['GET'])) webapp.mapper.connect( 'workflow_usage_contents', '/api/workflows/{workflow_id}/usage/{usage_id}', controller='workflows', action='workflow_usage_contents', conditions=dict(method=['GET'])) https://bitbucket.org/galaxy/galaxy-central/commits/479397aedd2b/ Changeset: 479397aedd2b User: jmchilton Date: 2014-08-08 15:16:55 Summary: More RESTful direct workflow creation from JSON. Previous route was "POST /api/workflows/upload", this still works but should be condisdered deprecated in favor of POSTing to /api/workflows with 'workflow' in the payload. Affected #: 3 files diff -r d7ebdeca53d28ac3d21e7e242629811a81f68082 -r 479397aedd2b4cb074ac978377f4d27fa92476a6 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -166,6 +166,7 @@ 'installed_repository_file', 'from_history_id', 'shared_workflow_id', + 'workflow', ] ) if len( ways_to_create.intersection( payload ) ) > 1: trans.response.status = 403 @@ -202,6 +203,9 @@ workflow_id = payload[ 'shared_workflow_id' ] return self.__api_import_shared_workflow( trans, workflow_id, payload ) + if 'workflow' in payload: + return self.__api_import_new_workflow( trans, payload, **kwd ) + workflow_id = payload.get( 'workflow_id', None ) if not workflow_id: trans.response.status = 403 @@ -389,15 +393,20 @@ return ( "Workflow '%s' successfully deleted" % stored_workflow.name ) @web.expose_api - def import_new_workflow(self, trans, payload, **kwd): + def import_new_workflow_deprecated(self, trans, payload, **kwd): """ POST /api/workflows/upload Importing dynamic workflows from the api. Return newly generated workflow id. Author: rpark # currently assumes payload['workflow'] is a json representation of a workflow to be inserted into the database + + Deprecated in favor to POST /api/workflows with encoded 'workflow' in + payload the same way. """ + return self.__api_import_new_workflow( trans, payload, **kwd ) + def __api_import_new_workflow( self, trans, payload, **kwd ): data = payload['workflow'] workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source="API" ) diff -r d7ebdeca53d28ac3d21e7e242629811a81f68082 -r 479397aedd2b4cb074ac978377f4d27fa92476a6 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -213,9 +213,8 @@ webapp.add_route( '/visualization/show/:visualization_name', controller='visualization', action='render', visualization_name=None ) - # "POST /api/workflows/import" => ``workflows.import_workflow()``. - # Defines a named route "import_workflow". - webapp.mapper.connect( 'import_workflow', '/api/workflows/upload', controller='workflows', action='import_new_workflow', conditions=dict( method=['POST'] ) ) + # Deprecated in favor of POST /api/workflows with 'workflow' in payload. + webapp.mapper.connect( 'import_workflow_deprecated', '/api/workflows/upload', controller='workflows', action='import_new_workflow_deprecated', conditions=dict( method=['POST'] ) ) webapp.mapper.connect( 'workflow_dict', '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) # Preserve the following download route for now for dependent applications -- deprecate at some point webapp.mapper.connect( 'workflow_dict', '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) diff -r d7ebdeca53d28ac3d21e7e242629811a81f68082 -r 479397aedd2b4cb074ac978377f4d27fa92476a6 test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -46,11 +46,21 @@ self._assert_status_code_is( index_response, 200 ) assert isinstance( index_response.json(), list ) - def test_import( self ): + def test_upload( self ): + self.__test_upload( use_deprecated_route=False ) + + def test_upload_deprecated( self ): + self.__test_upload( use_deprecated_route=True ) + + def __test_upload( self, use_deprecated_route ): data = dict( workflow=dumps( self.workflow_populator.load_workflow( name="test_import" ) ), ) - upload_response = self._post( "workflows/upload", data=data ) + if use_deprecated_route: + route = "workflows/upload" + else: + 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)" ) https://bitbucket.org/galaxy/galaxy-central/commits/ecc4c38e0529/ Changeset: ecc4c38e0529 User: jmchilton Date: 2014-08-08 15:16:55 Summary: Work toward making workflows API use newer standards. Convert workflow API to use new-style API decorator throughout. Improved workflow exception handling - now more explicit status code setting and returning of raw error strings in the API. Most obvious exceptional paths out of the API are now coming through MessageExceptions of things even more specific. Add API tests for many of these exceptional conditions. Use more helper methods to reduce method length, duplication. Affected #: 2 files diff -r 479397aedd2b4cb074ac978377f4d27fa92476a6 -r ecc4c38e0529fb3352ad0534e71929f6f6b29e7f lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -6,8 +6,9 @@ import logging from sqlalchemy import desc, or_ -from galaxy import exceptions, util, web +from galaxy import exceptions, util from galaxy.model.item_attrs import UsesAnnotations +from galaxy.managers import histories from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin from galaxy.web.base.controller import UsesHistoryMixin @@ -20,7 +21,11 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin, UsesAnnotations): - @web.expose_api + def __init__( self, app ): + super( BaseAPIController, self ).__init__( app ) + self.history_manager = histories.HistoryManager() + + @expose_api def index(self, trans, **kwd): """ GET /api/workflows @@ -54,30 +59,21 @@ rval.append(item) return rval - @web.expose_api + @expose_api def show(self, trans, id, **kwd): """ GET /api/workflows/{encoded_workflow_id} Displays information needed to run a workflow from the command line. """ - workflow_id = id - try: - decoded_workflow_id = trans.security.decode_id(workflow_id) - except TypeError: - trans.response.status = 400 - return "Malformed workflow id ( %s ) specified, unable to decode." % str(workflow_id) - try: - stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).get(decoded_workflow_id) - if stored_workflow.importable is False and stored_workflow.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: - trans.response.status = 400 - return("Workflow is neither importable, nor owned by or shared with current user") - except: - trans.response.status = 400 - return "That workflow does not exist." + stored_workflow = self.__get_stored_workflow( trans, id ) + if stored_workflow.importable is False and stored_workflow.user != trans.user and not trans.user_is_admin(): + 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=workflow_id) + item['url'] = url_for('workflow', id=id) item['owner'] = stored_workflow.user.username latest_workflow = stored_workflow.latest_workflow inputs = {} @@ -114,7 +110,7 @@ item['steps'] = steps return item - @web.expose_api + @expose_api def create(self, trans, payload, **kwd): """ POST /api/workflows @@ -167,10 +163,14 @@ 'from_history_id', 'shared_workflow_id', 'workflow', - ] ) - if len( ways_to_create.intersection( payload ) ) > 1: - trans.response.status = 403 - return "Only one among 'workflow_id', 'installed_repository_file', 'from_history_id' must be specified" + ] ).intersection( payload ) + if len( ways_to_create ) == 0: + message = "One parameter among - %s - must be specified" % ", ".join( ways_to_create ) + raise exceptions.RequestParameterMissingException( message ) + + if len( ways_to_create ) > 1: + message = "Only one parameter among - %s - must be specified" % ", ".join( ways_to_create ) + raise exceptions.RequestParameterInvalidException( message ) if 'installed_repository_file' in payload: workflow_controller = trans.webapp.controllers[ 'workflow' ] @@ -208,8 +208,8 @@ workflow_id = payload.get( 'workflow_id', None ) if not workflow_id: - trans.response.status = 403 - return "Either workflow_id, installed_repository_file or from_history_id must be specified" + message = "Invalid workflow_id specified." + raise exceptions.RequestParameterInvalidException( message ) # Pull other parameters out of payload. param_map = payload.get( 'parameters', {} ) @@ -238,34 +238,24 @@ history_param = payload.get('history', '') # Get workflow + accessibility check. - stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id)) - if stored_workflow.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: - trans.response.status = 400 - return("Workflow is not owned by or shared with current user") + stored_workflow = self.__get_stored_accessible_workflow( trans, workflow_id ) workflow = stored_workflow.latest_workflow # Sanity checks. - if not workflow: - trans.response.status = 400 - return "Workflow not found." if len( workflow.steps ) == 0: - trans.response.status = 400 - return "Workflow cannot be run because it does not have any steps" + raise exceptions.MessageException( "Workflow cannot be run because it does not have any steps" ) if workflow.has_cycles: - trans.response.status = 400 - return "Workflow cannot be run because it contains cycles" + raise exceptions.MessageException( "Workflow cannot be run because it contains cycles" ) if workflow.has_errors: - trans.response.status = 400 - return "Workflow cannot be run because of validation errors in some steps" + message = "Workflow cannot be run because of validation errors in some steps" + raise exceptions.MessageException( message ) # Get target history. if history_param.startswith('hist_id='): # Passing an existing history to use. - history = trans.sa_session.query(self.app.model.History).get(trans.security.decode_id(history_param[8:])) - if history.user != trans.user and not trans.user_is_admin(): - trans.response.status = 400 - return "Invalid History specified." + encoded_history_id = history_param[ 8: ] + history_id = self.__decode_id( trans, encoded_history_id, model_type="history" ) + history = self.history_manager.get( trans, history_id, check_ownership=True ) else: # Send workflow outputs to new history. history = self.app.model.History(name=history_param, user=trans.user) @@ -297,8 +287,8 @@ inputs[k]['id'] ) else: - trans.response.status = 400 - return "Unknown dataset source '%s' specified." % inputs[k]['src'] + message = "Unknown workflow input source '%s' specified." % inputs[k]['src'] + raise exceptions.RequestParameterInvalidException( message ) if add_to_history and content.history != history: content = content.copy() if isinstance( content, self.app.model.HistoryDatasetAssociation ): @@ -307,8 +297,8 @@ history.add_dataset_collection( content ) inputs[k]['hda'] = content # TODO: rename key to 'content', prescreen input ensure not populated explicitly except AssertionError: - trans.response.status = 400 - return "Invalid Dataset '%s' Specified" % inputs[k]['id'] + message = "Invalid workflow input '%s' specified" % inputs[k]['id'] + raise exceptions.ItemAccessibilityException( message ) # Run each step, connecting outputs to inputs replacement_dict = payload.get('replacement_params', {}) @@ -321,6 +311,8 @@ param_map=param_map, ) + # invoke may throw MessageExceptions on tool erors, failure + # to match up inputs, etc... outputs = invoke( trans=trans, workflow=workflow, @@ -340,30 +332,22 @@ return rval - @web.expose_api + @expose_api def workflow_dict( self, trans, workflow_id, **kwd ): """ GET /api/workflows/{encoded_workflow_id}/download Returns a selected workflow as a json dictionary. """ - try: - stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id)) - except Exception, e: - return ("Workflow with ID='%s' can not be found\n Exception: %s") % (workflow_id, str( e )) - # check to see if user has permissions to selected workflow - if stored_workflow.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: - trans.response.status = 400 - return("Workflow is not owned by or shared with current user") + stored_workflow = self.__get_stored_accessible_workflow( trans, workflow_id ) ret_dict = self._workflow_to_dict( trans, stored_workflow ) if not ret_dict: # This workflow has a tool that's missing from the distribution - trans.response.status = 400 - return "Workflow cannot be exported due to missing tools." + message = "Workflow cannot be exported due to missing tools." + raise exceptions.MessageException( message ) return ret_dict - @web.expose_api + @expose_api def delete( self, trans, id, **kwd ): """ DELETE /api/workflows/{encoded_workflow_id} @@ -392,7 +376,7 @@ # TODO: Unsure of response message to let api know that a workflow was successfully deleted return ( "Workflow '%s' successfully deleted" % stored_workflow.name ) - @web.expose_api + @expose_api def import_new_workflow_deprecated(self, trans, payload, **kwd): """ POST /api/workflows/upload @@ -512,3 +496,32 @@ if out is not None: return self.encode_all_ids( trans, out.to_dict('element'), True) return None + + def __get_stored_accessible_workflow( self, trans, workflow_id ): + stored_workflow = self.__get_stored_workflow( trans, workflow_id ) + + # check to see if user has permissions to selected workflow + if stored_workflow.user != trans.user and not trans.user_is_admin(): + if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: + message = "Workflow is not owned by or shared with current user" + raise exceptions.ItemAccessibilityException( message ) + + return stored_workflow + + def __get_stored_workflow( self, trans, workflow_id ): + try: + workflow_id = self.