May 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: jmchilton: Fix for previous commit.
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b94bb858d29b/ Changeset: b94bb858d29b User: jmchilton Date: 2014-05-16 05:05:04 Summary: Fix for previous commit. Affected #: 1 file diff -r 933d0f2847332024f1fdf40234e74930014794e6 -r b94bb858d29b39f5d8127414bd703ee8e4905281 lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -76,7 +76,7 @@ def __init__(self, **kwds): self.url = kwds.get('url') - self.manager_name = kwds.get("manager", "_default_") + self.manager_name = kwds.get("manager", None) or "_default_" self.connect_ssl = parse_amqp_connect_ssl_params(kwds.get('amqp_connect_ssl_args', None)) timeout = kwds.get('amqp_consumer_timeout', False) if timeout is False: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Bugfix: LWR - Fix manager name not passed into MQClientManager.
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/933d0f284733/ Changeset: 933d0f284733 User: jmchilton Date: 2014-05-16 04:57:54 Summary: Bugfix: LWR - Fix manager name not passed into MQClientManager. Affected #: 1 file diff -r 559c5f4d1bdb694f90826896e5ebc837afa9b4f2 -r 933d0f2847332024f1fdf40234e74930014794e6 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -51,7 +51,13 @@ for kwd in kwds.keys(): if kwd.startswith('amqp_connect_ssl_'): amqp_connect_ssl_args[kwd] = kwds[kwd] - client_manager_kwargs = {'transport_type': transport, 'cache': string_as_bool_or_none(cache), "url": url, 'amqp_connect_ssl_args': amqp_connect_ssl_args or None} + client_manager_kwargs = { + 'transport_type': transport, + 'cache': string_as_bool_or_none(cache), + "url": url, + 'amqp_connect_ssl_args': amqp_connect_ssl_args or None, + 'manager': kwds.get("manager", None), + } if 'amqp_consumer_timeout' in kwds: if kwds['amqp_consumer_timeout'] == 'None': client_manager_kwargs['amqp_consumer_timeout'] = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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

15 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fcd83883072c/ Changeset: fcd83883072c User: jmchilton Date: 2014-05-15 22:58:12 Summary: Fix GALAXY_SLOTS calculation for LSF. Thanks to Ilya Sytchev for the patch. Affected #: 1 file diff -r 47786821cd22eed10d1db9227b2ac18eff760374 -r fcd83883072c64b96ea0f12582fde3d05060b0f4 lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh --- a/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh +++ b/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh @@ -8,6 +8,8 @@ GALAXY_SLOTS="$NSLOTS" elif [ -f "$PBS_NODEFILE" ]; then GALAXY_SLOTS=`wc -l < $PBS_NODEFILE` +elif [ -n "$LSB_DJOB_NUMPROC" ]; then + GALAXY_SLOTS="$LSB_DJOB_NUMPROC" else GALAXY_SLOTS="1" unset GALAXY_SLOTS_CONFIGURED https://bitbucket.org/galaxy/galaxy-central/commits/559c5f4d1bdb/ Changeset: 559c5f4d1bdb User: jmchilton Date: 2014-05-15 22:58:58 Summary: Merge. Affected #: 1 file diff -r fcd83883072c64b96ea0f12582fde3d05060b0f4 -r 559c5f4d1bdb694f90826896e5ebc837afa9b4f2 lib/galaxy/webapps/galaxy/controllers/library_common.py --- a/lib/galaxy/webapps/galaxy/controllers/library_common.py +++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py @@ -473,6 +473,20 @@ dbkey = dbkey[0] file_formats = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ] file_formats.sort() + + def __ok_to_edit_metadata( ldda_id ): + #prevent modifying metadata when dataset is queued or running as input/output + #This code could be more efficient, i.e. by using mappers, but to prevent slowing down loading a History panel, we'll leave the code here for now + for job_to_dataset_association in trans.sa_session.query( self.app.model.JobToInputLibraryDatasetAssociation ) \ + .filter_by( ldda_id=ldda_id ) \ + .all() \ + + trans.sa_session.query( self.app.model.JobToOutputLibraryDatasetAssociation ) \ + .filter_by( ldda_id=ldda_id ) \ + .all(): + if job_to_dataset_association.job.state not in [ job_to_dataset_association.job.states.OK, job_to_dataset_association.job.states.ERROR, job_to_dataset_association.job.states.DELETED ]: + return False + return True + # See if we have any associated templates widgets = [] info_association, inherited = ldda.get_info_association() @@ -480,14 +494,18 @@ widgets = ldda.get_template_widgets( trans ) if params.get( 'change', False ): # The user clicked the Save button on the 'Change data type' form - if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: - trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) - trans.sa_session.flush() - message = "Data type changed for library dataset '%s'." % ldda.name - status = 'done' + if __ok_to_edit_metadata( ldda.id ): + if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: + trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) + trans.sa_session.flush() + message = "Data type changed for library dataset '%s'." % ldda.name + status = 'done' + else: + message = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype ) + status = 'error' else: - message = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype ) - status = 'error' + message = "This dataset is currently being used as input or output. You cannot change datatype until the jobs have completed or you have canceled them." + status = "error" elif params.get( 'save', False ): # The user clicked the Save button on the 'Edit Attributes' form old_name = ldda.name @@ -501,33 +519,40 @@ ldda.name = new_name ldda.info = new_info ldda.message = new_message - # The following for loop will save all metadata_spec items - for name, spec in ldda.datatype.metadata_spec.items(): - if spec.get("readonly"): - continue - optional = params.get( "is_" + name, None ) - if optional and optional == 'true': - # optional element... == 'true' actually means it is NOT checked (and therefore ommitted) - setattr( ldda.metadata, name, None ) - else: - setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) - ldda.metadata.dbkey = dbkey - ldda.datatype.after_setting_metadata( ldda ) + if __ok_to_edit_metadata( ldda.id ): + # The following for loop will save all metadata_spec items + for name, spec in ldda.datatype.metadata_spec.items(): + if spec.get("readonly"): + continue + optional = params.get( "is_" + name, None ) + if optional and optional == 'true': + # optional element... == 'true' actually means it is NOT checked (and therefore ommitted) + setattr( ldda.metadata, name, None ) + else: + setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) + ldda.metadata.dbkey = dbkey + ldda.datatype.after_setting_metadata( ldda ) + message = "Attributes updated for library dataset '%s'." % ldda.name + status = 'done' + else: + message = "Attributes updated, but metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata." + status = 'warning' trans.sa_session.flush() - message = "Attributes updated for library dataset '%s'." % ldda.name - status = 'done' elif params.get( 'detect', False ): # The user clicked the Auto-detect button on the 'Edit Attributes' form - for name, spec in