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

commit/galaxy-central: jmchilton: Add data parameter tests to tool execution unit tests.
by commits-noreply＠bitbucket.org 14 Jan '14

14 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1afdcafa4b28/ Changeset: 1afdcafa4b28 User: jmchilton Date: 2014-01-14 15:00:57 Summary: Add data parameter tests to tool execution unit tests. Affected #: 2 files diff -r a976a0ceee2b9d5a57eb6eaef062d48ebcdff085 -r 1afdcafa4b28e246efc0c96987c63e469e2255e7 test/unit/tools/test_execution.py --- a/test/unit/tools/test_execution.py +++ b/test/unit/tools/test_execution.py @@ -9,6 +9,7 @@ from galaxy.tools import DefaultToolState from galaxy.tools.parameters import params_to_incoming from galaxy.util import parse_xml +from galaxy.util.bunch import Bunch from galaxy.util import string_to_object from galaxy.util import object_to_string from galaxy.util.odict import odict @@ -40,15 +41,31 @@ </tool> ''' +# A tool with data parameters (kind of like cat1) my favorite test tool :) +SIMPLE_CAT_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool"> + <command>cat "$param1" #for $r in $repeat# "$r.param2" #end for# < $out1</command> + <inputs> + <param type="data" format="tabular" name="param1" value="" /> + <repeat name="repeat1" label="Repeat 1"> + <param type="data" format="tabular" name="param2" value="" /> + </repeat> + </inputs> + <outputs> + <output name="out1" format="data" /> + </outputs> +</tool> +''' + class ToolExecutionTestCase( TestCase, UsesApp ): def setUp(self): self.setup_app() + self.history = galaxy.model.History() self.app.job_config["get_job_tool_configurations"] = lambda ids: None self.app.config.drmaa_external_runjob_script = "" self.app.config.tool_secret = "testsecret" - self.trans = MockTrans( self.app ) + self.trans = MockTrans( self.app, self.history ) self.tool_action = MockAction( self.trans ) self.tool_file = os.path.join( self.test_directory, "tool.xml" ) @@ -102,6 +119,29 @@ state = self.__assert_rerenders_tool_without_errors( template, template_vars ) assert len( state.inputs[ "repeat1" ] ) == 1 + def test_data_param_execute( self ): + self.__init_tool( SIMPLE_CAT_TOOL_CONTENTS ) + hda = self.__add_dataset(1) + # Execute tool action + template, template_vars = self.__handle_with_incoming( + param1=1, + runtool_btn="dummy", + ) + assert template == "tool_executed.mako" + # Tool 'executed' once, with hda as param1 + assert len( self.tool_action.execution_call_args ) == 1 + assert self.tool_action.execution_call_args[ 0 ][ "incoming" ][ "param1" ] == hda + + def test_data_param_state_update( self ): + self.__init_tool( SIMPLE_CAT_TOOL_CONTENTS ) + hda = self.__add_dataset( 1 ) + # Update state + template, template_vars = self.__handle_with_incoming( + param1=1, + ) + state = self.__assert_rerenders_tool_without_errors( template, template_vars ) + assert hda == state.inputs[ "param1" ] + def __handle_with_incoming( self, previous_state=None, **kwds ): """ Execute tool.handle_input with incoming specified by kwds (optionally extending a previous state). @@ -122,12 +162,21 @@ new_incoming.update( kwds ) return new_incoming + def __add_dataset( self, id, state='ok' ): + hda = galaxy.model.HistoryDatasetAssociation() + hda.id = id + hda.dataset = galaxy.model.Dataset() + hda.dataset.state = 'ok' + + self.trans.sa_session.model_objects[ galaxy.model.HistoryDatasetAssociation ][ id ] = hda + self.history.datasets.append( hda ) + return hda + def __assert_rerenders_tool_without_errors( self, template, template_vars ): assert template == "tool_form.mako" assert not template_vars[ "errors" ] state = template_vars[ "tool_state" ] return state - assert state.inputs[ "param1" ] == "moo" def __init_tool( self, tool_contents ): self.__write_tool( tool_contents ) @@ -174,6 +223,13 @@ class MockTrans( object ): - def __init__( self, app ): + def __init__( self, app, history ): self.app = app + self.history = history self.history = galaxy.model.History() + self.workflow_building_mode = False + self.webapp = Bunch( name="galaxy" ) + self.sa_session = self.app.model.context + + def get_history( self ): + return self.history diff -r a976a0ceee2b9d5a57eb6eaef062d48ebcdff085 -r 1afdcafa4b28e246efc0c96987c63e469e2255e7 test/unit/tools_support.py --- a/test/unit/tools_support.py +++ b/test/unit/tools_support.py @@ -3,11 +3,13 @@ so use of this should be limitted to tests of very 'extensive' classes. """ +from collections import defaultdict import os.path import tempfile import shutil from galaxy.util.bunch import Bunch +import galaxy.model from galaxy.model import mapping @@ -44,8 +46,47 @@ # Setup some attributes for downstream extension by specific tests. self.job_config = Bunch() - self.model = Bunch() + # Create self.model to mimic app.model. + self.model = Bunch( context=MockContext() ) + for module_member_name in dir( galaxy.model ): + module_member = getattr(galaxy.model, module_member_name) + if type( module_member ) == type: + self.model[ module_member_name ] = module_member self.toolbox = None self.object_store = None + +class MockContext(object): + + def __init__(self, model_objects=None): + self.expunged_all = False + self.flushed = False + self.model_objects = model_objects or defaultdict( lambda: {} ) + self.created_objects = [] + + def expunge_all(self): + self.expunged_all = True + + def query(self, clazz): + return MockQuery(self.model_objects.get(clazz)) + + def flush(self): + self.flushed = True + + def add(self, object): + self.created_objects.append(object) + + +class MockQuery(object): + + def __init__(self, class_objects): + self.class_objects = class_objects + + def filter_by(self, **kwds): + return Bunch(first=lambda: None) + + def get(self, id): + return self.class_objects.get(id, None) + + __all__ = [ UsesApp ] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fixes for mapping values in the Galaxy tool shed install methods.