__decode_id( trans, workflow_id ) + query = trans.sa_session.query( trans.app.model.StoredWorkflow ) + stored_workflow = query.get( workflow_id ) + except Exception: + raise exceptions.ObjectNotFound( "No such workflow found - invalid workflow identifier." ) + if stored_workflow is None: + raise exceptions.ObjectNotFound( "No such workflow found." ) + return stored_workflow + + def __decode_id( self, trans, workflow_id, model_type="workflow" ): + try: + return trans.security.decode_id( workflow_id ) + except Exception: + message = "Malformed %s id ( %s ) specified, unable to decode" % ( model_type, workflow_id ) + raise exceptions.MalformedId( message ) diff -r 479397aedd2b4cb074ac978377f4d27fa92476a6 -r ecc4c38e0529fb3352ad0534e71929f6f6b29e7f test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -9,6 +9,7 @@ from .helpers import skip_without_tool from base.interactor import delete_request # requests like delete +from galaxy.exceptions import error_codes # Workflow API TODO: @@ -24,6 +25,16 @@ self.dataset_populator = DatasetPopulator( self.galaxy_interactor ) self.dataset_collection_populator = DatasetCollectionPopulator( self.galaxy_interactor ) + def test_show_invalid_is_404( self ): + show_response = self._get( "workflow/%s" % self._random_key() ) + self._assert_status_code_is( show_response, 404 ) + + def test_cannot_show_private_workflow( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_not_importportable" ) + with self._different_user(): + show_response = self._get( "workflows/%s" % workflow_id ) + self._assert_status_code_is( show_response, 403 ) + def test_delete( self ): workflow_id = self.workflow_populator.simple_workflow( "test_delete" ) workflow_name = "test_delete (imported from API)" @@ -95,6 +106,29 @@ self._assert_status_code_is( run_workflow_response, 200 ) self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + 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 ) + with self._different_user(): + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 403 ) + + def test_404_on_invalid_workflow( self ): + workflow = self.workflow_populator.load_workflow( name="test_for_run_does_not_exist" ) + workflow_request, history_id = self._setup_workflow_run( workflow ) + workflow_request[ "workflow_id" ] = self._random_key() + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 404 ) + + def test_cannot_run_against_other_users_history( self ): + workflow = self.workflow_populator.load_workflow( name="test_for_run_does_not_exist" ) + workflow_request, history_id = self._setup_workflow_run( workflow ) + with self._different_user(): + other_history_id = self.dataset_populator.new_history() + workflow_request[ "history" ] = "hist_id=%s" % other_history_id + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 403 ) + @skip_without_tool( "cat1" ) @skip_without_tool( "collection_two_paired" ) def test_run_workflow_collection_params( self ): @@ -243,6 +277,20 @@ collection_step_state = loads( collection_step[ "tool_state" ] ) self.assertEquals( collection_step_state[ "collection_type" ], u"paired" ) + def test_empty_create( self ): + response = self._post( "workflows" ) + self._assert_status_code_is( response, 400 ) + self._assert_error_code_is( response, error_codes.USER_REQUEST_MISSING_PARAMETER ) + + def test_invalid_create_multiple_types( self ): + data = { + 'shared_workflow_id': '1234567890abcdef', + 'from_history_id': '1234567890abcdef' + } + response = self._post( "workflows", data ) + self._assert_status_code_is( response, 400 ) + self._assert_error_code_is( response, error_codes.USER_REQUEST_INVALID_PARAMETER ) + @skip_without_tool( "random_lines1" ) def test_extract_mapping_workflow_from_history( self ): history_id = self.dataset_populator.new_history() https://bitbucket.org/galaxy/galaxy-central/commits/a3ac64b85faa/ Changeset: a3ac64b85faa User: jmchilton Date: 2014-08-08 15:16:55 Summary: Allow workflow uploads to specify publishable/importable. Use new capabilities to improve workflow testing. Affected #: 3 files diff -r ecc4c38e0529fb3352ad0534e71929f6f6b29e7f -r a3ac64b85faa4e59d331277a801a2b5570a8ca7e lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1664,7 +1664,7 @@ session.flush() return imported_stored - def _workflow_from_dict( self, trans, data, source=None, add_to_menu=False ): + def _workflow_from_dict( self, trans, data, source=None, add_to_menu=False, publish=False ): """ Creates a workflow from a dict. Created workflow is stored in the database and returned. """ @@ -1752,6 +1752,7 @@ workflow.stored_workflow = stored stored.latest_workflow = workflow stored.user = trans.user + stored.published = publish if data[ 'annotation' ]: self.add_item_annotation( trans.sa_session, stored.user, stored, data[ 'annotation' ] ) diff -r ecc4c38e0529fb3352ad0534e71929f6f6b29e7f -r a3ac64b85faa4e59d331277a801a2b5570a8ca7e lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -12,6 +12,7 @@ from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin from galaxy.web.base.controller import UsesHistoryMixin +from galaxy.web.base.controller import SharableMixin from galaxy.workflow.extract import extract_workflow from galaxy.workflow.run import invoke from galaxy.workflow.run import WorkflowRunConfig @@ -19,7 +20,7 @@ log = logging.getLogger(__name__) -class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin, UsesAnnotations): +class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin, UsesAnnotations, SharableMixin): def __init__( self, app ): super( BaseAPIController, self ).__init__( app ) @@ -393,7 +394,22 @@ def __api_import_new_workflow( self, trans, payload, **kwd ): data = payload['workflow'] - workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source="API" ) + publish = util.string_as_bool( payload.get( "publish", False ) ) + # If 'publish' set, default to importable. + importable = util.string_as_bool( payload.get( "importable", publish ) ) + + if publish and not importable: + raise exceptions.RequestParameterInvalidException( "Published workflow must be importable." ) + + from_dict_kwds = dict( + source="API", + publish=publish, + ) + workflow, missing_tool_tups = self._workflow_from_dict( trans, data, **from_dict_kwds ) + + if importable: + self._make_item_accessible( trans.sa_session, workflow ) + trans.sa_session.flush() # galaxy workflow newly created id workflow_id = workflow.id @@ -433,9 +449,9 @@ except: raise exceptions.ObjectNotFound( "Malformed workflow id ( %s ) specified." % workflow_id ) if stored_workflow.importable is False: - raise exceptions.MessageException( 'The owner of this workflow has disabled imports via this link.' ) + raise exceptions.ItemAccessibilityException( 'The owner of this workflow has disabled imports via this link.' ) elif stored_workflow.deleted: - raise exceptions.MessageException( "You can't import this workflow because it has been deleted." ) + raise exceptions.ItemDeletionException( "You can't import this workflow because it has been deleted." ) imported_workflow = self._import_shared_workflow( trans, stored_workflow ) item = imported_workflow.to_dict( value_mapper={ 'id': trans.security.encode_id } ) encoded_id = trans.security.encode_id(imported_workflow.id) diff -r ecc4c38e0529fb3352ad0534e71929f6f6b29e7f -r a3ac64b85faa4e59d331277a801a2b5570a8ca7e test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -75,6 +75,26 @@ self._assert_status_code_is( upload_response, 200 ) self._assert_user_has_workflow_with_name( "test_import (imported from API)" ) + def test_import_deprecated( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_import_published_deprecated", publish=True ) + with self._different_user(): + other_import_response = self.__import_workflow( workflow_id ) + self._assert_status_code_is( other_import_response, 200 ) + self._assert_user_has_workflow_with_name( "imported: test_import_published_deprecated (imported from API)") + + def test_not_importable_prevents_import( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_not_importportable" ) + with self._different_user(): + other_import_response = self.__import_workflow( workflow_id ) + self._assert_status_code_is( other_import_response, 403 ) + + def test_import_published( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_import_published", publish=True ) + with self._different_user(): + other_import_response = self.__import_workflow( workflow_id, deprecated_route=True ) + self._assert_status_code_is( other_import_response, 200 ) + self._assert_user_has_workflow_with_name( "imported: test_import_published (imported from API)") + def test_export( self ): uploaded_workflow_id = self.workflow_populator.simple_workflow( "test_for_export" ) download_response = self._get( "workflows/%s/download" % uploaded_workflow_id ) @@ -609,3 +629,16 @@ self._assert_status_code_is( index_response, 200 ) names = map( lambda w: w[ "name" ], index_response.json() ) return names + + def __import_workflow( self, workflow_id, deprecated_route=False ): + if deprecated_route: + route = "workflows/import" + import_data = dict( + workflow_id=workflow_id, + ) + else: + route = "workflows" + import_data = dict( + shared_workflow_id=workflow_id, + ) + return self._post( route, import_data ) https://bitbucket.org/galaxy/galaxy-central/commits/de2e33813275/ Changeset: de2e33813275 User: jmchilton Date: 2014-08-09 15:15:11 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #452) More RESTful workflow API (attempt 3) Affected #: 4 files diff -r fcbd2849ebd17a80e66e0fbdac9df7bb37f88fa2 -r de2e33813275b89a04e7de4e95b21f6d2e100d4e lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1664,7 +1664,7 @@ session.flush() return imported_stored - def _workflow_from_dict( self, trans, data, source=None, add_to_menu=False ): + def _workflow_from_dict( self, trans, data, source=None, add_to_menu=False, publish=False ): """ Creates a workflow from a dict. Created workflow is stored in the database and returned. """ @@ -1752,6 +1752,7 @@ workflow.stored_workflow = stored stored.latest_workflow = workflow stored.user = trans.user + stored.published = publish if data[ 'annotation' ]: self.add_item_annotation( trans.sa_session, stored.user, stored, data[ 'annotation' ] ) diff -r fcbd2849ebd17a80e66e0fbdac9df7bb37f88fa2 -r de2e33813275b89a04e7de4e95b21f6d2e100d4e lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -6,11 +6,13 @@ import logging from sqlalchemy import desc, or_ -from galaxy import exceptions, util, web +from galaxy import exceptions, util from galaxy.model.item_attrs import UsesAnnotations +from galaxy.managers import histories from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin from galaxy.web.base.controller import UsesHistoryMixin +from galaxy.web.base.controller import SharableMixin from galaxy.workflow.extract import extract_workflow from galaxy.workflow.run import invoke from galaxy.workflow.run import WorkflowRunConfig @@ -18,9 +20,13 @@ log = logging.getLogger(__name__) -class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin, UsesAnnotations): +class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin, UsesAnnotations, SharableMixin): - @web.expose_api + def __init__( self, app ): + super( BaseAPIController, self ).__init__( app ) + self.history_manager = histories.HistoryManager() + + @expose_api def index(self, trans, **kwd): """ GET /api/workflows @@ -54,30 +60,21 @@ rval.append(item) return rval - @web.expose_api + @expose_api def show(self, trans, id, **kwd): """ GET /api/workflows/{encoded_workflow_id} Displays information needed to run a workflow from the command line. """ - workflow_id = id - try: - decoded_workflow_id = trans.security.decode_id(workflow_id) - except TypeError: - trans.response.status = 400 - return "Malformed workflow id ( %s ) specified, unable to decode." % str(workflow_id) - try: - stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).get(decoded_workflow_id) - if stored_workflow.importable is False and stored_workflow.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: - trans.response.status = 400 - return("Workflow is neither importable, nor owned by or shared with current user") - except: - trans.response.status = 400 - return "That workflow does not exist." + stored_workflow = self.__get_stored_workflow( trans, id ) + if stored_workflow.importable is False and stored_workflow.user != trans.user and not trans.user_is_admin(): + 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=workflow_id) + item['url'] = url_for('workflow', id=id) item['owner'] = stored_workflow.user.username latest_workflow = stored_workflow.latest_workflow inputs = {} @@ -114,7 +111,7 @@ item['steps'] = steps return item - @web.expose_api + @expose_api def create(self, trans, payload, **kwd): """ POST /api/workflows @@ -161,10 +158,20 @@ :param workflow_name: If from_history_id is set - name of the workflow to create when extracting a workflow from history :type workflow_name: str """ + ways_to_create = set( [ + 'workflow_id', + 'installed_repository_file', + 'from_history_id', + 'shared_workflow_id', + 'workflow', + ] ).intersection( payload ) + if len( ways_to_create ) == 0: + message = "One parameter among - %s - must be specified" % ", ".join( ways_to_create ) + raise exceptions.RequestParameterMissingException( message ) - if len( set( ['workflow_id', 'installed_repository_file', 'from_history_id'] ).intersection( payload ) ) > 1: - trans.response.status = 403 - return "Only one among 'workflow_id', 'installed_repository_file', 'from_history_id' must be specified" + if len( ways_to_create ) > 1: + message = "Only one parameter among - %s - must be specified" % ", ".join( ways_to_create ) + raise exceptions.RequestParameterInvalidException( message ) if 'installed_repository_file' in payload: workflow_controller = trans.webapp.controllers[ 'workflow' ] @@ -193,10 +200,17 @@ item[ 'url' ] = url_for( 'workflow', id=item[ 'id' ] ) return item + if 'shared_workflow_id' in payload: + workflow_id = payload[ 'shared_workflow_id' ] + return self.__api_import_shared_workflow( trans, workflow_id, payload ) + + if 'workflow' in payload: + return self.__api_import_new_workflow( trans, payload, **kwd ) + workflow_id = payload.get( 'workflow_id', None ) if not workflow_id: - trans.response.status = 403 - return "Either workflow_id, installed_repository_file or from_history_id must be specified" + message = "Invalid workflow_id specified." + raise exceptions.RequestParameterInvalidException( message ) # Pull other parameters out of payload. param_map = payload.get( 'parameters', {} ) @@ -225,34 +239,24 @@ history_param = payload.get('history', '') # Get workflow + accessibility check. - stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id)) - if stored_workflow.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: - trans.response.status = 400 - return("Workflow is not owned by or shared with current user") + stored_workflow = self.__get_stored_accessible_workflow( trans, workflow_id ) workflow = stored_workflow.latest_workflow # Sanity checks. - if not workflow: - trans.response.status = 400 - return "Workflow not found." if len( workflow.steps ) == 0: - trans.response.status = 400 - return "Workflow cannot be run because it does not have any steps" + raise exceptions.MessageException( "Workflow cannot be run because it does not have any steps" ) if workflow.has_cycles: - trans.response.status = 400 - return "Workflow cannot be run because it contains cycles" + raise exceptions.MessageException( "Workflow cannot be run because it contains cycles" ) if workflow.has_errors: - trans.response.status = 400 - return "Workflow cannot be run because of validation errors in some steps" + message = "Workflow cannot be run because of validation errors in some steps" + raise exceptions.MessageException( message ) # Get target history. if history_param.startswith('hist_id='): # Passing an existing history to use. - history = trans.sa_session.query(self.app.model.History).get(trans.security.decode_id(history_param[8:])) - if history.user != trans.user and not trans.user_is_admin(): - trans.response.status = 400 - return "Invalid History specified." + encoded_history_id = history_param[ 8: ] + history_id = self.