[galaxy-commits] commit/galaxy-central: 2 new changesets

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7094bb55cc8a/ Changeset: 7094bb55cc8a User: jmchilton Date: 2014-06-29 20:31:33 Summary: Spelling fix in method name. Affected #: 2 files diff -r 381a36069c14bf20c98955c01ab00e7838257943 -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2931,7 +2931,7 @@ Find any additional datasets generated by a tool and attach (for cases where number of outputs is not known in advance). """ - return output_collect.collect_primary_datatasets( self, output, job_working_directory ) + return output_collect.collect_primary_datasets( self, output, job_working_directory ) def to_dict( self, trans, link_details=False, io_details=False ): """ Returns dict of tool. """ diff -r 381a36069c14bf20c98955c01ab00e7838257943 -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c lib/galaxy/tools/parameters/output_collect.py --- a/lib/galaxy/tools/parameters/output_collect.py +++ b/lib/galaxy/tools/parameters/output_collect.py @@ -14,7 +14,7 @@ DEFAULT_EXTRA_FILENAME_PATTERN = r"primary_DATASET_ID_(?P<designation>[^_]+)_(?P<visible>[^_]+)_(?P<ext>[^_]+)(_(?P<dbkey>[^_]+))?" -def collect_primary_datatasets( tool, output, job_working_directory ): +def collect_primary_datasets( tool, output, job_working_directory ): app = tool.app sa_session = tool.sa_session new_primary_datasets = {} https://bitbucket.org/galaxy/galaxy-central/commits/4de240e5a781/ Changeset: 4de240e5a781 User: jmchilton Date: 2014-06-29 20:31:33 Summary: Allow discovered datasets to use input data format in 'ext' definition. Affected #: 4 files diff -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c -r 4de240e5a7819c768b8267c19e477530dab54370 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1181,6 +1181,13 @@ out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] ) inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets ] ) + input_ext = 'data' + for _, data in inp_data.items(): + # For loop odd, but sort simulating behavior in galaxy.tools.actions + if not data: + continue + input_ext = data.ext + param_dict = dict( [ ( p.name, p.value ) for p in job.parameters ] ) # why not re-use self.param_dict here? ##dunno...probably should, this causes tools.parameters.basic.UnvalidatedValue to be used in following methods instead of validated and transformed values during i.e. running workflows param_dict = self.tool.params_from_strings( param_dict, self.app ) # Check for and move associated_files @@ -1191,7 +1198,7 @@ # Create generated output children and primary datasets and add to param_dict collected_datasets = { 'children': self.tool.collect_child_datasets(out_data, self.working_directory), - 'primary': self.tool.collect_primary_datasets(out_data, self.working_directory) + 'primary': self.tool.collect_primary_datasets(out_data, self.working_directory, input_ext) } param_dict.update({'__collected_datasets__': collected_datasets}) # Certain tools require tasks to be completed after job execution diff -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c -r 4de240e5a7819c768b8267c19e477530dab54370 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2926,12 +2926,12 @@ self.sa_session.flush() return children - def collect_primary_datasets( self, output, job_working_directory ): + def collect_primary_datasets( self, output, job_working_directory, input_ext ): """ Find any additional datasets generated by a tool and attach (for cases where number of outputs is not known in advance). """ - return output_collect.collect_primary_datasets( self, output, job_working_directory ) + return output_collect.collect_primary_datasets( self, output, job_working_directory, input_ext ) def to_dict( self, trans, link_details=False, io_details=False ): """ Returns dict of tool. """ diff -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c -r 4de240e5a7819c768b8267c19e477530dab54370 lib/galaxy/tools/parameters/output_collect.py --- a/lib/galaxy/tools/parameters/output_collect.py +++ b/lib/galaxy/tools/parameters/output_collect.py @@ -14,7 +14,7 @@ DEFAULT_EXTRA_FILENAME_PATTERN = r"primary_DATASET_ID_(?P<designation>[^_]+)_(?P<visible>[^_]+)_(?P<ext>[^_]+)(_(?P<dbkey>[^_]+))?" -def collect_primary_datasets( tool, output, job_working_directory ): +def collect_primary_datasets( tool, output, job_working_directory, input_ext ): app = tool.app sa_session = tool.sa_session new_primary_datasets = {} @@ -66,6 +66,8 @@ designation = fields_match.designation visible = fields_match.visible ext = fields_match.ext + if ext == "input": + ext = input_ext dbkey = fields_match.dbkey # Create new primary dataset primary_data = app.model.HistoryDatasetAssociation( extension=ext, diff -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c -r 4de240e5a7819c768b8267c19e477530dab54370 test/functional/tools/multi_output_configured.xml --- a/test/functional/tools/multi_output_configured.xml +++ b/test/functional/tools/multi_output_configured.xml @@ -8,19 +8,24 @@ echo "1" > subdir2/CUSTOM_1.txt; echo "2" > subdir2/CUSTOM_2.tabular; echo "3" > subdir2/CUSTOM_3.txt; + mkdir subdir3; + echo "Foo" > subdir3/Foo; </command><inputs> - <param name="input" type="integer" value="7" /> + <param name="num_param" type="integer" value="7" /> + <param name="input" type="data" /></inputs><outputs><data format="txt" name="report"><discover_datasets pattern="__designation_and_ext__" directory="subdir1" /><discover_datasets pattern="CUSTOM_(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;.+)" directory="subdir2" /> + <discover_datasets pattern="__designation__" directory="subdir3" ext="input" /></data></outputs><tests><test> - <param name="input" value="7" /> + <param name="num_param" value="7" /> + <param name="input" ftype="txt" value="simple_line.txt"/><output name="report"><assert_contents><has_line line="Hello" /> @@ -37,6 +42,9 @@ <discovered_dataset designation="2" ftype="tabular"><assert_contents><has_line line="2" /></assert_contents></discovered_dataset> + <discovered_dataset designation="Foo" ftype="txt"> + <assert_contents><has_line line="Foo" /></assert_contents> + </discovered_dataset></output></test></tests> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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