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

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/aa75079bf2cb/ Changeset: aa75079bf2cb Branch: admin_cleanup_datasets_fix User: lance_parsons Date: 2014-12-03 19:50:56+00:00 Summary: Added pkg_resources to load required Mako package Affected #: 1 file diff -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 -r aa75079bf2cb6e5a03774442aed99e2c16e540f5 scripts/cleanup_datasets/admin_cleanup_datasets.py --- a/scripts/cleanup_datasets/admin_cleanup_datasets.py +++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py @@ -47,10 +47,10 @@ log.addHandler(logging.StreamHandler(sys.stdout)) from cleanup_datasets import CleanupDatasetsApplication -#import pkg_resources +import pkg_resources #pkg_resources.require("SQLAlchemy >= 0.4") -#pkg_resources.require("Mako") +pkg_resources.require("Mako") from mako.template import Template import time https://bitbucket.org/galaxy/galaxy-central/commits/2cdf98534410/ Changeset: 2cdf98534410 User: natefoo Date: 2014-12-04 15:33:52+00:00 Summary: Merged in lance_parsons/galaxy-central-pull-requests/admin_cleanup_datasets_fix (pull request #586) Added pkg_resources to load required Mako package Affected #: 1 file diff -r 171511af9fcf2689e2761cf79e2cf02ff8324acc -r 2cdf98534410d48b1a10c03eec30901979955aca scripts/cleanup_datasets/admin_cleanup_datasets.py --- a/scripts/cleanup_datasets/admin_cleanup_datasets.py +++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py @@ -47,10 +47,10 @@ log.addHandler(logging.StreamHandler(sys.stdout)) from cleanup_datasets import CleanupDatasetsApplication -#import pkg_resources +import pkg_resources #pkg_resources.require("SQLAlchemy >= 0.4") -#pkg_resources.require("Mako") +pkg_resources.require("Mako") from mako.template import Template import time 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 #575)
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/171511af9fcf/ Changeset: 171511af9fcf User: jmchilton Date: 2014-12-04 14:50:45+00:00 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #575) Allow using attribute 'optional' for data column parameters. Affected #: 2 files diff -r 100a7353b7faf9815783ec7f1245bb539a1b2717 -r 171511af9fcf2689e2761cf79e2cf02ff8324acc lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1130,7 +1130,13 @@ SelectToolParameter.__init__( self, tool, elem ) self.tool = tool self.numerical = string_as_bool( elem.get( "numerical", False )) - self.force_select = string_as_bool( elem.get( "force_select", True )) + # Allow specifing force_select for backward compat., but probably + # should use optional going forward for consistency with other + # parameters. + if "force_select" in elem.attrib: + self.force_select = string_as_bool( elem.get( "force_select" ) ) + else: + self.force_select = not string_as_bool( elem.get( "optional", False ) ) self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) self.ref_input = None diff -r 100a7353b7faf9815783ec7f1245bb539a1b2717 -r 171511af9fcf2689e2761cf79e2cf02ff8324acc test/unit/tools/test_column_parameters.py --- a/test/unit/tools/test_column_parameters.py +++ b/test/unit/tools/test_column_parameters.py @@ -13,6 +13,21 @@ class DataColumnParameterTestCase( TestCase, tools_support.UsesApp ): + def test_not_optional_by_default(self): + assert not self.__param_optional() + + def test_force_select_disable(self): + self.other_attributes = 'force_select="false"' + assert self.__param_optional() + + def test_optional_override(self): + self.other_attributes = 'optional="true"' + assert self.__param_optional() + + def __param_optional(self): + # TODO: don't break abstraction, try setting null value instead + return not self.param.force_select + def test_from_html(self): value = self.param.from_html("3", self.trans, { "input_tsv": self.build_ready_hda() } ) assert value == "3" 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 04 Dec '14