by commits-noreply＠bitbucket.org 13 Jan '14

13 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a976a0ceee2b/ Changeset: a976a0ceee2b User: greg Date: 2014-01-13 22:54:40 Summary: Fixes for mapping values in the Galaxy tool shed install methods. Affected #: 1 file diff -r c2f2b62f5435a328eb0e54cbee00ce2fd3f668fc -r a976a0ceee2b9d5a57eb6eaef062d48ebcdff085 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -66,8 +66,9 @@ exported_workflows.append( display_dict ) return exported_workflows - def __get_value_mapper( self, trans ): - value_mapper = { 'id' : trans.security.encode_id } + def __get_value_mapper( self, trans, tool_shed_repository ): + value_mapper={ 'id' : trans.security.encode_id( tool_shed_repository.id ), + 'error_message' : tool_shed_repository.error_message or '' } return value_mapper @web.expose_api @@ -142,7 +143,7 @@ for tool_shed_repository in trans.install_model.context.query( trans.app.install_model.ToolShedRepository ) \ .order_by( trans.app.install_model.ToolShedRepository.table.c.name ): tool_shed_repository_dict = \ - tool_shed_repository.to_dict( value_mapper=self.__get_value_mapper( trans ) ) + tool_shed_repository.to_dict( value_mapper=self.__get_value_mapper( trans, tool_shed_repository ) ) tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', action='show', id=trans.security.encode_id( tool_shed_repository.id ) ) @@ -336,7 +337,7 @@ tool_path, install_tool_dependencies, reinstalling=False ) - tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=self.__get_value_mapper( trans ) ) + tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=self.__get_value_mapper( trans, tool_shed_repository ) ) tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', action='show', id=trans.security.encode_id( tool_shed_repository.id ) ) @@ -471,7 +472,7 @@ repair_dict = repository_util.repair_tool_shed_repository( trans, repository, encoding_util.tool_shed_encode( repo_info_dict ) ) - repository_dict = repository.to_dict( value_mapper=self.__get_value_mapper( trans ) ) + repository_dict = repository.to_dict( value_mapper=self.__get_value_mapper( trans, repository ) ) repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', action='show', id=trans.security.encode_id( repository.id ) ) @@ -538,7 +539,7 @@ if tool_shed_repository is None: log.debug( "Unable to locate tool_shed_repository record for id %s." % ( str( id ) ) ) return {} - tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=self.__get_value_mapper( trans ) ) + tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=self.__get_value_mapper( trans, tool_shed_repository ) ) tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', action='show', id=trans.security.encode_id( tool_shed_repository.id ) ) 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: Add more state handling tests...
by commits-noreply＠bitbucket.org 13 Jan '14

13 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c2f2b62f5435/ Changeset: c2f2b62f5435 User: jmchilton Date: 2014-01-13 22:14:33 Summary: Add more state handling tests... ... to tool execution unit tests. Affected #: 1 file diff -r 76979aa9d343e94dfcf22ce1458a145fbc9c7218 -r c2f2b62f5435a328eb0e54cbee00ce2fd3f668fc test/unit/tools/test_execution.py --- a/test/unit/tools/test_execution.py +++ b/test/unit/tools/test_execution.py @@ -7,14 +7,16 @@ import galaxy.model from galaxy.tools import Tool from galaxy.tools import DefaultToolState +from galaxy.tools.parameters import params_to_incoming from galaxy.util import parse_xml from galaxy.util import string_to_object from galaxy.util import object_to_string from galaxy.util.odict import odict from tools_support import UsesApp -EXAMPLE_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool"> - <command>echo "$text" < $out1</command> +# Simple tool with just one text parameter and output. +SIMPLE_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool"> + <command>echo "$param1" < $out1</command><inputs><param type="text" name="param1" value="" /></inputs> @@ -23,6 +25,21 @@ </outputs></tool>''' +# Tool with a repeat parameter, to test state update. +REPEAT_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool"> + <command>echo "$param1" #for $r in $repeat# "$r.param2" #end for# < $out1</command> + <inputs> + <param type="text" name="param1" value="" /> + <repeat name="repeat1" label="Repeat 1"> + <param type="text" name="param2" value="" /> + </repeat> + </inputs> + <outputs> + <output name="out1" format="data" /> + </outputs> +</tool> +''' + class ToolExecutionTestCase( TestCase, UsesApp ): @@ -39,27 +56,82 @@ self.tear_down_app() def test_state_new( self ): - self.__write_tool( EXAMPLE_TOOL_CONTENTS ) - self.__setup_tool( ) - template, template_vars = self.tool.handle_input( - trans=self.trans, - incoming=dict( param1="moo" ) + self.__init_tool( SIMPLE_TOOL_CONTENTS ) + template, template_vars = self.__handle_with_incoming( + param1="moo", # no runtool_btn, just rerenders the form mako with tool # state populated. ) + state = self.__assert_rerenders_tool_without_errors( template, template_vars ) + assert state.inputs[ "param1" ] == "moo" + + def test_execute( self ): + self.__init_tool( SIMPLE_TOOL_CONTENTS ) + template, template_vars = self.__handle_with_incoming( + param1="moo", + runtool_btn="dummy", + ) + assert template == "tool_executed.mako" + + def test_repeat_state_updates( self ): + self.__init_tool( REPEAT_TOOL_CONTENTS ) + + # Fresh state contains no repeat elements + template, template_vars = self.__handle_with_incoming() + state = self.__assert_rerenders_tool_without_errors( template, template_vars ) + assert len( state.inputs[ "repeat1" ] ) == 0 + + # Hitting add button adds repeat element + template, template_vars = self.__handle_with_incoming( + repeat1_add="dummy", + ) + state = self.__assert_rerenders_tool_without_errors( template, template_vars ) + assert len( state.inputs[ "repeat1" ] ) == 1 + + # Hitting add button again adds another repeat element + template, template_vars = self.__handle_with_incoming( state, **{ + "repeat1_add": "dummy", + "repeat1_0|param2": "moo2", + } ) + state = self.