ldda.datatype.metadata_spec.items(): - # We need to be careful about the attributes we are resetting - if name not in [ 'name', 'info', 'dbkey' ]: - if spec.get( 'default' ): - setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) - ldda.datatype.set_meta( ldda ) - ldda.datatype.after_setting_metadata( ldda ) + if __ok_to_edit_metadata( ldda.id ): + for name, spec in ldda.datatype.metadata_spec.items(): + # We need to be careful about the attributes we are resetting + if name not in [ 'name', 'info', 'dbkey' ]: + if spec.get( 'default' ): + setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) + message = "Attributes have been queued to be updated for library dataset '%s'." % ldda.name + status = 'done' + trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming = { 'input1':ldda } ) + else: + message = "This dataset is currently being used as input or output. You cannot change metadata until the jobs have completed or you have canceled them." + status = 'error' trans.sa_session.flush() - message = "Information updated for library dataset '%s'." % ldda.name - status = 'done' elif params.get( 'change_extended_metadata', False): em_string = util.restore_text( params.get("extended_metadata", "") ) if len(em_string): 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: dan: Have auto-detect metadata option in library use external set metadata process.
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/331232edbe8f/ Changeset: 331232edbe8f User: dan Date: 2014-05-15 22:25:44 Summary: Have auto-detect metadata option in library use external set metadata process. Affected #: 1 file diff -r 47786821cd22eed10d1db9227b2ac18eff760374 -r 331232edbe8f30eef4814cc01ac1cb3db4bd09e7 lib/galaxy/webapps/galaxy/controllers/library_common.py --- a/lib/galaxy/webapps/galaxy/controllers/library_common.py +++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py @@ -473,6 +473,20 @@ dbkey = dbkey[0] file_formats = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ] file_formats.sort() + + def __ok_to_edit_metadata( ldda_id ): + #prevent modifying metadata when dataset is queued or running as input/output + #This code could be more efficient, i.e. by using mappers, but to prevent slowing down loading a History panel, we'll leave the code here for now + for job_to_dataset_association in trans.sa_session.query( self.app.model.JobToInputLibraryDatasetAssociation ) \ + .filter_by( ldda_id=ldda_id ) \ + .all() \ + + trans.sa_session.query( self.app.model.JobToOutputLibraryDatasetAssociation ) \ + .filter_by( ldda_id=ldda_id ) \ + .all(): + if job_to_dataset_association.job.state not in [ job_to_dataset_association.job.states.OK, job_to_dataset_association.job.states.ERROR, job_to_dataset_association.job.states.DELETED ]: + return False + return True + # See if we have any associated templates widgets = [] info_association, inherited = ldda.get_info_association() @@ -480,14 +494,18 @@ widgets = ldda.get_template_widgets( trans ) if params.get( 'change', False ): # The user clicked the Save button on the 'Change data type' form - if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: - trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) - trans.sa_session.flush() - message = "Data type changed for library dataset '%s'." % ldda.name - status = 'done' + if __ok_to_edit_metadata( ldda.id ): + if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: + trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) + trans.sa_session.flush() + message = "Data type changed for library dataset '%s'." % ldda.name + status = 'done' + else: + message = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype ) + status = 'error' else: - message = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype ) - status = 'error' + message = "This dataset is currently being used as input or output. You cannot change datatype until the jobs have completed or you have canceled them." + status = "error" elif params.get( 'save', False ): # The user clicked the Save button on the 'Edit Attributes' form old_name = ldda.name @@ -501,33 +519,40 @@ ldda.name = new_name ldda.info = new_info ldda.message = new_message - # The following for loop will save all metadata_spec items - for name, spec in ldda.datatype.metadata_spec.items(): - if spec.get("readonly"): - continue - optional = params.get( "is_" + name, None ) - if optional and optional == 'true': - # optional element... == 'true' actually means it is NOT checked (and therefore ommitted) - setattr( ldda.metadata, name, None ) - else: - setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) - ldda.metadata.dbkey = dbkey - ldda.datatype.after_setting_metadata( ldda ) + if __ok_to_edit_metadata( ldda.id ): + # The following for loop will save all metadata_spec items + for name, spec in ldda.datatype.metadata_spec.items(): + if spec.get("readonly"): + continue + optional = params.get( "is_" + name, None ) + if optional and optional == 'true': + # optional element... == 'true' actually means it is NOT checked (and therefore ommitted) + setattr( ldda.metadata, name, None ) + else: + setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) + ldda.metadata.dbkey = dbkey + ldda.datatype.after_setting_metadata( ldda ) + message = "Attributes updated for library dataset '%s'." % ldda.name + status = 'done' + else: + message = "Attributes updated, but metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata." + status = 'warning' trans.sa_session.flush() - message = "Attributes updated for library dataset '%s'." % ldda.name - status = 'done' elif params.get( 'detect', False ): # The user clicked the Auto-detect button on the 'Edit Attributes' form - for name, spec in ldda.datatype.metadata_spec.items(): - # We need to be careful about the attributes we are resetting - if name not in [ 'name', 'info', 'dbkey' ]: - if spec.get( 'default' ): - setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) - ldda.datatype.set_meta( ldda ) - ldda.datatype.after_setting_metadata( ldda ) + if __ok_to_edit_metadata( ldda.id ): + for name, spec in ldda.datatype.metadata_spec.items(): + # We need to be careful about the attributes we are resetting + if name not in [ 'name', 'info', 'dbkey' ]: + if spec.get( 'default' ): + setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) + message = "Attributes have been queued to be updated for library dataset '%s'." % ldda.name + status = 'done' + trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming = { 'input1':ldda } ) + else: + message = "This dataset is currently being used as input or output. You cannot change metadata until the jobs have completed or you have canceled them." + status = 'error' trans.sa_session.flush() - message = "Information updated for library dataset '%s'." % ldda.name - status = 'done' elif params.get( 'change_extended_metadata', False): em_string = util.restore_text( params.get("extended_metadata", "") ) if len(em_string): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Fix incorrect LWR comment.
