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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<i> - installation of these additional repositories is required</i>" % folder_label if trans.webapp.name == 'galaxy': col_span_str = 'colspan="4"' - elif folder.label == 'Installation errors': - folder_label = "%s<i> - no functional tests were run for any tools in this changeset revision</i>" % folder_label elif folder.label == 'Invalid repository dependencies': folder_label = "%s<i> - click the repository dependency to see why it is invalid</i>" % 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:<br>' 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:<br>' 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 <b>Skip automated testing of tools in this revision</b> checked</li>' + message += '<li>the latest installable revision has <b>Skip automated testing of tools in this ' + message += 'revision</b> checked if the repository type is <b>Unrestricted</b> or <b>Skip ' + message += 'automated testing of this tool dependency recipe</b> checked if the repository ' + message += 'type is <b>Tool dependency definition</b></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:<br>' 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:<br>' message += '<ul>' - message += '<li>the latest installable revision contains at least 1 tool</li>' - message += '<li>the latest installable revision has <b>Skip automated testing of tools in this revision</b> checked</li>' + message += '<li>the latest installable revision has <b>Skip automated testing of tools in this ' + message += 'revision</b> checked if the repository type is <b>Unrestricted</b> or <b>Skip ' + message += 'automated testing of this tool dependency recipe</b> checked if the repository ' + message += 'type is <b>Tool dependency definition</b></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 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 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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commit/galaxy-central: guerler: Charts: Adjust chart data volume
by commits-noreply＠bitbucket.org 13 Jan '14

13 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1b7293faeb8f/ Changeset: 1b7293faeb8f User: guerler Date: 2014-01-13 17:54:52 Summary: Charts: Adjust chart data volume Affected #: 1 file diff -r 129e16a1e9463663631823a7afb04f7aa4f3e051 -r 1b7293faeb8ffb0778726f9541e8247c6010d2d8 config/plugins/visualizations/charts/static/models/datasets.js --- a/config/plugins/visualizations/charts/static/models/datasets.js +++ b/config/plugins/visualizations/charts/static/models/datasets.js @@ -8,7 +8,7 @@ optionsDefault : { limit : 20, pace : 1000, - max : 10 + max : 5 }, // list 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: Increase chart data volume limit
by commits-noreply＠bitbucket.org 13 Jan '14

13 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/129e16a1e946/ Changeset: 129e16a1e946 User: guerler Date: 2014-01-13 17:18:56 Summary: Charts: Increase chart data volume limit Affected #: 1 file diff -r 9bc3fa17c15d00a219fe8053af4072b4a4217507 -r 129e16a1e9463663631823a7afb04f7aa4f3e051 config/plugins/visualizations/charts/static/models/datasets.js --- a/config/plugins/visualizations/charts/static/models/datasets.js +++ b/config/plugins/visualizations/charts/static/models/datasets.js @@ -8,7 +8,7 @@ optionsDefault : { limit : 20, pace : 1000, - max : 2 + max : 10 }, // list 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: Eliminate simplejson for real this time. Update WebHelpers to v 1.3 (no longer requires simplejson), fix deprecated 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/9bc3fa17c15d/ Changeset: 9bc3fa17c15d User: dannon Date: 2014-01-13 16:54:20 Summary: Eliminate simplejson for real this time. Update WebHelpers to v 1.3 (no longer requires simplejson), fix deprecated methods. Affected #: 2 files diff -r 4eeac1dbfce3f399312e58e92d820e1153ba1a09 -r 9bc3fa17c15d00a219fe8053af4072b4a4217507 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -26,7 +26,6 @@ pysam = 0.4.2 pysqlite = 2.5.6 python_lzo = 1.08_2.03_static -simplejson = 2.1.1 threadframe = 0.2 guppy = 0.1.8 SQLAlchemy = 0.7.9 @@ -61,7 +60,7 @@ Tempita = 0.5.1 twill = 0.9 WebError = 0.8a -WebHelpers = 0.2 +WebHelpers = 1.3 WebOb = 0.8.5 wsgiref = 0.1.2 Babel = 0.9.4 diff -r 4eeac1dbfce3f399312e58e92d820e1153ba1a09 -r 9bc3fa17c15d00a219fe8053af4072b4a4217507 lib/galaxy/web/framework/helpers/__init__.py --- a/lib/galaxy/web/framework/helpers/__init__.py +++ b/lib/galaxy/web/framework/helpers/__init__.py @@ -1,14 +1,19 @@ -import pkg_resources +""" +Galaxy web framework helpers +""" -pkg_resources.require( "WebHelpers" ) -from webhelpers import date, stylesheet_link_tag, javascript_include_tag, url_for +import time +from cgi import escape +from datetime import datetime, timedelta +from galaxy import eggs +from galaxy.util import hash_util +from galaxy.util.json import to_json_string +eggs.require( "WebHelpers" ) +from webhelpers import date +from webhelpers.html.tags import stylesheet_link, javascript_link -from galaxy.util.json import to_json_string -from galaxy.util import hash_util -from datetime import datetime, timedelta -import time - -from cgi import escape +eggs.require( "Routes" ) +from routes import url_for server_starttime = int(time.time()) @@ -25,6 +30,9 @@ return date.distance_of_time_in_words( x, datetime.utcnow() ).replace("about", "~") + " ago" def iff( a, b, c ): + """ + Ternary shortcut + """ if a: return b else: @@ -48,7 +56,7 @@ Cache-bust with time that server started running on """ - return "\n".join( [ stylesheet_link_tag( "/static/style/" + name + ".css?v=%s" % server_starttime ) for name in args ] ) + return "\n".join( [ stylesheet_link( "/static/style/" + name + ".css?v=%s" % server_starttime ) for name in args ] ) def js_helper( prefix, *args ): """ @@ -57,7 +65,7 @@ Cache-bust with time that server started running on """ - return "\n".join( [ javascript_include_tag( prefix + name + ".js?v=%s" % server_starttime ) for name in args ] ) + return "\n".join( [ javascript_link( prefix + name + ".js?v=%s" % server_starttime ) for name in args ] ) def js( *args ): """ 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: dan: Update create_applet_tag_peekcreate_applet_tag_peek of images.py (used for e.g. GMAJ) to display an error message is Java is not installed/enabled for the browser.
by commits-noreply＠bitbucket.org 13 Jan '14

13 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4eeac1dbfce3/ Changeset: 4eeac1dbfce3 User: dan Date: 2014-01-13 16:35:44 Summary: Update create_applet_tag_peekcreate_applet_tag_peek of images.py (used for e.g. GMAJ) to display an error message is Java is not installed/enabled for the browser. Affected #: 1 file diff -r c250b1cfc60fe2b56ddcf18e2cf2543631d4c26f -r 4eeac1dbfce3f399312e58e92d820e1153ba1a09 lib/galaxy/datatypes/images.py --- a/lib/galaxy/datatypes/images.py +++ b/lib/galaxy/datatypes/images.py @@ -213,7 +213,6 @@ def create_applet_tag_peek( class_name, archive, params ): text = """ -<object classid="java:%s" type="application/x-java-applet" height="30" width="200" align="center" > @@ -221,17 +220,14 @@ for name, value in params.iteritems(): text += """<param name="%s" value="%s"/>""" % ( name, value ) text += """ -<object classid="clsid:8AD9C840-044E-11D1-B3E9-00805F499D93" height="30" width="200" ><param name="code" value="%s" /><param name="archive" value="%s"/>""" % ( class_name, archive ) for name, value in params.iteritems(): text += """<param name="%s" value="%s"/>""" % ( name, value ) - text += """</object> - + text += """<div class="errormessage">You must install and enable Java in your browser in order to access this applet.<div></object></object> - """ return """<div><p align="center">%s</p></div>""" % text 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: 3 new changesets
by commits-noreply＠bitbucket.org 13 Jan '14

13 Jan '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2588b7b42ecd/ Changeset: 2588b7b42ecd User: jmchilton Date: 2014-01-13 15:58:22 Summary: Non-exhaustive tools related PEP-8 fixes. Fixes for api/tools.py, tools/__init__.py, and tools/parameters/{__init__.py,basic.py}. Affected #: 4 files diff -r e40e2965ac65f3a52778838e2a6879aadaf18add -r 2588b7b42ecdd9998c878f70420c75543bd5219d lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -20,7 +20,7 @@ from math import isinf from galaxy import eggs -eggs.require( "MarkupSafe" ) #MarkupSafe must load before mako +eggs.require( "MarkupSafe" ) # MarkupSafe must load before mako eggs.require( "Mako" ) eggs.require( "elementtree" ) eggs.require( "Paste" ) @@ -69,11 +69,13 @@ log = logging.getLogger( __name__ ) -WORKFLOW_PARAMETER_REGULAR_EXPRESSION = re.compile( '''\$\{.+?\}''' ) +WORKFLOW_PARAMETER_REGULAR_EXPRESSION = re.compile( '''\$\{.+?\}''' ) + class ToolNotFoundException( Exception ): pass + def to_dict_helper( obj, kwargs ): """ Helper function that provides the appropriate kwargs to to_dict an object. """ @@ -83,6 +85,7 @@ return obj.to_dict( **kwargs ) + class ToolBox( object, Dictifiable ): """Container for a collection of tools""" @@ -421,6 +424,7 @@ return self.app.install_model.context.query( self.app.install_model.ToolVersion ) \ .filter( self.app.install_model.ToolVersion.table.c.tool_id == tool_id ) \ .first() + def __get_tool_shed_repository( self, tool_shed, name, owner, installed_changeset_revision ): return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ) \ .filter( and_( self.app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed, @@ -730,8 +734,8 @@ # Produce panel. rval = [] kwargs = dict( - trans = trans, - link_details = True + trans=trans, + link_details=True ) for elt in panel_elts: rval.append( to_dict_helper( elt, kwargs ) ) @@ -798,7 +802,6 @@ return None - class ToolSection( object, Dictifiable ): """ A group of tools with similar type/purpose that will be displayed as a @@ -828,8 +831,8 @@ section_dict = super( ToolSection, self ).to_dict() section_elts = [] kwargs = dict( - trans = trans, - link_details = link_details + trans=trans, + link_details=link_details ) for elt in self.elems.values(): section_elts.append( to_dict_helper( elt, kwargs ) ) @@ -837,6 +840,7 @@ return section_dict + class ToolSectionLabel( object, Dictifiable ): """ A label for a set of tools that can be displayed above groups of tools @@ -850,6 +854,7 @@ self.id = elem.get( "id" ) self.version = elem.get( "version" ) or '' + class DefaultToolState( object ): """ Keeps track of the state of a users interaction with a tool between @@ -860,6 +865,7 @@ self.page = 0 self.rerun_remap_job_id = None self.inputs = None + def encode( self, tool, app, secure=True ): """ Convert the data to a string @@ -877,6 +883,7 @@ return "%s:%s" % ( a, b ) else: return value + def decode( self, value, tool, app, secure=True ): """ Restore the state from a string @@ -896,6 +903,7 @@ self.rerun_remap_job_id = None self.inputs = params_from_strings( tool.inputs, values, app, ignore_errors=True ) + class ToolOutput( object, Dictifiable ): """ Represents an output datasets produced by a tool. For backward @@ -907,7 +915,7 @@ dict_collection_visible_keys = ( 'name', 'format', 'label', 'hidden' ) def __init__( self, name, format=None, format_source=None, metadata_source=None, - parent=None, label=None, filters = None, actions = None, hidden=False ): + parent=None, label=None, filters=None, actions=None, hidden=False ): self.name = name self.format = format self.format_source = format_source @@ -993,16 +1001,19 @@ # Parse XML element containing configuration self.parse( root, guid=guid ) self.external_runJob_script = app.config.drmaa_external_runjob_script + @property def sa_session( self ): """Returns a SQLAlchemy session""" return self.app.model.context + @property def tool_version( self ): """Return a ToolVersion if one exists for our id""" return self.app.install_model.context.query( self.app.install_model.ToolVersion ) \ .filter( self.app.install_model.ToolVersion.table.c.tool_id == self.id ) \ .first() + @property def tool_versions( self ): # If we have versions, return them. @@ -1010,6 +1021,7 @@ if tool_version: return tool_version.get_versions( self.app ) return [] + @property def tool_version_ids( self ): # If we have versions, return a list of their tool_ids. @@ -1017,6 +1029,7 @@ if tool_version: return tool_version.get_version_ids( self.app ) return [] + @property def tool_shed_repository( self ): # If this tool is included in an installed tool shed repository, return it. @@ -1075,7 +1088,7 @@ :returns: galaxy.jobs.JobDestination -- The destination definition and runner parameters. """ return self.app.job_config.get_destination(self.__get_job_tool_configuration(job_params=job_params).destination) - + def get_panel_section( self ): for key, item in self.app.toolbox.integrated_tool_panel.items(): if item: @@ -1099,7 +1112,7 @@ # Get the (user visible) name of the tool self.name = root.get( "name" ) if not self.name: - raise Exception, "Missing tool 'name'" + raise Exception( "Missing tool 'name'" ) # Get the UNIQUE id for the tool self.old_id = root.get( "id" ) if guid is None: @@ -1107,7 +1120,7 @@ else: self.id = guid if not self.id: - raise Exception, "Missing tool 'id'" + raise Exception( "Missing tool 'id'" ) self.version = root.get( "version" ) if not self.version: # For backward compatibility, some tools may not have versions yet. @@ -1127,7 +1140,7 @@ # Command line (template). Optional for tools that do not invoke a local program command = root.find("command") if command is not None and command.text is not None: - self.command = command.text.lstrip() # get rid of leading whitespace + self.command = command.text.lstrip() # get rid of leading whitespace # Must pre-pend this AFTER processing the cheetah command template self.interpreter = command.get( "interpreter", None ) else: @@ -1169,14 +1182,15 @@ self_ids = [ self.id.lower() ] if self.old_id != self.id: # Handle toolshed guids - self_ids = [ self.id.lower(), self.id.lower().rsplit('/',1)[0], self.old_id.lower() ] + self_ids = [ self.id.lower(), self.id.lower().rsplit('/', 1)[0], self.old_id.lower() ] self.all_ids = self_ids # In the toolshed context, there is no job config. if 'job_config' in dir(self.app): self.job_tool_configurations = self.app.job_config.get_job_tool_configurations(self_ids) # Is this a 'hidden' tool (hidden in tool menu) self.hidden = xml_text(root, "hidden") - if self.hidden: self.hidden = string_as_bool(self.hidden) + if self.hidden: + self.hidden = string_as_bool(self.hidden) # Load any tool specific code (optional) Edit: INS 5/29/2007, # allow code files to have access to the individual tool's # "module" if it has one. Allows us to reuse code files, etc. @@ -1186,7 +1200,7 @@ for hook_elem in code_elem.findall("hook"): for key, value in hook_elem.items(): # map hook to function - self.hook_map[key]=value + self.hook_map[key] = value file_name = code_elem.get("file") code_path = os.path.join( self.tool_dir, file_name ) execfile( code_path, self.code_namespace ) @@ -1308,7 +1322,7 @@ elif len( enctypes ) == 1: self.enctype = enctypes.pop() else: - raise Exception, "Conflicting required enctypes: %s" % str( enctypes ) + raise Exception( "Conflicting required enctypes: %s" % str( enctypes ) ) # Check if the tool either has no parameters or only hidden (and # thus hardcoded) FIXME: hidden parameters aren't # parameters at all really, and should be passed in a different @@ -1318,6 +1332,7 @@ if not isinstance( param, ( HiddenToolParameter, BaseURLToolParameter ) ): self.input_required = True break + def parse_help( self, root ): """ Parse the help text for the tool. Formatted in reStructuredText, but @@ -1365,6 +1380,7 @@ # Pad out help pages to match npages ... could this be done better? while len( self.help_by_page ) < self.npages: self.help_by_page.append( self.help ) + def parse_outputs( self, root ): """ Parse <outputs> elements and fill in self.outputs (keyed by name) @@ -1601,6 +1617,7 @@ else: display = None return display, inputs + def parse_input_elem( self, parent_elem, enctypes, context=None ): """ Parse a parent element whose children are inputs -- these could be @@ -1653,7 +1670,7 @@ input_elem = elem.find( "param" ) assert input_elem is not None, "<conditional> must have a child <param>" group.test_param = self.parse_param_elem( input_elem, enctypes, context ) - possible_cases = list( group.test_param.legal_values ) #store possible cases, undefined whens will have no inputs + possible_cases = list( group.test_param.legal_values ) # store possible cases, undefined whens will have no inputs # Must refresh when test_param changes group.test_param.refresh_on_change = True # And a set of possible cases @@ -1694,6 +1711,7 @@ param.ref_input = context[ param.data_ref ] self.input_params.append( param ) return rval + def parse_param_elem( self, input_elem, enctypes, context ): """ Parse a single "<param>" element and return a ToolParameter instance. @@ -1777,12 +1795,14 @@ raise Exception( "'get_param_html_map' only supported for simple paramters" ) rval[key] = param.get_html( trans, other_values=other_values ) return rval + def get_param( self, key ): """ Returns the parameter named `key` or None if there is no such parameter. """ return self.inputs.get( key, None ) + def get_hook(self, name): """ Returns an object from the code file referenced by `code_namespace` @@ -1795,6 +1815,7 @@ elif name in self.code_namespace: return self.code_namespace[name] return None + def visit_inputs( self, value, callback ): """ Call the function `callback` on each parameter of this tool. Visits @@ -1811,6 +1832,7 @@ callback( "", input, value[input.name] ) else: input.visit_inputs( "", value[input.name], callback ) + def handle_input( self, trans, incoming, history=None, old_errors=None, process_state='update', source='html' ): """ Process incoming parameters for this tool from the dict `incoming`, @@ -1955,6 +1977,7 @@ [ self.find_fieldstorage( y ) for y in x.values() ] elif type( x ) is types.ListType: [ self.find_fieldstorage( y ) for y in x ] + def handle_interrupted( self, trans, inputs ): """ Upon handling inputs, if it appears that we have received an incomplete @@ -2320,6 +2343,7 @@ errors[ input.name ] = error state[ input.name ] = value return errors + @property def params_with_missing_data_table_entry( self ): """ @@ -2333,6 +2357,7 @@ if options and options.missing_tool_data_table_name and input_param not in params: params.append( input_param ) return params + @property def params_with_missing_index_file( self ): """ @@ -2346,6 +2371,7 @@ if options and options.missing_index_file and input_param not in params: params.append( input_param ) return params + def get_static_param_values( self, trans ): """ Returns a map of parameter names and values if the tool does not @@ -2361,6 +2387,7 @@ else: raise Exception( "Unexpected parameter type" ) return args + def execute( self, trans, incoming={}, set_output_hid=True, history=None, **kwargs ): """ Execute the tool using parameter values in `incoming`. This just @@ -2369,10 +2396,13 @@ when run will build the tool's outputs, e.g. `DefaultToolAction`. """ return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) + def