diff --git a/lib/galaxy/jobs/runners/drmaa.py b/lib/galaxy/jobs/runners/drmaa.py index 62206f165d1..1fb01e89927 100644 --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -15,7 +15,6 @@ from galaxy.jobs import JobDestination from galaxy.jobs.handler import DEFAULT_JOB_PUT_FAILURE_MESSAGE from galaxy.jobs.runners import AsynchronousJobState, AsynchronousJobRunner from galaxy.util import asbool -from pulsar.managers.util.drmaa import DrmaaSessionFactory drmaa = None @@ -62,6 +61,7 @@ class DRMAAJobRunner( AsynchronousJobRunner ): 'feature, please install it or correct the ' 'following error:\n%s: %s' % (exc.__class__.__name__, str(exc))) + from pulsar.managers.util.drmaa import DrmaaSessionFactory # Subclasses may need access to state constants self.drmaa_job_states = drmaa.JobState diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py index 9b010c144ec..d70fd8fe53a 100644 --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -7,7 +7,7 @@ from six import string_types from galaxy import model from galaxy.exceptions import ObjectInvalid from galaxy.model import LibraryDatasetDatasetAssociation -from galaxy.tools.parameters.basic import DataCollectionToolParameter, DataToolParameter +from galaxy.tools.parameters.basic import DataCollectionToolParameter, DataToolParameter, RuntimeValue from galaxy.tools.parameters.wrapped import WrappedParameters from galaxy.tools.parameters import update_param from galaxy.util import ExecutionTimer @@ -54,8 +54,8 @@ class DefaultToolAction( object ): def visitor( input, value, prefix, parent=None, **kwargs ): def process_dataset( data, formats=None ): - if not data: - return data + if not data or isinstance( data, RuntimeValue ): + return None if formats is None: formats = input.formats if not data.datatype.matches_any( formats ): diff --git a/lib/galaxy/web/security/__init__.py b/lib/galaxy/web/security/__init__.py index 29726ee6ea9..4a2ed331a97 100644 --- a/lib/galaxy/web/security/__init__.py +++ b/lib/galaxy/web/security/__init__.py @@ -54,13 +54,13 @@ class SecurityHelper( object ): # Encrypt return id_cipher.encrypt( s ).encode( 'hex' ) - def encode_dict_ids( self, a_dict, kind=None ): + def encode_dict_ids( self, a_dict, kind=None, skip_startswith=None ): """ Encode all ids in dictionary. Ids are identified by (a) an 'id' key or (b) a key that ends with '_id' """ for key, val in a_dict.items(): - if key == 'id' or key.endswith('_id'): + if key == 'id' or key.endswith('_id') and ( skip_startswith is None or not key.startswith( skip_startswith ) ): a_dict[ key ] = self.encode_id( val, kind=kind ) return a_dict diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py index fd88db5f7b4..26f97f8e7c1 100644 --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -284,7 +284,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ): # so it's possible to figure out which newly created elements # correspond with which tool file outputs output_dict[ 'output_name' ] = output_name - outputs.append( trans.security.encode_dict_ids( output_dict ) ) + outputs.append( trans.security.encode_dict_ids( output_dict, skip_startswith="metadata_" ) ) for job in vars.get('jobs', []): rval[ 'jobs' ].append( self.encode_all_ids( trans, job.to_dict( view='collection' ), recursive=True ) ) diff --git a/test-data/biom1_metadata_test.txt b/test-data/biom1_metadata_test.txt new file mode 100644 index 00000000000..c4514806f24 --- /dev/null +++ b/test-data/biom1_metadata_test.txt @@ -0,0 +1,11 @@ +table_rows: __ob__u__sq__2__sq__, u__sq__3__sq__, u__sq__4__sq__, u__sq__5__sq__, u__sq__8__sq__, u__sq__9__sq__, u__sq__10__sq__, u__sq__11__sq__, u__sq__12__sq__, u__sq__14__sq__, u__sq__15__sq__, u__sq__16__sq__, u__sq__17__sq__, u__sq__18__sq__, u__sq__22__sq__, u__sq__23__sq__, u__sq__25__sq__, u__sq__28__sq__, u__sq__29__sq____cb__ +table_matrix_element_type: float +table_format: Biological Observation Matrix 1.0.0 +table_generated_by: BIOM-Format 2.1.5 +table_matrix_type: sparse +table_shape: __ob__19, 2__cb__ +table_format_url: http://biom-format.org +table_date: 2016-05-26T16:43:45.614267 +table_type: OTU table +table_id: None +table_columns: __ob__u__sq__SAMPLE_1__sq__, u__sq__SAMPLE_2__sq____cb__ \ No newline at end of file diff --git a/test-data/input_taxonomy.biom1 b/test-data/input_taxonomy.biom1 new file mode 100644 index 00000000000..e1c0a5315fb --- /dev/null +++ b/test-data/input_taxonomy.biom1 @@ -0,0 +1 @@ +{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2016-05-26T16:43:45.614267","type": "OTU table","matrix_element_type": "float","shape": [19, 2],"data": [[1,0,160.0],[1,1,242.0],[6,0,1.0],[6,1,1.0],[7,0,3.0],[7,1,4.0],[12,0,13.0],[12,1,36.0],[14,0,1.0],[14,1,5.0],[15,0,1.0],[16,0,1.0],[16,1,3.0]],"rows": [{"id": "2", "metadata": {"taxonomy": ["d__Archaea"]}},{"id": "3", "metadata": {"taxonomy": ["d__Bacteria"]}},{"id": "4", "metadata": {"taxonomy": ["d__Archaea", "p__Crenarchaeota"]}},{"id": "5", "metadata": {"taxonomy": ["d__Archaea", "p__Euryarchaeota"]}},{"id": "8", "metadata": {"taxonomy": ["d__Bacteria", "p__AC1"]}},{"id": "9", "metadata": {"taxonomy": ["d__Bacteria", "p__AD3"]}},{"id": "10", "metadata": {"taxonomy": ["d__Bacteria", "p__Acidobacteria"]}},{"id": "11", "metadata": {"taxonomy": ["d__Bacteria", "p__Actinobacteria"]}},{"id": "12", "metadata": {"taxonomy": ["d__Bacteria", "p__AncK6"]}},{"id": "14", "metadata": {"taxonomy": ["d__Bacteria", "p__Armatimonadetes"]}},{"id": "15", "metadata": {"taxonomy": ["d__Bacteria", "p__BHI80-139"]}},{"id": "16", "metadata": {"taxonomy": ["d__Bacteria", "p__BRC1"]}},{"id": "17", "metadata": {"taxonomy": ["d__Bacteria", "p__Bacteroidetes"]}},{"id": "18", "metadata": {"taxonomy": ["d__Bacteria", "p__CD12"]}},{"id": "22", "metadata": {"taxonomy": ["d__Bacteria", "p__Chlorobi"]}},{"id": "23", "metadata": {"taxonomy": ["d__Bacteria", "p__Chloroflexi"]}},{"id": "25", "metadata": {"taxonomy": ["d__Bacteria", "p__Cyanobacteria"]}},{"id": "28", "metadata": {"taxonomy": ["d__Bacteria", "p__EM19"]}},{"id": "29", "metadata": {"taxonomy": ["d__Bacteria", "p__EM3"]}}],"columns": [{"id": "SAMPLE_1", "metadata": null},{"id": "SAMPLE_2", "metadata": null}]} \ No newline at end of file diff --git a/test/functional/tools/metadata_biom1.xml b/test/functional/tools/metadata_biom1.xml new file mode 100644 index 00000000000..e20ec3652a0 --- /dev/null +++ b/test/functional/tools/metadata_biom1.xml @@ -0,0 +1,28 @@ + + cp "${input_metadata_values}" "${output_of_input_metadata}" + + table_rows: ${input_biom1.metadata.table_rows} +table_matrix_element_type: ${input_biom1.metadata.table_matrix_element_type} +table_format: ${input_biom1.metadata.table_format} +table_generated_by: ${input_biom1.metadata.table_generated_by} +table_matrix_type: ${input_biom1.metadata.table_matrix_type} +table_shape: ${input_biom1.metadata.table_shape} +table_format_url: ${input_biom1.metadata.table_format_url} +table_date: ${input_biom1.metadata.table_date} +table_type: ${input_biom1.metadata.table_type} +table_id: ${input_biom1.metadata.table_id} +table_columns: ${input_biom1.metadata.table_columns} + + + + + + + + + + + + + + diff --git a/test/functional/tools/sample_datatypes_conf.xml b/test/functional/tools/sample_datatypes_conf.xml index 28cb5ff2df7..3891cad99c4 100644 --- a/test/functional/tools/sample_datatypes_conf.xml +++ b/test/functional/tools/sample_datatypes_conf.xml @@ -13,5 +13,6 @@ + - \ No newline at end of file + diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml index 60c7d5edb54..bbbeed7395f 100644 --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -24,6 +24,7 @@ +