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/47786821cd22/ Changeset: 47786821cd22 User: jmchilton Date: 2014-05-15 21:59:57 Summary: Fix incorrect LWR comment. Affected #: 1 file diff -r a50b64b9d70704542eba7dd69410c2a25c54e2a3 -r 47786821cd22eed10d1db9227b2ac18eff760374 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -108,7 +108,7 @@ sleep( 2 ) job_state = self.__find_watched_job( job_id ) if not job_state: - log.warn( "Failed to find job corresponding to final status %s in %s" % ( full_status, self.watched ) ) + log.warn( "Failed to find job corresponding to status %s in %s" % ( full_status, self.watched ) ) else: self.__update_job_state_for_lwr_status(job_state, full_status["status"]) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Merged in jmchilton/galaxy-central-fork-1 (pull request #389)
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a50b64b9d707/ Changeset: a50b64b9d707 User: jmchilton Date: 2014-05-15 20:49:44 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #389) Small Column Parameter Enhancements Affected #: 2 files diff -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b -r a50b64b9d70704542eba7dd69410c2a25c54e2a3 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1096,7 +1096,13 @@ self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) self.ref_input = None + # Legacy style default value specification... self.default_value = elem.get( "default_value", None ) + if self.default_value is None: + # Newer style... more in line with other parameters. + self.default_value = elem.get( "value", None ) + if self.default_value is not None: + self.default_value = ColumnListParameter._strip_c( self.default_value ) self.is_dynamic = True self.usecolnames = string_as_bool( elem.get( "use_header_names", False )) @@ -1105,10 +1111,6 @@ Label convention prepends column number with a 'c', but tool uses the integer. This removes the 'c' when entered into a workflow. """ - def _strip_c( column ): - if column.startswith( 'c' ): - column = column.strip().lower()[1:] - return column if self.multiple: #split on newline and , if value: @@ -1120,16 +1122,22 @@ column2 = column2.strip() if column2: column_list.append( column2 ) - value = map( _strip_c, column_list ) + value = map( ColumnListParameter._strip_c, column_list ) else: value = [] else: if value: - value = _strip_c( value ) + value = ColumnListParameter._strip_c( value ) else: value = None return super( ColumnListParameter, self ).from_html( value, trans, context ) + @staticmethod + def _strip_c(column): + if column.startswith( 'c' ): + column = column.strip().lower()[1:] + return column + def get_column_list( self, trans, other_values ): """ Generate a select list containing the columns of the associated diff -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b -r a50b64b9d70704542eba7dd69410c2a25c54e2a3 test/unit/tools/test_column_parameters.py --- /dev/null +++ b/test/unit/tools/test_column_parameters.py @@ -0,0 +1,97 @@ +""" Tests for tool parameters, more tests exist in test_data_parameters.py and +test_select_parameters.py. +""" + +from unittest import TestCase +from galaxy.tools.parameters import basic +from galaxy.util import bunch +from galaxy import model +from elementtree.ElementTree import XML + +import tools_support + + +class DataColumnParameterTestCase( TestCase, tools_support.UsesApp ): + + def test_from_html(self): + value = self.param.from_html("3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == "3" + + def test_from_html_strips_c(self): + value = self.param.from_html("c1", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == "1" + + def test_multiple_from_html(self): + self.multiple = True + value = self.param.from_html("1,2,3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == ["1", "2", "3"] + + def test_multiple_from_html_with_c(self): + self.multiple = True + value = self.param.from_html("c1,c2,c3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == ["1", "2", "3"] + + def test_get_initial_value_default(self): + self.assertEqual( '1', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_legacy(self): + self.other_attributes = "default_value='2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_newstyle(self): + self.other_attributes = "value='2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_newstyle_strips_c(self): + self.other_attributes = "value='c2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def setUp( self ): + self.setup_app( mock_model=False ) + self.mock_tool = bunch.Bunch( + app=self.app, + tool_type="default", + ) + self.test_history = model.History() + self.app.model.context.add( self.test_history ) + self.app.model.context.flush() + self.trans = bunch.Bunch( + app=self.app, + get_history=lambda: self.test_history, + get_current_user_roles=lambda: [], + workflow_building_mode=False, + webapp=bunch.Bunch( name="galaxy" ), + ) + + self.type = "data_column" + self.other_attributes = "" + self.set_data_ref = "input_tsv" + self.multiple = False + self.optional = False + self._param = None + + def build_ready_hda(self): + hist = model.History() + self.app.model.context.add( hist ) + ready_hda = hist.add_dataset( model.HistoryDatasetAssociation( extension='interval', create_dataset=True, sa_session=self.app.model.context ) ) + ready_hda.set_dataset_state( 'ok' ) + return ready_hda + + @property + def param( self ): + if not self._param: + multi_text = "" + if self.multiple: + multi_text = 'multiple="True"' + optional_text = "" + if self.optional: + optional_text = 'optional="True"' + data_ref_text = "" + if self.set_data_ref: + data_ref_text = 'data_ref="input_tsv"' + template_xml = '''<param name="my_name" type="%s" %s %s %s %s></param>''' + self.param_xml = XML( template_xml % ( self.type, data_ref_text, multi_text, optional_text, self.other_attributes ) ) + self._param = basic.ColumnListParameter( self.mock_tool, self.param_xml ) + self._param.ref_input = bunch.Bunch(formats=[model.datatypes_registry.get_datatype_by_extension("tabular")]) + + return self._param Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/707b69b09eb4/ Changeset: 707b69b09eb4 User: jmchilton Date: 2014-05-12 19:01:14 Summary: Unit test case for tool column parameters. Ever more duplication