__assert_rerenders_tool_without_errors( template, template_vars ) + assert len( state.inputs[ "repeat1" ] ) == 2 + assert state.inputs[ "repeat1" ][ 0 ][ "param2" ] == "moo2" + + # Hitting remove drops a repeat element + template, template_vars = self.__handle_with_incoming( state, repeat1_1_remove="dummy" ) + state = self.__assert_rerenders_tool_without_errors( template, template_vars ) + assert len( state.inputs[ "repeat1" ] ) == 1 + + def __handle_with_incoming( self, previous_state=None, **kwds ): + """ Execute tool.handle_input with incoming specified by kwds + (optionally extending a previous state). + """ + if previous_state: + incoming = self.__to_incoming( previous_state, **kwds) + else: + incoming = kwds + return self.tool.handle_input( + trans=self.trans, + incoming=incoming, + ) + + def __to_incoming( self, state, **kwds ): + new_incoming = {} + params_to_incoming( new_incoming, self.tool.inputs, state.inputs, self.app ) + new_incoming[ "tool_state" ] = self.__state_to_string( state ) + new_incoming.update( kwds ) + return new_incoming + + def __assert_rerenders_tool_without_errors( self, template, template_vars ): assert template == "tool_form.mako" assert not template_vars[ "errors" ] state = template_vars[ "tool_state" ] + return state assert state.inputs[ "param1" ] == "moo" - def test_execute( self ): - self.__write_tool( EXAMPLE_TOOL_CONTENTS ) + def __init_tool( self, tool_contents ): + self.__write_tool( tool_contents ) self.__setup_tool( ) - template, template_vars = self.tool.handle_input( - trans=self.trans, - incoming=dict( param1="moo", runtool_btn="dummy" ) - ) - assert template == "tool_executed.mako" def __setup_tool( self ): tree = parse_xml( self.tool_file ) @@ -80,9 +152,12 @@ tool_state.inputs = inputs return tool_state + def __state_to_string( self, tool_state ): + return object_to_string( tool_state.encode( self.tool, self.app ) ) + def __inputs_to_state_string( self, inputs ): tool_state = self.__inputs_to_state( inputs ) - return object_to_string( tool_state.encode( self.tool, self.app ) ) + return self.__state_to_string( tool_state ) class MockAction( object ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Don't mess with the label of the installation errors container in the tool shed.
by commits-noreply＠bitbucket.org 13 Jan '14

13 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/76979aa9d343/ Changeset: 76979aa9d343 User: greg Date: 2014-01-13 22:02:47 Summary: Don't mess with the label of the installation errors container in the tool shed. Affected #: 1 file diff -r ab61a1b51a608183922301aa8bdb48a1d98c0f9b -r 76979aa9d343e94dfcf22ce1458a145fbc9c7218 templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -263,8 +263,6 @@ folder_label = "%s - installation of these additional repositories is required" % folder_label if trans.webapp.name == 'galaxy': col_span_str = 'colspan="4"' - elif folder.label == 'Installation errors': - folder_label = "%s - no functional tests were run for any tools in this changeset revision" % folder_label elif folder.label == 'Invalid repository dependencies': folder_label = "%s - click the repository dependency to see why it is invalid" % folder_label elif folder.label == 'Invalid tool dependencies': 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: greg: Fixes and code cleanup for the tool shed's "Latest revision" queries.
by commits-noreply＠bitbucket.org 13 Jan '14

13 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ab61a1b51a60/ Changeset: ab61a1b51a60 User: greg Date: 2014-01-13 21:49:40 Summary: Fixes and code cleanup for the tool shed's "Latest revision" queries. Affected #: 5 files diff -r 757ede99b3dee051a9d41b61bbef6a1afaaae35c -r ab61a1b51a608183922301aa8bdb48a1d98c0f9b lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -311,9 +311,9 @@ message = 'This list contains repositories that match the following criteria: ' message += '<ul>' message += '<li>you are authorized to update them</li>' - message += '<li>the latest installable revision contains at least 1 tool</li>' message += '<li>the latest installable revision is not missing any tool test components</li>' - message += '<li>the latest installable revision has installation errors (the repository itself, repository dependencies or tool dependencies)</li>' + message += '<li>the latest installable revision has installation errors (the repository itself, ' + message += 'repository dependencies or tool dependencies)</li>' message += '</ul>' kwd[ 'message' ] = message kwd[ 'status' ] = 'warning' @@ -340,8 +340,10 @@ message = 'This list contains repositories that match the following criteria: ' message += '<ul>' message += '<li>you are authorized to update them</li>' - message += '<li>the latest installable revision contains at least 1 tool</li>' - message += '<li>the latest installable revision has Skip automated testing of tools in this revision checked</li>' + message += '<li>the latest installable revision has Skip automated testing of tools in this ' + message += 'revision checked if the repository type is Unrestricted or Skip ' + message += 'automated testing of this tool dependency recipe checked if the repository ' + message += 'type is Tool dependency definition</li>' message += '</ul>' kwd[ 'message' ] = message kwd[ 'status' ] = 'warning' @@ -566,9 +568,9 @@ if 'message' not in kwd: message = 'This list contains repositories that match the following criteria: ' message += '<ul>' - message += '<li>the latest installable revision contains at least 1 tool</li>' message += '<li>the latest installable revision is not missing any tool test components</li>' - message += '<li>the latest installable revision has installation errors (the repository itself, repository dependencies or tool dependencies)</li>' + message += '<li>the latest installable revision has installation errors (the repository itself, ' + message += 'repository dependencies or tool dependencies)</li>' message += '</ul>' kwd[ 'message' ] = message kwd[ 'status' ] = 'warning' @@ -649,8 +651,10 @@ if 'message' not in kwd: message = 'This list contains repositories that match the following criteria: ' message += '<ul>' - message += '<li>the latest installable revision contains at least 1 tool</li>' - message += '<li>the latest installable revision has Skip automated testing of tools in this revision checked</li>' + message += '<li>the latest installable revision has Skip automated testing of tools in this ' + message += 'revision checked if the repository type is Unrestricted or Skip ' + message += 'automated testing of this tool dependency recipe checked if the repository ' + message += 'type is Tool dependency definition</li>' message += '</ul>' kwd[ 'message' ] = message kwd[ 'status' ] = 'warning' diff -r 757ede99b3dee051a9d41b61bbef6a1afaaae35c -r ab61a1b51a608183922301aa8bdb48a1d98c0f9b lib/galaxy/webapps/tool_shed/model/__init__.py --- a/lib/galaxy/webapps/tool_shed/model/__init__.py +++ b/lib/galaxy/webapps/tool_shed/model/__init__.py @@ -238,10 +238,10 @@ 'has_repository_dependencies', 'includes_datatypes', 'includes_tools', 'includes_tool_dependencies', 'includes_tools_for_display_in_tool_panel', 'includes_workflows' ) - def __init__( self, id=None, repository_id=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False, downloadable=False, - missing_test_components=None, tools_functionally_correct=False, do_not_test=False, test_install_error=False, time_last_tested=None, - tool_test_results=None, has_repository_dependencies=False, includes_datatypes=False, includes_tools=False, includes_tool_dependencies=False, - includes_workflows=False ): + def __init__( self, id=None, repository_id=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False, + downloadable=False, missing_test_components=None, tools_functionally_correct=False, do_not_test=False, + test_install_error=False, time_last_tested=None, tool_test_results=None, has_repository_dependencies=False, + includes_datatypes=False, includes_tools=False, includes_tool_dependencies=False, includes_workflows=False ): self.id = id self.repository_id = repository_id self.changeset_revision = changeset_revision diff -r 757ede99b3dee051a9d41b61bbef6a1afaaae35c -r ab61a1b51a608183922301aa8bdb48a1d98c0f9b lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -1693,12 +1693,11 @@ def filter_by_latest_downloadable_changeset_revision_that_has_failing_tool_tests( trans, repository ): """ - Inspect the latest installable changeset revision for the received repository to see if it includes at least 1 tool that has at least 1 failing test. + Inspect the latest downloadable changeset revision for the received repository to see if it + includes at least 1 tool that has at least 1 failing test. This will filter out repositories + of type tool_dependency_definition. """ - encoded_repository_id = trans.security.encode_id( repository.id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - tip_ctx = str( repo.changectx( repo.changelog.tip() ) ) - repository_metadata = get_latest_installable_repository_metadata_if_it_includes_tools( trans, repository ) + repository_metadata = get_latest_downloadable_repository_metadata_if_it_includes_tools( trans, repository ) if repository_metadata \ and repository_metadata.tool_test_results is not None \ and not repository_metadata.missing_test_components \ @@ -1709,109 +1708,135 @@ def filter_by_latest_downloadable_changeset_revision_that_has_missing_tool_test_components( trans, repository ): """ - Inspect the latest installable changeset revision for the received repository to see if it includes tools that are either missing functional tests - or functional test data. If the changset revision includes tools, but is missing tool test components, return the changeset revision hash. + Inspect the latest downloadable changeset revision for the received repository to see if it + includes tools that are either missing functional tests or functional test data. If the + changset revision includes tools but is missing tool test components, return the changeset + revision hash. This will filter out repositories of type tool_dependency_definition. """ - encoded_repository_id = trans.security.encode_id( repository.id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - tip_ctx = str( repo.changectx( repo.changelog.tip() ) ) - repository_metadata = get_latest_installable_repository_metadata_if_it_includes_tools( trans, repository ) + repository_metadata = get_latest_downloadable_repository_metadata_if_it_includes_tools( trans, repository ) if repository_metadata and repository_metadata.missing_test_components: return repository_metadata.changeset_revision return None def filter_by_latest_downloadable_changeset_revision_that_has_no_failing_tool_tests( trans, repository ): """ - Inspect the latest installable changeset revision for the received repository to see if it includes tools with no failing tests. + Inspect the latest downloadable changeset revision for the received repository to see if it + includes tools with no failing tests. This will filter out repositories of type tool_dependency_definition. """ - encoded_repository_id = trans.security.encode_id( repository.id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - tip_ctx = str( repo.changectx( repo.changelog.tip() ) ) - repository_metadata = get_latest_installable_repository_metadata_if_it_includes_tools( trans, repository ) - if repository_metadata and not repository_metadata.missing_test_components and repository_metadata.tools_functionally_correct: + repository_metadata = get_latest_downloadable_repository_metadata_if_it_includes_tools( trans, repository ) + if repository_metadata is not None and \ + not repository_metadata.missing_test_components and \ + repository_metadata.tools_functionally_correct: return repository_metadata.changeset_revision return None def filter_by_latest_metadata_changeset_revision_that_has_invalid_tools( trans, repository ): """ - Inspect the latest changeset revision with associated metadata for the received repository to see if it has invalid tools. + Inspect the latest changeset revision with associated metadata for the received repository + to see if it has invalid tools. This will filter out repositories of type tool_dependency_definition. """ - encoded_repository_id = trans.security.encode_id( repository.id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - tip_ctx = str( repo.changectx( repo.changelog.tip() ) ) repository_metadata = get_latest_repository_metadata_if_it_includes_invalid_tools( trans, repository ) - if repository_metadata: + if