params_to_strings( self, params, app ): return params_to_strings( self.inputs, params, app ) + def params_from_strings( self, params, app, ignore_errors=False ): return params_from_strings( self.inputs, params, app, ignore_errors ) + def check_and_update_param_values( self, values, trans, update_values=True, allow_workflow_parameters=False ): """ Check that all parameters have values, and fill in with default @@ -2382,6 +2412,7 @@ messages = {} self.check_and_update_param_values_helper( self.inputs, values, trans, messages, update_values=update_values, allow_workflow_parameters=allow_workflow_parameters ) return messages + def check_and_update_param_values_helper( self, inputs, values, trans, messages, context=None, prefix="", update_values=True, allow_workflow_parameters=False ): """ Recursive helper for `check_and_update_param_values_helper` @@ -2438,6 +2469,7 @@ messages[ input.name ] = "Value no longer valid for '%s%s', replaced with default" % ( prefix, input.label ) if update_values: values[ input.name ] = input.get_initial_value( trans, context ) + def handle_unvalidated_param_values( self, input_values, app ): """ Find any instances of `UnvalidatedValue` within input_values and @@ -2448,6 +2480,7 @@ if not self.check_values: return self.handle_unvalidated_param_values_helper( self.inputs, input_values, app ) + def handle_unvalidated_param_values_helper( self, inputs, input_values, app, context=None, prefix="" ): """ Recursive helper for `handle_unvalidated_param_values` @@ -2488,6 +2521,7 @@ % ( prefix, input.label, e ) raise LateValidationError( message ) input_values[ input.name ] = value + def handle_job_failure_exception( self, e ): """ Called by job.fail when an exception is generated to allow generation @@ -2499,6 +2533,7 @@ if isinstance( e, LateValidationError ): message = e.message return message + def build_param_dict( self, incoming, input_datasets, output_datasets, output_paths, job_working_directory ): """ Build the dictionary of parameters for substituting into the command @@ -2754,6 +2789,7 @@ # Remove newlines redirect_url_params = redirect_url_params.replace( "\n", " " ).replace( "\r", " " ) return redirect_url_params + def parse_redirect_url( self, data, param_dict ): """ Parse the REDIRECT_URL tool param. Tools that send data to an external @@ -2793,6 +2829,7 @@ USERNAME = 'Anonymous' redirect_url += "&USERNAME=%s" % USERNAME return redirect_url + def call_hook( self, hook_name, *args, **kwargs ): """ Call the custom code hook function identified by 'hook_name' if any, @@ -2808,15 +2845,19 @@ original_message = e.args[0] e.args = ( "Error in '%s' hook '%s', original message: %s" % ( self.name, hook_name, original_message ), ) raise + def exec_before_job( self, app, inp_data, out_data, param_dict={} ): pass - def exec_after_process( self, app, inp_data, out_data, param_dict, job = None ): + + def exec_after_process( self, app, inp_data, out_data, param_dict, job=None ): pass - def job_failed( self, job_wrapper, message, exception = False ): + + def job_failed( self, job_wrapper, message, exception=False ): """ Called when a job has failed """ pass + def collect_associated_files( self, output, job_working_directory ): """ Find extra files in the job working directory and move them into @@ -2835,10 +2876,11 @@ for f in files: self.app.object_store.update_from_file(hda.dataset, extra_dir=extra_dir, - alt_name = f, - file_name = os.path.join(root, f), - create = True, - preserve_symlinks = True ) + alt_name=f, + file_name=os.path.join(root, f), + create=True, + preserve_symlinks=True + ) # Clean up after being handled by object store. # FIXME: If the object (e.g., S3) becomes async, this will # cause issues so add it to the object store functionality? @@ -2848,6 +2890,7 @@ except Exception, e: log.debug( "Error in collect_associated_files: %s" % ( e ) ) continue + def collect_child_datasets( self, output, job_working_directory ): """ Look for child dataset files, create HDA and attach to parent. @@ -2858,9 +2901,9 @@ for name, outdata in output.items(): filenames = [] if 'new_file_path' in self.app.config.collect_outputs_from: - filenames.extend( glob.glob(os.path.join(self.app.config.new_file_path,"child_%i_*" % outdata.id) ) ) + filenames.extend( glob.glob(os.path.join(self.app.config.new_file_path, "child_%i_*" % outdata.id) ) ) if 'job_working_directory' in self.app.config.collect_outputs_from: - filenames.extend( glob.glob(os.path.join(job_working_directory,"child_%i_*" % outdata.id) ) ) + filenames.extend( glob.glob(os.path.join(job_working_directory, "child_%i_*" % outdata.id) ) ) for filename in filenames: if not name in children: children[name] = {} @@ -2909,12 +2952,14 @@ # Need to update all associated output hdas, i.e. history was # shared with job running for dataset in outdata.dataset.history_associations: - if outdata == dataset: continue + if outdata == dataset: + continue # Create new child dataset - child_data = child_dataset.copy( parent_id = dataset.id ) + child_data = child_dataset.copy( parent_id=dataset.id ) self.sa_session.add( child_data ) self.sa_session.flush() return children + def collect_primary_datasets( self, output, job_working_directory ): """ Find any additional datasets generated by a tool and attach (for @@ -2937,9 +2982,9 @@ for name, outdata in output.items(): filenames = [] if 'new_file_path' in self.app.config.collect_outputs_from: - filenames.extend( glob.glob(os.path.join(self.app.config.new_file_path,"primary_%i_*" % outdata.id) ) ) + filenames.extend( glob.glob(os.path.join(self.app.config.new_file_path, "primary_%i_*" % outdata.id) ) ) if 'job_working_directory' in self.app.config.collect_outputs_from: - filenames.extend( glob.glob(os.path.join(job_working_directory,"primary_%i_*" % outdata.id) ) ) + filenames.extend( glob.glob(os.path.join(job_working_directory, "primary_%i_*" % outdata.id) ) ) for filename in filenames: if not name in primary_datasets: primary_datasets[name] = {} @@ -2948,8 +2993,10 @@ parent_id = int(fields.pop(0)) designation = fields.pop(0) visible = fields.pop(0).lower() - if visible == "visible": visible = True - else: visible = False + if visible == "visible": + visible = True + else: + visible = False ext = fields.pop(0).lower() dbkey = outdata.dbkey if fields: @@ -2999,7 +3046,8 @@ # Need to update all associated output hdas, i.e. history was # shared with job running for dataset in outdata.dataset.history_associations: - if outdata == dataset: continue + if outdata == dataset: + continue new_data = primary_data.copy() dataset.history.add( new_data ) self.sa_session.add( new_data ) @@ -3029,7 +3077,7 @@ if io_details: tool_dict[ 'inputs' ] = [ input.to_dict( trans ) for input in self.inputs.values() ] tool_dict[ 'outputs' ] = [ output.to_dict() for output in self.outputs.values() ] - + tool_dict[ 'panel_section_id' ], tool_dict[ 'panel_section_name' ] = self.get_panel_section() return tool_dict @@ -3044,6 +3092,7 @@ JSONified within the contents of an output dataset """ tool_type = 'output_parameter_json' + def _prepare_json_list( self, param_list ): rval = [] for value in param_list: @@ -3054,6 +3103,7 @@ else: rval.append( str( value ) ) return rval + def _prepare_json_param_dict( self, param_dict ): rval = {} for key, value in param_dict.iteritems(): @@ -3064,11 +3114,12 @@ else: rval[ key ] = str( value ) return rval + def exec_before_job( self, app, inp_data, out_data, param_dict=None ): if param_dict is None: param_dict = {} json_params = {} - json_params[ 'param_dict' ] = self._prepare_json_param_dict( param_dict ) #it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? + json_params[ 'param_dict' ] = self._prepare_json_param_dict( param_dict ) # it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? json_params[ 'output_data' ] = [] json_params[ 'job_config' ] = dict( GALAXY_DATATYPES_CONF_FILE=param_dict.get( 'GALAXY_DATATYPES_CONF_FILE' ), GALAXY_ROOT_DIR=param_dict.get( 'GALAXY_ROOT_DIR' ), TOOL_PROVIDED_JOB_METADATA_FILE=jobs.TOOL_PROVIDED_JOB_METADATA_FILE ) json_filename = None @@ -3078,12 +3129,12 @@ #allow multiple files to be created file_name = str( wrapped_data ) extra_files_path = str( wrapped_data.files_path ) - data_dict = dict( out_data_name = out_name, - ext = data.ext, - dataset_id = data.dataset.id, - hda_id = data.id, - file_name = file_name, - extra_files_path = extra_files_path ) + data_dict = dict( out_data_name=out_name, + ext=data.ext, + dataset_id=data.dataset.id, + hda_id=data.id, + file_name=file_name, + extra_files_path=extra_files_path ) json_params[ 'output_data' ].append( data_dict ) if json_filename is None: json_filename = file_name @@ -3091,6 +3142,7 @@ out.write( json.dumps( json_params ) ) out.close() + class DataSourceTool( OutputParameterJSONTool ): """ Alternate implementation of Tool for data_source tools -- those that @@ -3101,11 +3153,13 @@ def _build_GALAXY_URL_parameter( self ): return ToolParameter.build( self, ElementTree.XML( '<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=%s" />' % self.id ) ) + def parse_inputs( self, root ): super( DataSourceTool, self ).parse_inputs( root ) if 'GALAXY_URL' not in self.inputs: self.inputs[ 'GALAXY_URL' ] = self._build_GALAXY_URL_parameter() self.inputs_by_page[0][ 'GALAXY_URL' ] = self.inputs[ 'GALAXY_URL' ] + def exec_before_job( self, app, inp_data, out_data, param_dict=None ): if param_dict is None: param_dict = {} @@ -3115,7 +3169,7 @@ name = param_dict.get( 'name' ) json_params = {} - json_params[ 'param_dict' ] = self._prepare_json_param_dict( param_dict ) #it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? + json_params[ 'param_dict' ] = self._prepare_json_param_dict( param_dict ) # it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? json_params[ 'output_data' ] = [] json_params[ 'job_config' ] = dict( GALAXY_DATATYPES_CONF_FILE=param_dict.get( 'GALAXY_DATATYPES_CONF_FILE' ), GALAXY_ROOT_DIR=param_dict.get( 'GALAXY_ROOT_DIR' ), TOOL_PROVIDED_JOB_METADATA_FILE=jobs.TOOL_PROVIDED_JOB_METADATA_FILE ) json_filename = None @@ -3138,12 +3192,12 @@ data.extension = cur_data_type file_name = str( wrapped_data ) extra_files_path = str( wrapped_data.files_path ) - data_dict = dict( out_data_name = out_name, - ext = data.ext, - dataset_id = data.dataset.id, - hda_id = data.id, - file_name = file_name, - extra_files_path = extra_files_path ) + data_dict = dict( out_data_name=out_name, + ext=data.ext, + dataset_id=data.dataset.id, + hda_id=data.id, + file_name=file_name, + extra_files_path=extra_files_path ) json_params[ 'output_data' ].append( data_dict ) if json_filename is None: json_filename = file_name @@ -3151,15 +3205,18 @@ out.write( json.dumps( json_params ) ) out.close() + class AsyncDataSourceTool( DataSourceTool ): tool_type = 'data_source_async' def _build_GALAXY_URL_parameter( self ): return ToolParameter.build( self, ElementTree.XML( '<param name="GALAXY_URL" type="baseurl" value="/async/%s" />' % self.id ) ) + class DataDestinationTool( Tool ): tool_type = 'data_destination' + class SetMetadataTool( Tool ): """ Tool implementation for special tool that sets metadata on an existing @@ -3167,8 +3224,8 @@ """ tool_type = 'set_metadata' requires_setting_metadata = False - - def exec_after_process( self, app, inp_data, out_data, param_dict, job = None ): + + def exec_after_process( self, app, inp_data, out_data, param_dict, job=None ): for name, dataset in inp_data.iteritems(): external_metadata = JobExternalOutputMetadataWrapper( job ) if external_metadata.external_metadata_set_successfully( dataset, app.model.context ): @@ -3191,23 +3248,28 @@ dataset.set_peek() self.sa_session.add( dataset ) self.sa_session.flush() - def job_failed( self, job_wrapper, message, exception = False ): + + def job_failed( self, job_wrapper, message, exception=False ): job = job_wrapper.sa_session.query( model.Job ).get( job_wrapper.job_id ) if job: inp_data = {} for dataset_assoc in job.input_datasets: inp_data[dataset_assoc.name] = dataset_assoc.dataset - return self.exec_after_process( job_wrapper.app, inp_data, {}, job_wrapper.get_param_dict(), job = job ) + return self.exec_after_process( job_wrapper.app, inp_data, {}, job_wrapper.get_param_dict(), job=job ) + class ExportHistoryTool( Tool ): tool_type = 'export_history' + class ImportHistoryTool( Tool ): tool_type = 'import_history' + class GenomeIndexTool( Tool ): tool_type = 'index_genome' + class DataManagerTool( OutputParameterJSONTool ): tool_type = 'manage_data' default_tool_action = DataManagerToolAction @@ -3218,9 +3280,9 @@ if self.data_manager_id is None: self.data_manager_id = self.id - def exec_after_process( self, app, inp_data, out_data, param_dict, job = None, **kwds ): + def exec_after_process( self, app, inp_data, out_data, param_dict, job=None, **kwds ): #run original exec_after_process - super( DataManagerTool, self ).exec_after_process( app, inp_data, out_data, param_dict, job = job, **kwds ) + super( DataManagerTool, self ).exec_after_process( app, inp_data, out_data, param_dict, job=job, **kwds ) #process results of tool if job and job.state == job.states.ERROR: return @@ -3267,8 +3329,8 @@ for tool_class in [ Tool, DataDestinationTool, SetMetadataTool, DataSourceTool, AsyncDataSourceTool, DataManagerTool ]: tool_types[ tool_class.tool_type ] = tool_class + # ---- Utility classes to be factored out ----------------------------------- - class TracksterConfig: """ Trackster configuration encapsulation. """ @@ -3282,6 +3344,7 @@ actions.append( SetParamAction.parse( action_elt ) ) return TracksterConfig( actions ) + class SetParamAction: """ Set parameter action. """ @@ -3294,10 +3357,12 @@ """ Parse action from element. """ return SetParamAction( elt.get( "name" ), elt.get( "output_name" ) ) + class BadValue( object ): def __init__( self, value ): self.value = value + class ToolStdioRegex( object ): """ This is a container for the <stdio> element's regex subelement. @@ -3313,6 +3378,7 @@ self.error_level = "fatal" self.desc = "" + class ToolStdioExitCode( object ): """ This is a container for the <stdio> element's <exit_code> subelement. @@ -3532,6 +3598,6 @@ else: return incoming.get( key, default ) + class InterruptedUpload( Exception ): pass - diff -r e40e2965ac65f3a52778838e2a6879aadaf18add -r 2588b7b42ecdd9998c878f70420c75543bd5219d lib/galaxy/tools/parameters/__init__.py --- a/lib/galaxy/tools/parameters/__init__.py +++ b/lib/galaxy/tools/parameters/__init__.py @@ -6,6 +6,7 @@ from grouping import * from galaxy.util.json import * + def visit_input_values( inputs, input_values, callback, name_prefix="", label_prefix="" ): """ Given a tools parameter definition (`inputs`) and a specific set of @@ -35,11 +36,12 @@ else: new_value = callback( input, input_values[input.name], - prefixed_name = name_prefix + input.name, - prefixed_label = label_prefix + input.label ) + prefixed_name=name_prefix + input.name, + prefixed_label=label_prefix + input.label ) if new_value: input_values[input.name] = new_value + def check_param( trans, param, incoming_value, param_values, source='html' ): """ Check the value of a single parameter `param`. The value in @@ -62,12 +64,13 @@ # Then do any further validation on the value param.validate( filtered_value, trans.history ) elif value is None and isinstance( param, SelectToolParameter ): - # An empty select list or column list - param.validate( value, trans.history ) + # An empty select list or column list + param.validate( value, trans.history ) except ValueError, e: error = str( e ) return value, error + def params_to_strings( params, param_values, app ): """ Convert a dictionary of parameter values to a dictionary of strings @@ -83,6 +86,7 @@ rval[ key ] = str( to_json_string( value ) ) return rval + def params_from_strings( params, param_values, app, ignore_errors=False ): """ Convert a dictionary of strings as produced by `params_to_strings` @@ -98,6 +102,7 @@ rval[ key ] = value return rval + def params_to_incoming( incoming, inputs, input_values, app, name_prefix="" ): """ Given a tool's parameter definition (`inputs`) and a specific set of @@ -119,4 +124,3 @@ params_to_incoming( incoming, input.cases[current].inputs, values, app, new_name_prefix ) else: incoming[ name_prefix + input.name ] = input.to_html_value( input_values.get( input.name ), app ) - diff -r e40e2965ac65f3a52778838e2a6879aadaf18add -r 2588b7b42ecdd9998c878f70420c75543bd5219d lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1441,10 +1441,11 @@ for opt in option['options']: recurse_option( option_list, opt ) rval = [] - recurse_option( rval, get_base_option( value, self.get_options( other_values = other_values ) ) ) + recurse_option( rval, get_base_option( value, self.get_options( other_values=other_values ) ) ) return rval or [value] - if value is None: return "None" + if value is None: + return "None" rval = [] if self.hierarchy == "exact": rval = value @@ -1483,8 +1484,9 @@ if value == option['value']: return option['name'] rval = get_option_display( value, option['options'] ) - if rval: return rval - return None #not found + if rval: + return rval + return None # not found if isinstance( value, UnvalidatedValue ): suffix = "\n(value not yet validated)" @@ -1524,12 +1526,12 @@ options = [] try: options = self.get_options( trans, {} ) - except KeyError, key_err: + except KeyError: # will sometimes error if self.is_dynamic and self.filtered # bc we dont/cant fill out other_values above ({}) pass - d[ 'options' ] = options; + d[ 'options' ] = options return d @@ -1762,7 +1764,7 @@ if v: if v.deleted: raise ValueError( "The previously selected dataset has been previously deleted" ) - if v.dataset.state in [galaxy.model.Dataset.states.ERROR, galaxy.model.Dataset.states.DISCARDED ]: + if v.dataset.state in [ galaxy.model.Dataset.states.ERROR, galaxy.model.Dataset.states.DISCARDED ]: raise ValueError( "The previously selected dataset has entered an unusable state" ) return rval @@ -1794,7 +1796,8 @@ return app.model.context.query( app.model.HistoryDatasetAssociation ).get( int( value ) ) def to_param_dict_string( self, value, other_values={} ): - if value is None: return "None" + if value is None: + return "None" return value.file_name def value_to_display_text( self, value, app ): @@ -1828,12 +1831,13 @@ if self.tool is None or self.tool.has_multiple_pages or not hasattr( trans, 'workflow_building_mode' ) or trans.workflow_building_mode: return False if other_values is None: - return True # we don't know other values, so we can't check, assume ok + return True # we don't know other values, so we can't check, assume ok converter_safe = [True] - def visitor( prefix, input, value, parent = None ): + + def visitor( prefix, input, value, parent=None ): if isinstance( input, SelectToolParameter ) and self.name in input.get_dependencies(): if input.is_dynamic and ( input.dynamic_options or ( not input.dynamic_options and not input.options ) or not input.options.converter_safe ): - converter_safe[0] = False #This option does not allow for conversion, i.e. uses contents of dataset file to generate options + converter_safe[0] = False # This option does not allow for conversion, i.e. uses contents of dataset file to generate options self.tool.visit_inputs( other_values, visitor ) return False not in converter_safe @@ -1960,21 +1964,24 @@ # self.html = form_builder.HiddenField( self.name, trans.history.id ).get_html() # return self.html -parameter_types = dict( text = TextToolParameter, - integer = IntegerToolParameter, - float = FloatToolParameter, - boolean = BooleanToolParameter, - genomebuild = GenomeBuildParameter, - select = SelectToolParameter, - data_column = ColumnListParameter, - hidden = HiddenToolParameter, - hidden_data = HiddenDataToolParameter, - baseurl = BaseURLToolParameter, - file = FileToolParameter, - ftpfile = FTPFileToolParameter, - data = DataToolParameter, - library_data = LibraryDatasetToolParameter, - drill_down = DrillDownSelectToolParameter ) +parameter_types = dict( + text=TextToolParameter, + integer=IntegerToolParameter, + float=FloatToolParameter, + boolean=BooleanToolParameter, + genomebuild=GenomeBuildParameter, + select=SelectToolParameter, + data_column=ColumnListParameter, + hidden=HiddenToolParameter, + hidden_data=HiddenDataToolParameter, + baseurl=BaseURLToolParameter, + file=FileToolParameter, + ftpfile=FTPFileToolParameter, + data=DataToolParameter, + library_data=LibraryDatasetToolParameter, + drill_down=DrillDownSelectToolParameter +) + class UnvalidatedValue( object ): """ @@ -1993,4 +2000,3 @@ runtime. """ pass - diff -r e40e2965ac65f3a52778838e2a6879aadaf18add -r 2588b7b42ecdd9998c878f70420c75543bd5219d lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -1,9 +1,11 @@ import urllib from galaxy import web, util -from galaxy.web.base.controller import BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin, UsesHistoryMixin +from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import UsesVisualizationMixin +from galaxy.web.base.controller import UsesHistoryMixin from galaxy.visualization.genomes import GenomeRegion -from galaxy.util.json import to_json_string, from_json_string +from galaxy.util.json import to_json_string from galaxy.visualization.data_providers.genome import * import logging @@ -47,7 +49,7 @@ GET /api/tools/{tool_id} Returns tool information, including parameters and inputs. """ - io_details = util.string_as_bool( kwd.get( 'io_details', False ) ) + io_details = util.string_as_bool( kwd.get( 'io_details', False ) ) link_details = util.string_as_bool( kwd.get( 'link_details', False ) ) try: id = urllib.unquote_plus( id ) @@ -96,7 +98,7 @@ for k, v in payload.iteritems(): if k.startswith("files_") or k.startswith("__files_"): inputs[k] = v - + #for inputs that are coming from the Library, copy them into the history input_patch = {} for k, v in inputs.iteritems(): @@ -112,7 +114,7 @@ inputs['runtool_btn'] = 'Execute' # TODO: encode data ids and decode ids. # TODO: handle dbkeys - params = util.Params( inputs, sanitize = False ) + params = util.Params( inputs, sanitize=False ) # process_state will be 'populate' or 'update'. When no tool # state is specified in input - it will be 'populate', and # tool will fully expand repeat and conditionals when building @@ -140,8 +142,8 @@ for output_name, output in output_datasets: output_dict = output.to_dict() #add the output name back into the output data structure - #so it's possible to figure out which newly created elements - #correspond with which tool file outputs + #so it's possible to figure out which newly created elements + #correspond with which tool file outputs output_dict['output_name'] = output_name outputs.append( trans.security.encode_dict_ids( output_dict ) ) return rval @@ -185,14 +187,13 @@ # HACK: add run button so that tool.handle_input will run tool. kwargs['runtool_btn'] = 'Execute' - params = util.Params( kwargs, sanitize = False ) + params = util.Params( kwargs, sanitize=False ) template, vars = tool.handle_input( trans, params.__dict__, history=target_history ) # TODO: check for errors and ensure that output dataset is available. output_datasets = vars[ 'out_data' ].values() return self.add_track_async( trans, output_datasets[0].id ) - def _rerun_tool( self, trans, payload, **kwargs ): """ Rerun a tool to produce a new output dataset that corresponds to a @@ -363,7 +364,7 @@ continue input_dataset = jida.dataset - if input_dataset is None: #optional dataset and dataset wasn't selected + if input_dataset is None: # optional dataset and dataset wasn't selected tool_params[ jida.name ] = None elif run_on_regions and 'data' in input_dataset.datatype.data_sources: # Dataset is indexed and hence a subset can be extracted and used @@ -407,7 +408,7 @@ # Set metadata. # TODO: set meta internally if dataset is small enough? trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, - trans, incoming = { 'input1':new_dataset }, + trans, incoming={ 'input1': new_dataset }, overwrite=False, job_params={ "source" : "trackster" } ) # Add HDA subset association. subset_association = trans.app.model.HistoryDatasetAssociationSubset( hda=input_dataset, subset=new_dataset, location=regions_str ) @@ -450,5 +451,5 @@ dataset_dict = output_dataset.to_dict() dataset_dict[ 'id' ] = trans.security.encode_id( dataset_dict[ 'id' ] ) - dataset_dict[ 'track_config' ] = self.get_new_track_config( trans, output_dataset ); + dataset_dict[ 'track_config' ] = self.get_new_track_config( trans, output_dataset ) return dataset_dict https://bitbucket.org/galaxy/galaxy-central/commits/14ab802d0209/ Changeset: 14ab802d0209 User: jmchilton Date: 2014-01-13 15:58:22 Summary: Initial work on tool execution unit tests. Going to be doing some more work on tool state stuff so it will be good to have a way to test that. This also brings in test/unit/tools_support.py from Pull Request #287 (would be overkill for just these tests, but it is useful for future tests coming down the pipe.) Affected #: 3 files diff -r 2588b7b42ecdd9998c878f70420c75543bd5219d -r 14ab802d020997e1acfdce191d912b702624b96f test/unit/tools/test_execution.py --- /dev/null +++ b/test/unit/tools/test_execution.py @@ -0,0 +1,104 @@ +""" Test Tool execution and state handling logic. +""" +import os + +from unittest import TestCase + +import galaxy.model +from galaxy.tools import Tool +from galaxy.tools import DefaultToolState +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> + <inputs> + <param type="text" name="param1" value="" /> + </inputs> + <outputs> + <output name="out1" format="data" /> + </outputs> +</tool>''' + + +class ToolExecutionTestCase( TestCase, UsesApp ): + + def setUp(self): + self.setup_app() + 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.tool_action = MockAction( self.trans ) + self.tool_file = os.path.join( self.test_directory, "tool.xml" ) + + def tearDown(self): + 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" ) + # no runtool_btn, just rerenders the form mako with tool + # state populated. + ) + assert template == "tool_form.mako" + assert not template_vars[ "errors" ] + state = template_vars[ "tool_state" ] + assert state.inputs[ "param1" ] == "moo" + + def test_execute( self ): + self.__write_tool( EXAMPLE_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 ) + self.tool = Tool( self.tool_file, tree.getroot(), self.app ) + self.tool.tool_action = self.tool_action + + def __write_tool( self, contents ): + open( self.tool_file, "w" ).write( contents ) + + def __string_to_state( self, state_string ): + encoded_state = string_to_object( state_string ) + state = DefaultToolState() + state.decode( encoded_state, self.tool, self.app ) + return state + + def __inputs_to_state( self, inputs ): + tool_state = DefaultToolState() + tool_state.inputs = inputs + return tool_state + + 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 ) ) + + +class MockAction( object ): + + def __init__( self, expected_trans ): + self.expected_trans = expected_trans + self.execution_call_args = [] + + def execute( self, tool, trans, **kwds ): + assert self.expected_trans == trans + self.execution_call_args.append( kwds ) + return None, odict(dict(out1="1")) + + +class MockTrans( object ): + + def __init__( self, app ): + self.app = app + self.history = galaxy.model.History() diff -r 2588b7b42ecdd9998c878f70420c75543bd5219d -r 14ab802d020997e1acfdce191d912b702624b96f test/unit/tools_support.py --- /dev/null +++ b/test/unit/tools_support.py @@ -0,0 +1,51 @@ +""" Module contains test fixtures meant to aide in the testing of jobs and +tool evaluation. Such extensive "fixtures" are something of an anti-pattern +so use of this should be limitted to tests of very 'extensive' classes. +""" + +import os.path +import tempfile +import shutil + +from galaxy.util.bunch import Bunch +from galaxy.model import mapping + + +class UsesApp( object ): + + def setup_app( self ): + # The following line is needed in order to create + # HistoryDatasetAssociations - ideally the model classes would be + # usable without the ORM infrastructure in place. + mapping.init( "/tmp", "sqlite:///:memory:", create_tables=True ) + self.test_directory = tempfile.mkdtemp() + self.app = MockApp(self.test_directory) + + def tear_down_app( self ): + shutil.rmtree( self.test_directory ) + + +class MockApp( object ): + + def __init__( self, test_directory ): + + self.datatypes_registry = Bunch( + integrated_datatypes_configs='/galaxy/integrated_datatypes_configs.xml', + get_datatype_by_extension=lambda ext: Bunch(), + ) + + self.config = Bunch( + outputs_to_working_directory=False, + new_file_path=os.path.join(test_directory, "new_files"), + tool_data_path=os.path.join(test_directory, "tools"), + root=os.path.join(test_directory, "galaxy"), + admin_users="mary(a)example.com", + ) + + # Setup some attributes for downstream extension by specific tests. + self.job_config = Bunch() + self.model = Bunch() + self.toolbox = None + self.object_store = None + +__all__ = [ UsesApp ] https://bitbucket.org/galaxy/galaxy-central/commits/c250b1cfc60f/ Changeset: c250b1cfc60f User: jmchilton Date: 2014-01-13 15:58:22 Summary: Initial work on tools API functional tests. Just tests some simple indexing and tool execution. Tons more one can and should test. Affected #: 1 file diff -r 14ab802d020997e1acfdce191d912b702624b96f -r c250b1cfc60fe2b56ddcf18e2cf2543631d4c26f test/functional/api/test_tools.py --- /dev/null +++ b/test/functional/api/test_tools.py @@ -0,0 +1,102 @@ +# Test tools API. +from itertools import chain +from json import dumps +import time + +from base import api +from operator import itemgetter + + +class ToolsTestCase( api.ApiTestCase ): + + def test_index( self ): + index = self._get( "tools" ) + tools_index = index.json() + # In panels by default, so flatten out sections... + tools = list( chain( *map( itemgetter( "elems" ), tools_index ) ) ) + tool_ids = map( itemgetter( "id" ), tools ) + assert "upload1" in tool_ids + assert "cat1" in tool_ids + + def test_no_panel_index( self ): + index = self._get( "tools", data=dict(in_panel="false") ) + tools_index = index.json() + # No need to flatten out sections, with in_panel=False, only tools are + # returned. + tool_ids = map( itemgetter( "id" ), tools_index ) + assert "upload1" in tool_ids + assert "cat1" in tool_ids + + def test_upload1_paste( self ): + history_id = self._new_history() + payload = self._upload_payload( history_id, 'Hello World' ) + create_response = self._post( "tools", data=payload ) + self._assert_has_keys( create_response.json(), 'outputs' ) + + def test_run_cat1( self ): + history_id = self._new_history() + new_dataset = self._new_dataset( history_id ) + dataset_id = new_dataset[ 'id' ] + payload = self._run_tool_payload( + tool_id='cat1', + inputs=dict( + input1=dict( + src='hda', + id=dataset_id + ), + ), + history_id=history_id, + ) + create_response = self._post( "tools", data=payload ) + self._assert_status_code_is( create_response, 200 ) + self._assert_has_keys( create_response.json(), 'outputs' ) + self._wait_for_history( history_id, assert_ok=True ) + + def _new_dataset( self, history_id, content='TestData123', **kwds ): + payload = self._upload_payload( history_id, content, **kwds ) + run_response = self._post( "tools", data=payload ) + self._assert_status_code_is( run_response, 200 ) + return run_response.json()["outputs"][0] + + def _wait_for_history( self, history_id, assert_ok=False ): + while True: + history_details_response = self._get( "histories/%s" % history_id ) + self._assert_status_code_is( history_details_response, 200 ) + history_state = history_details_response.json()[ "state" ] + if history_state not in [ "running", "queued" ]: + break + time.sleep( .1 ) + if assert_ok: + self.assertEquals( history_state, 'ok' ) + + def _new_history( self, **kwds ): + name = kwds.get( "name", "API Test History" ) + create_history_response = self._post( "histories", data=dict( name=name ) ) + self._assert_status_code_is( create_history_response, 200 ) + history_id = create_history_response.json()[ "id" ] + return history_id + + def _upload_payload( self, history_id, content, **kwds ): + name = kwds.get( "name", "Test Dataset" ) + dbkey = kwds.get( "dbkey", "?" ) + file_type = kwds.get( "file_type", 'txt' ) + upload_params = { + 'files_0|NAME': name, + 'files_0|url_paste': content, + 'dbkey': dbkey, + 'file_type': file_type, + } + return self._run_tool_payload( + tool_id='upload1', + inputs=upload_params, + history_id=history_id, + upload_type='upload_dataset' + ) + + def _run_tool_payload( self, tool_id, inputs, history_id, **kwds ): + return dict( + tool_id=tool_id, + inputs=dumps(inputs), + history_id=history_id, + **kwds + ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Update sample data for visualization plugin
by commits-noreply＠bitbucket.org 13 Jan '14

13 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e40e2965ac65/ Changeset: e40e2965ac65 User: guerler Date: 2014-01-13 12:17:24 Summary: Update sample data for visualization plugin Affected #: 1 file diff -r bc7445cda44439e787dcc0ead93f0a512fa6e0c3 -r e40e2965ac65f3a52778838e2a6879aadaf18add config/plugins/visualizations/charts/sample.txt --- a/config/plugins/visualizations/charts/sample.txt +++ b/config/plugins/visualizations/charts/sample.txt @@ -1,1 +1,9 @@ -43 55 63 99 28 85 20 31 47 14 1 63 94 83 94 74 7 73 51 7 8 34 2 94 87 21 72 51 3 84 5 50 40 30 59 43 19 77 30 80 22 55 69 43 77 72 12 54 53 56 36 34 81 28 59 64 54 29 57 69 57 90 93 32 45 98 40 16 52 83 6 17 39 86 10 11 38 69 19 50 67 51 47 22 58 27 65 49 92 96 \ No newline at end of file +43 55 63 99 28 85 20 31 47 14 +1 63 94 83 94 74 7 73 51 7 +8 34 2 94 87 21 72 51 3 84 +5 50 40 30 59 43 19 77 30 80 +22 55 69 43 77 72 12 54 53 56 +36 34 81 28 59 64 54 29 57 69 +57 90 93 32 45 98 40 16 52 83 +6 17 39 86 10 11 38 69 19 50 +67 51 47 22 58 27 65 49 92 96 \ 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: guerler: Sample data for visualization plugin
by commits-noreply＠bitbucket.org 13 Jan '14

13 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bc7445cda444/ Changeset: bc7445cda444 User: guerler Date: 2014-01-13 12:14:39 Summary: Sample data for visualization plugin Affected #: 1 file diff -r 6f56754324a6cd91d9e4afccd1d268ca22861093 -r bc7445cda44439e787dcc0ead93f0a512fa6e0c3 config/plugins/visualizations/charts/sample.txt --- /dev/null +++ b/config/plugins/visualizations/charts/sample.txt @@ -0,0 +1,1 @@ +43 55 63 99 28 85 20 31 47 14 1 63 94 83 94 74 7 73 51 7 8 34 2 94 87 21 72 51 3 84 5 50 40 30 59 43 19 77 30 80 22 55 69 43 77 72 12 54 53 56 36 34 81 28 59 64 54 29 57 69 57 90 93 32 45 98 40 16 52 83 6 17 39 86 10 11 38 69 19 50 67 51 47 22 58 27 65 49 92 96 \ 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: guerler: Visualization plugin: Wrapper for nvd3/d3
by commits-noreply＠bitbucket.org 13 Jan '14

13 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6f56754324a6/ Changeset: 6f56754324a6 User: guerler Date: 2014-01-13 11:53:01 Summary: Visualization plugin: Wrapper for nvd3/d3 Affected #: 28 files diff -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a -r 6f56754324a6cd91d9e4afccd1d268ca22861093 config/plugins/visualizations/charts/config/charts.xml --- /dev/null +++ b/config/plugins/visualizations/charts/config/charts.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "../../visualization.dtd"> +<visualization name="charts"> + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test> + <to_param param_attr="id">dataset_id</to_param> + </data_source> + </data_sources> + <params> + <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> + </params> + <template>charts.mako</template> +</visualization> diff -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a -r 6f56754324a6cd91d9e4afccd1d268ca22861093 config/plugins/visualizations/charts/static/app.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/app.js @@ -0,0 +1,67 @@ +// dependencies +define(['library/portlet', 'library/ui', 'library/utils', + 'main', 'viewport', 'create', 'config', + 'models/datasets', 'models/chart', 'models/charts', 'models/types'], + function( Portlet, Ui, Utils, + Main, Viewport, Create, Config, + Datasets, Chart, Charts, Types + ) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(options) + { + // link options + this.options = options; + + // link galaxy + this.modal = parent.Galaxy.modal; + + // create chart objects + this.types = new Types(); + this.chart = new Chart(); + this.charts = new Charts(this); + + // create dataset handler + this.datasets = new Datasets(this); + + // create views + this.main = new Main(this); + this.viewport = new Viewport(this); + this.config = new Config(this); + this.create = new Create(this); + + // portlet + this.portlet = new Portlet({icon : 'fa-bar-chart-o', label : 'Charts'}); + this.portlet.append(this.main.$el); + this.portlet.append(this.config.$el); + this.portlet.append(this.create.$el); + + // append main + this.main.append(this.viewport.$el); + + // create + this.config.$el.hide(); + this.create.$el.hide(); + + // set elements + this.setElement(this.portlet.$el); + }, + + // execute command + execute: function(options) { + }, + + // unload + onunload: function() { + }, + + // log + log: function(location, message) { + console.log(location + ' ' + message); + } +}); + +}); \ No newline at end of file diff -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a -r 6f56754324a6cd91d9e4afccd1d268ca22861093 config/plugins/visualizations/charts/static/charts/bardiagram.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/bardiagram.js @@ -0,0 +1,34 @@ +// dependencies +define(['library/utils'], function(Utils) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + this.chart = options.chart; + }, + + // render + refresh : function(data) + { + // add graph to screen + var self = this; + nv.addGraph(function() { + self.d3_chart = nv.models.multiBarChart(); + + self.d3_chart.xAxis.tickFormat(d3.format('.2f')) + self.d3_chart.yAxis.tickFormat(d3.format('.1f')) + + d3.select(self.options.svg_id) + .datum(data) + .call(self.d3_chart); + + nv.utils.windowResize(self.d3_chart.update); + }); + } +}); + +}); \ No newline at end of file diff -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a -r 6f56754324a6cd91d9e4afccd1d268ca22861093 config/plugins/visualizations/charts/static/charts/horizontal.