in these parameters tests, I need to find some time to refactor... Affected #: 1 file diff -r 8e2135ee278aa44eb5a8da04a392bfa44efc0279 -r 707b69b09eb4be515be228a8fb2bf7a771a1bbac test/unit/tools/test_column_parameters.py --- /dev/null +++ b/test/unit/tools/test_column_parameters.py @@ -0,0 +1,89 @@ +""" Tests for tool parameters, more tests exist in test_data_parameters.py and +test_select_parameters.py. +""" + +from unittest import TestCase +from galaxy.tools.parameters import basic +from galaxy.util import bunch +from galaxy import model +from elementtree.ElementTree import XML + +import tools_support + + +class DataColumnParameterTestCase( TestCase, tools_support.UsesApp ): + + def test_from_html(self): + value = self.param.from_html("3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == "3" + + def test_from_html_strips_c(self): + value = self.param.from_html("c1", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == "1" + + def test_multiple_from_html(self): + self.multiple = True + value = self.param.from_html("1,2,3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == ["1", "2", "3"] + + def test_multiple_from_html_with_c(self): + self.multiple = True + value = self.param.from_html("c1,c2,c3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == ["1", "2", "3"] + + def test_get_initial_value_default(self): + self.assertEqual( '1', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_legacy(self): + self.other_attributes = "default_value='2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def setUp( self ): + self.setup_app( mock_model=False ) + self.mock_tool = bunch.Bunch( + app=self.app, + tool_type="default", + ) + self.test_history = model.History() + self.app.model.context.add( self.test_history ) + self.app.model.context.flush() + self.trans = bunch.Bunch( + app=self.app, + get_history=lambda: self.test_history, + get_current_user_roles=lambda: [], + workflow_building_mode=False, + webapp=bunch.Bunch( name="galaxy" ), + ) + + self.type = "data_column" + self.other_attributes = "" + self.set_data_ref = "input_tsv" + self.multiple = False + self.optional = False + self._param = None + + def build_ready_hda(self): + hist = model.History() + self.app.model.context.add( hist ) + ready_hda = hist.add_dataset( model.HistoryDatasetAssociation( extension='interval', create_dataset=True, sa_session=self.app.model.context ) ) + ready_hda.set_dataset_state( 'ok' ) + return ready_hda + + @property + def param( self ): + if not self._param: + multi_text = "" + if self.multiple: + multi_text = 'multiple="True"' + optional_text = "" + if self.optional: + optional_text = 'optional="True"' + data_ref_text = "" + if self.set_data_ref: + data_ref_text = 'data_ref="input_tsv"' + template_xml = '''<param name="my_name" type="%s" %s %s %s %s></param>''' + self.param_xml = XML( template_xml % ( self.type, data_ref_text, multi_text, optional_text, self.other_attributes ) ) + self._param = basic.ColumnListParameter( self.mock_tool, self.param_xml ) + self._param.ref_input = bunch.Bunch(formats=[model.datatypes_registry.get_datatype_by_extension("tabular")]) + + return self._param https://bitbucket.org/galaxy/galaxy-central/commits/6171bcdb7333/ Changeset: 6171bcdb7333 User: jmchilton Date: 2014-05-12 19:01:14 Summary: Allow c to appear in default value for Column parameters, allow specification with value attribute. Ideas purposed by Peter Cock here - http://dev.list.galaxyproject.org/Default-value-for-data-column-not-working…. Affected #: 2 files diff -r 707b69b09eb4be515be228a8fb2bf7a771a1bbac -r 6171bcdb7333fd7a1bfa3986768ad425e28cf8f6 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1096,7 +1096,13 @@ self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) self.ref_input = None + # Legacy style default value specification... self.default_value = elem.get( "default_value", None ) + if self.default_value is None: + # Newer style... more in line with other parameters. + self.default_value = elem.get( "value", None ) + if self.default_value is not None: + self.default_value = ColumnListParameter._strip_c( self.default_value ) self.is_dynamic = True self.usecolnames = string_as_bool( elem.get( "use_header_names", False )) @@ -1105,10 +1111,6 @@ Label convention prepends column number with a 'c', but tool uses the integer. This removes the 'c' when entered into a workflow. """ - def _strip_c( column ): - if column.startswith( 'c' ): - column = column.strip().lower()[1:] - return column if self.multiple: #split on newline and , if value: @@ -1120,16 +1122,22 @@ column2 = column2.strip() if column2: column_list.append( column2 ) - value = map( _strip_c, column_list ) + value = map( ColumnListParameter._strip_c, column_list ) else: value = [] else: if value: - value = _strip_c( value ) + value = ColumnListParameter._strip_c( value ) else: value = None return super( ColumnListParameter, self ).from_html( value, trans, context ) + @staticmethod + def _strip_c(column): + if column.startswith( 'c' ): + column = column.strip().lower()[1:] + return column + def get_column_list( self, trans, other_values ): """ Generate a select list containing the columns of the associated diff -r 707b69b09eb4be515be228a8fb2bf7a771a1bbac -r 6171bcdb7333fd7a1bfa3986768ad425e28cf8f6 test/unit/tools/test_column_parameters.py --- a/test/unit/tools/test_column_parameters.py +++ b/test/unit/tools/test_column_parameters.py @@ -38,6 +38,14 @@ self.other_attributes = "default_value='2'" self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + def test_get_initial_value_override_newstyle(self): + self.other_attributes = "value='2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_newstyle_strips_c(self): + self.other_attributes = "value='c2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + def setUp( self ): self.setup_app( mock_model=False ) self.mock_tool = bunch.Bunch( https://bitbucket.org/galaxy/galaxy-central/commits/a50b64b9d707/ Changeset: a50b64b9d707 User: jmchilton Date: 2014-05-15 20:49:44 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #389) Small Column Parameter Enhancements Affected #: 2 files diff -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b -r a50b64b9d70704542eba7dd69410c2a25c54e2a3 