__decode_id( trans, encoded_history_id, model_type="history" ) + history = self.history_manager.get( trans, history_id, check_ownership=True ) else: # Send workflow outputs to new history. history = self.app.model.History(name=history_param, user=trans.user) @@ -284,8 +288,8 @@ inputs[k]['id'] ) else: - trans.response.status = 400 - return "Unknown dataset source '%s' specified." % inputs[k]['src'] + message = "Unknown workflow input source '%s' specified." % inputs[k]['src'] + raise exceptions.RequestParameterInvalidException( message ) if add_to_history and content.history != history: content = content.copy() if isinstance( content, self.app.model.HistoryDatasetAssociation ): @@ -294,8 +298,8 @@ history.add_dataset_collection( content ) inputs[k]['hda'] = content # TODO: rename key to 'content', prescreen input ensure not populated explicitly except AssertionError: - trans.response.status = 400 - return "Invalid Dataset '%s' Specified" % inputs[k]['id'] + message = "Invalid workflow input '%s' specified" % inputs[k]['id'] + raise exceptions.ItemAccessibilityException( message ) # Run each step, connecting outputs to inputs replacement_dict = payload.get('replacement_params', {}) @@ -308,6 +312,8 @@ param_map=param_map, ) + # invoke may throw MessageExceptions on tool erors, failure + # to match up inputs, etc... outputs = invoke( trans=trans, workflow=workflow, @@ -327,30 +333,22 @@ return rval - @web.expose_api + @expose_api def workflow_dict( self, trans, workflow_id, **kwd ): """ GET /api/workflows/{encoded_workflow_id}/download Returns a selected workflow as a json dictionary. """ - try: - stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id)) - except Exception, e: - return ("Workflow with ID='%s' can not be found\n Exception: %s") % (workflow_id, str( e )) - # check to see if user has permissions to selected workflow - if stored_workflow.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: - trans.response.status = 400 - return("Workflow is not owned by or shared with current user") + stored_workflow = self.__get_stored_accessible_workflow( trans, workflow_id ) ret_dict = self._workflow_to_dict( trans, stored_workflow ) if not ret_dict: # This workflow has a tool that's missing from the distribution - trans.response.status = 400 - return "Workflow cannot be exported due to missing tools." + message = "Workflow cannot be exported due to missing tools." + raise exceptions.MessageException( message ) return ret_dict - @web.expose_api + @expose_api def delete( self, trans, id, **kwd ): """ DELETE /api/workflows/{encoded_workflow_id} @@ -379,19 +377,39 @@ # TODO: Unsure of response message to let api know that a workflow was successfully deleted return ( "Workflow '%s' successfully deleted" % stored_workflow.name ) - @web.expose_api - def import_new_workflow(self, trans, payload, **kwd): + @expose_api + def import_new_workflow_deprecated(self, trans, payload, **kwd): """ POST /api/workflows/upload Importing dynamic workflows from the api. Return newly generated workflow id. Author: rpark # currently assumes payload['workflow'] is a json representation of a workflow to be inserted into the database + + Deprecated in favor to POST /api/workflows with encoded 'workflow' in + payload the same way. """ + return self.__api_import_new_workflow( trans, payload, **kwd ) + def __api_import_new_workflow( self, trans, payload, **kwd ): data = payload['workflow'] - workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source="API" ) + publish = util.string_as_bool( payload.get( "publish", False ) ) + # If 'publish' set, default to importable. + importable = util.string_as_bool( payload.get( "importable", publish ) ) + + if publish and not importable: + raise exceptions.RequestParameterInvalidException( "Published workflow must be importable." ) + + from_dict_kwds = dict( + source="API", + publish=publish, + ) + workflow, missing_tool_tups = self._workflow_from_dict( trans, data, **from_dict_kwds ) + + if importable: + self._make_item_accessible( trans.sa_session, workflow ) + trans.sa_session.flush() # galaxy workflow newly created id workflow_id = workflow.id @@ -409,7 +427,7 @@ return item @expose_api - def import_shared_workflow(self, trans, payload, **kwd): + def import_shared_workflow_deprecated(self, trans, payload, **kwd): """ POST /api/workflows/import Import a workflow shared by other users. @@ -423,14 +441,17 @@ workflow_id = payload.get('workflow_id', None) if workflow_id is None: raise exceptions.ObjectAttributeMissingException( "Missing required parameter 'workflow_id'." ) + self.__api_import_shared_workflow( trans, workflow_id, payload ) + + def __api_import_shared_workflow( self, trans, workflow_id, payload, **kwd ): try: stored_workflow = self.get_stored_workflow( trans, workflow_id, check_ownership=False ) except: raise exceptions.ObjectNotFound( "Malformed workflow id ( %s ) specified." % workflow_id ) if stored_workflow.importable is False: - raise exceptions.MessageException( 'The owner of this workflow has disabled imports via this link.' ) + raise exceptions.ItemAccessibilityException( 'The owner of this workflow has disabled imports via this link.' ) elif stored_workflow.deleted: - raise exceptions.MessageException( "You can't import this workflow because it has been deleted." ) + raise exceptions.ItemDeletionException( "You can't import this workflow because it has been deleted." ) imported_workflow = self._import_shared_workflow( trans, stored_workflow ) item = imported_workflow.to_dict( value_mapper={ 'id': trans.security.encode_id } ) encoded_id = trans.security.encode_id(imported_workflow.id) @@ -491,3 +512,32 @@ if out is not None: return self.encode_all_ids( trans, out.to_dict('element'), True) return None + + def __get_stored_accessible_workflow( self, trans, workflow_id ): + stored_workflow = self.__get_stored_workflow( trans, workflow_id ) + + # check to see if user has permissions to selected workflow + if stored_workflow.user != trans.user and not trans.user_is_admin(): + if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: + message = "Workflow is not owned by or shared with current user" + raise exceptions.ItemAccessibilityException( message ) + + return stored_workflow + + def __get_stored_workflow( self, trans, workflow_id ): + try: + workflow_id = self.__decode_id( trans, workflow_id ) + query = trans.sa_session.query( trans.app.model.StoredWorkflow ) + stored_workflow = query.get( workflow_id ) + except Exception: + raise exceptions.ObjectNotFound( "No such workflow found - invalid workflow identifier." ) + if stored_workflow is None: + raise exceptions.ObjectNotFound( "No such workflow found." ) + return stored_workflow + + def __decode_id( self, trans, workflow_id, model_type="workflow" ): + try: + return trans.security.decode_id( workflow_id ) + except Exception: + message = "Malformed %s id ( %s ) specified, unable to decode" % ( model_type, workflow_id ) + raise exceptions.MalformedId( message ) diff -r fcbd2849ebd17a80e66e0fbdac9df7bb37f88fa2 -r de2e33813275b89a04e7de4e95b21f6d2e100d4e lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -213,13 +213,13 @@ webapp.add_route( '/visualization/show/:visualization_name', controller='visualization', action='render', visualization_name=None ) - # "POST /api/workflows/import" => ``workflows.import_workflow()``. - # Defines a named route "import_workflow". - webapp.mapper.connect( 'import_workflow', '/api/workflows/upload', controller='workflows', action='import_new_workflow', conditions=dict( method=['POST'] ) ) + # Deprecated in favor of POST /api/workflows with 'workflow' in payload. + webapp.mapper.connect( 'import_workflow_deprecated', '/api/workflows/upload', controller='workflows', action='import_new_workflow_deprecated', conditions=dict( method=['POST'] ) ) webapp.mapper.connect( 'workflow_dict', '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) # Preserve the following download route for now for dependent applications -- deprecate at some point webapp.mapper.connect( 'workflow_dict', '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) - webapp.mapper.connect( 'import_shared_workflow', '/api/workflows/import', controller='workflows', action='import_shared_workflow', conditions=dict( method=['POST'] ) ) + # Deprecated in favor of POST /api/workflows with shared_workflow_id in payload. + webapp.mapper.connect( 'import_shared_workflow_deprecated', '/api/workflows/import', controller='workflows', action='import_shared_workflow_deprecated', conditions=dict( method=['POST'] ) ) webapp.mapper.connect( 'workflow_usage', '/api/workflows/{workflow_id}/usage', controller='workflows', action='workflow_usage', conditions=dict(method=['GET'])) webapp.mapper.connect( 'workflow_usage_contents', '/api/workflows/{workflow_id}/usage/{usage_id}', controller='workflows', action='workflow_usage_contents', conditions=dict(method=['GET'])) diff -r fcbd2849ebd17a80e66e0fbdac9df7bb37f88fa2 -r de2e33813275b89a04e7de4e95b21f6d2e100d4e test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -9,6 +9,7 @@ from .helpers import skip_without_tool from base.interactor import delete_request # requests like delete +from galaxy.exceptions import error_codes # Workflow API TODO: @@ -24,6 +25,16 @@ self.dataset_populator = DatasetPopulator( self.galaxy_interactor ) self.dataset_collection_populator = DatasetCollectionPopulator( self.galaxy_interactor ) + def test_show_invalid_is_404( self ): + show_response = self._get( "workflow/%s" % self._random_key() ) + self._assert_status_code_is( show_response, 404 ) + + def test_cannot_show_private_workflow( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_not_importportable" ) + with self._different_user(): + show_response = self._get( "workflows/%s" % workflow_id ) + self._assert_status_code_is( show_response, 403 ) + def test_delete( self ): workflow_id = self.workflow_populator.simple_workflow( "test_delete" ) workflow_name = "test_delete (imported from API)" @@ -46,14 +57,44 @@ self._assert_status_code_is( index_response, 200 ) assert isinstance( index_response.json(), list ) - def test_import( self ): + def test_upload( self ): + self.__test_upload( use_deprecated_route=False ) + + def test_upload_deprecated( self ): + self.__test_upload( use_deprecated_route=True ) + + def __test_upload( self, use_deprecated_route ): data = dict( workflow=dumps( self.workflow_populator.load_workflow( name="test_import" ) ), ) - upload_response = self._post( "workflows/upload", data=data ) + if use_deprecated_route: + route = "workflows/upload" + else: + 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)" ) + def test_import_deprecated( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_import_published_deprecated", publish=True ) + with self._different_user(): + other_import_response = self.__import_workflow( workflow_id ) + self._assert_status_code_is( other_import_response, 200 ) + self._assert_user_has_workflow_with_name( "imported: test_import_published_deprecated (imported from API)") + + def test_not_importable_prevents_import( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_not_importportable" ) + with self._different_user(): + other_import_response = self.__import_workflow( workflow_id ) + self._assert_status_code_is( other_import_response, 403 ) + + def test_import_published( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_import_published", publish=True ) + with self._different_user(): + other_import_response = self.__import_workflow( workflow_id, deprecated_route=True ) + self._assert_status_code_is( other_import_response, 200 ) + self._assert_user_has_workflow_with_name( "imported: test_import_published (imported from API)") + def test_export( self ): uploaded_workflow_id = self.workflow_populator.simple_workflow( "test_for_export" ) download_response = self._get( "workflows/%s/download" % uploaded_workflow_id ) @@ -85,6 +126,29 @@ self._assert_status_code_is( run_workflow_response, 200 ) self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + 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 ) + with self._different_user(): + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 403 ) + + def test_404_on_invalid_workflow( self ): + workflow = self.workflow_populator.load_workflow( name="test_for_run_does_not_exist" ) + workflow_request, history_id = self._setup_workflow_run( workflow ) + workflow_request[ "workflow_id" ] = self._random_key() + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 404 ) + + def test_cannot_run_against_other_users_history( self ): + workflow = self.workflow_populator.load_workflow( name="test_for_run_does_not_exist" ) + workflow_request, history_id = self._setup_workflow_run( workflow ) + with self._different_user(): + other_history_id = self.dataset_populator.new_history() + workflow_request[ "history" ] = "hist_id=%s" % other_history_id + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 403 ) + @skip_without_tool( "cat1" ) @skip_without_tool( "collection_two_paired" ) def test_run_workflow_collection_params( self ): @@ -233,6 +297,20 @@ collection_step_state = loads( collection_step[ "tool_state" ] ) self.assertEquals( collection_step_state[ "collection_type" ], u"paired" ) + def test_empty_create( self ): + response = self._post( "workflows" ) + self._assert_status_code_is( response, 400 ) + self._assert_error_code_is( response, error_codes.USER_REQUEST_MISSING_PARAMETER ) + + def test_invalid_create_multiple_types( self ): + data = { + 'shared_workflow_id': '1234567890abcdef', + 'from_history_id': '1234567890abcdef' + } + response = self._post( "workflows", data ) + self._assert_status_code_is( response, 400 ) + self._assert_error_code_is( response, error_codes.USER_REQUEST_INVALID_PARAMETER ) + @skip_without_tool( "random_lines1" ) def test_extract_mapping_workflow_from_history( self ): history_id = self.dataset_populator.new_history() @@ -551,3 +629,16 @@ self._assert_status_code_is( index_response, 200 ) names = map( lambda w: w[ "name" ], index_response.json() ) return names + + def __import_workflow( self, workflow_id, deprecated_route=False ): + if deprecated_route: + route = "workflows/import" + import_data = dict( + workflow_id=workflow_id, + ) + else: + route = "workflows" + import_data = dict( + shared_workflow_id=workflow_id, + ) + return self._post( route, import_data ) 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 08 Aug '14