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/horizontal.js @@ -0,0 +1,33 @@ +// dependencies +define(['library/utils'], function(Utils) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + this.chart = options.chart; + }, + + // render + refresh : function(data) + { + // add graph to screen + var self = this; + nv.addGraph(function() { + self.d3_chart = nv.models.multiBarHorizontalChart(); + + self.d3_chart.xAxis.tickFormat(function() { return ''; }); + + d3.select(self.options.svg_id) + .datum(data) + .call(self.d3_chart); + + nv.utils.windowResize(self.d3_chart.update); + }); + } +}); + +}); \ No newline at end of file diff -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a -r 6f56754324a6cd91d9e4afccd1d268ca22861093 config/plugins/visualizations/charts/static/charts/line.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/line.js @@ -0,0 +1,39 @@ +// dependencies +define(['library/utils'], function(Utils) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + this.chart = options.chart; + }, + + // render + refresh : function(data) + { + // add graph to screen + var self = this; + nv.addGraph(function() { + self.chart_3d = nv.models.lineChart(); + + self.chart_3d.xAxis + .tickFormat(d3.format(',f')); + + self.chart_3d.yAxis + .tickFormat(d3.format(',.2f')); + + d3.select(self.options.svg_id) + .datum(data) + .call(self.chart_3d); + + nv.utils.windowResize(self.chart_3d.update); + + return self.chart_3d; + }); + } +}); + +}); \ No newline at end of file diff -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a -r 6f56754324a6cd91d9e4afccd1d268ca22861093 config/plugins/visualizations/charts/static/charts/linewithfocus.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/linewithfocus.js @@ -0,0 +1,37 @@ +// dependencies +define(['library/utils'], function(Utils) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + this.chart = options.chart; + }, + + // render + refresh : function(data) + { + // add graph to screen + var self = this; + nv.addGraph(function() { + self.chart_3d = nv.models.lineWithFocusChart(); + + self.chart_3d.xAxis + .tickFormat(d3.format(',f')); + + self.chart_3d.yAxis + .tickFormat(d3.format(',.2f')); + + d3.select(self.options.svg_id) + .datum(data) + .call(self.chart_3d); + + nv.utils.windowResize(self.chart_3d.update); + }); + } +}); + +}); \ No newline at end of file diff -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a -r 6f56754324a6cd91d9e4afccd1d268ca22861093 config/plugins/visualizations/charts/static/charts/piechart.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/piechart.js @@ -0,0 +1,59 @@ +// dependencies +define(['library/utils'], function(Utils) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + this.chart = options.chart; + }, + + // render + refresh : function() + { + // add graph to screen + var self = this; + nv.addGraph(function(data) { + 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); + + d3.select(self.options.svg_id) + .datum(self._data()) + .transition().duration(1200) + .attr('height', 250) + .attr('width', 250) + .call(self.chart_3d); + + nv.utils.windowResize(self.chart_3d.update); + }); + }, + + _data : function() { + return [ + { + key: "Cumulative Return", + values: [ + { + key : "CDS / Options" , + y : 29.765957771107 + }, + { + key : "Options" , + y : 19.765957771107 + }, + { + key : "Other" , + y : 12.765957771107 + }] + }]; + } +}); + +}); \ No newline at end of file diff -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a -r 6f56754324a6cd91d9e4afccd1d268ca22861093 config/plugins/visualizations/charts/static/charts/scatterplot.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/scatterplot.js @@ -0,0 +1,37 @@ +// dependencies +define(['library/utils'], function(Utils) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + this.chart = options.chart; + }, + + // render + refresh : function(data) + { + // add graph to screen + var self = this; + nv.addGraph(function() { + self.d3_chart = nv.models.scatterChart() + .showDistX(true) + .showDistY(true) + .color(d3.scale.category10().range()); + + self.d3_chart.xAxis.tickFormat(d3.format('.02f')) + self.d3_chart.yAxis.tickFormat(d3.format('.02f')) + + d3.select(self.options.svg_id) + .datum(data) + .call(self.d3_chart); + + nv.utils.windowResize(self.d3_chart.update); + }); + } +}); + +}); \ No newline at end of file diff -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a -r 6f56754324a6cd91d9e4afccd1d268ca22861093 config/plugins/visualizations/charts/static/charts/stackedarea.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/stackedarea.js @@ -0,0 +1,59 @@ +// dependencies +define(['library/utils'], function(Utils) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + this.chart = options.chart; + }, + + // render + refresh : function(data) + { + // add graph to screen + var self = this; + nv.addGraph(function() { + // check data + var valid = true; + var length = 0; + for (var key in data) { + // evalute length + if (length == 0) { + length = data[key].values.length; + } else { + if (length != data[key].values.length) { + valid = false; + break; + } + } + } + if (!valid) { + return; + } + + // make plot + self.d3_chart = nv.models.stackedAreaChart() + .x(function(d) { + return d.x + }) + .y(function(d) { + return d.y + }) + .clipEdge(true); + + self.d3_chart.xAxis.tickFormat(function() { return ''; }); + + d3.select(self.options.svg_id) + .datum(data) + .call(self.d3_chart); + + nv.utils.windowResize(self.d3_chart.update); + }); + } +}); + +}); \ No newline at end of file diff -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a -r 6f56754324a6cd91d9e4afccd1d268ca22861093 config/plugins/visualizations/charts/static/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/config.js @@ -0,0 +1,219 @@ +// dependencies +define(['library/portlet', 'library/table', 'library/ui', 'library/utils', 'models/group'], + function(Portlet, Table, Ui, Utils, Group) { + +// chart config +return Backbone.View.extend( +{ + // model + group: new Group(), + + // columns + columns: [], + + // initialize + initialize: function(app, options) { + // link app + this.app = app; + + // get current chart object + this.chart = this.app.chart; + + // ui elements + this.message = new Ui.Message(); + this.label = new Ui.Input({placeholder: 'Group label'}); + this.table = new Table({content: 'No data column.'}); + + // add table to portlet + var self = this; + this.portlet = new Portlet({ + icon : 'fa-edit', + label : 'Define group properties:', + operations : { + 'save' : new Ui.ButtonIcon({ + icon : 'fa-save', + tooltip : 'Save', + onclick : function() { + // save/add group + self._saveGroup(); + } + }), + 'back' : new Ui.ButtonIcon({ + icon : 'fa-caret-left', + tooltip : 'Return', + onclick : function() { + self.$el.hide(); + self.app.create.$el.show(); + } + }) + } + }); + this.portlet.append(this.message.$el); + this.portlet.append(this.label.$el); + this.portlet.append(this.table.$el); + + // add element + this.setElement(this.portlet.$el); + + // change + var self = this; + this.chart.on('change:dataset_id', function() { + self._refreshDataset(); + }); + this.chart.on('change:type', function() { + self._refreshType(); + }); + this.group.on('change:label', function() { + self._refreshLabel(); + }); + this.group.on('change', function() { + self._refreshGroup(); + }); + }, + + // show + show: function() { + this.$el.show(); + }, + + // reset + reset: function() { + this.group.reset(); + this.group.set('id', Utils.uuid()); + this.group.set('label', 'Group label'); + }, + + // update dataset + _refreshDataset: function() { + // identify datasets + var dataset_id = this.chart.get('dataset_id'); + + // check if dataset is available + if (!dataset_id) { + return; + } + + // get dataset + var dataset = this.app.datasets.get({id : dataset_id}); + + // check + if (!dataset) { + this.app.log('Config::render()', 'Failed to retrieve dataset.'); + return; + } + + // configure columns + this.columns = []; + var meta = dataset.metadata_column_types; + for (var key in meta){ + this.columns.push({ + 'label' : key + ' [' + meta[key] + ']', + 'value' : key + }); + } + + // update select fields + for (var key in this.list) { + this.list[key].update(this.columns); + } + }, + + // update + _refreshType: function() { + // configure chart type + var self = this; + var chart_type = this.chart.get('type'); + if (chart_type) { + var chart_settings = this.app.types.get(chart_type); + + // table + this.table.removeAll(); + this.list = {}; + for (var id in chart_settings.data) { + // create select field + var data_def = chart_settings.data[id]; + var select = new Ui.Select({ + id : 'select_' + id, + gid : id, + data : this.columns, + onchange : function(value) { + self.group.set(this.gid, value); + } + }); + + // add row to table + this.table.add(data_def.title); + this.table.add(select.$el); + this.table.append(id); + + // add select field to list + this.list[id] = select; + } + } + }, + + // update + _refreshGroup: function() { + // update select fields + for (var id in this.list) { + var col = this.group.get(id); + if (col === undefined) { + col = 0; + } + this.list[id].value(col); + } + }, + + // update label + _refreshLabel: function() { + var label_text = this.group.get('label'); + if (label_text === undefined) { + label_text = ''; + } + this.label.value(label_text); + }, + + // create group + _saveGroup: function() { + // get current chart + var chart = this.chart; + + // update group object + var group = this.group; + for (var key in this.list) { + group.set(key, this.list[key].value()); + } + + // add label + group.set({ + dataset_id : this.chart.get('dataset_id'), + label : this.label.value(), + date : Utils.time() + }); + + // validate + if (!group.get('label')) { + this.message.update({message : 'Please enter a label for your group.'}); + return; + } + + // get groups of current chart + var groups = this.chart.groups; + + // create/update group + var group_update = groups.get(group.id); + if (group_update) { + group_update.set(group.attributes); + } else { + groups.add(group.clone()); + } + + // hide + this.$el.hide(); + + // update main + this.app.create.$el.show(); + } +}); + +}); \ No newline at end of file diff -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a -r 6f56754324a6cd91d9e4afccd1d268ca22861093 config/plugins/visualizations/charts/static/create.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/create.js @@ -0,0 +1,189 @@ +// dependencies +define(['library/portlet', 'library/table', 'library/ui', 'library/utils', 'models/chart', 'groups'], + function(Portlet, Table, Ui, Utils, Chart, Groups) { + +// widget +return Backbone.View.extend( +{ + // defaults options + optionsDefault: { + header : true, + content : 'No content available.' + }, + + // current chart + chart : null, + + // initialize + initialize: function(app, options) + { + // link application + this.app = app; + + // get current chart object + this.chart = this.app.chart; + + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // main elements + this.message = new Ui.Message(); + this.title = new Ui.Input({placeholder: 'Chart title'}); + this.dataset = new Ui.Input({value : app.options.dataset.id, disabled: true}); + + // configure dataset + this.groups = new Groups(this.app); + + // table + var self = this; + this.table = new Table({ + header : false, + onconfirm : function(type) { + if (self.chart.groups.length > 0) { + // show modal + self.app.modal.show({ + title : 'Switching the chart type?', + body : 'You configured data sources. If you switch chart types your configurations will be removed.', + buttons : { + 'Cancel' : function() { + // hide modal + self.app.modal.hide(); + }, + 'Continue' : function() { + // hide modal + self.app.modal.hide(); + + // confirm + self.table.confirm(type); + } + } + }); + } else { + // confirm + self.table.confirm(type); + } + }, + onchange : function(type) { + // update chart type + self.chart.set({type: type}); + + // reset groups + self.chart.groups.reset(); + }, + content: 'No chart types available' + }); + + // add types + var types_n = 0; + var types = app.types.attributes; + for (var id in types){ + var chart_type = types[id]; + this.table.add (++types_n + '.'); + this.table.add (chart_type.title); + this.table.append(id); + } + + // add table to portlet + var self = this; + this.portlet = new Portlet({ + icon : 'fa-edit', + label : 'Create a new chart:', + operations : { + 'save' : new Ui.ButtonIcon({ + icon : 'fa-save', + tooltip : 'Save', + onclick : function() { + self._saveChart(); + } + }), + 'back' : new Ui.ButtonIcon({ + icon : 'fa-caret-left', + tooltip : 'Return', + onclick : function() { + self.$el.hide(); + self.app.main.$el.show(); + } + }) + } + }); + this.portlet.append(this.message.$el); + this.portlet.append((new Ui.Label({ label : 'Provide a chart title:'})).$el); + this.portlet.append(this.title.$el); + this.portlet.append((new Ui.Label({ label : 'Select a dataset:'})).$el); + this.portlet.append(this.dataset.$el); + this.portlet.append((new Ui.Label({ label : 'Select a chart type:'})).$el); + this.portlet.append(this.table.$el); + this.portlet.append(this.groups.$el); + + // elements + this.setElement(this.portlet.$el); + + // events + var self = this; + this.chart.on('change:title', function(chart) { + self.title.value(chart.get('title')); + }); + this.chart.on('change:type', function(chart) { + self.table.value(chart.get('type')); + }); + }, + + // reset + reset: function() { + this.chart.reset(); + this.chart.set('id', Utils.uuid()); + this.chart.set('dataset_id', app.options.dataset.id); + this.chart.set('type', 'bardiagram'); + this.chart.set('title', 'Chart title'); + }, + + // set chart + setChart: function(new_chart) { + this.chart.copy(new_chart); + }, + + // create chart + _saveChart: function() { + // update chart data + this.chart.set({ + type : this.table.value(), + title : this.title.value(), + dataset_id : this.dataset.value(), + date : Utils.time() + }); + + // validate + if (!this.chart.get('title')) { + this.message.update({message : 'Please enter a title for your chart.'}); + return; + } + + if (!this.chart.get('type')) { + this.message.update({message : 'Please select a chart type.'}); + return; + } + + if (this.chart.groups.length == 0) { + this.message.update({message : 'Please configure at least one data source.'}); + return; + } + + // create/get chart + var current = this.app.charts.get(this.chart.id); + if (!current) { + current = this.chart.clone(); + this.app.charts.add(current); + } + + // update chart model + current.copy(this.chart); + + // hide + this.$el.hide(); + + // update main + this.app.main.$el.show(); + } +}); + +}); \ No newline at end of file diff -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a -r 6f56754324a6cd91d9e4afccd1d268ca22861093 config/plugins/visualizations/charts/static/groups.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/groups.js @@ -0,0 +1,154 @@ +// dependencies +define(['library/portlet', 'library/table', 'library/ui', 'library/utils'], function(Portlet, Table, Ui, Utils) { + +// chart config +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + // link app + this.app = app; + + // get current chart object + this.chart = this.app.chart; + + // table + this.table = new Table({ + content : 'Add data sources to this table.', + ondblclick : function(group_id) { + // get group + var group = self.app.chart.groups.get(group_id); + + // show edit + self.app.create.$el.hide(); + self.app.config.show(); + self.app.config.group.set(group.attributes); + } + }); + + // add table to portlet + var self = this; + this.portlet = new Portlet({ + icon : '', + label : 'Configure data sources:', + height : 100, + operations : { + 'new' : new Ui.ButtonIcon({ + icon : 'fa-plus', + tooltip: 'Create', + onclick: function() { + self.app.create.$el.hide(); + self.app.config.show(); + self.app.config.reset(); + } + }), + 'edit' : new Ui.ButtonIcon({ + icon : 'fa-pencil', + tooltip: 'Edit', + onclick: function() { + // check if element has been selected + var group_id = self.table.value(); + if (!group_id) { + return; + } + + // get group + var group = self.app.chart.groups.get(group_id); + + // show edit + self.app.create.$el.hide(); + self.app.config.show(); + self.app.config.group.set(group.attributes); + } + }), + 'delete' : new Ui.ButtonIcon({ + icon : 'fa-minus', + tooltip: 'Delete', + onclick: function() { + // check if element has been selected + var id = self.table.value(); + if (!id) { + return; + } + // remove group from chart + self.chart.groups.remove(id); + } + }) + } + }); + this.portlet.append(this.table.$el); + + // add element + this.setElement(this.portlet.$el); + + // change + var self = this; + this.chart.on('change', function() { + self._refresh(); + }); + this.chart.on('reset', function() { + self._removeGroupAll(); + }); + this.chart.on('change:type', function() { + self.app.config.trigger('change'); + }); + this.chart.groups.on('add', function(group) { + self._addGroup(group); + }); + this.chart.groups.on('remove', function(group) { + self._removeGroup(group); + }); + this.chart.groups.on('reset', function(group) { + self._removeGroupAll(); + }); + this.chart.groups.on('change', function(group) { + self._removeGroup(group); + self._addGroup(group); + }); + }, + + // refresh + _refresh: function() { + this._removeGroupAll(); + var self = this; + var groups = this.chart.groups; + if (groups) { + groups.each(function(group) { self._addGroup(group); }); + } + }, + + // add + _addGroup: function(group) { + // make custom info string + var info = '['; + var chart_type = this.chart.get('type'); + if (chart_type) { + var chart_settings = this.app.types.get(chart_type); + for (var key in chart_settings.data) { + info += key + '=' + group.get(key) + ', ' + } + } + info = info.substring(0, info.length - 2) + ']'; + + // add to table + this.table.add(group.get('label')); + this.table.add(info); + this.table.add('Last changed: ' + group.get('date')); + this.table.prepend(group.id); + this.table.value(group.id); + }, + + // remove + _removeGroup: function(group) { + // remove from to table + this.table.remove(group.id); + }, + + // data config reset + _removeGroupAll: function() { + // reset options table + this.table.removeAll(); + } +}); + +}); \ No newline at end of file diff -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a -r 6f56754324a6cd91d9e4afccd1d268ca22861093 config/plugins/visualizations/charts/static/library/portlet.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/library/portlet.js @@ -0,0 +1,142 @@ +// dependencies +define(['library/utils'], function(Utils) { + +// return +return Backbone.View.extend( +{ + // visibility + visible: false, + + // defaults options + optionsDefault: { + label : '', + icon : 'fa-tasks', + buttons : null, + body : null, + height : null, + operations : null, + placement : 'bottom', + overflow : 'auto' + }, + + // content + $content : null, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(this.options)); + + // link content + this.$content = this.$el.find('#content'); + + // set content height + if (this.options.height) { + this.$el.find('#body').css('height', this.options.height); + this.$el.find('#content').css('overflow', this.options.overflow); + } + + // append buttons + this.$buttons = $(this.el).find('#buttons'); + if (this.options.buttons) { + // link functions + var self = this; + $.each(this.options.buttons, function(name, item) { + self.$buttons.append(item.