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1096,7 +1096,13 @@ self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) self.ref_input = None + # Legacy style default value specification... self.default_value = elem.get( "default_value", None ) + if self.default_value is None: + # Newer style... more in line with other parameters. + self.default_value = elem.get( "value", None ) + if self.default_value is not None: + self.default_value = ColumnListParameter._strip_c( self.default_value ) self.is_dynamic = True self.usecolnames = string_as_bool( elem.get( "use_header_names", False )) @@ -1105,10 +1111,6 @@ Label convention prepends column number with a 'c', but tool uses the integer. This removes the 'c' when entered into a workflow. """ - def _strip_c( column ): - if column.startswith( 'c' ): - column = column.strip().lower()[1:] - return column if self.multiple: #split on newline and , if value: @@ -1120,16 +1122,22 @@ column2 = column2.strip() if column2: column_list.append( column2 ) - value = map( _strip_c, column_list ) + value = map( ColumnListParameter._strip_c, column_list ) else: value = [] else: if value: - value = _strip_c( value ) + value = ColumnListParameter._strip_c( value ) else: value = None return super( ColumnListParameter, self ).from_html( value, trans, context ) + @staticmethod + def _strip_c(column): + if column.startswith( 'c' ): + column = column.strip().lower()[1:] + return column + def get_column_list( self, trans, other_values ): """ Generate a select list containing the columns of the associated diff -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b -r a50b64b9d70704542eba7dd69410c2a25c54e2a3 test/unit/tools/test_column_parameters.py --- /dev/null +++ b/test/unit/tools/test_column_parameters.py @@ -0,0 +1,97 @@ +""" Tests for tool parameters, more tests exist in test_data_parameters.py and +test_select_parameters.py. +""" + +from unittest import TestCase +from galaxy.tools.parameters import basic +from galaxy.util import bunch +from galaxy import model +from elementtree.ElementTree import XML + +import tools_support + + +class DataColumnParameterTestCase( TestCase, tools_support.UsesApp ): + + def test_from_html(self): + value = self.param.from_html("3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == "3" + + def test_from_html_strips_c(self): + value = self.param.from_html("c1", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == "1" + + def test_multiple_from_html(self): + self.multiple = True + value = self.param.from_html("1,2,3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == ["1", "2", "3"] + + def test_multiple_from_html_with_c(self): + self.multiple = True + value = self.param.from_html("c1,c2,c3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == ["1", "2", "3"] + + def test_get_initial_value_default(self): + self.assertEqual( '1', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_legacy(self): + self.other_attributes = "default_value='2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_newstyle(self): + self.other_attributes = "value='2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_newstyle_strips_c(self): + self.other_attributes = "value='c2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def setUp( self ): + self.setup_app( mock_model=False ) + self.mock_tool = bunch.Bunch( + app=self.app, + tool_type="default", + ) + self.test_history = model.History() + self.app.model.context.add( self.test_history ) + self.app.model.context.flush() + self.trans = bunch.Bunch( + app=self.app, + get_history=lambda: self.test_history, + get_current_user_roles=lambda: [], + workflow_building_mode=False, + webapp=bunch.Bunch( name="galaxy" ), + ) + + self.type = "data_column" + self.other_attributes = "" + self.set_data_ref = "input_tsv" + self.multiple = False + self.optional = False + self._param = None + + def build_ready_hda(self): + hist = model.History() + self.app.model.context.add( hist ) + ready_hda = hist.add_dataset( model.HistoryDatasetAssociation( extension='interval', create_dataset=True, sa_session=self.app.model.context ) ) + ready_hda.set_dataset_state( 'ok' ) + return ready_hda + + @property + def param( self ): + if not self._param: + multi_text = "" + if self.multiple: + multi_text = 'multiple="True"' + optional_text = "" + if self.optional: + optional_text = 'optional="True"' + data_ref_text = "" + if self.set_data_ref: + data_ref_text = 'data_ref="input_tsv"' + template_xml = '''<param name="my_name" type="%s" %s %s %s %s></param>''' + self.param_xml = XML( template_xml % ( self.type, data_ref_text, multi_text, optional_text, self.other_attributes ) ) + self._param = basic.ColumnListParameter( self.mock_tool, self.param_xml ) + self._param.ref_input = bunch.Bunch(formats=[model.datatypes_registry.get_datatype_by_extension("tabular")]) + + return self._param 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 #387)
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/44ac8fc8f7b6/ Changeset: 44ac8fc8f7b6 User: jmchilton Date: 2014-05-15 20:43:43 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #387) Recursive Tool Parameter Dictification Affected #: 2 files diff -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -53,6 +53,9 @@ return group_dict class Repeat( Group ): + + dict_collection_visible_keys = ( 'name', 'type', 'title', 'help', 'default', 'min', 'max' ) + type = "repeat" def __init__( self ): Group.