repository_metadata is not None: return repository_metadata.changeset_revision return None def filter_by_latest_downloadable_changeset_revision_that_has_test_install_errors( trans, repository ): """ - Inspect the latest installable changeset revision for the received repository to see if it has tool test installation errors. + Inspect the latest downloadable changeset revision for the received repository to see if + it has tool test installation errors. This will return repositories of type unrestricted + as well as type tool_dependency_definition. """ - encoded_repository_id = trans.security.encode_id( repository.id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - tip_ctx = str( repo.changectx( repo.changelog.tip() ) ) - repository_metadata = get_latest_installable_repository_metadata_if_it_includes_tools( trans, repository ) - if repository_metadata \ - and repository_metadata.test_install_error \ - and not repository_metadata.missing_test_components: + repository_metadata = get_latest_downloadable_repository_metadata_if_it_has_test_install_errors( trans, repository ) + # Filter further by eliminating repositories that are missing test components. + if repository_metadata is not None and not repository_metadata.missing_test_components: return repository_metadata.changeset_revision return None def filter_by_latest_downloadable_changeset_revision_with_skip_tests_checked( trans, repository ): """ - Inspect the latest installable changeset revision for the received repository to see if skip tests is checked. + Inspect the latest downloadable changeset revision for the received repository to see if skip tests + is checked. This will return repositories of type unrestricted as well as type tool_dependency_definition. """ - encoded_repository_id = trans.security.encode_id( repository.id ) - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - tip_ctx = str( repo.changectx( repo.changelog.tip() ) ) - repository_metadata = get_latest_installable_repository_metadata_if_it_includes_tools( trans, repository ) - if repository_metadata and repository_metadata.skip_tool_tests: + repository_metadata = get_latest_downloadable_repository_metadata( trans, repository ) + # The skip_tool_tests attribute is a SkipToolTest table mapping backref to the RepositoryMetadata table. + if repository_metadata is not None and repository_metadata.skip_tool_tests: return repository_metadata.changeset_revision return None -def get_latest_repository_metadata_if_it_includes_invalid_tools( trans, repository ): - """Return the latest repository_metadata record for the received repository that contains invalid tools if one exists.""" +def get_latest_downloadable_repository_metadata( trans, repository ): + """ + Return the latest downloadable repository_metadata record for the received repository. This will + return repositories of type unrestricted as well as type tool_dependency_definition. + """ encoded_repository_id = trans.security.encode_id( repository.id ) repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) tip_ctx = str( repo.changectx( repo.changelog.tip() ) ) repository_metadata = None try: repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, tip_ctx ) - if repository_metadata: - metadata = repository_metadata.metadata - if metadata and 'invalid_tools' in metadata: - return repository_metadata - return None + if repository_metadata is not None and repository_metadata.downloadable: + return repository_metadata return None except: - latest_installable_revision = suc.get_previous_metadata_changeset_revision( repository, repo, tip_ctx, downloadable=False ) - if latest_installable_revision == suc.INITIAL_CHANGELOG_HASH: + latest_downloadable_revision = suc.get_previous_metadata_changeset_revision( repository, repo, tip_ctx, downloadable=True ) + if latest_downloadable_revision == suc.INITIAL_CHANGELOG_HASH: return None - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, latest_installable_revision ) - if repository_metadata: - metadata = repository_metadata.metadata - if metadata and 'invalid_tools' in metadata: - return repository_metadata - return None + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, + encoded_repository_id, + latest_downloadable_revision ) + if repository_metadata is not None and repository_metadata.downloadable: + return repository_metadata return None -def get_latest_installable_repository_metadata_if_it_includes_tools( trans, repository ): - """Return the latest installable repository_metadata record for the received repository that contains valid tools if one exists.""" +def get_latest_downloadable_repository_metadata_if_it_includes_tools( trans, repository ): + """ + Return the latest downloadable repository_metadata record for the received repository if its + includes_tools attribute is True. This will filter out repositories of type tool_dependency_definition. + """ + repository_metadata = get_latest_downloadable_repository_metadata( trans, repository ) + if repository_metadata is not None and repository_metadata.includes_tools: + return repository_metadata + return None + +def get_latest_downloadable_repository_metadata_if_it_has_test_install_errors( trans, repository ): + """ + Return the latest downloadable repository_metadata record for the received repository if its + test_install_error attribute is True. This will return repositories of type unrestricted as + well as type tool_dependency_definition. + """ + repository_metadata = get_latest_downloadable_repository_metadata( trans, repository ) + if repository_metadata is not None and repository_metadata.test_install_error: + return repository_metadata + return None + +def get_latest_repository_metadata( trans, repository ): + """ + Return the latest repository_metadata record for the received repository if it exists. This will + return repositories of type unrestricted as well as type tool_dependency_definition. + """ encoded_repository_id = trans.security.encode_id( repository.id ) repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) tip_ctx = str( repo.changectx( repo.changelog.tip() ) ) - repository_metadata = None try: repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, tip_ctx ) - if repository_metadata and