08 Aug '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d0133648ddb9/ Changeset: d0133648ddb9 User: jmchilton Date: 2014-08-08 17:42:20 Summary: Cleanup unused parameter left over in workflow controller. Affected #: 1 file diff -r 5f663734a26e8e2d1c462320741c86c9b5d9aef6 -r d0133648ddb96fc3e0c030c86802e0b6186b7f92 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1226,7 +1226,7 @@ url_for( controller='workflow', action='run', id=workflow_id ) ) ) @web.expose - def run( self, trans, id, history_id=None, multiple_input_mode="product", hide_fixed_params=False, **kwargs ): + def run( self, trans, id, history_id=None, hide_fixed_params=False, **kwargs ): stored = self.get_stored_workflow( trans, id, check_ownership=False ) user = trans.get_user() if stored.user != user: @@ -1269,7 +1269,7 @@ # been POSTed # List to gather values for the template invocations = [] - for (kwargs, multi_input_keys) in _expand_multiple_inputs(kwargs, mode=multiple_input_mode): + for (kwargs, multi_input_keys) in _expand_multiple_inputs(kwargs): for step in workflow.steps: step.upgrade_messages = {} # Connections by input name @@ -1653,9 +1653,9 @@ return " on %s and %s" % (", ".join(instance_ds_names[0:-1]), instance_ds_names[-1]) -def _expand_multiple_inputs(kwargs, mode): +def _expand_multiple_inputs(kwargs): (single_inputs, matched_multi_inputs, multiplied_multi_inputs) = \ - _split_inputs(kwargs, mode) + _split_inputs(kwargs) # Build up every combination of inputs to be run together. input_combos = _extend_with_matched_combos(single_inputs, matched_multi_inputs) @@ -1714,7 +1714,7 @@ return new_inputs -def _split_inputs(kwargs, mode): +def _split_inputs(kwargs): """ """ input_keys = filter(lambda a: a.endswith('|input'), kwargs) https://bitbucket.org/galaxy/galaxy-central/commits/fcbd2849ebd1/ Changeset: fcbd2849ebd1 User: jmchilton Date: 2014-08-08 17:42:20 Summary: Some PEP-8 fixes for lib/galaxy/webapps/galaxy/controllers/workflow.py. Affected #: 1 file diff -r d0133648ddb96fc3e0c030c86802e0b6186b7f92 -r fcbd2849ebd17a80e66e0fbdac9df7bb37f88fa2 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -51,7 +51,7 @@ use_panels = True title = "Saved Workflows" model_class = model.StoredWorkflow - default_filter = { "name" : "All", "tags": "All" } + default_filter = { "name": "All", "tags": "All" } default_sort_key = "-update_time" columns = [ grids.TextColumn( "Name", key="name", attach_popup=True, filterable="advanced" ), @@ -62,10 +62,11 @@ ] columns.append( grids.MulticolFilterColumn( - "Search", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", visible=False, filterable="standard" ) - ) + "Search", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", visible=False, filterable="standard" + ) + ) operations = [ grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), grids.GridOperation( "Run", condition=( lambda item: not item.deleted ), async_compatible=False ), @@ -95,19 +96,24 @@ ] columns.append( grids.MulticolFilterColumn( - "Search name, annotation, owner, and tags", - cols_to_filter=[ columns[0], columns[1], columns[2], columns[4] ], - key="free-text-search", visible=False, filterable="standard" ) - ) + "Search name, annotation, owner, and tags", + cols_to_filter=[ columns[0], columns[1], columns[2], columns[4] ], + key="free-text-search", visible=False, filterable="standard" + ) + ) operations = [ - grids.GridOperation( "Import", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( action="imp" ) ), - grids.GridOperation( "Save as File", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( action="export_to_file" ) ), + grids.GridOperation( + "Import", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( action="imp") + ), + grids.GridOperation( + "Save as File", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( action="export_to_file" ) + ), ] def build_initial_query( self, trans, **kwargs ): @@ -275,7 +281,7 @@ user_item_rating = 0 ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, stored_workflow ) return trans.fill_template_mako( "workflow/display.mako", item=stored_workflow, item_data=stored_workflow.latest_workflow.steps, - user_item_rating=user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) + user_item_rating=user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) @web.expose def get_item_content_async( self, trans, id ): @@ -390,7 +396,7 @@ # Do import. stored = self.get_stored_workflow( trans, id, check_ownership=False ) - if stored.importable == False: + if stored.importable is False: return trans.show_error_message( "The owner of this workflow has disabled imports via this link.<br>You can %s" % referer_message, use_panels=True ) elif stored.deleted: return trans.show_error_message( "You can't import this workflow because it has been deleted.<br>You can %s" % referer_message, use_panels=True ) @@ -415,7 +421,7 @@ if 'annotation' in kwargs: # Set workflow annotation; sanitize annotation before adding it. annotation = sanitize_html( kwargs[ 'annotation' ], 'utf-8', 'text/html' ) - self.add_item_annotation( trans.sa_session, trans.get_user(), stored, annotation ) + self.add_item_annotation( trans.sa_session, trans.get_user(), stored, annotation ) trans.sa_session.flush() return trans.fill_template( 'workflow/edit_attributes.mako', stored=stored, @@ -511,7 +517,7 @@ """ Returns workflow's name and link. """ stored = self.get_stored_workflow( trans, id ) - return_dict = { "name" : stored.name, "link" : url_for(controller='workflow', action="display_by_username_and_slug", username=stored.user.username, slug=stored.slug ) } + return_dict = { "name": stored.name, "link": url_for(controller='workflow', action="display_by_username_and_slug", username=stored.user.username, slug=stored.slug ) } return return_dict @web.expose @@ -583,8 +589,8 @@ return self.editor( trans, id=trans.security.encode_id(stored_workflow.id )) else: return form( url_for(controller="workflow", action="create"), "Create New Workflow", submit_text="Create", use_panels=True ) \ - .add_text( "workflow_name", "Workflow Name", value="Unnamed workflow" ) \ - .add_text( "workflow_annotation", "Workflow Annotation", value="", help="A description of the workflow; annotation is shown alongside shared or published workflows." ) + .add_text( "workflow_name", "Workflow Name", value="Unnamed workflow" ) \ + .add_text( "workflow_annotation", "Workflow Annotation", value="", help="A description of the workflow; annotation is shown alongside shared or published workflows." ) @web.expose def delete( self, trans, id=None ): @@ -665,7 +671,7 @@ module = module_factory.new( trans, type, **kwargs ) return { 'type': module.type, - 'name': module.get_name(), + 'name': module.get_name(), 'tool_id': module.get_tool_id(), 'tool_state': module.get_state(), 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ), @@ -750,9 +756,9 @@ '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' : [] + 'annotation': annotation_str, + 'post_job_actions': {}, + 'workflow_outputs': [] } # Connections input_connections = step.input_connections @@ -838,8 +844,8 @@ 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) + 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 @@ -932,18 +938,19 @@ workflow_content = json.dumps( workflow_dict, indent=4, sort_keys=True ) # Create myExperiment request. - request_raw = trans.fill_template( "workflow/myexp_export.mako", \ - workflow_name=workflow_dict['name'], \ - workflow_description=workflow_dict['annotation'], \ - workflow_content=workflow_content, \ - workflow_svg=self._workflow_to_svg_canvas( trans, stored ).standalone_xml() - ) + request_raw = trans.fill_template( + "workflow/myexp_export.mako", + workflow_name=workflow_dict['name'], + workflow_description=workflow_dict['annotation'], + workflow_content=workflow_content, + workflow_svg=self._workflow_to_svg_canvas( trans, stored ).standalone_xml() + ) # strip() b/c myExperiment XML parser doesn't allow white space before XML; utf-8 handles unicode characters. request = unicode( request_raw.strip(), 'utf-8' ) # Do request and get result. auth_header = base64.b64encode( '%s:%s' % ( myexp_username, myexp_password )) - headers = { "Content-type": "text/xml", "Accept": "text/xml", "Authorization" : "Basic %s" % auth_header } + headers = { "Content-type": "text/xml", "Accept": "text/xml", "Authorization": "Basic %s" % auth_header } myexp_url = trans.app.config.get( "myexperiment_url", self.__myexp_url ) conn = httplib.HTTPConnection( myexp_url ) # NOTE: blocks web thread. @@ -958,14 +965,14 @@ myexp_workflow_id = parser.tag_content workflow_list_str = " <br>Return to <a href='%s'>workflow list." % url_for( controller='workflow', action='list' ) if myexp_workflow_id: - return trans.show_message( \ + return trans.show_message( """Workflow '%s' successfully exported to myExperiment. <br/><a href="http://%s/workflows/%s">Click here to view the workflow on myExperiment</a> %s """ % ( stored.name, myexp_url, myexp_workflow_id, workflow_list_str ), use_panels=True ) else: - return trans.show_error_message( \ - "Workflow '%s' could not be exported to myExperiment. Error: %s %s" % \ + return trans.show_error_message( + "Workflow '%s' could not be exported to myExperiment. Error: %s %s" % ( stored.name, response_data, workflow_list_str ), use_panels=True ) @web.json_pretty @@ -1205,10 +1212,10 @@ jobs, warnings = summarize( trans ) # Render return trans.fill_template( - "workflow/build_from_current_history.mako", - jobs=jobs, - warnings=warnings, - history=history + "workflow/build_from_current_history.mako", + jobs=jobs, + warnings=warnings, + history=history ) else: stored_workflow = extract_workflow( @@ -1223,7 +1230,7 @@ workflow_id = trans.security.encode_id( stored_workflow.id ) return trans.show_message( 'Workflow "%s" created from current history. You can <a href="%s" target="_parent">edit</a> or <a href="%s">run</a> the workflow.' % ( workflow_name, url_for( controller='workflow', action='editor', id=workflow_id ), - url_for( controller='workflow', action='run', id=workflow_id ) ) ) + url_for( controller='workflow', action='run', id=workflow_id ) ) ) @web.expose def run( self, trans, id, history_id=None, hide_fixed_params=False, **kwargs ): @@ -1350,8 +1357,8 @@ trans.sa_session.flush() if invocations: return trans.fill_template( "workflow/run_complete.mako", - workflow=stored, - invocations=invocations ) + workflow=stored, + invocations=invocations ) else: # Prepare each step missing_tools = [] @@ -1388,24 +1395,27 @@ step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections ) if missing_tools: stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored ) - return trans.fill_template("workflow/run.mako", - steps=[], - workflow=stored, - hide_fixed_params=hide_fixed_params, - missing_tools=missing_tools) + return trans.fill_template( + "workflow/run.mako", + steps=[], + workflow=stored, + hide_fixed_params=hide_fixed_params, + missing_tools=missing_tools + ) # Render the form stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored ) return trans.fill_template( - "workflow/run.mako", - steps=workflow.steps, - workflow=stored, - has_upgrade_messages=has_upgrade_messages, - step_version_changes=step_version_changes, - errors=errors, - incoming=kwargs, - history_id=history_id, - hide_fixed_params=hide_fixed_params, - enable_unique_defaults=trans.app.config.enable_unique_workflow_defaults) + "workflow/run.mako", + steps=workflow.steps, + workflow=stored, + has_upgrade_messages=has_upgrade_messages, + step_version_changes=step_version_changes, + errors=errors, + incoming=kwargs, + history_id=history_id, + hide_fixed_params=hide_fixed_params, + enable_unique_defaults=trans.app.config.enable_unique_workflow_defaults + ) finally: # restore the active history if saved_history is not None: @@ -1484,12 +1494,12 @@ step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections ) # Render the form return trans.fill_template( - "workflow/tag_outputs.mako", - steps=workflow.steps, - workflow=stored, - has_upgrade_messages=has_upgrade_messages, - errors=errors, - incoming=kwargs + "workflow/tag_outputs.mako", + steps=workflow.steps, + workflow=stored, + has_upgrade_messages=has_upgrade_messages, + errors=errors, + incoming=kwargs ) @web.expose @@ -1539,7 +1549,7 @@ shared_by_others=shared_by_others, ids_in_menu=ids_in_menu, message=message, - refresh_frames=['tools'] ) + refresh_frames=refresh_frames ) def _workflow_to_svg_canvas( self, trans, stored ): workflow = stored.latest_workflow @@ -1619,17 +1629,17 @@ if len(step_dict['data_inputs']) > 0: box_height += 15 sep_y = y + len(step_dict['data_inputs']) * line_px + 40 - text.append( svgfig.Line(x-margin, sep_y, x+width-margin, sep_y).SVG() ) # + text.append( svgfig.Line(x - margin, sep_y, x + width - margin, sep_y).SVG() ) # input/output box - boxes.append( svgfig.Rect(x-margin, y+30, x+width-margin, y+30+box_height, fill="#ffffff").SVG() ) + boxes.append( svgfig.Rect(x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff").SVG() ) for conn, output_dict in step_dict['input_connections'].iteritems(): in_coords = in_pos[step_dict['id']][conn] out_conn_pos = out_pos[output_dict['id']][output_dict['output_name']] adjusted = (out_conn_pos[0] + widths[output_dict['id']], out_conn_pos[1]) - text.append( svgfig.SVG("circle", cx=out_conn_pos[0]+widths[output_dict['id']]-margin, cy=out_conn_pos[1]-margin, r=5, fill="#ffffff" ) ) - connectors.append( svgfig.Line(adjusted[0], adjusted[1]-margin, in_coords[0]-10, in_coords[1], arrow_end="true" ).SVG() ) + text.append( svgfig.SVG("circle", cx=out_conn_pos[0] + widths[output_dict['id']] - margin, cy=out_conn_pos[1] - margin, r=5, fill="#ffffff" ) ) + connectors.append( svgfig.Line(adjusted[0], adjusted[1] - margin, in_coords[0] - 10, in_coords[1], arrow_end="true" ).SVG() ) canvas.append(connectors) canvas.append(boxes) @@ -1654,16 +1664,14 @@ def _expand_multiple_inputs(kwargs): - (single_inputs, matched_multi_inputs, multiplied_multi_inputs) = \ - _split_inputs(kwargs) + (single_inputs, matched_multi_inputs, multiplied_multi_inputs) = _split_inputs(kwargs) # Build up every combination of inputs to be run together. input_combos = _extend_with_matched_combos(single_inputs, matched_multi_inputs) input_combos = _extend_with_multiplied_combos(input_combos, multiplied_multi_inputs) # Input name that are multiply specified - multi_input_keys = \ - matched_multi_inputs.keys() + multiplied_multi_inputs.keys() + multi_input_keys = matched_multi_inputs.keys() + multiplied_multi_inputs.keys() for input_combo in input_combos: for key, value in input_combo.iteritems(): 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: natefoo: Bug fix for display site changes.