__init__( self ) @@ -117,6 +120,16 @@ rval.append( rval_dict ) return rval + def to_dict( self, trans, view='collection', value_mapper=None ): + repeat_dict = super( Repeat, self ).to_dict( trans, view=view, value_mapper=value_mapper ) + + def input_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + repeat_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() ) + return repeat_dict + + class UploadDataset( Group ): type = "upload_dataset" def __init__( self ): @@ -517,7 +530,29 @@ rval[ child_input.name ] = child_input.get_initial_value( trans, child_context, history=history ) return rval -class ConditionalWhen( object ): + def to_dict( self, trans, view='collection', value_mapper=None ): + cond_dict = super( Conditional, self ).to_dict( trans, view=view, value_mapper=value_mapper ) + + def nested_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + cond_dict[ "cases" ] = map( nested_to_dict, self.cases ) + cond_dict[ "test_param" ] = nested_to_dict( self.test_param ) + return cond_dict + + +class ConditionalWhen( object, Dictifiable ): + dict_collection_visible_keys = ( 'value', ) + def __init__( self ): self.value = None self.inputs = None + + def to_dict( self, trans, view='collection', value_mapper=None ): + when_dict = super( ConditionalWhen, self ).to_dict( view=view, value_mapper=value_mapper ) + + def input_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + when_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() ) + return when_dict diff -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -25,6 +25,49 @@ tool_ids = map( itemgetter( "id" ), tools_index ) assert "upload1" in tool_ids + @skip_without_tool( "cat1" ) + def test_show_repeat( self ): + tool_info = self._show_valid_tool( "cat1" ) + parameters = tool_info[ "inputs" ] + assert len( parameters ) == 2 + assert parameters[ 0 ][ "name" ] == "input1" + assert parameters[ 1 ][ "name" ] == "queries" + + repeat_info = parameters[ 1 ] + self._assert_has_keys( repeat_info, "min", "max", "title", "help" ) + repeat_params = repeat_info[ "inputs" ] + assert len( repeat_params ) == 1 + assert repeat_params[ 0 ][ "name" ] == "input2" + + @skip_without_tool( "random_lines1" ) + def test_show_conditional( self ): + tool_info = self._show_valid_tool( "random_lines1" ) + + cond_info = tool_info[ "inputs" ][ 2 ] + self._assert_has_keys( cond_info, "cases", "test_param" ) + self._assert_has_keys( cond_info[ "test_param" ], 'name', 'type', 'label', 'help' ) + + cases = cond_info[ "cases" ] + assert len( cases ) == 2 + case1 = cases[ 0 ] + self._assert_has_keys( case1, "value", "inputs" ) + assert case1[ "value" ] == "no_seed" + assert len( case1[ "inputs" ] ) == 0 + + case2 = cases[ 1 ] + self._assert_has_keys( case2, "value", "inputs" ) + case2_inputs = case2[ "inputs" ] + assert len( case2_inputs ) == 1 + self._assert_has_keys( case2_inputs[ 0 ], 'name', 'type', 'label', 'help' ) + assert case2_inputs[ 0 ][ "name" ] == "seed" + + def _show_valid_tool( self, tool_id ): + tool_show_response = self._get( "tools/%s" % tool_id, data=dict( io_details=True ) ) + self._assert_status_code_is( tool_show_response, 200 ) + tool_info = tool_show_response.json() + self._assert_has_keys( tool_info, "inputs", "outputs", "panel_section_id" ) + return tool_info + def test_upload1_paste( self ): history_id = self.dataset_populator.new_history() payload = self.dataset_populator.upload_payload( history_id, 'Hello World' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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

15 May '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/73b85f86a9d5/ Changeset: 73b85f86a9d5 User: jmchilton Date: 2014-05-09 00:55:00 Summary: Improvements to to_dict for Repeat tool parameters. Expand out nested parameters and more information about the repeat itself. Affected #: 2 files diff -r f2f32d8b8a06ff370145360b5c75c90e2e2447a9 -r 73b85f86a9d5231fbccb8d442d819365cc33b6e9 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -53,6 +53,9 @@ return group_dict class Repeat( Group ): + + dict_collection_visible_keys = ( 'name', 'type', 'title', 'help', 'default', 'min', 'max' ) + type = "repeat" def __init__( self ): Group.__init__( self ) @@ -117,6 +120,16 @@ rval.append( rval_dict ) return rval + def to_dict( self, trans, view='collection', value_mapper=None ): + repeat_dict = super( Repeat, self ).to_dict( trans, view=view, value_mapper=value_mapper ) + + def input_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + repeat_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() ) + return repeat_dict + + class UploadDataset( Group ): type = "upload_dataset" def __init__( self ): diff -r f2f32d8b8a06ff370145360b5c75c90e2e2447a9 -r 73b85f86a9d5231fbccb8d442d819365cc33b6e9 test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -25,6 +25,23 @@ tool_ids = map( itemgetter( "id" ), tools_index ) assert "upload1" in tool_ids + @skip_without_tool( "cat1" ) + def test_show_repeat( self ): + tool_show_response = self._get( "tools/cat1", data=dict( io_details=True ) ) + self._assert_status_code_is( tool_show_response, 200 ) + tool_info = tool_show_response.json() + self._assert_has_keys( tool_info, "inputs", "outputs", "panel_section_id" ) + parameters = tool_info[ "inputs" ] + assert len( parameters ) == 2 + assert parameters[ 0 ][ "name" ] == "input1" + assert parameters[ 1 ][ "name" ] == "queries" + + repeat_info = parameters[ 1 ] + self._assert_has_keys( repeat_info, "min", "max", "title", "help" ) + repeat_params = repeat_info[ "inputs" ] + assert len( repeat_params ) == 1 + assert repeat_params[ 0 ][ "name" ] == "input2" + def test_upload1_paste( self ): history_id = self.dataset_populator.new_history() payload = self.dataset_populator.upload_payload( history_id, 'Hello World' ) https://bitbucket.org/galaxy/galaxy-central/commits/b411c3c86936/ Changeset: b411c3c86936 User: jmchilton Date: 2014-05-09 00:55:00 Summary: Improvements to to_dict for Conditional tool parameters. Expand out nested test_param parameter and cases. Affected #: 2 files diff -r 73b85f86a9d5231fbccb8d442d819365cc33b6e9 -r b411c3c8693660a3291f0f537c61ba0b978e1813 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -530,7 +530,29 @@ rval[ child_input.name ] = child_input.get_initial_value( trans, child_context, history=history ) return rval -class ConditionalWhen( object ): + def to_dict( self, trans, view='collection', value_mapper=None ): + cond_dict = super( Conditional, self ).to_dict( trans, view=view, value_mapper=value_mapper ) + + def nested_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + cond_dict[ "cases" ] = map( nested_to_dict, self.cases ) + cond_dict[ "test_param" ] = nested_to_dict( self.test_param ) + return cond_dict + + +class ConditionalWhen( object, Dictifiable ): + dict_collection_visible_keys = ( 'value', ) + def __init__( self ): self.value = None self.inputs = None + + def to_dict( self, trans, view='collection', value_mapper=None ): + when_dict = super( ConditionalWhen, self ).to_dict( view=view, value_mapper=value_mapper ) + + def