04 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/df52b3de192d/ Changeset: df52b3de192d User: jmchilton Date: 2014-11-25 15:57:49+00:00 Summary: Allow using attribute 'optional' for data column parameters. For consistency with other parameters, has the opposite effect of 'force_select'. Affected #: 2 files diff -r 69a6f901230540012d38f17adb1995d96f6a5dba -r df52b3de192d2edeffedd6fe325ecce6c3c33ddc lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1125,7 +1125,13 @@ SelectToolParameter.__init__( self, tool, elem ) self.tool = tool self.numerical = string_as_bool( elem.get( "numerical", False )) - self.force_select = string_as_bool( elem.get( "force_select", True )) + # Allow specifing force_select for backward compat., but probably + # should use optional going forward for consistency with other + # parameters. + if "force_select" in elem.attrib: + self.force_select = string_as_bool( elem.get( "force_select" ) ) + else: + self.force_select = not string_as_bool( elem.get( "optional", False ) ) self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) self.ref_input = None diff -r 69a6f901230540012d38f17adb1995d96f6a5dba -r df52b3de192d2edeffedd6fe325ecce6c3c33ddc test/unit/tools/test_column_parameters.py --- a/test/unit/tools/test_column_parameters.py +++ b/test/unit/tools/test_column_parameters.py @@ -13,6 +13,21 @@ class DataColumnParameterTestCase( TestCase, tools_support.UsesApp ): + def test_not_optional_by_default(self): + assert not self.__param_optional() + + def test_force_select_disable(self): + self.other_attributes = 'force_select="false"' + assert self.__param_optional() + + def test_optional_override(self): + self.other_attributes = 'optional="true"' + assert self.__param_optional() + + def __param_optional(self): + # TODO: don't break abstraction, try setting null value instead + return not self.param.force_select + def test_from_html(self): value = self.param.from_html("3", self.trans, { "input_tsv": self.build_ready_hda() } ) assert value == "3" https://bitbucket.org/galaxy/galaxy-central/commits/171511af9fcf/ Changeset: 171511af9fcf User: jmchilton Date: 2014-12-04 14:50:45+00:00 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #575) Allow using attribute 'optional' for data column parameters. Affected #: 2 files diff -r 100a7353b7faf9815783ec7f1245bb539a1b2717 -r 171511af9fcf2689e2761cf79e2cf02ff8324acc lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1130,7 +1130,13 @@ SelectToolParameter.__init__( self, tool, elem ) self.tool = tool self.numerical = string_as_bool( elem.get( "numerical", False )) - self.force_select = string_as_bool( elem.get( "force_select", True )) + # Allow specifing force_select for backward compat., but probably + # should use optional going forward for consistency with other + # parameters. + if "force_select" in elem.attrib: + self.force_select = string_as_bool( elem.get( "force_select" ) ) + else: + self.force_select = not string_as_bool( elem.get( "optional", False ) ) self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) self.ref_input = None diff -r 100a7353b7faf9815783ec7f1245bb539a1b2717 -r 171511af9fcf2689e2761cf79e2cf02ff8324acc test/unit/tools/test_column_parameters.py --- a/test/unit/tools/test_column_parameters.py +++ b/test/unit/tools/test_column_parameters.py @@ -13,6 +13,21 @@ class DataColumnParameterTestCase( TestCase, tools_support.UsesApp ): + def test_not_optional_by_default(self): + assert not self.__param_optional() + + def test_force_select_disable(self): + self.other_attributes = 'force_select="false"' + assert self.__param_optional() + + def test_optional_override(self): + self.other_attributes = 'optional="true"' + assert self.__param_optional() + + def __param_optional(self): + # TODO: don't break abstraction, try setting null value instead + return not self.param.force_select + def test_from_html(self): value = self.param.from_html("3", self.trans, { "input_tsv": self.build_ready_hda() } ) assert value == "3" 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: Merged in dan/galaxy-central-prs/stable (pull request #584)