repository_metadata.includes_tools and repository_metadata.downloadable: + return repository_metadata + except: + latest_downloadable_revision = suc.get_previous_metadata_changeset_revision( repository, repo, tip_ctx, downloadable=False ) + if latest_downloadable_revision == suc.INITIAL_CHANGELOG_HASH: + return None + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, + encoded_repository_id, + latest_downloadable_revision ) + return repository_metadata + +def get_latest_repository_metadata_if_it_includes_invalid_tools( trans, repository ): + """ + Return the latest repository_metadata record for the received repository that contains invalid + tools if one exists. This will filter out repositories of type tool_dependency_definition. + """ + repository_metadata = get_latest_repository_metadata( trans, repository ) + if repository_metadata is not None: + metadata = repository_metadata.metadata + if metadata is not None and 'invalid_tools' in metadata: return repository_metadata - return None - except: - latest_installable_revision = suc.get_previous_metadata_changeset_revision( repository, repo, tip_ctx, downloadable=True ) - if latest_installable_revision == suc.INITIAL_CHANGELOG_HASH: - return None - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, latest_installable_revision ) - if repository_metadata and repository_metadata.includes_tools and repository_metadata.downloadable: - return repository_metadata - return None + return None diff -r 757ede99b3dee051a9d41b61bbef6a1afaaae35c -r ab61a1b51a608183922301aa8bdb48a1d98c0f9b test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -852,7 +852,7 @@ owner = repository_dependencies_dict.get( 'owner', None ) changeset_revision = repository_dependencies_dict.get( 'changeset_revision', None ) if name is None or owner is None or changeset_revision is None: - log.debug( 'Skipping invalid repository_dependencies_dict due to missing name,owner or changeset_revision: %s' % \ + log.debug( 'Skipping invalid repository_dependencies_dict due to missing name, owner or changeset_revision: %s' % \ str( repository_dependencies_dict ) ) continue name = str( name ) diff -r 757ede99b3dee051a9d41b61bbef6a1afaaae35c -r ab61a1b51a608183922301aa8bdb48a1d98c0f9b test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -697,7 +697,7 @@ set_do_not_test = not is_latest_downloadable_revision params = dict( tools_functionally_correct=False, test_install_error=False, - do_not_test=str( set_do_not_test ) ) + do_not_test=set_do_not_test ) response_dict = \ install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, tool_test_results_dicts, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: inithello: Set the install and test wrapper script to only execute the repositories_with_tools tests if the previous tool_dependency_definitions test run completed.
by commits-noreply＠bitbucket.org 13 Jan '14

13 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/757ede99b3de/ Changeset: 757ede99b3de User: inithello Date: 2014-01-13 21:23:23 Summary: Set the install and test wrapper script to only execute the repositories_with_tools tests if the previous tool_dependency_definitions test run completed. Affected #: 1 file diff -r e464ef370c194f730297a81592fa83d7dc59bdbc -r 757ede99b3dee051a9d41b61bbef6a1afaaae35c install_and_test_tool_shed_repositories.sh --- a/install_and_test_tool_shed_repositories.sh +++ b/install_and_test_tool_shed_repositories.sh @@ -45,18 +45,27 @@ test_tool_dependency_definitions () { # Test installation of repositories of type tool_dependency_definition. + if [ -f /ToolDepsTest/stage_1_complete ] ; then + rm /ToolDepsTest/stage_1_complete + fi python test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py $* -v --with-nosehtml --html-report-file \ test/install_and_test_tool_shed_repositories/tool_dependency_definitions/run_functional_tests.html \ test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ - test/functional/test_toolbox.py + test/functional/test_toolbox.py + touch /ToolDepsTest/stage_1_complete } test_repositories_with_tools () { + if [ ! -f /ToolDepsTest/stage_1_complete ] ; then + echo 'Stage 1 did not complete its run, exiting.' + exit 1 + fi # Test installation of repositories that contain valid tools with defined functional tests and a test-data directory containing test files. python test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py $* -v --with-nosehtml --html-report-file \ test/install_and_test_tool_shed_repositories/repositories_with_tools/run_functional_tests.html \ test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ - test/functional/test_toolbox.py + test/functional/test_toolbox.py + rm /ToolDepsTest/stage_1_complete } which='both' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Charts: Update pie chart code
by commits-noreply＠bitbucket.org 13 Jan '14

13 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e464ef370c19/ Changeset: e464ef370c19 User: guerler Date: 2014-01-13 20:27:42 Summary: Charts: Update pie chart code Affected #: 1 file diff -r 5c5e543867c10731a2d4a4309f077d9b3e91d3a5 -r e464ef370c194f730297a81592fa83d7dc59bdbc config/plugins/visualizations/charts/static/charts/piechart.js --- a/config/plugins/visualizations/charts/static/charts/piechart.js +++ b/config/plugins/visualizations/charts/static/charts/piechart.js @@ -12,47 +12,25 @@ }, // render - refresh : function() + refresh : function(data) { // add graph to screen var self = this; - nv.addGraph(function(data) { + nv.addGraph(function() { self.chart_3d = nv.models.pieChart() .x(function(d) { return d.key }) .y(function(d) { return d.y }) - .color(d3.scale.category10().range()) - .height(250) - .width(250); + .showLabels(true); d3.select(self.options.svg_id) - .datum(self._data()) + .datum(data) .transition().duration(1200) - .attr('height', 250) - .attr('width', 250) .call(self.chart_3d); nv.utils.windowResize(self.chart_3d.update); + + return self.chart_3d; }); - }, - - _data : function() { - return [ - { - key: "Cumulative Return", - values: [ - { - key : "CDS / Options" , - y : 29.765957771107 - }, - { - key : "Options" , - y : 19.765957771107 - }, - { - key : "Other" , - y : 12.765957771107 - }] - }]; } }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: HDA API: silently fail any update to the None value