input_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + when_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() ) + return when_dict diff -r 73b85f86a9d5231fbccb8d442d819365cc33b6e9 -r b411c3c8693660a3291f0f537c61ba0b978e1813 test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -27,10 +27,7 @@ @skip_without_tool( "cat1" ) def test_show_repeat( self ): - tool_show_response = self._get( "tools/cat1", data=dict( io_details=True ) ) - self._assert_status_code_is( tool_show_response, 200 ) - tool_info = tool_show_response.json() - self._assert_has_keys( tool_info, "inputs", "outputs", "panel_section_id" ) + tool_info = self._show_valid_tool( "cat1" ) parameters = tool_info[ "inputs" ] assert len( parameters ) == 2 assert parameters[ 0 ][ "name" ] == "input1" @@ -42,6 +39,35 @@ assert len( repeat_params ) == 1 assert repeat_params[ 0 ][ "name" ] == "input2" + @skip_without_tool( "random_lines1" ) + def test_show_conditional( self ): + tool_info = self._show_valid_tool( "random_lines1" ) + + cond_info = tool_info[ "inputs" ][ 2 ] + self._assert_has_keys( cond_info, "cases", "test_param" ) + self._assert_has_keys( cond_info[ "test_param" ], 'name', 'type', 'label', 'help' ) + + cases = cond_info[ "cases" ] + assert len( cases ) == 2 + case1 = cases[ 0 ] + self._assert_has_keys( case1, "value", "inputs" ) + assert case1[ "value" ] == "no_seed" + assert len( case1[ "inputs" ] ) == 0 + + case2 = cases[ 1 ] + self._assert_has_keys( case2, "value", "inputs" ) + case2_inputs = case2[ "inputs" ] + assert len( case2_inputs ) == 1 + self._assert_has_keys( case2_inputs[ 0 ], 'name', 'type', 'label', 'help' ) + assert case2_inputs[ 0 ][ "name" ] == "seed" + + def _show_valid_tool( self, tool_id ): + tool_show_response = self._get( "tools/%s" % tool_id, data=dict( io_details=True ) ) + self._assert_status_code_is( tool_show_response, 200 ) + tool_info = tool_show_response.json() + self._assert_has_keys( tool_info, "inputs", "outputs", "panel_section_id" ) + return tool_info + def test_upload1_paste( self ): history_id = self.dataset_populator.new_history() payload = self.dataset_populator.upload_payload( history_id, 'Hello World' ) https://bitbucket.org/galaxy/galaxy-central/commits/44ac8fc8f7b6/ Changeset: 44ac8fc8f7b6 User: jmchilton Date: 2014-05-15 20:43:43 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #387) Recursive Tool Parameter Dictification Affected #: 2 files diff -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -53,6 +53,9 @@ return group_dict class Repeat( Group ): + + dict_collection_visible_keys = ( 'name', 'type', 'title', 'help', 'default', 'min', 'max' ) + type = "repeat" def __init__( self ): Group.__init__( self ) @@ -117,6 +120,16 @@ rval.append( rval_dict ) return rval + def to_dict( self, trans, view='collection', value_mapper=None ): + repeat_dict = super( Repeat, self ).to_dict( trans, view=view, value_mapper=value_mapper ) + + def input_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + repeat_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() ) + return repeat_dict + + class UploadDataset( Group ): type = "upload_dataset" def __init__( self ): @@ -517,7 +530,29 @@ rval[ child_input.name ] = child_input.get_initial_value( trans, child_context, history=history ) return rval -class ConditionalWhen( object ): + def to_dict( self, trans, view='collection', value_mapper=None ): + cond_dict = super( Conditional, self ).to_dict( trans, view=view, value_mapper=value_mapper ) + + def nested_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + cond_dict[ "cases" ] = map( nested_to_dict, self.cases ) + cond_dict[ "test_param" ] = nested_to_dict( self.test_param ) + return cond_dict + + +class ConditionalWhen( object, Dictifiable ): + dict_collection_visible_keys = ( 'value', ) + def __init__( self ): self.value = None self.inputs = None + + def to_dict( self, trans, view='collection', value_mapper=None ): + when_dict = super( ConditionalWhen, self ).to_dict( view=view, value_mapper=value_mapper ) + + def input_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + when_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() ) + return when_dict diff -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -25,6 +25,49 @@ tool_ids = map( itemgetter( "id" ), tools_index ) assert "upload1" in tool_ids + @skip_without_tool( "cat1" ) + def test_show_repeat( self ): + tool_info = self._show_valid_tool( "cat1" ) + parameters = tool_info[ "inputs" ] + assert len( parameters ) == 2 + assert parameters[ 0 ][ "name" ] == "input1" + assert parameters[ 1 ][ "name" ] == "queries" + + repeat_info = parameters[ 1 ] + self._assert_has_keys( repeat_info, "min", "max", "title", "help" ) + repeat_params = repeat_info[ "inputs" ] + assert len( repeat_params ) == 1 + assert repeat_params[ 0 ][ "name" ] == "input2" + + @skip_without_tool( "random_lines1" ) + def test_show_conditional( self ): + tool_info = self._show_valid_tool( "random_lines1" ) + + cond_info = tool_info[ "inputs" ][ 2 ] + self._assert_has_keys( cond_info, "cases", "test_param" ) + self._assert_has_keys( cond_info[ "test_param" ], 'name', 'type', 'label', 'help' ) + + cases = cond_info[ "cases" ] + assert len( cases ) == 2 + case1 = cases[ 0 ] + self._assert_has_keys( case1, "value", "inputs" ) + assert case1[ "value" ] == "no_seed" + assert len( case1[ "inputs" ] ) == 0 + + case2 = cases[ 1 ] + self._assert_has_keys( case2, "value", "inputs" ) + case2_inputs = case2[ "inputs" ] + assert len( case2_inputs ) == 1 + self._assert_has_keys( case2_inputs[ 0 ], 'name', 'type', 'label', 'help' ) + assert case2_inputs[ 0 ][ "name" ] == "seed" + + def _show_valid_tool( self, tool_id ): + tool_show_response = self._get( "tools/%s" % tool_id, data=dict( io_details=True ) ) + self._assert_status_code_is( tool_show_response, 200 ) + tool_info = tool_show_response.json() + self._assert_has_keys( tool_info, "inputs", "outputs", "panel_section_id" ) + return tool_info + def test_upload1_paste( self ): history_id = self.dataset_populator.new_history() payload = self.dataset_populator.upload_payload( history_id, 'Hello World' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Change paired collections terminology from left/right to forward/reverse.