$el); + }); + } else { + this.$buttons.remove(); + } + + // append operations + this.$operations = $(this.el).find('#operations'); + if (this.options.operations) { + // link functions + var self = this; + $.each(this.options.operations, function(name, item) { + self.$operations.append(item.$el); + }); + } + + // add body + if(this.options.body) { + this.append(this.options.body); + } + }, + + // append + append: function($el) { + this.$content.append(Utils.wrap($el)); + }, + + // content + content: function() { + return this.$content; + }, + + // hide modal + show: function(){ + // fade in + this.$el.fadeIn('fast'); + + // set flag + this.visible = true; + }, + + // hide modal + hide: function(){ + // fade out + this.$el.fadeOut('fast'); + + // set flag + this.visible = false; + }, + + // enable buttons + enableButton: function(name) { + this.$buttons.find('#' + String(name).toLowerCase()).prop('disabled', false); + }, + + // disable buttons + disableButton: function(name) { + this.$buttons.find('#' + String(name).toLowerCase()).prop('disabled', true); + }, + + // fill regular modal template + template: function(options) { + var tmpl = '<div class="toolForm">'; + + if (options.label) { + tmpl += '<div id="title" class="toolFormTitle" style="padding-bottom: 7px;">' + + '<div id="operations" style="float: right;"></div>' + + '<div>'; + + if (options.icon) + tmpl += '<i style="font-size: 1.2em" class="icon fa ' + options.icon + '"> </i>'; + + tmpl += options.label + + '</div>' + + '</div>'; + } + tmpl += '<div id="body" class="toolFormBody">'; + + if (options.placement == 'top') { + tmpl += '<div id="buttons" class="buttons" style="height: 50px; padding: 10px;"></div>'; + } + + tmpl += '<div id="content" class="content" style="height: inherit; padding: 10px;"></div>'; + + if (options.placement == 'bottom') { + tmpl += '<div id="buttons" class="buttons" style="height: 50px; padding: 10px;"></div>'; + } + + tmpl += '</div>' + + '</div>'; + return tmpl; + } +}); + +}); diff -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a -r 6f56754324a6cd91d9e4afccd1d268ca22861093 config/plugins/visualizations/charts/static/library/table.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/library/table.js @@ -0,0 +1,188 @@ +// dependencies +define(['library/utils'], function(Utils) { + +// return +return Backbone.View.extend( +{ + // current row + row: null, + + // count rows + row_count: 0, + + // defaults options + optionsDefault: { + content : 'No content available.', + onchange : null, + ondblclick : null, + onconfirm : null + }, + + // events + events : { + 'click' : 'onclick', + 'dblclick' : 'ondblclick' + }, + + // first + first: true, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(options)); + + // initialize row + this.row = $('<tr></tr>'); + }, + + // add header cell + addHeader: function($el) { + var wrapper = $('<th></th>'); + wrapper.append($el); + this.row.append(wrapper); + }, + + // header + appendHeader: function() { + // append header row + $(this.el).find('thead').append(this.row); + + // row + this.row = $('<tr></tr>'); + }, + + // add row cell + add: function($el) { + var wrapper = $('<td></td>'); + wrapper.append($el); + this.row.append(wrapper); + }, + + // append + append: function(id) { + this.commit(id); + }, + + // prepend + prepend: function(id) { + this.commit(id, true); + }, + + // commit + commit: function(id, prepend) { + // add + this.row.attr('id', id); + + // add row + if (prepend) { + $(this.el).find('tbody').prepend(this.row); + } else { + $(this.el).find('tbody').append(this.row); + } + + // row + this.row = $('<tr></tr>'); + + // row count + this.row_count++; + this.refresh(); + }, + + // remove + remove: function(id) { + $(this.el).find('#' + id).remove(); + this.row_count--; + this.refresh(); + }, + + // remove + removeAll: function() { + $(this.el).find('tbody').html(''); + this.row_count = 0; + this.refresh(); + }, + + // value + value: function(new_value) { + // get current id/value + this.before = this.$el.find('.current').attr('id'); + + // check if new_value is defined + if (new_value !== undefined) { + this.$el.find('tr').removeClass('current'); + if (new_value) { + this.$el.find('#' + new_value).addClass('current'); + } + } + + // get current id/value + var after = this.$el.find('.current').attr('id'); + if(after === undefined) { + return null; + } else { + // fire onchange + if (after != this.before && this.options.onchange) { + this.options.onchange(new_value); + } + + // return current value + return after; + } + }, + + // cancel last change + confirm: function(new_value) { + this.value(new_value); + }, + + // onclick + onclick: function(e) { + // get values + var old_value = this.value(); + var new_value = $(e.target).closest('tr').attr('id'); + + // check equality + if (new_value && old_value != new_value) { + if (this.options.onconfirm) { + this.options.onconfirm(new_value); + } else { + this.confirm(new_value); + } + } + }, + + // onclick + ondblclick: function(e) { + var value = this.value(); + if (value && this.options.ondblclick) { + this.options.ondblclick(value); + } + }, + + // refresh + refresh: function() { + if (this.row_count == 0) { + this.$el.find('tmessage').show(); + } else { + this.$el.find('tmessage').hide(); + } + }, + + // load html template + template: function(options) + { + return '<div>' + + '<table class="grid">' + + '<thead></thead>' + + '<tbody style="cursor: pointer;"></tbody>' + + '</table>' + + '<tmessage>' + options.content + '</tmessage>' + + '<div>'; + } +}); + +}); diff -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a -r 6f56754324a6cd91d9e4afccd1d268ca22861093 config/plugins/visualizations/charts/static/library/ui.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/library/ui.js @@ -0,0 +1,472 @@ +// dependencies +define(['library/utils', 'library/ui.select'], function(Utils, Select) { + +// plugin +var Label = Backbone.View.extend( +{ + // options + optionsDefault: { + label : '' + }, + + // initialize + initialize : function(options) { + // get options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(this.options)); + }, + + // template + template: function(options) { + return '<label><b>' + options.label + '</b></label>'; + }, + + // value + value: function() { + return options.label; + } +}); + +// plugin +var Button = Backbone.View.extend( +{ + // options + optionsDefault: { + label : '', + float : 'right', + cls : 'btn-default', + type : 'submit', + icon : '' + }, + + // initialize + initialize : function(options) { + // get options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(this.options)); + + // add event + $(this.el).on('click', options.onclick); + }, + + // element + template: function(options) { + var str = '<button type="' + options.type + '" style="margin-right: 5px; float: ' + options.float + ';" type="button" class="btn ' + options.cls + '">'; + if (options.icon) { + str += '<i class="icon fa ' + options.icon + '"></i> ' ; + } + str += options.label + + '</button>'; + return str; + } +}); + +// plugin +var Anchor = Backbone.View.extend( +{ + // options + optionsDefault: { + label : '' + }, + + // initialize + initialize : function(options) { + // get options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(this.options)); + + // add event + $(this.el).on('click', options.onclick); + }, + + // element + template: function(options) { + return '<div><a href="javascript:void(0)">' + options.label + '</a></div>'; + } +}); + +// plugin +var Message = Backbone.View.extend( +{ + // options + optionsDefault: { + message : '', + status : 'info', + persistent : false + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement('<div></div>'); + }, + + // update + update : function(options) { + // get options + this.options = Utils.merge(options, this.optionsDefault); + + // show message + if (options.message != '') { + this.$el.html(this.template(this.options)); + this.$el.fadeIn(); + + // check if message is persistent + if (!options.persistent) { + // set timer + var self = this; + window.setTimeout(function() { + if (self.$el.is(':visible')) { + self.$el.fadeOut(); + } else { + self.$el.hide(); + } + }, 3000); + } + } else { + this.$el.fadeOut(); + } + }, + + // element + template: function(options) { + return '<div class="alert alert-' + options.status + '" style="padding: 2px 2px 2px 10px;">' + options.message + '</div>'; + } +}); + +// plugin +var Searchbox = Backbone.View.extend( +{ + // options + optionsDefault: { + onclick : null, + searchword : '' + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(this.options)); + + // add click event + var self = this; + if (this.options.onclick) { + this.$el.on('submit', function(e) { + var search_field = self.$el.find('#search'); + self.options.onclick(search_field.val()); + }); + } + }, + + // element + template: function(options) { + return '<div class="search">' + + '<form onsubmit="return false;">' + + '<input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="' + options.searchword + '">' + + '<button type="submit" class="btn search-btn">' + + '<i class="fa fa-search"></i>' + + '</button>' + + '</form>' + + '</div>'; + } +}); + +// plugin +var Title = Backbone.View.extend( +{ + // options + optionsDefault: { + label : 'Unlabeled', + body : null + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(this.options)); + + if (this.options.body) { + this.$el.find('.body').append(this.options.body); + } + }, + + // element + template: function(options) { + return '<div id="title" class="title">' + + options.label + ':' + + '</div>'; + } +}); + +// tab +var ButtonMenu = Backbone.View.extend( +{ + // main options + options: + { + id : '', + title : '', + target : '', + href : '', + onunload : null, + onclick : null, + visible : true, + icon : null, + tag : '' + }, + + // optional sub menu + $menu: null, + + // initialize + initialize: function (options) + { + // read in defaults + if (options) + this.options = _.defaults(options, this.options); + + // add template for tab + this.setElement($(this._template(this.options))); + + // find root + var $root = $(this.el).find('.root'); + + // link head + var self = this; + $root.on('click', function(e) + { + // prevent default + e.preventDefault(); + + // add click event + if(self.options.onclick) { + self.options.onclick(); + } + }); + + // visiblity + if (!this.options.visible) + this.hide(); + }, + + // show + show: function() + { + $(this.el).show(); + }, + + // hide + hide: function() + { + $(this.el).hide(); + }, + + // add menu item + addMenu: function (options) + { + // menu option defaults + var menuOptions = { + title : '', + target : '', + href : '', + onclick : null, + divider : false, + icon : null + } + + // read in defaults + if (options) + menuOptions = _.defaults(options, menuOptions); + + // check if submenu element is available + if (!this.$menu) + { + // insert submenu element into root + $(this.el).append(this._templateMenu()); + + // update element link + this.$menu = $(this.el).find('.menu'); + } + + // create + var $item = $(this._templateMenuItem(menuOptions)); + + // add events + $item.on('click', function(e) + { + // prevent default + e.preventDefault(); + + // add click event + if(menuOptions.onclick) { + menuOptions.onclick(); + } + }); + + // append menu + this.$menu.append($item); + + // append divider + if (menuOptions.divider) + this.$menu.append($(this._templateDivider())); + }, + + // fill template header + _templateMenuItem: function (options) + { + var tmpl = '<li>' + + '<a href="' + options.href + '" target="' + options.target + '">'; + + if (options.icon) + tmpl += '<i class="fa ' + options.icon + '"></i>'; + + tmpl += ' ' + options.title + + '</a>' + + '</li>'; + return tmpl; + }, + + // fill template header + _templateMenu: function () + { + return '<ul class="menu dropdown-menu pull-right" role="menu"></ul>'; + }, + + _templateDivider: function() + { + return '<li class="divider"></li>'; + }, + + // fill template + _template: function (options) + { + // start template + var tmpl = '<div id="' + options.id + '" class="button-menu btn-group">' + + '<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">'; + + if (options.icon) + tmpl += '<i class="fa ' + options.icon + '"></i>'; + + '</button>' + + '</div>'; + + // return template + return tmpl; + } +}); + +// plugin +var ButtonIcon = Backbone.View.extend( +{ + // options + optionsDefault: { + label : '', + float : 'right', + cls : 'icon-btn', + type : 'submit', + icon : '', + tooltip : '' + }, + + // initialize + initialize : function(options) { + // get options + if (options) + this.options = _.defaults(options, this.optionsDefault); + else + this.options = this.optionsDefault; + + // create new element + this.setElement(this.template(this.options)); + + // add event + $(this.el).on('click', options.onclick); + + // add tooltip + $(this.el).tooltip({title: options.tooltip, placement: 'bottom'}); + }, + + // element + template: function(options) { + var str = '<a style="margin-right: 5px; float: ' + options.float + ';" class="' + options.cls + '">'; + if (options.icon) { + str += '<i class="icon fa ' + options.icon + '"></i>'; + } + str += options.label + + '</a>'; + return str; + } +}); + + +// plugin +var Input = Backbone.View.extend( +{ + // options + optionsDefault: { + value : '', + type : 'text', + placeholder : '', + disabled : false + }, + + // initialize + initialize : function(options) { + // get options + if (options) + this.options = _.defaults(options, this.optionsDefault); + else + this.options = this.optionsDefault; + + // create new element + this.setElement(this.template(this.options)); + + // disable input field + if (this.options.disabled) { + this.$el.prop('disabled', true); + } + }, + + // value + value : function (new_val) { + if (new_val !== undefined) { + this.$el.val(new_val); + } + return this.$el.val(); + }, + + // element + template: function(options) { + return '<input id="' + options.id + '" type="' + options.type + '" value="' + options.value + '" placeholder="' + options.placeholder + '" class="form-control">'; + } +}); + +// return +return { + Label : Label, + Button : Button, + ButtonIcon : ButtonIcon, + Input : Input, + Anchor : Anchor, + Message : Message, + Searchbox : Searchbox, + Title : Title, + Select : Select, + ButtonMenu : ButtonMenu +} +}); diff -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a -r 6f56754324a6cd91d9e4afccd1d268ca22861093 config/plugins/visualizations/charts/static/library/ui.select.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/library/ui.select.js @@ -0,0 +1,117 @@ +// dependencies +define(['library/utils'], function(Utils) { + + +// plugin +return Backbone.View.extend( +{ + // options + optionsDefault: { + id : '', + cls : '' + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(this.options)); + + // add change event + var self = this; + if (this.options.onchange) { + this.$el.on('change', function() { self.options.onchange(self.value()) }); + } + }, + + // value + value : function (new_val) { + if (new_val !== undefined) { + this.$el.val(new_val); + } + return this.$el.val(); + }, + + // label + label : function () { + return this.$el.find('option:selected').text(); + }, + + // disabled + disabled: function() { + return this.$el.is(':disabled'); + }, + + // render + update: function(options) { + // selected + var selected = this.$el.val(); + + // remove all options + $(this.el).find('option').remove(); + + // add new options + for (var key in options.data) { + $(this.el).append(this.templateOption(options.data[key])); + } + + // check if selected value exists + var exists = 0 != $(this.el).find('option[value=' + selected + ']').length; + + // add selected value + if (exists) + $(this.el).val(selected); + }, + + // update from url + updateUrl : function(options, callback) { + // get json + var self = this; + Utils.get(options.url, function(json) { + // write data into array + var data = []; + for (key in json) { + data.push({label: json[key].name, value: json[key].id}); + } + + // check if disabled. do not update disabled select elements. + if (!self.disabled()) { + self.update({data: data}); + } + + // callback + if (callback) { + callback(); + } + }); + }, + + // option + templateOption: function(options) { + return '<option value="' + options.value + '">' + options.label + '</option>'; + }, + + // element + template: function(options) { + var tmpl = '<select id="' + options.id + '" class="select ' + options.cls + ' ' + options.id + '">'; + for (key in options.data) { + // options + var item = options.data[key]; + + // identify selected value + var tag = ''; + if (item.value == options.selected || item.value == '') { + tag = 'selected'; + } + + // add template string + tmpl += '<option value="' + item.value + '" ' + tag + '>' + item.label + '</option>'; + } + tmpl += '</select>'; + return tmpl; + } +}); + +}); This diff is so big that we needed to truncate the remainder. 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: 2 new changesets
by commits-noreply＠bitbucket.org 12 Jan '14