by commits-noreply＠bitbucket.org 13 Jan '14

13 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5c5e543867c1/ Changeset: 5c5e543867c1 User: carlfeberhard Date: 2014-01-13 20:12:33 Summary: HDA API: silently fail any update to the None value Affected #: 3 files diff -r 6fe7f3ce1acd2263cbc57d34d83b99b3b58e6ea3 -r 5c5e543867c10731a2d4a4309f077d9b3e91d3a5 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -385,6 +385,8 @@ ) validated_payload = {} for key, val in payload.items(): + if val is None: + continue if key in ( 'name', 'genome_build', 'misc_info', 'annotation' ): val = self.validate_and_sanitize_basestring( key, val ) #TODO: need better remap system or eliminate the need altogether diff -r 6fe7f3ce1acd2263cbc57d34d83b99b3b58e6ea3 -r 5c5e543867c10731a2d4a4309f077d9b3e91d3a5 static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -41,7 +41,7 @@ purged : false, // sniffed datatype (sam, tabular, bed, etc.) - data_type : null, + data_type : '', // size in bytes file_size : 0, file_ext : '', @@ -52,7 +52,8 @@ misc_blurb : '', misc_info : '', - tags : null + tags : [], + annotation : '' }, /** fetch location of this HDA's history in the api */ diff -r 6fe7f3ce1acd2263cbc57d34d83b99b3b58e6ea3 -r 5c5e543867c10731a2d4a4309f077d9b3e91d3a5 static/scripts/packed/mvc/dataset/hda-model.js --- a/static/scripts/packed/mvc/dataset/hda-model.js +++ b/static/scripts/packed/mvc/dataset/hda-model.js @@ -1,1 +1,1 @@ -define([],function(){var d=Backbone.Model.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:null},urlRoot:galaxy_config.root+"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("id")},urls:function(){var i=this.get("id");if(!i){return{}}var h={purge:galaxy_config.root+"datasets/"+i+"/purge_async",display:galaxy_config.root+"datasets/"+i+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+i+"/edit",download:galaxy_config.root+"datasets/"+i+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+i,rerun:galaxy_config.root+"tool_runner/rerun?id="+i,show_params:galaxy_config.root+"datasets/"+i+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+i,set:galaxy_config.root+"dataset/annotate_async?id="+i},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+i+"&metadata_name="};return h},initialize:function(h){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",d.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(i,h){this.log(this+" has changed state:",i,h);if(this.inReadyState()){this.trigger("state:ready",i,h,this.previous("state"))}})},toJSON:function(){var h=Backbone.Model.prototype.toJSON.call(this);h.misc_info=jQuery.trim(h.misc_info);return h},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(i,j){var h=true;if((!i)&&(this.get("deleted")||this.get("purged"))){h=false}if((!j)&&(!this.get("visible"))){h=false}return h},hidden:function(){return !this.get("visible")},inReadyState:function(){var h=_.contains(d.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||h)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function c(h){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},h)},undelete:function a(h){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},h)},hide:function b(h){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},h)},unhide:function g(h){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},h)},purge:function f(h){if(this.get("purged")){return jQuery.when()}h=h||{};h.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var i=this,j=jQuery.ajax(h);j.done(function(m,k,l){i.set({deleted:true,purged:true})});j.fail(function(o,k,n){var l=_l("Unable to purge dataset");var m=("Removal of datasets by users is not allowed in this Galaxy instance");if(o.responseJSON&&o.responseJSON.error){l=o.responseJSON.error}else{if(o.responseText.indexOf(m)!==-1){l=m}}o.responseText=l;i.trigger("error",i,o,h,_l(l),{error:l})});return j},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},searchAttribute:function(j,h){var i=this.get(j);if(!h||(i===undefined||i===null)){return false}if(_.isArray(i)){return this._searchArrayAttribute(i,h)}return(i.toString().toLowerCase().indexOf(h.toLowerCase())!==-1)},_searchArrayAttribute:function(i,h){h=h.toLowerCase();return _.any(i,function(j){return(j.toString().toLowerCase().indexOf(h.toLowerCase())!==-1)})},search:function(h){var i=this;return _.filter(this.searchAttributes,function(j){return i.searchAttribute(j,h)})},matches:function(i){var k="=",h=i.split(k);if(h.length>=2){var j=h[0];j=this.searchAliases[j]||j;return this.searchAttribute(j,h[1])}return !!this.search(i).length},matchesAll:function(i){var h=this;i=i.match(/(".*"|\w*=".*"|\S*)/g).filter(function(j){return !!j});return _.all(i,function(j){j=j.replace(/"/g,"");return h.matches(j)})},toString:function(){var h=this.get("id")||"";if(this.get("name")){h=this.get("hid")+' :"'+this.get("name")+'",'+h}return"HDA("+h+")"}});d.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};d.READY_STATES=[d.STATES.NEW,d.STATES.OK,d.STATES.EMPTY,d.STATES.PAUSED,d.STATES.FAILED_METADATA,d.STATES.NOT_VIEWABLE,d.STATES.DISCARDED,d.STATES.ERROR];d.NOT_READY_STATES=[d.STATES.UPLOAD,d.STATES.QUEUED,d.STATES.RUNNING,d.STATES.SETTING_METADATA];var e=Backbone.Collection.extend(LoggableMixin).extend({model:d,urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(i,h){h=h||{};this.historyId=h.historyId},ids:function(){return this.map(function(h){return h.id})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(i){if(!i.inReadyState()){h.push(i.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];var i=new e(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new e(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(k,j){var i=jQuery.Deferred(),h=this.length,m=[];if(!h){i.resolve([]);return i}var l=this.chain().reverse().map(function(o,n){return function(){var p=k.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){m.push(q);if(l.length){l.shift()()}else{i.resolve(m)}})}}).value();l.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(l){var m=i.get(l.id);if(!m){return l}var k=m.toJSON();_.extend(k,l);return k});Backbone.Collection.prototype.set.call(this,j,h)},toString:function(){return(["HDACollection(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryDatasetAssociation:d,HDACollection:e}}); \ No newline at end of file +define([],function(){var d=Backbone.Model.