by commits-noreply＠bitbucket.org 07 Aug '14

07 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5f663734a26e/ Changeset: 5f663734a26e User: natefoo Date: 2014-08-07 17:35:20 Summary: Bug fix for display site changes. Affected #: 3 files diff -r 103697ebdd339377424063fba0459cb3cc2b707c -r 5f663734a26e8e2d1c462320741c86c9b5d9aef6 lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py +++ b/lib/galaxy/datatypes/genetics.py @@ -85,7 +85,7 @@ if not dataset.dbkey: dataset.dbkey = 'hg18' # punt! if dataset.has_data(): - for site_name, site_url in app.build_sites.get_ucsc_by_build(dataset.dbkey): + for site_name, site_url in app.build_sites.get_ucsc_sites_by_build(dataset.dbkey): if site_name in app.config.ucsc_display_sites: site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs internal_url = "%s" % url_for( controller='dataset', diff -r 103697ebdd339377424063fba0459cb3cc2b707c -r 5f663734a26e8e2d1c462320741c86c9b5d9aef6 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -234,7 +234,7 @@ # Filter UCSC sites to only those that are supported by this build and # enabled. valid_sites = [ ( name, url ) - for name, url in app.build_sites.get_ucsc_by_build( dataset.dbkey ) + for name, url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ) if name in app.config.ucsc_display_sites ] if not valid_sites: return [] @@ -750,7 +750,7 @@ ret_val = [] seqid, start, stop = self.get_estimated_display_viewport( dataset ) if seqid is not None: - for site_name, site_url in app.build_sites.get_ucsc_by_build( dataset.dbkey ): + for site_name, site_url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ): if site_name in app.config.ucsc_display_sites: redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % @@ -1103,7 +1103,7 @@ ret_val = [] chrom, start, stop = self.get_estimated_display_viewport( dataset ) if chrom is not None: - for site_name, site_url in app.build_sites.get_ucsc_by_build( dataset.dbkey ): + for site_name, site_url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ): if site_name in app.config.ucsc_display_sites: redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % ( site_url, dataset.dbkey, chrom, start, stop ) ) link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url ) @@ -1285,7 +1285,7 @@ ret_val = [] chrom, start, stop = self.get_estimated_display_viewport(dataset) if chrom is not None: - for site_name, site_url in app.build_sites.get_ucsc_by_build(dataset.dbkey): + for site_name, site_url in app.build_sites.get_ucsc_sites_by_build(dataset.dbkey): if site_name in app.config.ucsc_display_sites: internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) ) diff -r 103697ebdd339377424063fba0459cb3cc2b707c -r 5f663734a26e8e2d1c462320741c86c9b5d9aef6 lib/galaxy/util/build_sites.py --- a/lib/galaxy/util/build_sites.py +++ b/lib/galaxy/util/build_sites.py @@ -38,7 +38,7 @@ self._build_sites['ucsc'] = self.read_build_sites( self._app.config.ucsc_build_sites ) self._build_sites['gbrowse'] = self.read_build_sites( self._app.config.gbrowse_build_sites ) - def get_site_by_build( self, site_type, build ): + def _get_site_by_build( self, site_type, build ): sites = [] for site in self._build_sites[site_type]: if build in site['builds']: 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 07 Aug '14

07 Aug '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d7bf7ad5c578/ Changeset: d7bf7ad5c578 Branch: next-stable User: jmchilton Date: 2014-08-07 15:35:43 Summary: Bugfix: Deal with BibTeX fields in a case insensitive fashion. Would have thought the parser would have done this already - oh well. Affected #: 2 files diff -r 3976f4d59bc0d7b65575e7573f13fb7470c9bf53 -r d7bf7ad5c578e7d27a4a94c559ef336b2eb3eab0 static/scripts/mvc/citation/citation-model.js --- a/static/scripts/mvc/citation/citation-model.js +++ b/static/scripts/mvc/citation/citation-model.js @@ -18,12 +18,19 @@ var bibtex = this.attributes.content; var entry = new BibtexParser(bibtex).entries[0]; this.entry = entry; + this._fields = {}; + var rawFields = entry.Fields; + for(key in rawFields) { + var value = rawFields[ key ]; + var lowerKey = key.toLowerCase(); + this._fields[ lowerKey ] = value; + } }, entryType: function() { return this.entry.EntryType; }, fields: function() { - return this.entry.Fields; + return this._fields; } } ); diff -r 3976f4d59bc0d7b65575e7573f13fb7470c9bf53 -r d7bf7ad5c578e7d27a4a94c559ef336b2eb3eab0 static/scripts/mvc/citation/citation-view.js --- a/static/scripts/mvc/citation/citation-view.js +++ b/static/scripts/mvc/citation/citation-view.js @@ -55,9 +55,9 @@ this._asSentence(fields.note); } var doiUrl = ""; - if( fields.DOI ) { - doiUrl = 'http://dx.doi.org/' + fields.DOI; - ref += '[<a href="' + doiUrl + '">doi:' + fields.DOI + "</a>]"; + if( fields.doi ) { + doiUrl = 'http://dx.doi.org/' + fields.doi; + ref += '[<a href="' + doiUrl + '">doi:' + fields.doi + "</a>]"; } var url = fields.url || doiUrl; if( url ) { https://bitbucket.org/galaxy/galaxy-central/commits/ee8efcfd787f/ Changeset: ee8efcfd787f Branch: next-stable User: jmchilton Date: 2014-08-07 15:35:43 Summary: Relax BibTeX parsing and accept header to handle figshare DOIs. For instance 10.6084/m9.figshare.979190 reported by Michael Crusoe. JavaScript parser didn't like @data entries produced by figshare and when requesting the entry dx.doi.org returns a 403 response for type accept type text/bibliography, also allowing application/x-bibtex fixes this. Interestingly dx.doi.org throws 500 exceptions if application/x-bibtex is the only acceptable type or appears first for some other DOIs. Affected #: 2 files diff -r d7bf7ad5c578e7d27a4a94c559ef336b2eb3eab0 -r ee8efcfd787f93c77eb4e451084d64ce4dc6b85e lib/galaxy/managers/citations.py --- a/lib/galaxy/managers/citations.py +++ b/lib/galaxy/managers/citations.py @@ -49,7 +49,7 @@ def _raw_get_bibtex( self, doi ): dx_url = "http://dx.doi.org/" + doi - headers = {'Accept': "text/bibliography; style=bibtex" } + headers = {'Accept': 'text/bibliography; style=bibtex, application/x-bibtex'} req = urllib2.Request(dx_url, data="", headers=headers) response = urllib2.urlopen(req) bibtex = response.read() diff -r d7bf7ad5c578e7d27a4a94c559ef336b2eb3eab0 -r ee8efcfd787f93c77eb4e451084d64ce4dc6b85e static/scripts/libs/bibtex.js --- a/static/scripts/libs/bibtex.js +++ b/static/scripts/libs/bibtex.js @@ -93,6 +93,7 @@ 'booklet' : 14, 'masterthesis' : 15, 'conference' : 16 + ,'data' : 999 // Galaxy MOD: Handle @data citations coming from figshare. } /** @private */ this.MACROS_ = { 'jan' : 'January', https://bitbucket.org/galaxy/galaxy-central/commits/990bc0688199/ Changeset: 990bc0688199 Branch: next-stable User: jmchilton Date: 2014-08-07 15:36:18 Summary: Pack scripts. Affected #: 3 files diff -r ee8efcfd787f93c77eb4e451084d64ce4dc6b85e -r 990bc0688199410ab08d5e8a418770b516c6f4e2 static/scripts/packed/libs/bibtex.js --- a/static/scripts/packed/libs/bibtex.js +++ b/static/scripts/packed/libs/bibtex.js @@ -1,1 +1,1 @@ -function BibtexParser(c){if(typeof c=="string"){var d={};var a=[];function b(f){a.push(f)}var e=BibtexParser.call(d,b);e.parse(c);return{entries:a,errors:e.getErrors()}}if(typeof c!="function"){throw"Invalid parser construction."}this.STATES_={ENTRY_OR_JUNK:0,OBJECT_TYPE:1,ENTRY_KEY:2,KV_KEY:3,EQUALS:4,KV_VALUE:5};this.DATA_={};this.CALLBACK_=c;this.CHAR_=0;this.LINE_=1;this.CHAR_IN_LINE_=0;this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.PARSETMP_={};this.SKIPTILLEOL_=false;this.VALBRACES_=null;this.BRACETYPE_=null;this.BRACECOUNT_=0;this.STATE_=this.STATES_.ENTRY_OR_JUNK;this.ERRORS_=[];this.ENTRY_TYPES_={inproceedings:1,proceedings:2,article:3,techreport:4,misc:5,mastersthesis:6,book:7,phdthesis:8,incollection:9,unpublished:10,inbook:11,manual:12,periodical:13,booklet:14,masterthesis:15,conference:16};this.MACROS_={jan:"January",feb:"February",mar:"March",apr:"April",may:"May",jun:"June",jul:"July",aug:"August",sep:"September",oct:"October",nov:"November",dec:"December",Jan:"January",Feb:"February",Mar:"March",Apr:"April",May:"May",Jun:"June",Jul:"July",Aug:"August",Sep:"September",Oct:"October",Nov:"November",Dec:"December"};this.getErrors=function(){return this.ERRORS_};this.parse=function(f){for(var g=0;g<f.length;g++){this.processCharacter_(f[g])}};this.error_=function(f){this.ERRORS_.push([this.LINE_,this.CHAR_IN_LINE_,this.CHAR_,f])};this.processEntry_=function(){var h=this.DATA_;if(h.Fields){for(var k in h.Fields){var p=h.Fields[k];for(var j=0;j<this.CHARCONV_.length;j++){var q=this.CHARCONV_[j][0];var n=this.CHARCONV_[j][1];p=p.replace(q,n)}p=p.replace(/[\n\r\t]/g," ").replace(/\s\s+/g," ").replace(/^\s+|\s+$/g,"");var l=p.length;var g="";for(var j=0;j<l;j++){var m=p[j];var o=false;if(m=="\\"&&j<l-1){m=p[++j]}else{if(m=="{"||m=="}"){o=true}}if(!o){g+=m}}h.Fields[k]=g}}if(h.ObjectType=="string"){for(var k in h.Fields){this.MACROS_[k]=h.Fields[k]}}else{this.CALLBACK_(h)}};this.processCharacter_=function(l){this.CHAR_++;this.CHAR_IN_LINE_++;if(l=="\n"){this.LINE_++;this.CHAR_IN_LINE_=1}if(this.SKIPTILLEOL_){if(l=="\n"){this.SKIPTILLEOL_=false}return}if(this.SKIPCOMMENT_&&l=="%"){this.SKIPTILLEOL_=true;return}if(this.SKIPWS_&&/\s/.test(l)){return}this.SKIPWS_=false;this.SKIPCOMMENT_=false;this.SKIPTILLEOL_=false;var f=true;while(f){f=false;switch(this.STATE_){case this.STATES_.ENTRY_OR_JUNK:if(l=="@"){this.STATE_=this.STATES_.OBJECT_TYPE;this.DATA_={ObjectType:""}}this.BRACETYPE_=null;this.SKIPWS_=true;this.SKIPCOMMENT_=true;break;case this.STATES_.OBJECT_TYPE:if(/[A-Za-z]/.test(l)){this.DATA_.ObjectType+=l.toLowerCase();this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{var i=this.DATA_.ObjectType;if(i=="comment"){this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{if(i=="string"){this.DATA_.ObjectType=i;this.DATA_.Fields={};this.BRACETYPE_=l;this.BRACECOUNT_=1;this.STATE_=this.STATES_.KV_KEY;this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.PARSETMP_={Key:""}}else{if(i=="preamble"){this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{if(i in this.ENTRY_TYPES_){this.DATA_.ObjectType="entry";this.DATA_.EntryType=i;this.DATA_.EntryKey="";this.STATE_=this.STATES_.ENTRY_KEY;f=true}else{this.error_('Unrecognized object type: "'+this.DATA_.ObjectType+'"');this.STATE_=this.STATES_.ENTRY_OR_JUNK}}}}}break;case this.STATES_.ENTRY_KEY:if((l==="{"||l==="(")&&this.BRACETYPE_==null){this.BRACETYPE_=l;this.BRACECOUNT_=1;this.SKIPWS_=true;this.SKIPCOMMENT_=true;break}if(/[,%\s]/.test(l)){if(this.DATA_.EntryKey.length<1){this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{if(this.BRACETYPE_==null){this.error_("No opening brace for object.");this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{this.SKIPWS_=true;this.SKIPCOMMENT_=true;f=true;this.STATE_=this.STATES_.KV_KEY;this.PARSETMP_.Key="";this.DATA_.Fields={}}}}else{this.DATA_.EntryKey+=l;this.SKIPWS_=false;this.SKIPCOMMENT_=false}break;case this.STATES_.KV_KEY:if((l=="}"&&this.BRACETYPE_=="{")||(l==")"&&this.BRACETYPE_=="(")){this.processEntry_();this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.ENTRY_OR_JUNK;break}if(/[\-A-Za-z:]/.test(l)){this.PARSETMP_.Key+=l;this.SKIPWS_=false;this.SKIPCOMMENT_=false}else{if(this.PARSETMP_.Key.length<1){this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.EQUALS;f=true}}break;case this.STATES_.EQUALS:if((l=="}"&&this.BRACETYPE_=="{")||(l==")"&&this.BRACETYPE_=="(")){this.error_('Key-value pair has key "'+this.PARSETMP_.Key+'", but no 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this.ERRORS_};this.parse=function(f){for(var g=0;g<f.length;g++){this.processCharacter_(f[g])}};this.error_=function(f){this.ERRORS_.push([this.LINE_,this.CHAR_IN_LINE_,this.CHAR_,f])};this.processEntry_=function(){var h=this.DATA_;if(h.Fields){for(var k in h.Fields){var p=h.Fields[k];for(var j=0;j<this.CHARCONV_.length;j++){var q=this.CHARCONV_[j][0];var n=this.CHARCONV_[j][1];p=p.replace(q,n)}p=p.replace(/[\n\r\t]/g," ").replace(/\s\s+/g," ").replace(/^\s+|\s+$/g,"");var l=p.length;var g="";for(var j=0;j<l;j++){var m=p[j];var o=false;if(m=="\\"&&j<l-1){m=p[++j]}else{if(m=="{"||m=="}"){o=true}}if(!o){g+=m}}h.Fields[k]=g}}if(h.ObjectType=="string"){for(var k in h.Fields){this.MACROS_[k]=h.Fields[k]}}else{this.CALLBACK_(h)}};this.processCharacter_=function(l){this.CHAR_++;this.CHAR_IN_LINE_++;if(l=="\n"){this.LINE_++;this.CHAR_IN_LINE_=1}if(this.SKIPTILLEOL_){if(l=="\n"){this.SKIPTILLEOL_=false}return}if(this.SKIPCOMMENT_&&l=="%"){this.SKIPTILLEOL_=true;return}if(this.SKIPWS_&&/\s/.test(l)){return}this.SKIPWS_=false;this.SKIPCOMMENT_=false;this.SKIPTILLEOL_=false;var f=true;while(f){f=false;switch(this.STATE_){case this.STATES_.ENTRY_OR_JUNK:if(l=="@"){this.STATE_=this.STATES_.OBJECT_TYPE;this.DATA_={ObjectType:""}}this.BRACETYPE_=null;this.SKIPWS_=true;this.SKIPCOMMENT_=true;break;case this.STATES_.OBJECT_TYPE:if(/[A-Za-z]/.test(l)){this.DATA_.ObjectType+=l.toLowerCase();this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{var i=this.DATA_.ObjectType;if(i=="comment"){this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{if(i=="string"){this.DATA_.ObjectType=i;this.DATA_.Fields={};this.BRACETYPE_=l;this.BRACECOUNT_=1;this.STATE_=this.STATES_.KV_KEY;this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.PARSETMP_={Key:""}}else{if(i=="preamble"){this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{if(i in this.ENTRY_TYPES_){this.DATA_.ObjectType="entry";this.DATA_.EntryType=i;this.DATA_.EntryKey="";this.STATE_=this.STATES_.ENTRY_KEY;f=true}else{this.error_('Unrecognized object type: "'+this.DATA_.ObjectType+'"');this.STATE_=this.STATES_.ENTRY_OR_JUNK}}}}}break;case this.STATES_.ENTRY_KEY:if((l==="{"||l==="(")&&this.BRACETYPE_==null){this.BRACETYPE_=l;this.BRACECOUNT_=1;this.SKIPWS_=true;this.SKIPCOMMENT_=true;break}if(/[,%\s]/.test(l)){if(this.DATA_.EntryKey.length<1){this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{if(this.BRACETYPE_==null){this.error_("No opening brace for object.");this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{this.SKIPWS_=true;this.SKIPCOMMENT_=true;f=true;this.STATE_=this.STATES_.KV_KEY;this.PARSETMP_.Key="";this.DATA_.Fields={}}}}else{this.DATA_.EntryKey+=l;this.SKIPWS_=false;this.SKIPCOMMENT_=false}break;case this.STATES_.KV_KEY:if((l=="}"&&this.BRACETYPE_=="{")||(l==")"&&this.BRACETYPE_=="(")){this.processEntry_();this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.ENTRY_OR_JUNK;break}if(/[\-A-Za-z:]/.test(l)){this.PARSETMP_.Key+=l;this.SKIPWS_=false;this.SKIPCOMMENT_=false}else{if(this.PARSETMP_.Key.length<1){this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.EQUALS;f=true}}break;case this.STATES_.EQUALS:if((l=="}"&&this.BRACETYPE_=="{")||(l==")"&&this.BRACETYPE_=="(")){this.error_('Key-value pair has key "'+this.PARSETMP_.Key+'", but no value.');this.processEntry_();this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.ENTRY_OR_JUNK;break}if(l=="="){this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.KV_VALUE;this.PARSETMP_.Value="";this.VALBRACES_={'"':[],"{":[]}}break;case this.STATES_.KV_VALUE:var k=this.VALBRACES_;var j=this.PARSETMP_.Value;var h=false;if(l=='"'||l=="{"||l=="}"||l==","){if(l==","){if(0===k['"'].length+k["{"].length){var g=this.PARSETMP_.Value.trim();if(g in this.MACROS_){this.PARSETMP_.Value=this.MACROS_[g]}else{this.error_("Reference to an undefined macro: "+g)}h=true}}if(l=='"'){if(0===k['"'].length+k["{"].length){k['"'].push(this.CHAR_);this.SKIPWS_=false;this.SKIPCOMMENT_=false;break}if(k['"'].length==1&&k["{"].length==0&&(j.length==0||j[j.length-1]!