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/caade2c602d6/ Changeset: caade2c602d6 Branch: stable User: natefoo Date: 2014-12-04 14:20:19+00:00 Summary: Merged in dan/galaxy-central-prs/stable (pull request #584) [STABLE] DatasetMatcher should check to see if hda is of the correct format before attempting to filter on e.g. metadata attributes (that may not exist for a non-expected format). Affected #: 1 file diff -r cfdd5c45c63eee193cdefa7767e9b43217238e88 -r caade2c602d65a005d54997e95fcb1a9eab6ea17 lib/galaxy/tools/parameters/dataset_matcher.py --- a/lib/galaxy/tools/parameters/dataset_matcher.py +++ b/lib/galaxy/tools/parameters/dataset_matcher.py @@ -39,26 +39,30 @@ return state_valid and ( not check_security or self.__can_access_dataset( dataset ) ) def valid_hda_match( self, hda, check_implicit_conversions=True, check_security=False ): - """ Return False of this parameter can not be matched to a the supplied + """ Return False of this parameter can not be matched to the supplied HDA, otherwise return a description of the match (either a HdaDirectMatch describing a direct match or a HdaImplicitMatch describing an implicit conversion.) """ + rval = False + formats = self.param.formats + if hda.datatype.matches_any( formats ): + rval = HdaDirectMatch( hda ) + else: + if not check_implicit_conversions: + return False + target_ext, converted_dataset = hda.find_conversion_destination( formats ) + if target_ext: + if converted_dataset: + hda = converted_dataset + if check_security and not self.__can_access_dataset( hda.dataset ): + return False + rval = HdaImplicitMatch( hda, target_ext ) + else: + return False if self.filter( hda ): return False - formats = self.param.formats - if hda.datatype.matches_any( formats ): - return HdaDirectMatch( hda ) - if not check_implicit_conversions: - return False - target_ext, converted_dataset = hda.find_conversion_destination( formats ) - if target_ext: - if converted_dataset: - hda = converted_dataset - if check_security and not self.__can_access_dataset( hda.dataset ): - return False - return HdaImplicitMatch( hda, target_ext ) - return False + return rval def hda_match( self, hda, check_implicit_conversions=True, ensure_visible=True ): """ If HDA is accessible, return information about whether it could 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 04 Dec '14

04 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f6914532d844/ Changeset: f6914532d844 Branch: stable User: dan Date: 2014-12-03 16:35:35+00:00 Summary: DatasetMatcher should check to see if hda is of the correct format before attempting to filter on e.g. metadata attributes (that may not exist for a non-expected format). Affected #: 1 file diff -r 26aab19109ce7956f29bfc4f5877e6950c0fae56 -r f6914532d8440041ee6741815355d36dac0c1b10 lib/galaxy/tools/parameters/dataset_matcher.py --- a/lib/galaxy/tools/parameters/dataset_matcher.py +++ b/lib/galaxy/tools/parameters/dataset_matcher.py @@ -39,26 +39,30 @@ return state_valid and ( not check_security or self.__can_access_dataset( dataset ) ) def valid_hda_match( self, hda, check_implicit_conversions=True, check_security=False ): - """ Return False of this parameter can not be matched to a the supplied + """ Return False of this parameter can not be matched to the supplied HDA, otherwise return a description of the match (either a HdaDirectMatch describing a direct match or a HdaImplicitMatch describing an implicit conversion.) """ + rval = False + formats = self.param.formats + if hda.datatype.matches_any( formats ): + rval = HdaDirectMatch( hda ) + else: + if not check_implicit_conversions: + return False + target_ext, converted_dataset = hda.find_conversion_destination( formats ) + if target_ext: + if converted_dataset: + hda = converted_dataset + if check_security and not self.__can_access_dataset( hda.dataset ): + return False + rval = HdaImplicitMatch( hda, target_ext ) + else: + return False if self.filter( hda ): return False - formats = self.param.formats - if hda.datatype.matches_any( formats ): - return HdaDirectMatch( hda ) - if not check_implicit_conversions: - return False - target_ext, converted_dataset = hda.find_conversion_destination( formats ) - if target_ext: - if converted_dataset: - hda = converted_dataset - if check_security and not self.