12 Jan '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/494b51bda9c1/ Changeset: 494b51bda9c1 User: jmchilton Date: 2014-01-12 05:40:18 Summary: Rework workflow functional testing so isn't tested by default... Meant to be used with a specific workflow, but nose is picking it up by default when no workflow has been specified. Affected #: 4 files diff -r c8c00d106c7a6883feaacca809b42fd7c107fe2a -r 494b51bda9c1a319672e92cce4ec17386cd65390 run_functional_tests.sh --- a/run_functional_tests.sh +++ b/run_functional_tests.sh @@ -51,7 +51,7 @@ python ./test/tool_shed/functional_tests.py -v --with-nosehtml --html-report-file ./test/tool_shed/run_functional_tests.html $2 fi elif [ $1 = '-workflow' ]; then - python ./scripts/functional_tests.py -v functional.test_workflow:WorkflowTestCase --with-nosehtml --html-report-file ./test/tool_shed/run_functional_tests.html -workflow $2 + python ./scripts/functional_tests.py -v functional.workflow:WorkflowTestCase --with-nosehtml --html-report-file ./test/tool_shed/run_functional_tests.html -workflow $2 elif [ $1 = '-data_managers' ]; then if [ ! $2 ]; then python ./scripts/functional_tests.py -v functional.test_data_managers --with-nosehtml --html-report-file run_functional_tests.html -data_managers diff -r c8c00d106c7a6883feaacca809b42fd7c107fe2a -r 494b51bda9c1a319672e92cce4ec17386cd65390 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -475,10 +475,10 @@ def _run_functional_test( testing_shed_tools=None ): workflow_test = __check_arg( '-workflow', param=True ) if workflow_test: - import functional.test_workflow - functional.test_workflow.WorkflowTestCase.workflow_test_file = workflow_test - functional.test_workflow.WorkflowTestCase.master_api_key = master_api_key - functional.test_workflow.WorkflowTestCase.user_api_key = get_user_api_key() + import functional.workflow + functional.workflow.WorkflowTestCase.workflow_test_file = workflow_test + functional.workflow.WorkflowTestCase.master_api_key = master_api_key + functional.workflow.WorkflowTestCase.user_api_key = get_user_api_key() data_manager_test = __check_arg( '-data_managers', param=False ) if data_manager_test: import functional.test_data_managers diff -r c8c00d106c7a6883feaacca809b42fd7c107fe2a -r 494b51bda9c1a319672e92cce4ec17386cd65390 test/functional/test_workflow.py --- a/test/functional/test_workflow.py +++ /dev/null @@ -1,185 +0,0 @@ -import os -import sys -from base.twilltestcase import TwillTestCase -from base.interactor import GalaxyInteractorApi, stage_data_in_history - -from galaxy.util import parse_xml -from galaxy.tools.test import parse_param_elem, require_file, test_data_iter, parse_output_elems -from json import load, dumps - -from logging import getLogger -log = getLogger( __name__ ) - - -class WorkflowTestCase( TwillTestCase ): - """ - Kind of a shell of a test case for running workflow tests. Probably - needs to look more like test_toolbox. - """ - workflow_test_file = None - user_api_key = None - master_api_key = None - - def test_workflow( self, workflow_test_file=None ): - maxseconds = 120 - workflow_test_file = workflow_test_file or WorkflowTestCase.workflow_test_file - assert workflow_test_file - workflow_test = parse_test_file( workflow_test_file ) - galaxy_interactor = GalaxyWorkflowInteractor( self ) - - # Calling workflow https://github.com/jmchilton/blend4j/blob/master/src/test/java/com/github/j… - - # Import workflow - workflow_id, step_id_map, output_defs = self.__import_workflow( galaxy_interactor, workflow_test.workflow ) - - # Stage data and history for workflow - test_history = galaxy_interactor.new_history() - stage_data_in_history( galaxy_interactor, workflow_test.test_data(), test_history ) - - # Build workflow parameters - uploads = galaxy_interactor.uploads - ds_map = {} - for step_index, input_dataset_label in workflow_test.input_datasets(): - # Upload is {"src": "hda", "id": hid} - try: - upload = uploads[ workflow_test.upload_name( input_dataset_label ) ] - except KeyError: - raise AssertionError( "Failed to find upload with label %s in uploaded datasets %s" % ( input_dataset_label, uploads ) ) - - ds_map[ step_id_map[ step_index ] ] = upload - - payload = { - "history": "hist_id=%s" % test_history, - "ds_map": dumps( ds_map ), - "workflow_id": workflow_id, - } - run_response = galaxy_interactor.run_workflow( payload ).json() - - outputs = run_response[ 'outputs' ] - if not len( outputs ) == len( output_defs ): - msg_template = "Number of outputs [%d] created by workflow execution does not equal expected number from input file [%d]." - msg = msg_template % ( len( outputs ), len( output_defs ) ) - raise AssertionError( msg ) - - galaxy_interactor.wait_for_ids( test_history, outputs ) - - for expected_output_def in workflow_test.outputs: - # Get the correct hid - name, outfile, attributes = expected_output_def - - output_data = outputs[ int( name ) ] - try: - galaxy_interactor.verify_output( test_history, output_data, outfile, attributes=attributes, shed_tool_id=None, maxseconds=maxseconds ) - except Exception: - for stream in ['stdout', 'stderr']: - stream_output = galaxy_interactor.get_job_stream( test_history, output_data, stream=stream ) - print >>sys.stderr, self._format_stream( stream_output, stream=stream, format=True ) - raise - - def __import_workflow( self, galaxy_interactor, workflow ): - """ - Import workflow into Galaxy and return id and mapping of step ids. - """ - workflow_info = galaxy_interactor.import_workflow( workflow ).json() - try: - workflow_id = workflow_info[ 'id' ] - except KeyError: - raise AssertionError( "Failed to find id for workflow import response %s" % workflow_info ) - - # Well ideally the local copy of the workflow would have the same step ids - # as the one imported through the API, but API workflow imports are 1-indexed - # and GUI exports 0-indexed as of mid-november 2013. - - imported_workflow = galaxy_interactor.read_workflow( workflow_id ) - #log.info("local %s\nimported%s" % (workflow, imported_workflow)) - step_id_map = {} - local_steps_ids = sorted( [ int( step_id ) for step_id in workflow[ 'steps' ].keys() ] ) - imported_steps_ids = sorted( [ int( step_id ) for step_id in imported_workflow[ 'steps' ].keys() ] ) - for local_step_id, imported_step_id in zip( local_steps_ids, imported_steps_ids ): - step_id_map[ local_step_id ] = imported_step_id - - output_defs = [] - for local_step_id in local_steps_ids: - step_def = workflow['steps'][ str( local_step_id ) ] - output_defs.extend( step_def.get( "outputs", [] ) ) - - return workflow_id, step_id_map, output_defs - - -def parse_test_file( workflow_test_file ): - tree = parse_xml( workflow_test_file ) - root = tree.getroot() - input_elems = root.findall( "input" ) - required_files = [] - dataset_dict = {} - for input_elem in input_elems: - name, value, attrib = parse_param_elem( input_elem ) - require_file( name, value, attrib, required_files ) - dataset_dict[ name ] = value - - outputs = parse_output_elems( root ) - - workflow_file_rel_path = root.get( 'file' ) - if not workflow_file_rel_path: - raise Exception( "Workflow test XML must declare file attribute pointing to workflow under test." ) - - # TODO: Normalize this path, prevent it from accessing arbitrary files on system. - worfklow_file_abs_path = os.path.join( os.path.dirname( workflow_test_file ), workflow_file_rel_path ) - - return WorkflowTest( - dataset_dict, - required_files, - worfklow_file_abs_path, - outputs=outputs, - ) - - -class WorkflowTest( object ): - - def __init__( self, dataset_dict, required_files, workflow_file, outputs ): - self.dataset_dict = dataset_dict - self.required_files = required_files - self.workflow = load( open( workflow_file, "r" ) ) - self.outputs = outputs - - def test_data( self ): - return test_data_iter( self.required_files ) - - def upload_name( self, input_dataset_label ): - return self.dataset_dict[ input_dataset_label ] - - def input_datasets( self ): - steps = self.workflow[ "steps" ] - log.info("in input_datasets with steps %s" % steps) - for step_index, step_dict in steps.iteritems(): - if step_dict.get( "name", None ) == "Input dataset": - yield int( step_index ), step_dict[ "inputs" ][0][ "name" ] - - -class GalaxyWorkflowInteractor(GalaxyInteractorApi): - - def __init__( self, twill_test_case ): - super(GalaxyWorkflowInteractor, self).__init__( twill_test_case ) - - def import_workflow( self, workflow_rep ): - payload = { "workflow": dumps( workflow_rep ) } - return self._post( "workflows/upload", data=payload ) - - def run_workflow( self, data ): - return self._post( "workflows", data=data ) - - def read_workflow( self, id ): - return self._get( "workflows/%s" % id ).json() - - def wait_for_ids( self, history_id, ids ): - self.twill_test_case.wait_for( lambda: not all( [ self.__dataset_ready( history_id, id ) for id in ids ] ), maxseconds=120 ) - - def __dataset_ready( self, history_id, id ): - contents = self._get( 'histories/%s/contents' % history_id ).json() - for content in contents: - - if content["id"] == id: - state = content[ 'state' ] - state_ready = self._state_ready( state, error_msg="Dataset creation failed for dataset with name %s." % content[ 'name' ] ) - return state_ready - return False diff -r c8c00d106c7a6883feaacca809b42fd7c107fe2a -r 494b51bda9c1a319672e92cce4ec17386cd65390 test/functional/workflow.py --- /dev/null +++ b/test/functional/workflow.py @@ -0,0 +1,185 @@ +import os +import sys +from base.twilltestcase import TwillTestCase +from base.interactor import GalaxyInteractorApi, stage_data_in_history + +from galaxy.util import parse_xml +from galaxy.tools.test import parse_param_elem, require_file, test_data_iter, parse_output_elems +from json import load, dumps + +from logging import getLogger +log = getLogger( __name__ ) + + +class WorkflowTestCase( TwillTestCase ): + """ + Kind of a shell of a test case for running workflow tests. Probably + needs to look more like test_toolbox. + """ + workflow_test_file = None + user_api_key = None + master_api_key = None + + def test_workflow( self, workflow_test_file=None ): + maxseconds = 120 + workflow_test_file = workflow_test_file or WorkflowTestCase.workflow_test_file + assert workflow_test_file + workflow_test = parse_test_file( workflow_test_file ) + galaxy_interactor = GalaxyWorkflowInteractor( self ) + + # Calling workflow https://github.com/jmchilton/blend4j/blob/master/src/test/java/com/github/j… + + # Import workflow + workflow_id, step_id_map, output_defs = self.__import_workflow( galaxy_interactor, workflow_test.workflow ) + + # Stage data and history for workflow + test_history = galaxy_interactor.new_history() + stage_data_in_history( galaxy_interactor, workflow_test.test_data(), test_history ) + + # Build workflow parameters + uploads = galaxy_interactor.uploads + ds_map = {} + for step_index, input_dataset_label in workflow_test.input_datasets(): + # Upload is {"src": "hda", "id": hid} + try: + upload = uploads[ workflow_test.upload_name( input_dataset_label ) ] + except KeyError: + raise AssertionError( "Failed to find upload with label %s in uploaded datasets %s" % ( input_dataset_label, uploads ) ) + + ds_map[ step_id_map[ step_index ] ] = upload + + payload = { + "history": "hist_id=%s" % test_history, + "ds_map": dumps( ds_map ), + "workflow_id": workflow_id, + } + run_response = galaxy_interactor.run_workflow( payload ).json() + + outputs = run_response[ 'outputs' ] + if not len( outputs ) == len( output_defs ): + msg_template = "Number of outputs [%d] created by workflow execution does not equal expected number from input file [%d]." + msg = msg_template % ( len( outputs ), len( output_defs ) ) + raise AssertionError( msg ) + + galaxy_interactor.wait_for_ids( test_history, outputs ) + + for expected_output_def in workflow_test.outputs: + # Get the correct hid + name, outfile, attributes = expected_output_def + + output_data = outputs[ int( name ) ] + try: + galaxy_interactor.verify_output( test_history, output_data, outfile, attributes=attributes, shed_tool_id=None, maxseconds=maxseconds ) + except Exception: + for stream in ['stdout', 'stderr']: + stream_output = galaxy_interactor.get_job_stream( test_history, output_data, stream=stream ) + print >>sys.stderr, self._format_stream( stream_output, stream=stream, format=True ) + raise + + def __import_workflow( self, galaxy_interactor, workflow ): + """ + Import workflow into Galaxy and return id and mapping of step ids. + """ + workflow_info = galaxy_interactor.import_workflow( workflow ).json() + try: + workflow_id = workflow_info[ 'id' ] + except KeyError: + raise AssertionError( "Failed to find id for workflow import response %s" % workflow_info ) + + # Well ideally the local copy of the workflow would have the same step ids + # as the one imported through the API, but API workflow imports are 1-indexed + # and GUI exports 0-indexed as of mid-november 2013. + + imported_workflow = galaxy_interactor.read_workflow( workflow_id ) + #log.info("local %s\nimported%s" % (workflow, imported_workflow)) + step_id_map = {} + local_steps_ids = sorted( [ int( step_id ) for step_id in workflow[ 'steps' ].keys() ] ) + imported_steps_ids = sorted( [ int( step_id ) for step_id in imported_workflow[ 'steps' ].keys() ] ) + for local_step_id, imported_step_id in zip( local_steps_ids, imported_steps_ids ): + step_id_map[ local_step_id ] = imported_step_id + + output_defs = [] + for local_step_id in local_steps_ids: + step_def = workflow['steps'][ str( local_step_id ) ] + output_defs.extend( step_def.get( "outputs", [] ) ) + + return workflow_id, step_id_map, output_defs + + +def parse_test_file( workflow_test_file ): + tree = parse_xml( workflow_test_file ) + root = tree.getroot() + input_elems = root.findall( "input" ) + required_files = [] + dataset_dict = {} + for input_elem in input_elems: + name, value, attrib = parse_param_elem( input_elem ) + require_file( name, value, attrib, required_files ) + dataset_dict[ name ] = value + + outputs = parse_output_elems( root ) + + workflow_file_rel_path = root.get( 'file' ) + if not workflow_file_rel_path: + raise Exception( "Workflow test XML must declare file attribute pointing to workflow under test." ) + + # TODO: Normalize this path, prevent it from accessing arbitrary files on system. + worfklow_file_abs_path = os.path.join( os.path.dirname( workflow_test_file ), workflow_file_rel_path ) + + return WorkflowTest( + dataset_dict, + required_files, + worfklow_file_abs_path, + outputs=outputs, + ) + + +class WorkflowTest( object ): + + def __init__( self, dataset_dict, required_files, workflow_file, outputs ): + self.dataset_dict = dataset_dict + self.required_files = required_files + self.workflow = load( open( workflow_file, "r" ) ) + self.outputs = outputs + + def test_data( self ): + return test_data_iter( self.required_files ) + + def upload_name( self, input_dataset_label ): + return self.dataset_dict[ input_dataset_label ] + + def input_datasets( self ): + steps = self.workflow[ "steps" ] + log.info("in input_datasets with steps %s" % steps) + for step_index, step_dict in steps.iteritems(): + if step_dict.get( "name", None ) == "Input dataset": + yield int( step_index ), step_dict[ "inputs" ][0][ "name" ] + + +class GalaxyWorkflowInteractor(GalaxyInteractorApi): + + def __init__( self, twill_test_case ): + super(GalaxyWorkflowInteractor, self).__init__( twill_test_case ) + + def import_workflow( self, workflow_rep ): + payload = { "workflow": dumps( workflow_rep ) } + return self._post( "workflows/upload", data=payload ) + + def run_workflow( self, data ): + return self._post( "workflows", data=data ) + + def read_workflow( self, id ): + return self._get( "workflows/%s" % id ).json() + + def wait_for_ids( self, history_id, ids ): + self.twill_test_case.wait_for( lambda: not all( [ self.__dataset_ready( history_id, id ) for id in ids ] ), maxseconds=120 ) + + def __dataset_ready( self, history_id, id ): + contents = self._get( 'histories/%s/contents' % history_id ).json() + for content in contents: + + if content["id"] == id: + state = content[ 'state' ] + state_ready = self._state_ready( state, error_msg="Dataset creation failed for dataset with name %s." % content[ 'name' ] ) + return state_ready + return False https://bitbucket.org/galaxy/galaxy-central/commits/c7986c31fd74/ Changeset: c7986c31fd74 User: jmchilton Date: 2014-01-12 05:40:18 Summary: More work on eliminating references to test_db_util.sa_session. ... tweaked styling of several functional tests (the non-toolbox,datamanager,workflow,api functional tests) along the way - mostly PEP-8 fixes and eliminating * imports. Did not modify tests which do not pass - but did not in the source where they fail inside a TODO. Affected #: 14 files diff -r 494b51bda9c1a319672e92cce4ec17386cd65390 -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a test/base/test_db_util.py --- a/test/base/test_db_util.py +++ b/test/base/test_db_util.py @@ -1,153 +1,223 @@ import galaxy.model from galaxy.model.orm import * -from functional.database_contexts import galaxy_context as sa_session +from functional import database_contexts +# Deprecated - import database_contexts and use galaxy_context +sa_session = database_contexts.galaxy_context from base.twilltestcase import * -import sys + + +def gx_context(): + return database_contexts.galaxy_context + def delete_obj( obj ): - sa_session.delete( obj ) - sa_session.flush() + gx_context().delete( obj ) + gx_context().flush() + + def delete_request_type_permissions( id ): - rtps = sa_session.query( galaxy.model.RequestTypePermissions ) \ - .filter( and_( galaxy.model.RequestTypePermissions.table.c.request_type_id==id ) ) \ + rtps = gx_context().query( galaxy.model.RequestTypePermissions ) \ + .filter( and_( galaxy.model.RequestTypePermissions.table.c.request_type_id == id ) ) \ .order_by( desc( galaxy.model.RequestTypePermissions.table.c.create_time ) ) for rtp in rtps: - sa_session.delete( rtp ) - sa_session.flush() + gx_context().delete( rtp ) + gx_context().flush() + + def delete_user_roles( user ): for ura in user.roles: - sa_session.delete( ura ) - sa_session.flush() + gx_context().delete( ura ) + gx_context().flush() + + def flush( obj ): - sa_session.add( obj ) - sa_session.flush() + gx_context().add( obj ) + gx_context().flush() + + def get_all_histories_for_user( user ): - return sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.user_id==user.id, - galaxy.model.History.table.c.deleted==False ) ) \ + return gx_context().query( galaxy.model.History ) \ + .filter( and_( galaxy.model.History.table.c.user_id == user.id, + galaxy.model.History.table.c.deleted == False ) ) \ .all() + + def get_dataset_permissions_by_dataset( dataset ): - return sa_session.query( galaxy.model.DatasetPermissions ) \ - .filter( galaxy.model.DatasetPermissions.table.c.dataset_id==dataset.id ) \ + return gx_context().query( galaxy.model.DatasetPermissions ) \ + .filter( galaxy.model.DatasetPermissions.table.c.dataset_id == dataset.id ) \ .all() + + def get_dataset_permissions_by_role( role ): - return sa_session.query( galaxy.model.DatasetPermissions ) \ + return gx_context().query( galaxy.model.DatasetPermissions ) \ .filter( galaxy.model.DatasetPermissions.table.c.role_id == role.id ) \ .first() + + def get_default_history_permissions_by_history( history ): - return sa_session.query( galaxy.model.DefaultHistoryPermissions ) \ - .filter( galaxy.model.DefaultHistoryPermissions.table.c.history_id==history.id ) \ + return gx_context().query( galaxy.model.DefaultHistoryPermissions ) \ + .filter( galaxy.model.DefaultHistoryPermissions.table.c.history_id == history.id ) \ .all() + + def get_default_history_permissions_by_role( role ): - return sa_session.query( galaxy.model.DefaultHistoryPermissions ) \ + return gx_context().query( galaxy.model.DefaultHistoryPermissions ) \ .filter( galaxy.model.DefaultHistoryPermissions.table.c.role_id == role.id ) \ .all() + + def get_default_user_permissions_by_role( role ): - return sa_session.query( galaxy.model.DefaultUserPermissions ) \ + return gx_context().query( galaxy.model.DefaultUserPermissions ) \ .filter( galaxy.model.DefaultUserPermissions.table.c.role_id == role.id ) \ .all() + + def get_default_user_permissions_by_user( user ): - return sa_session.query( galaxy.model.DefaultUserPermissions ) \ - .filter( galaxy.model.DefaultUserPermissions.table.c.user_id==user.id ) \ + return gx_context().query( galaxy.model.DefaultUserPermissions ) \ + .filter( galaxy.model.DefaultUserPermissions.table.c.user_id == user.id ) \ .all() + + def get_form( name ): - fdc_list = sa_session.query( galaxy.model.FormDefinitionCurrent ) \ + fdc_list = gx_context().query( galaxy.model.FormDefinitionCurrent ) \ .filter( galaxy.model.FormDefinitionCurrent.table.c.deleted == False ) \ .order_by( galaxy.model.FormDefinitionCurrent.table.c.create_time.desc() ) for fdc in fdc_list: - sa_session.refresh( fdc ) - sa_session.refresh( fdc.latest_form ) + gx_context().refresh( fdc ) + gx_context().refresh( fdc.latest_form ) if fdc.latest_form.name == name: return fdc.latest_form return None + + def get_folder( parent_id, name, description ): - return sa_session.query( galaxy.model.LibraryFolder ) \ - .filter( and_( galaxy.model.LibraryFolder.table.c.parent_id==parent_id, - galaxy.model.LibraryFolder.table.c.name==name, - galaxy.model.LibraryFolder.table.c.description==description ) ) \ + return gx_context().query( galaxy.model.LibraryFolder ) \ + .filter( and_( galaxy.model.LibraryFolder.table.c.parent_id == parent_id, + galaxy.model.LibraryFolder.table.c.name == name, + galaxy.model.LibraryFolder.table.c.description == description ) ) \ .first() + + def get_group_by_name( name ): - return sa_session.query( galaxy.model.Group ).filter( galaxy.model.Group.table.c.name==name ).first() + return gx_context().query( galaxy.model.Group ).filter( galaxy.model.Group.table.c.name == name ).first() + + def get_group_role_associations_by_group( group ): - return sa_session.query( galaxy.model.GroupRoleAssociation ) \ + return gx_context().query( galaxy.model.GroupRoleAssociation ) \ .filter( galaxy.model.GroupRoleAssociation.table.c.group_id == group.id ) \ .all() + + def get_group_role_associations_by_role( role ): - return sa_session.query( galaxy.model.GroupRoleAssociation ) \ + return gx_context().query( galaxy.model.GroupRoleAssociation ) \ .filter( galaxy.model.GroupRoleAssociation.table.c.role_id == role.id ) \ .all() + + def get_latest_dataset(): - return sa_session.query( galaxy.model.Dataset ) \ + return gx_context().query( galaxy.model.Dataset ) \ .order_by( desc( galaxy.model.Dataset.table.c.create_time ) ) \ .first() + + def get_latest_hda(): - return sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ + return gx_context().query( galaxy.model.HistoryDatasetAssociation ) \ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ .first() + + def get_latest_history_for_user( user ): - return sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==user.id ) ) \ + return gx_context().query( galaxy.model.History ) \ + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == user.id ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() + + def get_latest_ldda_by_name( name ): - return sa_session.query( galaxy.model.LibraryDatasetDatasetAssociation ) \ - .filter( and_( galaxy.model.LibraryDatasetDatasetAssociation.table.c.name==name, + return gx_context().query( galaxy.model.LibraryDatasetDatasetAssociation ) \ + .filter( and_( galaxy.model.LibraryDatasetDatasetAssociation.table.c.name == name, galaxy.model.LibraryDatasetDatasetAssociation.table.c.deleted == False ) ) \ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ) \ .first() + + def get_latest_lddas( limit ): - return sa_session.query( galaxy.model.LibraryDatasetDatasetAssociation ) \ + return gx_context().query( galaxy.model.LibraryDatasetDatasetAssociation ) \ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.update_time ) ) \ .limit( limit ) + + def get_library( name, description, synopsis ): - return sa_session.query( galaxy.model.Library ) \ - .filter( and_( galaxy.model.Library.table.c.name==name, - galaxy.model.Library.table.c.description==description, - galaxy.model.Library.table.c.synopsis==synopsis, - galaxy.model.Library.table.c.deleted==False ) ) \ + return gx_context().query( galaxy.model.Library ) \ + .filter( and_( galaxy.model.Library.table.c.name == name, + galaxy.model.Library.table.c.description == description, + galaxy.model.Library.table.c.synopsis == synopsis, + galaxy.model.Library.table.c.deleted == False ) ) \ .first() + + def get_private_role( user ): for role in user.all_roles(): if role.name == user.email and role.description == 'Private Role for %s' % user.email: return role raise AssertionError( "Private role not found for user '%s'" % user.email ) + + def get_request_by_name( name ): - return sa_session.query( galaxy.model.Request ) \ - .filter( and_( galaxy.model.Request.table.c.name==name, - galaxy.model.Request.table.c.deleted==False ) ) \ - .first() + return gx_context().query( galaxy.model.Request ) \ + .filter( and_( galaxy.model.Request.table.c.name == name, + galaxy.model.Request.table.c.deleted == False ) ) \ + .first() + + def get_request_type_by_name( name ): - return sa_session.query( galaxy.model.RequestType ) \ - .filter( and_( galaxy.model.RequestType.table.c.name==name ) ) \ + return gx_context().query( galaxy.model.RequestType ) \ + .filter( and_( galaxy.model.RequestType.table.c.name == name ) ) \ .order_by( desc( galaxy.model.RequestType.table.c.create_time ) ) \ .first() + + def get_role_by_name( name ): - return sa_session.query( galaxy.model.Role ).filter( galaxy.model.Role.table.c.name==name ).first() + return gx_context().query( galaxy.model.Role ).filter( galaxy.model.Role.table.c.name == name ).first() + + def get_user( email ): - return sa_session.query( galaxy.model.User ) \ - .filter( galaxy.model.User.table.c.email==email ) \ + return gx_context().query( galaxy.model.User ) \ + .filter( galaxy.model.User.table.c.email == email ) \ .first() + + def get_user_address( user, short_desc ): - return sa_session.query( galaxy.model.UserAddress ) \ - .filter( and_( galaxy.model.UserAddress.table.c.user_id==user.id, - galaxy.model.UserAddress.table.c.desc==short_desc, - galaxy.model.UserAddress.table.c.deleted==False ) ) \ + return gx_context().query( galaxy.model.UserAddress ) \ + .filter( and_( galaxy.model.UserAddress.table.c.user_id == user.id, + galaxy.model.UserAddress.table.c.desc == short_desc, + galaxy.model.UserAddress.table.c.deleted == False ) ) \ .order_by( desc( galaxy.model.UserAddress.table.c.create_time ) ) \ - .first() + .first() + + def get_user_group_associations_by_group( group ): - return sa_session.query( galaxy.model.UserGroupAssociation ) \ + return gx_context().query( galaxy.model.UserGroupAssociation ) \ .filter( galaxy.model.UserGroupAssociation.table.c.group_id == group.id ) \ .all() + + def get_user_info_form_definition(): return galaxy.model.FormDefinition.types.USER_INFO + + def get_user_role_associations_by_role( role ): - return sa_session.query( galaxy.model.UserRoleAssociation ) \ + return gx_context().query( galaxy.model.UserRoleAssociation ) \ .filter( galaxy.model.UserRoleAssociation.table.c.role_id == role.id ) \ .all() + + def mark_obj_deleted( obj ): obj.deleted = True - sa_session.add( obj ) - sa_session.flush() + gx_context().add( obj ) + gx_context().flush() + + def refresh( obj ): - sa_session.refresh( obj ) + gx_context().refresh( obj ) diff -r 494b51bda9c1a319672e92cce4ec17386cd65390 -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a test/functional/test_DNAse_flanked_genes.py --- a/test/functional/test_DNAse_flanked_genes.py +++ b/test/functional/test_DNAse_flanked_genes.py @@ -1,21 +1,24 @@ import galaxy.model from galaxy.model.orm import * -from base.test_db_util import sa_session +import database_contexts from base.twilltestcase import TwillTestCase """ A sample analysis""" + class AnalysisDNAseHSSFlankedGenes( TwillTestCase ): + def test_get_DNAseHSS_flanked_genes( self ): + sa_session = database_contexts.galaxy_context self.logout() self.login( email='test(a)bx.psu.edu' ) admin_user = sa_session.query( galaxy.model.User ) \ - .filter( galaxy.model.User.table.c.email=='test(a)bx.psu.edu' ) \ + .filter( galaxy.model.User.table.c.email == 'test(a)bx.psu.edu' ) \ .one() self.new_history( name='DNAseHSS_flanked_genes' ) history1 = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==admin_user.id ) ) \ + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == admin_user.id ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() track_params = dict( diff -r 494b51bda9c1a319672e92cce4ec17386cd65390 -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a test/functional/test_admin_features.py --- a/test/functional/test_admin_features.py +++ b/test/functional/test_admin_features.py @@ -1,5 +1,32 @@ -from base.twilltestcase import * -from base.test_db_util import * +from base.twilltestcase import TwillTestCase +from functional import database_contexts +import galaxy.model +from base.test_db_util import ( + get_user, + get_private_role, + get_all_histories_for_user, + get_latest_history_for_user, + get_default_history_permissions_by_history, + get_latest_dataset, + refresh, + flush, + get_group_by_name, + get_role_by_name, + get_user_group_associations_by_group, + get_default_history_permissions_by_role, + get_default_user_permissions_by_role, + get_user_role_associations_by_role, + get_group_role_associations_by_group, + get_dataset_permissions_by_role, + get_group_role_associations_by_role, +) + + +# Globals setup by these tests. +regular_user1 = regular_user2 = regular_user3 = admin_user = None +role_one = role_two = role_three = None +group_zero = group_one = group_two = None + class TestDataSecurity( TwillTestCase ): def test_000_initiate_users( self ): @@ -19,6 +46,7 @@ global admin_user admin_user = get_user( 'test(a)bx.psu.edu' ) assert admin_user is not None, 'Problem retrieving user with email "test(a)bx.psu.edu" from the database' + def test_005_create_new_user_account_as_admin( self ): """Testing creating a new user account as admin""" # Logged in as admin_user @@ -31,8 +59,9 @@ username='admin-user', redirect='' ) if not username_taken: - raise AssertionError, "The public name (%s) is already being used by another user, but no error was displayed" \ - % 'admin-user' + error_msg = "The public name (%s) is already being used by another user, but no error was displayed" % 'admin-user' + raise AssertionError( error_msg ) + # Test setting the user name to an invalid one. Note that the account must not exist in order # for this test to work as desired, so the email we're passing is important... previously_created, username_taken, invalid_username = self.create_new_account_as_admin( email='diff(a)you.com', @@ -40,7 +69,7 @@ username='h', redirect='' ) if not invalid_username: - raise AssertionError, "The public name (%s) is is invalid, but no error was displayed" % username + raise AssertionError( "The public name (%s) is is invalid, but no error was displayed" % 'diff(a)you.com' ) previously_created, username_taken, invalid_username = self.create_new_account_as_admin( email=email, password=password, username='regular-user3', @@ -61,7 +90,7 @@ raise AssertionError( '%d UserRoleAssociations were created for user %s when the admin created the account ( should have been 1 )' \ % ( len( regular_user3.roles ), regular_user3.email ) ) for ura in regular_user3.roles: - role = sa_session.query( galaxy.model.Role ).get( ura.role_id ) + role = database_contexts.galaxy_context.query( galaxy.model.Role ).get( ura.role_id ) if not previously_created and role.type != 'private': raise AssertionError( 'Role created for user %s when the admin created the account is not private, type is' \ % str( role.type ) ) @@ -73,9 +102,11 @@ # Make sure the user was not associated with any groups if regular_user3.groups: raise AssertionError( 'Groups were incorrectly associated with user %s when the admin created the account' % email ) + def test_010_reset_password_as_admin( self ): """Testing reseting a user password as admin""" self.reset_password_as_admin( user_id=self.security.encode_id( regular_user3.id ), password='testreset' ) + def test_015_login_after_password_reset( self ): """Testing logging in after an admin reset a password - tests DefaultHistoryPermissions for accounts created by an admin""" # logged in as admin_user @@ -84,7 +115,7 @@ # Make sure a History and HistoryDefaultPermissions exist for the user latest_history = get_latest_history_for_user( regular_user3 ) if not latest_history.user_id == regular_user3.id: - raise AssertionError( 'A history was not created for user %s when he logged in' % email ) + raise AssertionError( 'A history was not created for user %s when he logged in' % regular_user3.email ) if not latest_history.default_permissions: raise AssertionError( 'No DefaultHistoryPermissions were created for history id %d when it was created' % latest_history.id ) dhps = get_default_history_permissions_by_history( latest_history ) @@ -102,22 +133,25 @@ if dp.action != galaxy.model.Dataset.permitted_actions.DATASET_MANAGE_PERMISSIONS.action: raise AssertionError( 'The DatasetPermissions for dataset id %d is %s ( should have been %s )' \ % ( latest_dataset.id, - latest_dataset.actions.action, + latest_dataset.actions.action, galaxy.model.Dataset.permitted_actions.DATASET_MANAGE_PERMISSIONS.action ) ) self.logout() # Reset the password to the default for later tests self.login( email='test(a)bx.psu.edu' ) self.reset_password_as_admin( user_id=self.security.encode_id( regular_user3.id ), password='testuser' ) + def test_020_mark_user_deleted( self ): """Testing marking a user account as deleted""" # Logged in as admin_user self.mark_user_deleted( user_id=self.security.encode_id( regular_user3.id ), email=regular_user3.email ) if not regular_user3.active_histories: raise AssertionError( 'HistoryDatasetAssociations for regular_user3 were incorrectly deleted when the user was marked deleted' ) + def test_025_undelete_user( self ): """Testing undeleting a user account""" # Logged in as admin_user self.undelete_user( user_id=self.security.encode_id( regular_user3.id ), email=regular_user3.email ) + def test_030_create_role( self ): """Testing creating new role with 3 members ( and a new group named the same ), then renaming the role""" # Logged in as admin_user @@ -137,7 +171,7 @@ "One of the groups associated with this role is the newly created group with the same name." ] ) # Get the role object for later tests global role_one - role_one = sa_session.query( galaxy.model.Role ).filter( galaxy.model.Role.table.c.name==name ).first() + role_one = database_contexts.galaxy_context.query( galaxy.model.Role ).filter( galaxy.model.Role.table.c.name == name ).first() assert role_one is not None, 'Problem retrieving role named "Role One" from the database' # Make sure UserRoleAssociations are correct if len( role_one.users ) != len( in_user_ids ): @@ -156,13 +190,14 @@ group_zero = get_group_by_name( name ) # Rename the role rename = "Role One's been Renamed" - new_description="This is Role One's Re-described" + new_description = "This is Role One's Re-described" self.rename_role( self.security.encode_id( role_one.id ), name=rename, description=new_description ) self.visit_url( '%s/admin/roles' % self.url ) self.check_page_for_string( rename ) self.check_page_for_string( new_description ) # Reset the role back to the original name and description self.rename_role( self.security.encode_id( role_one.id ), name=name, description=description ) + def test_035_create_group( self ): """Testing creating new group with 3 members and 2 associated roles, then renaming it""" # Logged in as admin_user @@ -202,6 +237,7 @@ self.check_page_for_string( rename ) # Reset the group back to the original name self.rename_group( self.security.encode_id( group_one.id ), name=name ) + def test_040_add_members_and_role_to_group( self ): """Testing editing user membership and role associations of an existing group""" # Logged in as admin_user @@ -224,6 +260,7 @@ group_two.name, user_ids=user_ids, role_ids=role_ids ) + def test_045_create_role_with_user_and_group_associations( self ): """Testing creating a role with user and group associations""" # Logged in as admin_user @@ -233,9 +270,9 @@ # associate_users_and_groups_with_role() method. name = 'Role Two' description = 'This is Role Two' - user_ids=[ str( admin_user.id ) ] - group_ids=[ str( group_two.id ) ] - private_role=admin_user.email + user_ids = [ str( admin_user.id ) ] + group_ids = [ str( group_two.id ) ] + private_role = admin_user.email # Create the role self.create_role( name=name, description=description, @@ -263,15 +300,16 @@ refresh( group_two ) if len( group_two.roles ) != 2: raise AssertionError( '%d GroupRoleAssociations are associated with group id %d ( should be 2 )' % ( len( group_two.roles ), group_two.id ) ) + def test_050_change_user_role_associations( self ): """Testing changing roles associated with a user""" # Logged in as admin_user # Create a new role with no associations name = 'Role Three' description = 'This is Role Three' - user_ids=[] - group_ids=[] - private_role=admin_user.email + user_ids = [] + group_ids = [] + private_role = admin_user.email self.create_role( name=name, description=description, in_user_ids=user_ids, @@ -301,6 +339,7 @@ if len( admin_user.roles ) != 4: raise AssertionError( '%d UserRoleAssociations are associated with %s ( should be 4 )' % \ ( len( admin_user.roles ), admin_user.email ) ) + def test_055_mark_group_deleted( self ): """Testing marking a group as deleted""" # Logged in as admin_user @@ -314,6 +353,7 @@ raise AssertionError( '%s incorrectly lost all members when it was marked as deleted.' % group_two.name ) if not group_two.roles: raise AssertionError( '%s incorrectly lost all role associations when it was marked as deleted.' % group_two.name ) + def test_060_undelete_group( self ): """Testing undeleting a deleted group""" # Logged in as admin_user @@ -321,6 +361,7 @@ refresh( group_two ) if group_two.deleted: raise AssertionError( '%s was not correctly marked as not deleted.' % group_two.name ) + def test_065_mark_role_deleted( self ): """Testing marking a role as deleted""" # Logged in as admin_user @@ -335,10 +376,12 @@ raise AssertionError( '%s incorrectly lost all user associations when it was marked as deleted.' % role_two.name ) if not role_two.groups: raise AssertionError( '%s incorrectly lost all group associations when it was marked as deleted.' % role_two.name ) + def test_070_undelete_role( self ): """Testing undeleting a deleted role""" # Logged in as admin_user self.undelete_role( self.security.encode_id( role_two.id ), role_two.name ) + def test_075_purge_user( self ): """Testing purging a user account""" # Logged in as admin_user @@ -352,26 +395,27 @@ if len( regular_user3.default_permissions ) != 1: raise AssertionError( 'DefaultUserPermissions for user %s were not deleted.' % regular_user3.email ) for dup in regular_user3.default_permissions: - role = sa_session.query( galaxy.model.Role ).get( dup.role_id ) + role = database_contexts.galaxy_context.query( galaxy.model.Role ).get( dup.role_id ) if role.type != 'private': raise AssertionError( 'DefaultUserPermissions for user %s are not related with the private role.' % regular_user3.email ) # Make sure History deleted for history in regular_user3.histories: refresh( history ) if not history.deleted: - raise AssertionError( 'User %s has active history id %d after their account was marked as purged.' % ( regular_user3.email, hda.id ) ) + raise AssertionError( 'User %s has active history id %d after their account was marked as purged.' % ( regular_user3.email, history.id ) ) # NOTE: Not all hdas / datasets will be deleted at the time a history is deleted - the cleanup_datasets.py script # is responsible for this. # Make sure UserGroupAssociations deleted if regular_user3.groups: - raise AssertionError( 'User %s has active group id %d after their account was marked as purged.' % ( regular_user3.email, uga.id ) ) + raise AssertionError( 'User %s has active group after their account was marked as purged.' % ( regular_user3.email ) ) # Make sure UserRoleAssociations deleted EXCEPT FOR THE PRIVATE ROLE if len( regular_user3.roles ) != 1: raise AssertionError( 'UserRoleAssociations for user %s were not deleted.' % regular_user3.email ) for ura in regular_user3.roles: - role = sa_session.query( galaxy.model.Role ).get( ura.role_id ) + role = database_contexts.galaxy_context.query( galaxy.model.Role ).get( ura.role_id ) if role.type != 'private': raise AssertionError( 