="\\")){h=true}else{}}if(l=="{"){if(j.length==0||j[j.length-1]!="\\"){k["{"].push(this.CHAR_);this.SKIPWS_=false;this.SKIPCOMMENT_=false}else{}}if(l=="}"){if(0===k['"'].length+k["{"].length){var g=this.PARSETMP_.Value.trim();if(g in this.MACROS_){this.PARSETMP_.Value=this.MACROS_[g]}else{this.error_("Reference to an undefined macro: "+g)}f=true;h=true}else{if(j.length==0||j[j.length-1]!="\\"){if(k["{"].length>0){k["{"].splice(k["{"].length-1,1);if(0==k["{"].length+k['"'].length){h=true}else{}}}else{}}}}if(h){this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.KV_KEY;this.DATA_.Fields[this.PARSETMP_.Key]=this.PARSETMP_.Value;this.PARSETMP_={Key:""};this.VALBRACES_=null}else{this.PARSETMP_.Value+=l}break}}};this.CHARCONV_=[[/\\space /g,"\u0020"],[/\\textdollar /g,"\u0024"],[/\\textquotesingle /g,"\u0027"],[/\\ast /g,"\u002A"],[/\\textbackslash /g,"\u005C"],[/\\\^\{\}/g,"\u005E"],[/\\textasciigrave /g,"\u0060"],[/\\lbrace /g,"\u007B"],[/\\vert /g,"\u007C"],[/\\rbrace /g,"\u007D"],[/\\textasciitilde /g,"\u007E"],[/\\textexclamdown /g,"\u00A1"],[/\\textcent /g,"\u00A2"],[/\\textsterling /g,"\u00A3"],[/\\textcurrency /g,"\u00A4"],[/\\textyen 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/g,"\u2AB5"],[/\\succneqq /g,"\u2AB6"],[/\\precapprox /g,"\u2AB7"],[/\\succapprox /g,"\u2AB8"],[/\\precnapprox /g,"\u2AB9"],[/\\succnapprox /g,"\u2ABA"],[/\\subseteqq /g,"\u2AC5"],[/\\nsubseteqq /g,"\u2AC5-00338"],[/\\supseteqq /g,"\u2AC6"],[/\\nsupseteqq/g,"\u2AC6-00338"],[/\\subsetneqq /g,"\u2ACB"],[/\\supsetneqq /g,"\u2ACC"],[/\\ElsevierGlyph\{E30D\}/g,"\u2AEB"],[/\\Elztdcol /g,"\u2AF6"],[/\\ElsevierGlyph\{300A\}/g,"\u300A"],[/\\ElsevierGlyph\{300B\}/g,"\u300B"],[/\\ElsevierGlyph\{3018\}/g,"\u3018"],[/\\ElsevierGlyph\{3019\}/g,"\u3019"],[/\\openbracketleft /g,"\u301A"],[/\\openbracketright /g,"\u301B"]];return this}if(typeof module!=="undefined"&&module.exports){module.exports=BibtexParser}; \ No newline at end of file diff -r ee8efcfd787f93c77eb4e451084d64ce4dc6b85e -r 990bc0688199410ab08d5e8a418770b516c6f4e2 static/scripts/packed/mvc/citation/citation-model.js --- a/static/scripts/packed/mvc/citation/citation-model.js +++ b/static/scripts/packed/mvc/citation/citation-model.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","utils/localization"],function(a,e){var f=Backbone.Model.extend(a.LoggableMixin).extend({initialize:function(){var g=this.attributes.content;var h=new BibtexParser(g).entries[0];this.entry=h},entryType:function(){return this.entry.EntryType},fields:function(){return this.entry.Fields}});var b=Backbone.Collection.extend(a.LoggableMixin).extend({urlRoot:galaxy_config.root+"api",partial:true,model:f,});var d=b.extend({url:function(){return this.urlRoot+"/histories/"+this.history_id+"/citations"}});var c=b.extend({url:function(){return this.urlRoot+"/tools/"+this.tool_id+"/citations"},partial:false,});return{Citation:f,HistoryCitationCollection:d,ToolCitationCollection:c}}); \ No newline at end of file +define(["mvc/base-mvc","utils/localization"],function(a,e){var f=Backbone.Model.extend(a.LoggableMixin).extend({initialize:function(){var g=this.attributes.content;var i=new BibtexParser(g).entries[0];this.entry=i;this._fields={};var k=i.Fields;for(key in k){var j=k[key];var h=key.toLowerCase();this._fields[h]=j}},entryType:function(){return this.entry.EntryType},fields:function(){return this._fields}});var b=Backbone.Collection.extend(a.LoggableMixin).extend({urlRoot:galaxy_config.root+"api",partial:true,model:f,});var d=b.extend({url:function(){return this.urlRoot+"/histories/"+this.history_id+"/citations"}});var c=b.extend({url:function(){return this.urlRoot+"/tools/"+this.tool_id+"/citations"},partial:false,});return{Citation:f,HistoryCitationCollection:d,ToolCitationCollection:c}}); \ No newline at end of file diff -r ee8efcfd787f93c77eb4e451084d64ce4dc6b85e -r 990bc0688199410ab08d5e8a418770b516c6f4e2 static/scripts/packed/mvc/citation/citation-view.js --- a/static/scripts/packed/mvc/citation/citation-view.js +++ b/static/scripts/packed/mvc/citation/citation-view.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,d,c){var b=Backbone.View.extend({tagName:"div",className:"citations",render:function(){this.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var j=this.model;var i=j.entryType();var k=j.fields();var g="";var n=this._asSentence((k.author?k.author:"")+(k.year?(" ("+k.year+")"):""))+" ";var m=k.title||"";var h=k.pages?("pp. "+k.pages):"";var o=k.address;if(i=="article"){g=n+this._asSentence(m)+(k.journal?("In <em>"+k.journal+", "):"")+(k.volume?k.volume:"")+(k.number?("("+k.number+"), "):", ")+this._asSentence(h)+this._asSentence(k.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=n+this._asSentence(m)+(k.booktitle?("In <em>"+k.booktitle+", "):"")+(h?h:"")+(o?", "+o:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=n+this._asSentence(m)+(k.howpublished?k.howpublished+". ":"")+(k.note?k.note+".":"")}else{if(i=="techreport"){g=n+". "+this._asSentence(m)+this._asSentence(k.institution)+this._asSentence(k.number)+this._asSentence(k.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=this._asSentence(n)+" "+this._formatBookInfo(k)}else{g=this._asSentence(n)+" "+this._asSentence(m)+this._asSentence(k.howpublished)+this._asSentence(k.note)}}}}}var l="";if(k.DOI){l="http://dx.doi.org/"+k.DOI;g+='[<a href="'+l+'">doi:'+k.DOI+"</a>]"}var f=k.url||l;if(f){g+='[<a href="'+f+'">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return(f&&f.trim())?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".citations-formatted").append(f.render().el);var h=this.$(".citations-bibtex-text");h.val(h.val()+"\n\r"+g.attributes.content)},render:function(){this.$el.html(this.citationsElement());this.collection.each(function(f){this.renderCitation(f)},this);this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show();this.$(".citations-to-bibtex").hide();this.$(".citations-bibtex").show();this.$(".citations-formatted").hide();this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide();this.$(".citations-to-bibtex").show();this.$(".citations-bibtex").hide();this.$(".citations-formatted").show()},partialWarningElement:function(){if(this.collection.partial){return['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",].join("")}else{return""}},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:b,CitationListView:e}}); \ No newline at end of file +define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,d,c){var b=Backbone.View.extend({tagName:"div",className:"citations",render:function(){this.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var j=this.model;var i=j.entryType();var k=j.fields();var g="";var n=this._asSentence((k.author?k.author:"")+(k.year?(" ("+k.year+")"):""))+" ";var m=k.title||"";var h=k.pages?("pp. "+k.pages):"";var o=k.address;if(i=="article"){g=n+this._asSentence(m)+(k.journal?("In <em>"+k.journal+", "):"")+(k.volume?k.volume:"")+(k.number?("("+k.number+"), "):", ")+this._asSentence(h)+this._asSentence(k.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=n+this._asSentence(m)+(k.booktitle?("In <em>"+k.booktitle+", "):"")+(h?h:"")+(o?", "+o:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=n+this._asSentence(m)+(k.howpublished?k.howpublished+". ":"")+(k.note?k.note+".":"")}else{if(i=="techreport"){g=n+". "+this._asSentence(m)+this._asSentence(k.institution)+this._asSentence(k.number)+this._asSentence(k.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=this._asSentence(n)+" "+this._formatBookInfo(k)}else{g=this._asSentence(n)+" "+this._asSentence(m)+this._asSentence(k.howpublished)+this._asSentence(k.note)}}}}}var l="";if(k.doi){l="http://dx.doi.org/"+k.doi;g+='[<a href="'+l+'">doi:'+k.doi+"</a>]"}var f=k.url||l;if(f){g+='[<a href="'+f+'">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return(f&&f.trim())?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".citations-formatted").append(f.render().el);var h=this.$(".citations-bibtex-text");h.val(h.val()+"\n\r"+g.attributes.content)},render:function(){this.$el.html(this.citationsElement());this.collection.each(function(f){this.renderCitation(f)},this);this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show();this.$(".citations-to-bibtex").hide();this.$(".citations-bibtex").show();this.$(".citations-formatted").hide();this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide();this.$(".citations-to-bibtex").show();this.$(".citations-bibtex").hide();this.$(".citations-formatted").show()},partialWarningElement:function(){if(this.collection.partial){return['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",].join("")}else{return""}},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:b,CitationListView:e}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/103697ebdd33/ Changeset: 103697ebdd33 User: jmchilton Date: 2014-08-07 15:36:41 Summary: Merge next-stable. Affected #: 7 files diff -r 6ebb0a47a2a3088ba9ed313d8f323d7e1f5c9bb6 -r 103697ebdd339377424063fba0459cb3cc2b707c lib/galaxy/managers/citations.py --- a/lib/galaxy/managers/citations.py +++ b/lib/galaxy/managers/citations.py @@ -49,7 +49,7 @@ def _raw_get_bibtex( self, doi ): dx_url = "http://dx.doi.org/" + doi - headers = {'Accept': "text/bibliography; style=bibtex" } + headers = {'Accept': 'text/bibliography; style=bibtex, application/x-bibtex'} req = urllib2.Request(dx_url, data="", headers=headers) response = urllib2.urlopen(req) bibtex = response.read() diff -r 6ebb0a47a2a3088ba9ed313d8f323d7e1f5c9bb6 -r 103697ebdd339377424063fba0459cb3cc2b707c static/scripts/libs/bibtex.js --- a/static/scripts/libs/bibtex.js +++ b/static/scripts/libs/bibtex.js @@ -93,6 +93,7 @@ 'booklet' : 14, 'masterthesis' : 15, 'conference' : 16 + ,'data' : 999 // Galaxy MOD: Handle @data citations coming from figshare. } /** @private */ this.MACROS_ = { 'jan' : 'January', diff -r 6ebb0a47a2a3088ba9ed313d8f323d7e1f5c9bb6 -r 103697ebdd339377424063fba0459cb3cc2b707c static/scripts/mvc/citation/citation-model.js --- a/static/scripts/mvc/citation/citation-model.js +++ b/static/scripts/mvc/citation/citation-model.js @@ -18,12 +18,19 @@ var bibtex = this.attributes.content; var entry = new BibtexParser(bibtex).entries[0]; this.entry = entry; + this._fields = {}; + var rawFields = entry.Fields; + for(key in rawFields) { + var value = rawFields[ key ]; + var lowerKey = key.toLowerCase(); + this._fields[ lowerKey ] = value; + } }, entryType: function() { return this.entry.EntryType; }, fields: function() { - return this.entry.Fields; + return this._fields; } } ); diff -r 6ebb0a47a2a3088ba9ed313d8f323d7e1f5c9bb6 -r 103697ebdd339377424063fba0459cb3cc2b707c static/scripts/mvc/citation/citation-view.js --- a/static/scripts/mvc/citation/citation-view.js +++ b/static/scripts/mvc/citation/citation-view.js @@ -55,9 +55,9 @@ this._asSentence(fields.note); } var doiUrl = ""; - if( fields.DOI ) { - doiUrl = 'http://dx.doi.org/' + fields.DOI; - ref += '[<a href="' + doiUrl + '">doi:' + fields.DOI + "</a>]"; + if( fields.doi ) { + doiUrl = 'http://dx.doi.org/' + fields.doi; + ref += '[<a href="' + doiUrl + '">doi:' + fields.doi + "</a>]"; } var url = fields.url || doiUrl; if( url ) { diff -r 6ebb0a47a2a3088ba9ed313d8f323d7e1f5c9bb6 -r 103697ebdd339377424063fba0459cb3cc2b707c static/scripts/packed/libs/bibtex.js --- a/static/scripts/packed/libs/bibtex.js +++ b/static/scripts/packed/libs/bibtex.js @@ -1,1 +1,1 @@ -function BibtexParser(c){if(typeof c=="string"){var d={};var a=[];function b(f){a.push(f)}var e=BibtexParser.call(d,b);e.parse(c);return{entries:a,errors:e.getErrors()}}if(typeof c!="function"){throw"Invalid parser construction."