__can_access_dataset( hda.dataset ): - return False - return HdaImplicitMatch( hda, target_ext ) - return False + return rval def hda_match( self, hda, check_implicit_conversions=True, ensure_visible=True ): """ If HDA is accessible, return information about whether it could https://bitbucket.org/galaxy/galaxy-central/commits/caade2c602d6/ Changeset: caade2c602d6 Branch: stable User: natefoo Date: 2014-12-04 14:20:19+00:00 Summary: Merged in dan/galaxy-central-prs/stable (pull request #584) [STABLE] DatasetMatcher should check to see if hda is of the correct format before attempting to filter on e.g. metadata attributes (that may not exist for a non-expected format). Affected #: 1 file diff -r cfdd5c45c63eee193cdefa7767e9b43217238e88 -r caade2c602d65a005d54997e95fcb1a9eab6ea17 lib/galaxy/tools/parameters/dataset_matcher.py --- a/lib/galaxy/tools/parameters/dataset_matcher.py +++ b/lib/galaxy/tools/parameters/dataset_matcher.py @@ -39,26 +39,30 @@ return state_valid and ( not check_security or self.__can_access_dataset( dataset ) ) def valid_hda_match( self, hda, check_implicit_conversions=True, check_security=False ): - """ Return False of this parameter can not be matched to a the supplied + """ Return False of this parameter can not be matched to the supplied HDA, otherwise return a description of the match (either a HdaDirectMatch describing a direct match or a HdaImplicitMatch describing an implicit conversion.) """ + rval = False + formats = self.param.formats + if hda.datatype.matches_any( formats ): + rval = HdaDirectMatch( hda ) + else: + if not check_implicit_conversions: + return False + target_ext, converted_dataset = hda.find_conversion_destination( formats ) + if target_ext: + if converted_dataset: + hda = converted_dataset + if check_security and not self.__can_access_dataset( hda.dataset ): + return False + rval = HdaImplicitMatch( hda, target_ext ) + else: + return False if self.filter( hda ): return False - formats = self.param.formats - if hda.datatype.matches_any( formats ): - return HdaDirectMatch( hda ) - if not check_implicit_conversions: - return False - target_ext, converted_dataset = hda.find_conversion_destination( formats ) - if target_ext: - if converted_dataset: - hda = converted_dataset - if check_security and not self.__can_access_dataset( hda.dataset ): - return False - return HdaImplicitMatch( hda, target_ext ) - return False + return rval def hda_match( self, hda, check_implicit_conversions=True, ensure_visible=True ): """ If HDA is accessible, return information about whether it could 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 04 Dec '14

04 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ef86eb163f3f/ Changeset: ef86eb163f3f User: jmchilton Date: 2014-12-04 14:16:01+00:00 Summary: Easier debugging of API test problems. Affected #: 1 file diff -r 50fe8f57c2fbe71ec3ee7b7dd2b489a0d7c32d78 -r ef86eb163f3f66c046f7ca4ff0d829b38b0728d4 test/api/helpers.py --- a/test/api/helpers.py +++ b/test/api/helpers.py @@ -76,7 +76,11 @@ return run_response.json()["outputs"][0] def wait_for_history( self, history_id, assert_ok=False, timeout=DEFAULT_HISTORY_TIMEOUT ): - return wait_on_state( lambda: self.galaxy_interactor.get( "histories/%s" % history_id ), assert_ok=assert_ok, timeout=timeout ) + try: + return wait_on_state( lambda: self.galaxy_interactor.get( "histories/%s" % history_id ), assert_ok=assert_ok, timeout=timeout ) + except AssertionError: + self.galaxy_interactor._summarize_history_errors( history_id ) + raise def wait_for_job( self, job_id, assert_ok=False, timeout=DEFAULT_HISTORY_TIMEOUT ): return wait_on_state( lambda: self.galaxy_interactor.get( "jobs/%s" % job_id ), assert_ok=assert_ok, timeout=timeout ) https://bitbucket.org/galaxy/galaxy-central/commits/100a7353b7fa/ Changeset: 100a7353b7fa User: jmchilton Date: 2014-12-04 14:16:01+00:00 Summary: Remove seemingly unlinked to workflow action and template. Please let me know if I missed something. Affected #: 2 files diff -r ef86eb163f3f66c046f7ca4ff0d829b38b0728d4 -r 100a7353b7faf9815783ec7f1245bb539a1b2717 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -407,27 +407,6 @@ @web.expose @web.require_login( "use Galaxy workflows" ) - def edit_attributes( self, trans, id, **kwargs ): - # Get workflow and do error checking. - stored = self.get_stored_workflow( trans, id ) - if not stored: - error( "You do not own this workflow or workflow ID is invalid." ) - # Update workflow attributes if new values submitted. - if 'name' in kwargs: - # Rename workflow. - stored.name = sanitize_html( kwargs['name'] ) - 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 ) - trans.sa_session.flush() - return trans.fill_template( 'workflow/edit_attributes.mako', - stored=stored, - annotation=self.get_item_annotation_str( trans.sa_session, trans.user, stored ) - ) - - @web.expose - @web.require_login( "use Galaxy workflows" ) def rename( self, trans, id, new_name=None, **kwargs ): stored = self.get_stored_workflow( trans, id ) if new_name is not None: diff -r ef86eb163f3f66c046f7ca4ff0d829b38b0728d4 -r 100a7353b7faf9815783ec7f1245bb539a1b2717 templates/webapps/galaxy/workflow/edit_attributes.mako --- a/templates/webapps/galaxy/workflow/edit_attributes.mako +++ /dev/null @@ -1,66 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="title()">${_('Edit Workflow Attributes')}</%def> - -<%def name="stylesheets()"> - ${h.css( "base", "autocomplete_tagging" )} -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js( "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )} -</%def> - -%if msg: - ${render_msg( msg, messagetype )} -%endif - -<%def name="body()"> - <div class="toolForm"> - <div class="toolFormTitle">${_('Edit Workflow Attributes')}</div> - <div class="toolFormBody"> - <form name="edit_attributes" action="${h.url_for(controller='workflow', action='edit_attributes' )}" method="post"> - <input type="hidden" name="id" value="${trans.security.encode_id( stored.id )}"/> - <div class="form-row"> - <label> - Name: - </label> - <div style="float: left; width: 225px; margin-right: 10px;"> - <input type="text" name="name" value="${stored.name}" size="30"/> - </div> - <div style="clear: both"></div> - </div> - <%namespace file="/tagging_common.mako" import="render_individual_tagging_element" /> - <div class="form-row"> - <label> - Tags: - </label> - <div style="float: left; width: 265px; margin-right: 10px; border-style: inset; border-width: 1px; margin-left: 2px"> - <style> - .tag-area { - border: none; - } - </style> - ${render_individual_tagging_element(user=trans.get_user(), tagged_item=stored, elt_context="edit_attributes.mako", use_toggle_link=False, in_form=True, input_size="25")} - </div> - <div style="clear: both"></div> - <div class="toolParamHelp">Apply tags to make it easy to search for and find items with the same tag.</div> - </div> - <div class="form-row"> - <label> - Annotation / Notes: - </label> - <div style="float: left; width: 225px; margin-right: 10px;"> - <textarea name="annotation" cols="30" rows="2">${annotation}</textarea> - </div> - <div style="clear: both"></div> - <div class="toolParamHelp">Add an annotation notes to a workflow; annotations are available when a workflow is viewed.</div> - </div> - <div class="form-row"> - <input type="submit" name="save" value="${_('Save')}"/> - </div> - </form> - </div> - </div> -</%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Update tag latest_2014.10.06 for changeset 0e663285c743
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cfdd5c45c63e/ Changeset: cfdd5c45c63e Branch: stable User: natefoo Date: 2014-12-04 14:00:18+00:00 Summary: Update tag latest_2014.10.06 for changeset 0e663285c743 Affected #: 1 file diff -r 0e663285c74326737d4ff3c637d4c8aba8847755 -r cfdd5c45c63eee193cdefa7767e9b43217238e88 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -546ff6ef27b4b83e26ae228c292fd981173ac550 latest_2014.10.06 +0e663285c74326737d4ff3c637d4c8aba8847755 latest_2014.10.06 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 03 Dec '14