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f24bb5dde1f5/ Changeset: f24bb5dde1f5 User: jmchilton Date: 2014-05-15 20:01:36 Summary: Change paired collections terminology from left/right to forward/reverse. If you have paired datasets in your database they will no longer work - send me an e-mail and I can give you an SQL update statement. Affected #: 5 files diff -r b5a1cd130f71b20a25f1bf110b0e1e24843df4b7 -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 lib/galaxy/dataset_collections/types/paired.py --- a/lib/galaxy/dataset_collections/types/paired.py +++ b/lib/galaxy/dataset_collections/types/paired.py @@ -2,8 +2,10 @@ from galaxy.model import DatasetCollectionElement -LEFT_IDENTIFIER = "left" -RIGHT_IDENTIFIER = "right" +FORWARD_IDENTIFIER = "forward" +REVERSE_IDENTIFIER = "reverse" + +INVALID_IDENTIFIERS_MESSAGE = "Paired instance must define '%s' and '%s' datasets ." % ( FORWARD_IDENTIFIER, REVERSE_IDENTIFIER ) class PairedDatasetCollectionType( BaseDatasetCollectionType ): @@ -16,16 +18,16 @@ pass def build_collection( self, elements ): - left_dataset = elements.get("left", None) - right_dataset = elements.get("right", None) - if not left_dataset or not right_dataset: - self._validation_failed("Paired instance must define 'left' and 'right' datasets .") + forward_dataset = elements.get( FORWARD_IDENTIFIER, None ) + reverse_dataset = elements.get( REVERSE_IDENTIFIER, None ) + if not forward_dataset or not reverse_dataset: + self._validation_failed( INVALID_IDENTIFIERS_MESSAGE ) left_association = DatasetCollectionElement( - element=left_dataset, - element_identifier=LEFT_IDENTIFIER, + element=forward_dataset, + element_identifier=FORWARD_IDENTIFIER, ) right_association = DatasetCollectionElement( - element=right_dataset, - element_identifier=RIGHT_IDENTIFIER, + element=reverse_dataset, + element_identifier=REVERSE_IDENTIFIER, ) return self._new_collection_for_elements([left_association, right_association]) diff -r b5a1cd130f71b20a25f1bf110b0e1e24843df4b7 -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 test/api/helpers.py --- a/test/api/helpers.py +++ b/test/api/helpers.py @@ -292,8 +292,8 @@ hda1, hda2 = self.__datasets( history_id, count=2, contents=contents ) element_identifiers = [ - dict( name="left", src="hda", id=hda1[ "id" ] ), - dict( name="right", src="hda", id=hda2[ "id" ] ), + dict( name="forward", src="hda", id=hda1[ "id" ] ), + dict( name="reverse", src="hda", id=hda2[ "id" ] ), ] return element_identifiers diff -r b5a1cd130f71b20a25f1bf110b0e1e24843df4b7 -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -204,8 +204,8 @@ first_object = first_element[ "object" ] assert first_object[ "collection_type" ] == "paired" assert len( first_object[ "elements" ] ) == 2 - first_object_left_element = first_object[ "elements" ][ 0 ] - self.assertEquals( outputs[ 0 ][ "id" ], first_object_left_element[ "object" ][ "id" ] ) + first_object_forward_element = first_object[ "elements" ][ 0 ] + self.assertEquals( outputs[ 0 ][ "id" ], first_object_forward_element[ "object" ][ "id" ] ) @skip_without_tool( "cat1" ) def test_map_over_two_collections( self ): diff -r b5a1cd130f71b20a25f1bf110b0e1e24843df4b7 -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 test/functional/tools/collection_mixed_param.xml --- a/test/functional/tools/collection_mixed_param.xml +++ b/test/functional/tools/collection_mixed_param.xml @@ -13,8 +13,8 @@ <test><param name="f1"><collection type="paired"> - <element name="left" value="simple_line.txt" /> - <element name="right" value="simple_line_alternative.txt" /> + <element name="forward" value="simple_line.txt" /> + <element name="reverse" value="simple_line_alternative.txt" /></collection></param><param name="f2" value="simple_lines_both.txt" /> diff -r b5a1cd130f71b20a25f1bf110b0e1e24843df4b7 -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 test/functional/tools/collection_paired_test.xml --- a/test/functional/tools/collection_paired_test.xml +++ b/test/functional/tools/collection_paired_test.xml @@ -1,6 +1,6 @@ <tool id="collection_paired_test" name="paired_test" version="0.1.0"><command> - cat #for $f in $f1# ${f} #end for# >> $out1; + cat $f1.forward $f1.reverse >> $out1; </command><inputs><param name="f1" type="data_collection" collection_type="paired" /> @@ -12,8 +12,8 @@ <test><param name="f1"><collection type="paired"> - <element name="left" value="simple_line.txt" /> - <element name="right" value="simple_line_alternative.txt" /> + <element name="forward" value="simple_line.txt" /> + <element name="reverse" value="simple_line_alternative.txt" /></collection></param><output name="out1"> 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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