}this.STATES_={ENTRY_OR_JUNK:0,OBJECT_TYPE:1,ENTRY_KEY:2,KV_KEY:3,EQUALS:4,KV_VALUE:5};this.DATA_={};this.CALLBACK_=c;this.CHAR_=0;this.LINE_=1;this.CHAR_IN_LINE_=0;this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.PARSETMP_={};this.SKIPTILLEOL_=false;this.VALBRACES_=null;this.BRACETYPE_=null;this.BRACECOUNT_=0;this.STATE_=this.STATES_.ENTRY_OR_JUNK;this.ERRORS_=[];this.ENTRY_TYPES_={inproceedings:1,proceedings:2,article:3,techreport:4,misc:5,mastersthesis:6,book:7,phdthesis:8,incollection:9,unpublished:10,inbook:11,manual:12,periodical:13,booklet:14,masterthesis:15,conference:16};this.MACROS_={jan:"January",feb:"February",mar:"March",apr:"April",may:"May",jun:"June",jul:"July",aug:"August",sep:"September",oct:"October",nov:"November",dec:"December",Jan:"January",Feb:"February",Mar:"March",Apr:"April",May:"May",Jun:"June",Jul:"July",Aug:"August",Sep:"September",Oct:"October",Nov:"November",Dec:"December"};this.getErrors=function(){return this.ERRORS_};this.parse=function(f){for(var g=0;g<f.length;g++){this.processCharacter_(f[g])}};this.error_=function(f){this.ERRORS_.push([this.LINE_,this.CHAR_IN_LINE_,this.CHAR_,f])};this.processEntry_=function(){var h=this.DATA_;if(h.Fields){for(var k in h.Fields){var p=h.Fields[k];for(var j=0;j<this.CHARCONV_.length;j++){var q=this.CHARCONV_[j][0];var n=this.CHARCONV_[j][1];p=p.replace(q,n)}p=p.replace(/[\n\r\t]/g," ").replace(/\s\s+/g," ").replace(/^\s+|\s+$/g,"");var l=p.length;var g="";for(var j=0;j<l;j++){var m=p[j];var o=false;if(m=="\\"&&j<l-1){m=p[++j]}else{if(m=="{"||m=="}"){o=true}}if(!o){g+=m}}h.Fields[k]=g}}if(h.ObjectType=="string"){for(var k in h.Fields){this.MACROS_[k]=h.Fields[k]}}else{this.CALLBACK_(h)}};this.processCharacter_=function(l){this.CHAR_++;this.CHAR_IN_LINE_++;if(l=="\n"){this.LINE_++;this.CHAR_IN_LINE_=1}if(this.SKIPTILLEOL_){if(l=="\n"){this.SKIPTILLEOL_=false}return}if(this.SKIPCOMMENT_&&l=="%"){this.SKIPTILLEOL_=true;return}if(this.SKIPWS_&&/\s/.test(l)){return}this.SKIPWS_=false;this.SKIPCOMMENT_=false;this.SKIPTILLEOL_=false;var f=true;while(f){f=false;switch(this.STATE_){case this.STATES_.ENTRY_OR_JUNK:if(l=="@"){this.STATE_=this.STATES_.OBJECT_TYPE;this.DATA_={ObjectType:""}}this.BRACETYPE_=null;this.SKIPWS_=true;this.SKIPCOMMENT_=true;break;case this.STATES_.OBJECT_TYPE:if(/[A-Za-z]/.test(l)){this.DATA_.ObjectType+=l.toLowerCase();this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{var i=this.DATA_.ObjectType;if(i=="comment"){this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{if(i=="string"){this.DATA_.ObjectType=i;this.DATA_.Fields={};this.BRACETYPE_=l;this.BRACECOUNT_=1;this.STATE_=this.STATES_.KV_KEY;this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.PARSETMP_={Key:""}}else{if(i=="preamble"){this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{if(i in this.ENTRY_TYPES_){this.DATA_.ObjectType="entry";this.DATA_.EntryType=i;this.DATA_.EntryKey="";this.STATE_=this.STATES_.ENTRY_KEY;f=true}else{this.error_('Unrecognized object type: "'+this.DATA_.ObjectType+'"');this.STATE_=this.STATES_.ENTRY_OR_JUNK}}}}}break;case this.STATES_.ENTRY_KEY:if((l==="{"||l==="(")&&this.BRACETYPE_==null){this.BRACETYPE_=l;this.BRACECOUNT_=1;this.SKIPWS_=true;this.SKIPCOMMENT_=true;break}if(/[,%\s]/.test(l)){if(this.DATA_.EntryKey.length<1){this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{if(this.BRACETYPE_==null){this.error_("No opening brace for object.");this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{this.SKIPWS_=true;this.SKIPCOMMENT_=true;f=true;this.STATE_=this.STATES_.KV_KEY;this.PARSETMP_.Key="";this.DATA_.Fields={}}}}else{this.DATA_.EntryKey+=l;this.SKIPWS_=false;this.SKIPCOMMENT_=false}break;case this.STATES_.KV_KEY:if((l=="}"&&this.BRACETYPE_=="{")||(l==")"&&this.BRACETYPE_=="(")){this.processEntry_();this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.ENTRY_OR_JUNK;break}if(/[\-A-Za-z:]/.test(l)){this.PARSETMP_.Key+=l;this.SKIPWS_=false;this.SKIPCOMMENT_=false}else{if(this.PARSETMP_.Key.length<1){this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.EQUALS;f=true}}break;case this.STATES_.EQUALS:if((l=="}"&&this.BRACETYPE_=="{")||(l==")"&&this.BRACETYPE_=="(")){this.error_('Key-value pair has key "'+this.PARSETMP_.Key+'", but no 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/g,"\u2A54"],[/\\ElsevierGlyph\{E36E\}/g,"\u2A55"],[/\\ElOr /g,"\u2A56"],[/\\perspcorrespond /g,"\u2A5E"],[/\\Elzminhat /g,"\u2A5F"],[/\\ElsevierGlyph\{225A\}/g,"\u2A63"],[/\\stackrel\{*\}\{=\}/g,"\u2A6E"],[/\\Equal /g,"\u2A75"],[/\\leqslant /g,"\u2A7D"],[/\\nleqslant /g,"\u2A7D-00338"],[/\\geqslant /g,"\u2A7E"],[/\\ngeqslant /g,"\u2A7E-00338"],[/\\lessapprox /g,"\u2A85"],[/\\gtrapprox /g,"\u2A86"],[/\\lneq /g,"\u2A87"],[/\\gneq /g,"\u2A88"],[/\\lnapprox /g,"\u2A89"],[/\\gnapprox /g,"\u2A8A"],[/\\lesseqqgtr /g,"\u2A8B"],[/\\gtreqqless /g,"\u2A8C"],[/\\eqslantless /g,"\u2A95"],[/\\eqslantgtr /g,"\u2A96"],[/\\Pisymbol\{ppi020\}\{117\}/g,"\u2A9D"],[/\\Pisymbol\{ppi020\}\{105\}/g,"\u2A9E"],[/\\NestedLessLess /g,"\u2AA1"],[/\\NotNestedLessLess /g,"\u2AA1-00338"],[/\\NestedGreaterGreater /g,"\u2AA2"],[/\\NotNestedGreaterGreater /g,"\u2AA2-00338"],[/\\preceq /g,"\u2AAF"],[/\\not\\preceq /g,"\u2AAF-00338"],[/\\succeq /g,"\u2AB0"],[/\\not\\succeq /g,"\u2AB0-00338"],[/\\precneqq /g,"\u2AB5"],[/\\succneqq /g,"\u2AB6"],[/\\precapprox /g,"\u2AB7"],[/\\succapprox /g,"\u2AB8"],[/\\precnapprox /g,"\u2AB9"],[/\\succnapprox /g,"\u2ABA"],[/\\subseteqq /g,"\u2AC5"],[/\\nsubseteqq /g,"\u2AC5-00338"],[/\\supseteqq /g,"\u2AC6"],[/\\nsupseteqq/g,"\u2AC6-00338"],[/\\subsetneqq /g,"\u2ACB"],[/\\supsetneqq /g,"\u2ACC"],[/\\ElsevierGlyph\{E30D\}/g,"\u2AEB"],[/\\Elztdcol /g,"\u2AF6"],[/\\ElsevierGlyph\{300A\}/g,"\u300A"],[/\\ElsevierGlyph\{300B\}/g,"\u300B"],[/\\ElsevierGlyph\{3018\}/g,"\u3018"],[/\\ElsevierGlyph\{3019\}/g,"\u3019"],[/\\openbracketleft /g,"\u301A"],[/\\openbracketright /g,"\u301B"]];return this}if(typeof module!=="undefined"&&module.exports){module.exports=BibtexParser}; \ No newline at end of file +function BibtexParser(c){if(typeof c=="string"){var d={};var a=[];function b(f){a.push(f)}var e=BibtexParser.call(d,b);e.parse(c);return{entries:a,errors:e.getErrors()}}if(typeof c!="function"){throw"Invalid parser construction."}this.STATES_={ENTRY_OR_JUNK:0,OBJECT_TYPE:1,ENTRY_KEY:2,KV_KEY:3,EQUALS:4,KV_VALUE:5};this.DATA_={};this.CALLBACK_=c;this.CHAR_=0;this.LINE_=1;this.CHAR_IN_LINE_=0;this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.PARSETMP_={};this.SKIPTILLEOL_=false;this.VALBRACES_=null;this.BRACETYPE_=null;this.BRACECOUNT_=0;this.STATE_=this.STATES_.ENTRY_OR_JUNK;this.ERRORS_=[];this.ENTRY_TYPES_={inproceedings:1,proceedings:2,article:3,techreport:4,misc:5,mastersthesis:6,book:7,phdthesis:8,incollection:9,unpublished:10,inbook:11,manual:12,periodical:13,booklet:14,masterthesis:15,conference:16,data:999};this.MACROS_={jan:"January",feb:"February",mar:"March",apr:"April",may:"May",jun:"June",jul:"July",aug:"August",sep:"September",oct:"October",nov:"November",dec:"December",Jan:"January",Feb:"February",Mar:"March",Apr:"April",May:"May",Jun:"June",Jul:"July",Aug:"August",Sep:"September",Oct:"October",Nov:"November",Dec:"December"};this.getErrors=function(){return this.ERRORS_};this.parse=function(f){for(var g=0;g<f.length;g++){this.processCharacter_(f[g])}};this.error_=function(f){this.ERRORS_.push([this.LINE_,this.CHAR_IN_LINE_,this.CHAR_,f])};this.processEntry_=function(){var h=this.DATA_;if(h.Fields){for(var k in h.Fields){var p=h.Fields[k];for(var j=0;j<this.CHARCONV_.length;j++){var q=this.CHARCONV_[j][0];var n=this.CHARCONV_[j][1];p=p.replace(q,n)}p=p.replace(/[\n\r\t]/g," ").replace(/\s\s+/g," ").replace(/^\s+|\s+$/g,"");var l=p.length;var g="";for(var j=0;j<l;j++){var m=p[j];var o=false;if(m=="\\"&&j<l-1){m=p[++j]}else{if(m=="{"||m=="}"){o=true}}if(!o){g+=m}}h.Fields[k]=g}}if(h.ObjectType=="string"){for(var k in h.Fields){this.MACROS_[k]=h.Fields[k]}}else{this.CALLBACK_(h)}};this.processCharacter_=function(l){this.CHAR_++;this.CHAR_IN_LINE_++;if(l=="\n"){this.LINE_++;this.CHAR_IN_LINE_=1}if(this.SKIPTILLEOL_){if(l=="\n"){this.SKIPTILLEOL_=false}return}if(this.SKIPCOMMENT_&&l=="%"){this.SKIPTILLEOL_=true;return}if(this.SKIPWS_&&/\s/.test(l)){return}this.SKIPWS_=false;this.SKIPCOMMENT_=false;this.SKIPTILLEOL_=false;var f=true;while(f){f=false;switch(this.STATE_){case this.STATES_.ENTRY_OR_JUNK:if(l=="@"){this.STATE_=this.STATES_.OBJECT_TYPE;this.DATA_={ObjectType:""}}this.BRACETYPE_=null;this.SKIPWS_=true;this.SKIPCOMMENT_=true;break;case this.STATES_.OBJECT_TYPE:if(/[A-Za-z]/.test(l)){this.DATA_.ObjectType+=l.toLowerCase();this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{var i=this.DATA_.ObjectType;if(i=="comment"){this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{if(i=="string"){this.DATA_.ObjectType=i;this.DATA_.Fields={};this.BRACETYPE_=l;this.BRACECOUNT_=1;this.STATE_=this.STATES_.KV_KEY;this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.PARSETMP_={Key:""}}else{if(i=="preamble"){this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{if(i in this.ENTRY_TYPES_){this.DATA_.ObjectType="entry";this.DATA_.EntryType=i;this.DATA_.EntryKey="";this.STATE_=this.STATES_.ENTRY_KEY;f=true}else{this.error_('Unrecognized object type: "'+this.DATA_.ObjectType+'"');this.STATE_=this.STATES_.ENTRY_OR_JUNK}}}}}break;case this.STATES_.ENTRY_KEY:if((l==="{"||l==="(")&&this.BRACETYPE_==null){this.BRACETYPE_=l;this.BRACECOUNT_=1;this.SKIPWS_=true;this.SKIPCOMMENT_=true;break}if(/[,%\s]/.test(l)){if(this.DATA_.EntryKey.length<1){this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{if(this.BRACETYPE_==null){this.error_("No opening brace for 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in k){var j=k[key];var h=key.toLowerCase();this._fields[h]=j}},entryType:function(){return this.entry.EntryType},fields:function(){return this._fields}});var b=Backbone.Collection.extend(a.LoggableMixin).extend({urlRoot:galaxy_config.root+"api",partial:true,model:f,});var d=b.extend({url:function(){return this.urlRoot+"/histories/"+this.history_id+"/citations"}});var c=b.extend({url:function(){return this.urlRoot+"/tools/"+this.tool_id+"/citations"},partial:false,});return{Citation:f,HistoryCitationCollection:d,ToolCitationCollection:c}}); \ No newline at end of file diff -r 6ebb0a47a2a3088ba9ed313d8f323d7e1f5c9bb6 -r 103697ebdd339377424063fba0459cb3cc2b707c static/scripts/packed/mvc/citation/citation-view.js --- a/static/scripts/packed/mvc/citation/citation-view.js +++ b/static/scripts/packed/mvc/citation/citation-view.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,d,c){var b=Backbone.View.extend({tagName:"div",className:"citations",render:function(){this.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var j=this.model;var i=j.entryType();var k=j.fields();var g="";var n=this._asSentence((k.author?k.author:"")+(k.year?(" ("+k.year+")"):""))+" ";var m=k.title||"";var h=k.pages?("pp. "+k.pages):"";var o=k.address;if(i=="article"){g=n+this._asSentence(m)+(k.journal?("In <em>"+k.journal+", "):"")+(k.volume?k.volume:"")+(k.number?("("+k.number+"), "):", ")+this._asSentence(h)+this._asSentence(k.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=n+this._asSentence(m)+(k.booktitle?("In <em>"+k.booktitle+", "):"")+(h?h:"")+(o?", "+o:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=n+this._asSentence(m)+(k.howpublished?k.howpublished+". ":"")+(k.note?k.note+".":"")}else{if(i=="techreport"){g=n+". "+this._asSentence(m)+this._asSentence(k.institution)+this._asSentence(k.number)+this._asSentence(k.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=this._asSentence(n)+" "+this._formatBookInfo(k)}else{g=this._asSentence(n)+" "+this._asSentence(m)+this._asSentence(k.howpublished)+this._asSentence(k.note)}}}}}var l="";if(k.DOI){l="http://dx.doi.org/"+k.DOI;g+='[<a href="'+l+'">doi:'+k.DOI+"</a>]"}var f=k.url||l;if(f){g+='[<a href="'+f+'">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return(f&&f.trim())?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".citations-formatted").append(f.render().el);var h=this.$(".citations-bibtex-text");h.val(h.val()+"\n\r"+g.attributes.content)},render:function(){this.$el.html(this.citationsElement());this.collection.each(function(f){this.renderCitation(f)},this);this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show();this.$(".citations-to-bibtex").hide();this.$(".citations-bibtex").show();this.$(".citations-formatted").hide();this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide();this.$(".citations-to-bibtex").show();this.$(".citations-bibtex").hide();this.$(".citations-formatted").show()},partialWarningElement:function(){if(this.collection.partial){return['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",].join("")}else{return""}},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:b,CitationListView:e}}); \ No newline at end of file +define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,d,c){var b=Backbone.View.extend({tagName:"div",className:"citations",render:function(){this.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var j=this.model;var i=j.entryType();var k=j.fields();var g="";var n=this._asSentence((k.author?k.author:"")+(k.year?(" ("+k.year+")"):""))+" ";var m=k.title||"";var h=k.pages?("pp. "+k.pages):"";var o=k.address;if(i=="article"){g=n+this._asSentence(m)+(k.journal?("In <em>"+k.journal+", "):"")+(k.volume?k.volume:"")+(k.number?("("+k.number+"), "):", ")+this._asSentence(h)+this._asSentence(k.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=n+this._asSentence(m)+(k.booktitle?("In <em>"+k.booktitle+", "):"")+(h?h:"")+(o?", "+o:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=n+this._asSentence(m)+(k.howpublished?k.howpublished+". ":"")+(k.note?k.note+".":"")}else{if(i=="techreport"){g=n+". "+this._asSentence(m)+this._asSentence(k.institution)+this._asSentence(k.number)+this._asSentence(k.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=this._asSentence(n)+" "+this._formatBookInfo(k)}else{g=this._asSentence(n)+" "+this._asSentence(m)+this._asSentence(k.howpublished)+this._asSentence(k.note)}}}}}var l="";if(k.doi){l="http://dx.doi.org/"+k.doi;g+='[<a href="'+l+'">doi:'+k.doi+"</a>]"}var f=k.url||l;if(f){g+='[<a href="'+f+'">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return(f&&f.trim())?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".citations-formatted").append(f.render().el);var h=this.$(".citations-bibtex-text");h.val(h.val()+"\n\r"+g.attributes.content)},render:function(){this.$el.html(this.citationsElement());this.collection.each(function(f){this.renderCitation(f)},this);this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show();this.$(".citations-to-bibtex").hide();this.$(".citations-bibtex").show();this.$(".citations-formatted").hide();this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide();this.$(".citations-to-bibtex").show();this.$(".citations-bibtex").hide();this.$(".citations-formatted").show()},partialWarningElement:function(){if(this.collection.partial){return['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",].join("")}else{return""}},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:b,CitationListView:e}}); \ No newline at end of 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.