03 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0cfba5087d81/ Changeset: 0cfba5087d81 Branch: next-stable User: guerler Date: 2014-12-04 05:42:39+00:00 Summary: ToolForm: Fix error mapping Affected #: 3 files diff -r 97fdb9c106886f9f768b35b2cbe5fd164e95f3c7 -r 0cfba5087d81c4bd0add051cf1d0ab48d8a33cce client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -234,7 +234,11 @@ for (var i in head) { var new_id = i; if (id !== '') { - new_id = id + '|' + new_id; + var separator = '|'; + if (head instanceof Array) { + separator = '_'; + } + new_id = id + separator + new_id; } search (new_id, head[i]); } diff -r 97fdb9c106886f9f768b35b2cbe5fd164e95f3c7 -r 0cfba5087d81c4bd0add051cf1d0ab48d8a33cce static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -234,7 +234,11 @@ for (var i in head) { var new_id = i; if (id !== '') { - new_id = id + '|' + new_id; + var separator = '|'; + if (head instanceof Array) { + separator = '_'; + } + new_id = id + separator + new_id; } search (new_id, head[i]); } diff -r 97fdb9c106886f9f768b35b2cbe5fd164e95f3c7 -r 0cfba5087d81c4bd0add051cf1d0ab48d8a33cce static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(l,o){for(var j in o){var g=o[j];if(g.input){var q=g.input;var k=l;if(l!=""){k+="|"}k+=q.name;switch(q.type){case"repeat":var f="section-";var t=[];var n=null;for(var s in g){var m=s.indexOf(f);if(m!=-1){m+=f.length;t.push(parseInt(s.substr(m)));if(!n){n=s.substr(0,m)}}}t.sort(function(u,i){return u-i});var j=0;for(var h in t){b(k+"_"+j++,g[n+t[h]])}break;case"conditional":var r=a.app.field_list[q.id].value();if(d[q.test_param.type]){r=d[q.test_param.type](r)}c(k+"|"+q.test_param.name,q.id,r);var e=a.matchCase(q,r);if(e!=-1){b(k,o[q.id+"-section-"+e])}break;default:var p=a.app.field_list[q.id];var r=p.value();if(d[q.type]){r=d[q.type](r)}if(!p.skip){c(k,q.id,r)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.app.tree.job_ids[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file +define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(l,o){for(var j in o){var g=o[j];if(g.input){var q=g.input;var k=l;if(l!=""){k+="|"}k+=q.name;switch(q.type){case"repeat":var f="section-";var t=[];var n=null;for(var s in g){var m=s.indexOf(f);if(m!=-1){m+=f.length;t.push(parseInt(s.substr(m)));if(!n){n=s.substr(0,m)}}}t.sort(function(u,i){return u-i});var j=0;for(var h in t){b(k+"_"+j++,g[n+t[h]])}break;case"conditional":var r=a.app.field_list[q.id].value();if(d[q.test_param.type]){r=d[q.test_param.type](r)}c(k+"|"+q.test_param.name,q.id,r);var e=a.matchCase(q,r);if(e!=-1){b(k,o[q.id+"-section-"+e])}break;default:var p=a.app.field_list[q.id];var r=p.value();if(d[q.type]){r=d[q.type](r)}if(!p.skip){c(k,q.id,r)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.app.tree.job_ids[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(k,h){if(typeof h==="string"){var f=b.app.tree.job_ids[k];if(f){a[f]=h}}else{for(var g in h){var e=g;if(k!==""){var j="|";if(h instanceof Array){j="_"}e=k+j+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/50fe8f57c2fb/ Changeset: 50fe8f57c2fb User: guerler Date: 2014-12-04 05:43:07+00:00 Summary: Merge Affected #: 3 files diff -r 7591b8c658b50d484cacfa5aca61df0babfdaca2 -r 50fe8f57c2fbe71ec3ee7b7dd2b489a0d7c32d78 client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -234,7 +234,11 @@ for (var i in head) { var new_id = i; if (id !== '') { - new_id = id + '|' + new_id; + var separator = '|'; + if (head instanceof Array) { + separator = '_'; + } + new_id = id + separator + new_id; } search (new_id, head[i]); } diff -r 7591b8c658b50d484cacfa5aca61df0babfdaca2 -r 50fe8f57c2fbe71ec3ee7b7dd2b489a0d7c32d78 static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -234,7 +234,11 @@ for (var i in head) { var new_id = i; if (id !== '') { - new_id = id + '|' + new_id; + var separator = '|'; + if (head instanceof Array) { + separator = '_'; + } + new_id = id + separator + new_id; } search (new_id, head[i]); } diff -r 7591b8c658b50d484cacfa5aca61df0babfdaca2 -r 50fe8f57c2fbe71ec3ee7b7dd2b489a0d7c32d78 static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(l,o){for(var j in o){var g=o[j];if(g.input){var q=g.input;var k=l;if(l!=""){k+="|"}k+=q.name;switch(q.type){case"repeat":var f="section-";var t=[];var n=null;for(var s in g){var m=s.indexOf(f);if(m!=-1){m+=f.length;t.push(parseInt(s.substr(m)));if(!n){n=s.substr(0,m)}}}t.sort(function(u,i){return u-i});var j=0;for(var h in t){b(k+"_"+j++,g[n+t[h]])}break;case"conditional":var r=a.app.field_list[q.id].value();if(d[q.test_param.type]){r=d[q.test_param.type](r)}c(k+"|"+q.test_param.name,q.id,r);var e=a.matchCase(q,r);if(e!