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:"",file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:[],annotation:""},urlRoot:galaxy_config.root+"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("id")},urls:function(){var i=this.get("id");if(!i){return{}}var h={purge:galaxy_config.root+"datasets/"+i+"/purge_async",display:galaxy_config.root+"datasets/"+i+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+i+"/edit",download:galaxy_config.root+"datasets/"+i+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+i,rerun:galaxy_config.root+"tool_runner/rerun?id="+i,show_params:galaxy_config.root+"datasets/"+i+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+i,set:galaxy_config.root+"dataset/annotate_async?id="+i},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+i+"&metadata_name="};return h},initialize:function(h){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",d.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(i,h){this.log(this+" has 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b(h){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},h)},unhide:function g(h){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},h)},purge:function f(h){if(this.get("purged")){return jQuery.when()}h=h||{};h.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var i=this,j=jQuery.ajax(h);j.done(function(m,k,l){i.set({deleted:true,purged:true})});j.fail(function(o,k,n){var l=_l("Unable to purge dataset");var m=("Removal of datasets by users is not allowed in this Galaxy instance");if(o.responseJSON&&o.responseJSON.error){l=o.responseJSON.error}else{if(o.responseText.indexOf(m)!==-1){l=m}}o.responseText=l;i.trigger("error",i,o,h,_l(l),{error:l})});return j},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},searchAttribute:function(j,h){var i=this.get(j);if(!h||(i===undefined||i===null)){return false}if(_.isArray(i)){return this._searchArrayAttribute(i,h)}return(i.toString().toLowerCase().indexOf(h.toLowerCase())!==-1)},_searchArrayAttribute:function(i,h){h=h.toLowerCase();return _.any(i,function(j){return(j.toString().toLowerCase().indexOf(h.toLowerCase())!==-1)})},search:function(h){var i=this;return _.filter(this.searchAttributes,function(j){return i.searchAttribute(j,h)})},matches:function(i){var k="=",h=i.split(k);if(h.length>=2){var j=h[0];j=this.searchAliases[j]||j;return this.searchAttribute(j,h[1])}return !!this.search(i).length},matchesAll:function(i){var h=this;i=i.match(/(".*"|\w*=".*"|\S*)/g).filter(function(j){return !!j});return _.all(i,function(j){j=j.replace(/"/g,"");return h.matches(j)})},toString:function(){var h=this.get("id")||"";if(this.get("name")){h=this.get("hid")+' :"'+this.get("name")+'",'+h}return"HDA("+h+")"}});d.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};d.READY_STATES=[d.STATES.NEW,d.STATES.OK,d.STATES.EMPTY,d.STATES.PAUSED,d.STATES.FAILED_METADATA,d.STATES.NOT_VIEWABLE,d.STATES.DISCARDED,d.STATES.ERROR];d.NOT_READY_STATES=[d.STATES.UPLOAD,d.STATES.QUEUED,d.STATES.RUNNING,d.STATES.SETTING_METADATA];var e=Backbone.Collection.extend(LoggableMixin).extend({model:d,urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(i,h){h=h||{};this.historyId=h.historyId},ids:function(){return this.map(function(h){return h.id})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(i){if(!i.inReadyState()){h.push(i.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];var i=new e(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new e(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(k,j){var i=jQuery.Deferred(),h=this.length,m=[];if(!h){i.resolve([]);return i}var l=this.chain().reverse().map(function(o,n){return function(){var p=k.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){m.push(q);if(l.length){l.shift()()}else{i.resolve(m)}})}}).value();l.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(l){var m=i.get(l.id);if(!m){return l}var k=m.toJSON();_.extend(k,l);return k});Backbone.Collection.prototype.set.call(this,j,h)},toString:function(){return(["HDACollection(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryDatasetAssociation:d,HDACollection:e}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Require markupsafe loading prior to webhelpers. This is a new dependency, resulting in certain situations where loading order was incorrect and markupsafe can't be found.
by commits-noreply＠bitbucket.org 13 Jan '14

13 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6fe7f3ce1acd/ Changeset: 6fe7f3ce1acd User: dannon Date: 2014-01-13 18:51:05 Summary: Require markupsafe loading prior to webhelpers. This is a new dependency, resulting in certain situations where loading order was incorrect and markupsafe can't be found. Affected #: 1 file diff -r 696efd4df3ecf32aa33a55bacf470c3eb5357867 -r 6fe7f3ce1acd2263cbc57d34d83b99b3b58e6ea3 lib/galaxy/web/framework/helpers/__init__.py --- a/lib/galaxy/web/framework/helpers/__init__.py +++ b/lib/galaxy/web/framework/helpers/__init__.py @@ -8,6 +8,7 @@ from galaxy import eggs from galaxy.util import hash_util from galaxy.util.json import to_json_string +eggs.require( "MarkupSafe" ) #required by WebHelpers eggs.require( "WebHelpers" ) from webhelpers import date from webhelpers.html.tags import stylesheet_link, javascript_link 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: guerler: Charts: Fix comment
by commits-noreply＠bitbucket.org 13 Jan '14

13 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/696efd4df3ec/ Changeset: 696efd4df3ec User: guerler Date: 2014-01-13 18:46:05 Summary: Charts: Fix comment Affected #: 1 file diff -r 1b7293faeb8ffb0778726f9541e8247c6010d2d8 -r 696efd4df3ecf32aa33a55bacf470c3eb5357867 config/plugins/visualizations/charts/static/library/table.js --- a/config/plugins/visualizations/charts/static/library/table.js +++ b/config/plugins/visualizations/charts/static/library/table.js @@ -134,7 +134,7 @@ } }, - // cancel last change + // confirm new value confirm: function(new_value) { this.value(new_value); }, 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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