1 0

commit/galaxy-central: jmchilton: Fix more BibTeX problems caught by @peterjc.
by commits-noreply＠bitbucket.org 06 Aug '14

06 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6ebb0a47a2a3/ Changeset: 6ebb0a47a2a3 User: jmchilton Date: 2014-08-06 18:36:27 Summary: Fix more BibTeX problems caught by @peterjc. See https://bitbucket.org/galaxy/galaxy-central/commits/3e8dfd372918c90ee4b3726…. Thanks Peter! Affected #: 1 file diff -r 3e8dfd372918c90ee4b37267f0b7c03a291acb54 -r 6ebb0a47a2a3088ba9ed313d8f323d7e1f5c9bb6 tools/phenotype_association/lps.xml --- a/tools/phenotype_association/lps.xml +++ b/tools/phenotype_association/lps.xml @@ -308,12 +308,16 @@ journal = {Journal of Machine Learning Research}, year = {2007}, volume = {8}, - pages = {1519-1555}, + pages = {1519--1555}, }</citation> - <citation type="bibtex">@MISC{Shi08lasso-patternsearchalgorithm, + <citation type="bibtex">@ARTICLE{Shi08lasso-patternsearchalgorithm, author = {Weiliang Shi and Grace Wahba and Stephen Wright and Kristine Lee and Ronald Klein and Barbara Klein}, - title = { LASSO-Patternsearch Algorithm with Application to Ophthalmology and Genomic Data}, - year = {2008} + title = {LASSO-Patternsearch Algorithm with Application to Ophthalmology and Genomic Data}, + journal= {Stat Interface}, + year = {2008}, + volume = {1}, + number = {1}, + pages = {137--153} }</citation></citations></tool> 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: jmchilton: Fix citation problem in 39c9831 caught by @peterjc.
by commits-noreply＠bitbucket.org 06 Aug '14

06 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3e8dfd372918/ Changeset: 3e8dfd372918 User: jmchilton Date: 2014-08-06 18:31:50 Summary: Fix citation problem in 39c9831 caught by @peterjc. Affected #: 1 file diff -r 0e9c220ff8cd619c902aca574a07f208a2a30a21 -r 3e8dfd372918c90ee4b37267f0b7c03a291acb54 tools/phenotype_association/lps.xml --- a/tools/phenotype_association/lps.xml +++ b/tools/phenotype_association/lps.xml @@ -307,7 +307,8 @@ title = {An interior-point method for large-scale l1-regularized logistic regression}, journal = {Journal of Machine Learning Research}, year = {2007}, - volume = {2007} + volume = {8}, + pages = {1519-1555}, }</citation><citation type="bibtex">@MISC{Shi08lasso-patternsearchalgorithm, author = {Weiliang Shi and Grace Wahba and Stephen Wright and Kristine Lee and Ronald Klein and Barbara Klein}, 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: 2 new changesets
by commits-noreply＠bitbucket.org 06 Aug '14

06 Aug '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a57767f4ae8f/ Changeset: a57767f4ae8f Branch: next-stable User: dannon Date: 2014-08-06 16:16:22 Summary: Fix for conditionally using bucket_default in cloudlaunch. Affected #: 1 file diff -r 283f3be266eab2951f04cda8204fc24af22983ca -r a57767f4ae8f5e45ed04a123aae5be53c69ebe91 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py --- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py +++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py @@ -70,10 +70,18 @@ cfg = cloudman.CloudManConfig(key_id, secret, cluster_name, ami, instance_type, password, placement=zone) cml = cloudman.launch.CloudManLauncher(key_id, secret) - result = cml.launch(cluster_name, ami, instance_type, password, - cfg.kernel_id, cfg.ramdisk_id, cfg.key_name, - cfg.security_groups, cfg.placement, - bucket_default=bucket_default) + # This should probably be handled better on the bioblend side, but until + # an egg update can be made, this needs to conditionally include the + # parameter or not, even if the value is None. + if bucket_default: + result = cml.launch(cluster_name, ami, instance_type, password, + cfg.kernel_id, cfg.ramdisk_id, cfg.key_name, + cfg.security_groups, cfg.placement, + bucket_default=bucket_default) + else: + result = cml.launch(cluster_name, ami, instance_type, password, + cfg.kernel_id, cfg.ramdisk_id, cfg.key_name, + cfg.security_groups, cfg.placement) # result is a dict with sg_names, kp_name, kp_material, rs, and instance_id if not result['rs']: trans.response.status = 400 https://bitbucket.org/galaxy/galaxy-central/commits/3976f4d59bc0/ Changeset: 3976f4d59bc0 Branch: next-stable User: dannon Date: 2014-08-06 17:25:12 Summary: Merge. Affected #: 3 files diff -r a57767f4ae8f5e45ed04a123aae5be53c69ebe91 -r 3976f4d59bc0d7b65575e7573f13fb7470c9bf53 lib/galaxy/managers/citations.py --- a/lib/galaxy/managers/citations.py +++ b/lib/galaxy/managers/citations.py @@ -157,8 +157,8 @@ if self.raw_bibtex is DoiCitation.BIBTEX_UNSET: return """@MISC{%s, - DOI = '%s', - note = 'Failed to fetch BibTeX for DOI.' + DOI = {%s}, + note = {Failed to fetch BibTeX for DOI.} }""" % (self.__doi, self.__doi) else: return self.raw_bibtex diff -r a57767f4ae8f5e45ed04a123aae5be53c69ebe91 -r 3976f4d59bc0d7b65575e7573f13fb7470c9bf53 static/scripts/mvc/citation/citation-view.js --- a/static/scripts/mvc/citation/citation-view.js +++ b/static/scripts/mvc/citation/citation-view.js @@ -94,7 +94,7 @@ return info + "."; }, _asSentence: function(str) { - return str ? str + ". " : ""; + return (str && str.trim()) ? str + ". " : ""; } }); diff -r a57767f4ae8f5e45ed04a123aae5be53c69ebe91 -r 3976f4d59bc0d7b65575e7573f13fb7470c9bf53 static/scripts/packed/mvc/citation/citation-view.js --- a/static/scripts/packed/mvc/citation/citation-view.js +++ b/static/scripts/packed/mvc/citation/citation-view.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,d,c){var b=Backbone.View.extend({tagName:"div",className:"citations",render:function(){this.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var j=this.model;var i=j.entryType();var k=j.fields();var g="";var n=this._asSentence((k.author?k.author:"")+(k.year?(" ("+k.year+")"):""))+" ";var m=k.title||"";var h=k.pages?("pp. "+k.pages):"";var o=k.address;if(i=="article"){g=n+this._asSentence(m)+(k.journal?("In <em>"+k.journal+", "):"")+(k.volume?k.volume:"")+(k.number?("("+k.number+"), "):", ")+this._asSentence(h)+this._asSentence(k.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=n+this._asSentence(m)+(k.booktitle?("In <em>"+k.booktitle+", "):"")+(h?h:"")+(o?", "+o:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=n+this._asSentence(m)+(k.howpublished?k.howpublished+". ":"")+(k.note?k.note+".":"")}else{if(i=="techreport"){g=n+". "+this._asSentence(m)+this._asSentence(k.institution)+this._asSentence(k.number)+this._asSentence(k.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=this._asSentence(n)+" "+this._formatBookInfo(k)}else{g=this._asSentence(n)+" "+this._asSentence(m)+this._asSentence(k.howpublished)+this._asSentence(k.note)}}}}}var l="";if(k.DOI){l="http://dx.doi.org/"+k.DOI;g+='[<a href="'+l+'">doi:'+k.DOI+"</a>]"}var f=k.url||l;if(f){g+='[<a href="'+f+'">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return f?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".citations-formatted").append(f.render().el);var h=this.$(".citations-bibtex-text");h.val(h.val()+"\n\r"+g.attributes.content)},render:function(){this.$el.html(this.citationsElement());this.collection.each(function(f){this.renderCitation(f)},this);this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show();this.$(".citations-to-bibtex").hide();this.$(".citations-bibtex").show();this.$(".citations-formatted").hide();this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide();this.$(".citations-to-bibtex").show();this.$(".citations-bibtex").hide();this.$(".citations-formatted").show()},partialWarningElement:function(){if(this.collection.partial){return['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",].join("")}else{return""}},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:b,CitationListView:e}}); \ No newline at end of file +define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,d,c){var b=Backbone.View.extend({tagName:"div",className:"citations",render:function(){this.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var j=this.model;var i=j.entryType();var k=j.fields();var g="";var n=this._asSentence((k.author?k.author:"")+(k.year?(" ("+k.year+")"):""))+" ";var m=k.title||"";var h=k.pages?("pp. "+k.pages):"";var o=k.address;if(i=="article"){g=n+this._asSentence(m)+(k.journal?("In <em>"+k.journal+", "):"")+(k.volume?k.volume:"")+(k.number?("("+k.number+"), "):", ")+this._asSentence(h)+this._asSentence(k.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=n+this._asSentence(m)+(k.booktitle?("In <em>"+k.booktitle+", "):"")+(h?h:"")+(o?", "+o:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=n+this._asSentence(m)+(k.howpublished?k.howpublished+". ":"")+(k.note?k.note+".":"")}else{if(i=="techreport"){g=n+". "+this._asSentence(m)+this._asSentence(k.institution)+this._asSentence(k.number)+this._asSentence(k.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=this._asSentence(n)+" "+this._formatBookInfo(k)}else{g=this._asSentence(n)+" "+this._asSentence(m)+this._asSentence(k.howpublished)+this._asSentence(k.note)}}}}}var l="";if(k.DOI){l="http://dx.doi.org/"+k.DOI;g+='[<a href="'+l+'">doi:'+k.DOI+"</a>]"}var f=k.url||l;if(f){g+='[<a href="'+f+'">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return(f&&f.trim())?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".citations-formatted").append(f.render().el);var h=this.$(".citations-bibtex-text");h.val(h.val()+"\n\r"+g.attributes.content)},render:function(){this.$el.html(this.citationsElement());this.collection.each(function(f){this.renderCitation(f)},this);this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show();this.$(".citations-to-bibtex").hide();this.$(".citations-bibtex").show();this.$(".citations-formatted").hide();this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide();this.$(".citations-to-bibtex").show();this.$(".citations-bibtex").hide();this.$(".citations-formatted").show()},partialWarningElement:function(){if(this.collection.partial){return['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",].join("")}else{return""}},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:b,CitationListView:e}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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