=-1){b(k,o[q.id+"-section-"+e])}break;default:var p=a.app.field_list[q.id];var r=p.value();if(d[q.type]){r=d[q.type](r)}if(!p.skip){c(k,q.id,r)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.app.tree.job_ids[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file +define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(l,o){for(var j in o){var g=o[j];if(g.input){var q=g.input;var k=l;if(l!=""){k+="|"}k+=q.name;switch(q.type){case"repeat":var f="section-";var t=[];var n=null;for(var s in g){var m=s.indexOf(f);if(m!=-1){m+=f.length;t.push(parseInt(s.substr(m)));if(!n){n=s.substr(0,m)}}}t.sort(function(u,i){return u-i});var j=0;for(var h in t){b(k+"_"+j++,g[n+t[h]])}break;case"conditional":var r=a.app.field_list[q.id].value();if(d[q.test_param.type]){r=d[q.test_param.type](r)}c(k+"|"+q.test_param.name,q.id,r);var e=a.matchCase(q,r);if(e!=-1){b(k,o[q.id+"-section-"+e])}break;default:var p=a.app.field_list[q.id];var r=p.value();if(d[q.type]){r=d[q.type](r)}if(!p.skip){c(k,q.id,r)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.app.tree.job_ids[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(k,h){if(typeof h==="string"){var f=b.app.tree.job_ids[k];if(f){a[f]=h}}else{for(var g in h){var e=g;if(k!==""){var j="|";if(h instanceof Array){j="_"}e=k+j+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ 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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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 03 Dec '14

03 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/97fdb9c10688/ Changeset: 97fdb9c10688 Branch: next-stable User: guerler Date: 2014-12-04 04:49:15+00:00 Summary: Fix inf swapping for json Affected #: 1 file diff -r 06d53d20887d55bf27f412c2248741e940d5424f -r 97fdb9c106886f9f768b35b2cbe5fd164e95f3c7 lib/galaxy/util/json.py --- a/lib/galaxy/util/json.py +++ b/lib/galaxy/util/json.py @@ -48,6 +48,8 @@ return "__Infinity__" elif val == float("-inf"): return "__-Infinity__" + else: + return val else: return val https://bitbucket.org/galaxy/galaxy-central/commits/7591b8c658b5/ Changeset: 7591b8c658b5 User: guerler Date: 2014-12-04 04:49:43+00:00 Summary: Merge Affected #: 1 file diff -r 1deca66fc876e855e8f286b6f0cd610227276e48 -r 7591b8c658b50d484cacfa5aca61df0babfdaca2 lib/galaxy/util/json.py --- a/lib/galaxy/util/json.py +++ b/lib/galaxy/util/json.py @@ -48,6 +48,8 @@ return "__Infinity__" elif val == float("-inf"): return "__-Infinity__" + else: + return val else: return val 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: Re-attempt fix in 37cf9cd.
by commits-noreply＠bitbucket.org 03 Dec '14

03 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1deca66fc876/ Changeset: 1deca66fc876 User: jmchilton Date: 2014-12-04 03:38:37+00:00 Summary: Re-attempt fix in 37cf9cd. Affected #: 2 files diff -r f2e8f6fdeb720a4c1d4643306f45f13bb9fc8924 -r 1deca66fc876e855e8f286b6f0cd610227276e48 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2222,10 +2222,6 @@ raise ValueError( "History does not include a dataset collection of the correct type or containing the correct types of datasets" ) if value in [None, "None"]: return None - # would really like to not need to handle lists in here but - # doing it for uniformity with DataToolParameters for now. - if isinstance( value, list ): - value = value[ 0 ] if isinstance( value, str ) and value.find( "," ) > 0: value = [ int( value_part ) for value_part in value.split( "," ) ] elif isinstance( value, trans.app.model.HistoryDatasetCollectionAssociation ): diff -r f2e8f6fdeb720a4c1d4643306f45f13bb9fc8924 -r 1deca66fc876e855e8f286b6f0cd610227276e48 lib/galaxy/tools/parameters/meta.py --- a/lib/galaxy/tools/parameters/meta.py +++ b/lib/galaxy/tools/parameters/meta.py @@ -123,6 +123,10 @@ def __collection_multirun_parameter( value ): + is_batch = value.get( 'batch', False ) + if not is_batch: + return False + batch_values = util.listify( value[ 'values' ] ) if len( batch_values ) == 1: batch_over = batch_values[ 0 ] 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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