'UserRoleAssociations for user %s are not related with the private role.' % regular_user3.email ) + def test_080_manually_unpurge_user( self ): """Testing manually un-purging a user account""" # Logged in as admin_user @@ -381,6 +425,7 @@ regular_user3.purged = False regular_user3.deleted = False flush( regular_user3 ) + def test_085_purge_group( self ): """Testing purging a group""" # Logged in as admin_user @@ -394,6 +439,7 @@ raise AssertionError( "Purging the group did not delete the GroupRoleAssociations for group_id '%s'" % group_two.id ) # Undelete the group for later test runs self.undelete_group( self.security.encode_id( group_two.id ), group_two.name ) + def test_090_purge_role( self ): """Testing purging a role""" # Logged in as admin_user @@ -414,6 +460,7 @@ # Make sure there are no DatasetPermissionss if get_dataset_permissions_by_role( role_two ): raise AssertionError( "Purging the role did not delete the DatasetPermissionss for role_id '%s'" % role_two.id ) + def test_095_manually_unpurge_role( self ): """Testing manually un-purging a role""" # Logged in as admin_user @@ -422,6 +469,7 @@ role_two.purged = False flush( role_two ) self.undelete_role( self.security.encode_id( role_two.id ), role_two.name ) + def test_999_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to pass""" # Logged in as admin_user @@ -433,8 +481,8 @@ self.purge_role( self.security.encode_id( role.id ), role.name ) # Manually delete the role from the database refresh( role ) - sa_session.delete( role ) - sa_session.flush() + database_contexts.galaxy_context.delete( role ) + database_contexts.galaxy_context.flush() ################## # Eliminate all groups ################## @@ -443,8 +491,8 @@ self.purge_group( self.security.encode_id( group.id ), group.name ) # Manually delete the group from the database refresh( group ) - sa_session.delete( group ) - sa_session.flush() + database_contexts.galaxy_context.delete( group ) + database_contexts.galaxy_context.flush() ################## # Make sure all users are associated only with their private roles ################## diff -r 494b51bda9c1a319672e92cce4ec17386cd65390 -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a test/functional/test_data_security.py --- a/test/functional/test_data_security.py +++ b/test/functional/test_data_security.py @@ -1,7 +1,24 @@ -from base.twilltestcase import * -from base.test_db_util import * +import galaxy.model +from base.twilltestcase import TwillTestCase +from base.test_db_util import ( + get_user, + get_private_role, + get_latest_history_for_user, + get_default_history_permissions_by_history, + get_latest_dataset, + refresh, + get_default_user_permissions_by_user, + get_dataset_permissions_by_dataset, +) + +regular_user1 = regular_user2 = regular_user3 = None +admin_user = None +admin_user_private_role = regular_user1_private_role = None +regular_user2_private_role = None + class TestDataSecurity( TwillTestCase ): + def test_000_initiate_users( self ): """Ensuring all required user accounts exist""" self.logout() @@ -32,6 +49,7 @@ assert admin_user is not None, 'Problem retrieving user with email "test(a)bx.psu.edu" from the database' global admin_user_private_role admin_user_private_role = get_private_role( admin_user ) + def test_005_default_permissions( self ): """Testing initial settings for DefaultUserPermissions and DefaultHistoryPermissions""" # Logged in as admin_user @@ -59,7 +77,8 @@ # Try deleting the admin_user's private role self.manage_roles_and_groups_for_user( self.security.encode_id( admin_user.id ), out_role_ids=str( admin_user_private_role.id ), - strings_displayed = [ "You cannot eliminate a user's private role association." ] ) + strings_displayed=[ "You cannot eliminate a user's private role association." ] ) + def test_010_private_role_creation_and_default_history_permissions( self ): """Testing private role creation and changing DefaultHistoryPermissions for new histories""" # Logged in as admin_user @@ -127,6 +146,7 @@ if dps != dhps: raise AssertionError( 'DatasetPermissions "%s" for dataset id %d differ from DefaultHistoryPermissions "%s" for history id %d' \ % ( str( dps ), latest_dataset.id, str( dhps ), latest_history.id ) ) + def test_015_change_default_permissions_for_current_history( self ): """Testing changing DefaultHistoryPermissions for the current history""" # logged in a regular_user1 @@ -139,7 +159,6 @@ # Make sure these are in sorted order for later comparison actions_in = [ 'manage permissions' ] permissions_out = [ 'DATASET_ACCESS' ] - actions_out = [ 'access' ] # Change DefaultHistoryPermissions for the current history self.history_set_default_permissions( permissions_out=permissions_out, permissions_in=permissions_in, role_id=str( regular_user2_private_role.id ) ) if len( latest_history.default_permissions ) != len( actions_in ): @@ -168,6 +187,7 @@ if dps != dhps: raise AssertionError( 'DatasetPermissionss "%s" for dataset id %d differ from DefaultHistoryPermissions "%s"' \ % ( str( dps ), latest_dataset.id, str( dhps ) ) ) + def test_999_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to pass""" # Logged in as regular_user2 diff -r 494b51bda9c1a319672e92cce4ec17386cd65390 -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a test/functional/test_dataset_features.py --- a/test/functional/test_dataset_features.py +++ b/test/functional/test_dataset_features.py @@ -3,7 +3,7 @@ class TestDatasetFeatures( TwillTestCase ): - + def test_0000_initiate_users( self ): """Ensuring all required user accounts exist""" self.logout() @@ -18,18 +18,18 @@ self.new_history() latest_history = test_db_util.get_latest_history_for_user( admin_user ) assert latest_history is not None, "Problem retrieving latest_history from database" - + def test_0005_initiate_data( self ): '''Ensure that data exists for this test suite.''' self.upload_file( '1.bed' ) - + def test_0010_view_dataset_params( self ): '''Test viewing a dataset's parameters.''' hda = self.find_hda_by_dataset_name( '1.bed' ) assert hda is not None, 'Could not retrieve latest hda from history API.' self.visit_url( '/datasets/%s/show_params' % hda[ 'id'] ) self.check_for_strings( strings_displayed=[ '1.bed', 'uploaded' ] ) - + def test_0015_report_dataset_error( self ): '''Load and submit the report error form. This should show an error message, as the functional test instance should not be configured for email.''' hda = test_db_util.get_latest_hda() diff -r 494b51bda9c1a319672e92cce4ec17386cd65390 -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a test/functional/test_get_data.py --- a/test/functional/test_get_data.py +++ b/test/functional/test_get_data.py @@ -1,7 +1,12 @@ -import galaxy.model -from galaxy.model.orm import * from base.twilltestcase import TwillTestCase -from base.test_db_util import * +from base.test_db_util import ( + get_user, + get_latest_history_for_user, + get_latest_hda, +) + +admin_user = None + class UploadData( TwillTestCase ): @@ -25,7 +30,7 @@ self.is_history_empty() return get_latest_history_for_user( user ) - def test_0005_upload_file( self ): + def test_0005_upload_file( self ): """ Test uploading 1.bed, NOT setting the file format """ @@ -39,13 +44,13 @@ self.delete_history( id=self.security.encode_id( history.id ) ) - def test_0006_upload_file( self ): + def test_0006_upload_file( self ): """ Test uploading 1.bed.spaces, with space to tab selected, NOT setting the file format """ history = self.create_fresh_history( admin_user ) - self.upload_file( '1.bed.spaces', space_to_tab = True ) + self.upload_file( '1.bed.spaces', space_to_tab=True ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" self.verify_dataset_correctness( '1.bed', hid=str( hda.hid ) ) @@ -209,13 +214,13 @@ history = self.create_fresh_history( admin_user ) # lped data types include a ped_file and a map_file ( which is binary ) - self.upload_file( None, ftype='lped', metadata = [ { 'name':'base_name', 'value':'rgenetics' } ], composite_data = [ { 'name':'ped_file', 'value':'tinywga.ped' }, { 'name':'map_file', 'value':'tinywga.map'} ] ) + self.upload_file( None, ftype='lped', metadata=[ { 'name':'base_name', 'value':'rgenetics' } ], composite_data=[ { 'name':'ped_file', 'value':'tinywga.ped' }, { 'name':'map_file', 'value':'tinywga.map'} ] ) # Get the latest hid for testing hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" # We'll test against the resulting ped file and map file for correctness - self.verify_composite_datatype_file_content( 'tinywga.ped', str( hda.id ), base_name = 'rgenetics.ped' ) - self.verify_composite_datatype_file_content( 'tinywga.map', str( hda.id ), base_name = 'rgenetics.map' ) + self.verify_composite_datatype_file_content( 'tinywga.ped', str( hda.id ), base_name='rgenetics.ped' ) + self.verify_composite_datatype_file_content( 'tinywga.map', str( hda.id ), base_name='rgenetics.map' ) self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "metadata_base_name", "rgenetics", use_string_contains=True ) @@ -229,13 +234,13 @@ history = self.create_fresh_history( admin_user ) # lped data types include a ped_file and a map_file ( which is binary ) - self.upload_file( None, ftype='lped', metadata = [ { 'name':'base_name', 'value':'rgenetics' } ], composite_data = [ { 'name':'ped_file', 'value':'tinywga.ped', 'space_to_tab':True }, { 'name':'map_file', 'value':'tinywga.map'} ] ) + self.upload_file( None, ftype='lped', metadata=[ { 'name':'base_name', 'value':'rgenetics' } ], composite_data=[ { 'name':'ped_file', 'value':'tinywga.ped', 'space_to_tab':True }, { 'name':'map_file', 'value':'tinywga.map'} ] ) # Get the latest hid for testing hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" # We'll test against the resulting ped file and map file for correctness - self.verify_composite_datatype_file_content( 'tinywga.ped.space_to_tab', str( hda.id ), base_name = 'rgenetics.ped' ) - self.verify_composite_datatype_file_content( 'tinywga.map', str( hda.id ), base_name = 'rgenetics.map' ) + self.verify_composite_datatype_file_content( 'tinywga.ped.space_to_tab', str( hda.id ), base_name='rgenetics.ped' ) + self.verify_composite_datatype_file_content( 'tinywga.map', str( hda.id ), base_name='rgenetics.map' ) self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "metadata_base_name", "rgenetics", use_string_contains=True ) @@ -250,8 +255,8 @@ # pbed data types include a bim_file, a bed_file and a fam_file self.upload_file( None, ftype='pbed', - metadata = [ { 'name':'base_name', 'value':'rgenetics' } ], - composite_data = [ + metadata=[ { 'name':'base_name', 'value':'rgenetics' } ], + composite_data=[ { 'name':'bim_file', 'value':'tinywga.bim' }, { 'name':'bed_file', 'value':'tinywga.bed' }, { 'name':'fam_file', 'value':'tinywga.fam' } ]) @@ -259,9 +264,9 @@ hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" # We'll test against the resulting ped file and map file for correctness - self.verify_composite_datatype_file_content( 'tinywga.bim', str( hda.id ), base_name = 'rgenetics.bim' ) - self.verify_composite_datatype_file_content( 'tinywga.bed', str( hda.id ), base_name = 'rgenetics.bed' ) - self.verify_composite_datatype_file_content( 'tinywga.fam', str( hda.id ), base_name = 'rgenetics.fam' ) + self.verify_composite_datatype_file_content( 'tinywga.bim', str( hda.id ), base_name='rgenetics.bim' ) + self.verify_composite_datatype_file_content( 'tinywga.bed', str( hda.id ), base_name='rgenetics.bed' ) + self.verify_composite_datatype_file_content( 'tinywga.fam', str( hda.id ), base_name='rgenetics.fam' ) self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "metadata_base_name", "rgenetics", use_string_contains=True ) diff -r 494b51bda9c1a319672e92cce4ec17386cd65390 -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py +++ b/test/functional/test_history_functions.py @@ -4,6 +4,7 @@ from base.test_db_util import sa_session from base.twilltestcase import * + class TestHistory( TwillTestCase ): def test_000_history_behavior_between_logout_login( self ): @@ -16,7 +17,7 @@ global anonymous_history anonymous_history = ( sa_session.query( galaxy.model.History ) - .filter( and_( galaxy.model.History.table.c.deleted==False, galaxy.model.History.table.c.name==name ) ) + .filter( and_( galaxy.model.History.table.c.deleted == False, galaxy.model.History.table.c.name == name ) ) .order_by( desc( galaxy.model.History.table.c.create_time ) ) .first() ) @@ -26,7 +27,7 @@ self.login( email='test1(a)bx.psu.edu', username='regular-user1' ) global regular_user1 regular_user1 = sa_session.query( galaxy.model.User ) \ - .filter( galaxy.model.User.table.c.email=='test1(a)bx.psu.edu' ) \ + .filter( galaxy.model.User.table.c.email == 'test1(a)bx.psu.edu' ) \ .first() assert regular_user1 is not None, 'Problem retrieving user with email "test1(a)bx.psu.edu" from the database' # Current history should be anonymous_history @@ -39,21 +40,21 @@ self.login( email='test2(a)bx.psu.edu', username='regular-user2' ) global regular_user2 regular_user2 = sa_session.query( galaxy.model.User ) \ - .filter( galaxy.model.User.table.c.email=='test2(a)bx.psu.edu' ) \ + .filter( galaxy.model.User.table.c.email == 'test2(a)bx.psu.edu' ) \ .first() assert regular_user2 is not None, 'Problem retrieving user with email "test2(a)bx.psu.edu" from the database' self.logout() self.login( email='test3(a)bx.psu.edu', username='regular-user3' ) global regular_user3 regular_user3 = sa_session.query( galaxy.model.User ) \ - .filter( galaxy.model.User.table.c.email=='test3(a)bx.psu.edu' ) \ + .filter( galaxy.model.User.table.c.email == 'test3(a)bx.psu.edu' ) \ .first() assert regular_user3 is not None, 'Problem retrieving user with email "test3(a)bx.psu.edu" from the database' self.logout() self.login( email='test(a)bx.psu.edu', username='admin-user' ) global admin_user admin_user = sa_session.query( galaxy.model.User ) \ - .filter( galaxy.model.User.table.c.email=='test(a)bx.psu.edu' ) \ + .filter( galaxy.model.User.table.c.email == 'test(a)bx.psu.edu' ) \ .one() assert admin_user is not None, 'Problem retrieving user with email "test(a)bx.psu.edu" from the database' # Get the admin_user private role for later use @@ -66,8 +67,8 @@ if not admin_user_private_role: raise AssertionError( "Private role not found for user '%s'" % admin_user.email ) historyA = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==admin_user.id ) ) \ + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == admin_user.id ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() assert historyA is not None, "Problem retrieving historyA from database" @@ -76,8 +77,8 @@ self.logout() self.login( email=admin_user.email ) historyB = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==admin_user.id ) ) \ + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == admin_user.id ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() assert historyB is not None, "Problem retrieving historyB from database" @@ -87,23 +88,23 @@ """Testing deleting histories""" # Logged in as admin_user historyB = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==admin_user.id ) ) \ + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == admin_user.id ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() assert historyB is not None, "Problem retrieving historyB from database" self.delete_history( self.security.encode_id( historyB.id ) ) sa_session.refresh( historyB ) if not historyB.deleted: - raise AssertionError, "Problem deleting history id %d" % historyB.id + raise AssertionError( "Problem deleting history id %d" % historyB.id ) # Since we deleted the current history, make sure the history frame was refreshed self.check_history_for_string( 'Your history is empty.' ) # We'll now test deleting a list of histories # After deleting the current history, a new one should have been created global history1 history1 = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==admin_user.id ) ) \ + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == admin_user.id ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() assert history1 is not None, "Problem retrieving history1 from database" @@ -111,8 +112,8 @@ self.new_history( name=urllib.quote( 'history2' ) ) global history2 history2 = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==admin_user.id ) ) \ + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == admin_user.id ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() assert history2 is not None, "Problem retrieving history2 from database" @@ -123,26 +124,26 @@ self.check_history_for_string( 'Your history is empty.' ) try: self.view_stored_active_histories( strings_displayed=[ history1.name ] ) - raise AssertionError, "History %s is displayed in the active history list after it was deleted" % history1.name + raise AssertionError( "History %s is displayed in the active history list after it was deleted" % history1.name ) except: pass self.view_stored_deleted_histories( strings_displayed=[ history1.name ] ) try: self.view_stored_active_histories( strings_displayed=[ history2.name ] ) - raise AssertionError, "History %s is displayed in the active history list after it was deleted" % history2.name + raise AssertionError( "History %s is displayed in the active history list after it was deleted" % history2.name ) except: pass self.view_stored_deleted_histories( strings_displayed=[ history2.name ] ) sa_session.refresh( history1 ) if not history1.deleted: - raise AssertionError, "Problem deleting history id %d" % history1.id + raise AssertionError( "Problem deleting history id %d" % history1.id ) if not history1.default_permissions: - raise AssertionError, "Default permissions were incorrectly deleted from the db for history id %d when it was deleted" % history1.id + raise AssertionError( "Default permissions were incorrectly deleted from the db for history id %d when it was deleted" % history1.id ) sa_session.refresh( history2 ) if not history2.deleted: - raise AssertionError, "Problem deleting history id %d" % history2.id + raise AssertionError( "Problem deleting history id %d" % history2.id ) if not history2.default_permissions: - raise AssertionError, "Default permissions were incorrectly deleted from the db for history id %d when it was deleted" % history2.id + raise AssertionError( "Default permissions were incorrectly deleted from the db for history id %d when it was deleted" % history2.id ) # Current history is empty self.history_options( user=True ) @@ -151,12 +152,12 @@ # Logged in as admin_user global history3 history3 = sa_session.query( galaxy.model.History ) \ - .filter( galaxy.model.History.table.c.deleted==False ) \ + .filter( galaxy.model.History.table.c.deleted == False ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() assert history3 is not None, "Problem retrieving history3 from database" if history3.deleted: - raise AssertionError, "History id %d deleted when it should not be" % latest_history.id + raise AssertionError( "History id %d deleted when it should not be" % latest_history.id ) self.rename_history( self.security.encode_id( history3.id ), history3.name, new_name=urllib.quote( 'history 3' ) ) sa_session.refresh( history3 ) @@ -192,7 +193,7 @@ # Make sure history3 is now accessible. sa_session.refresh( history3 ) if not history3.importable: - raise AssertionError, "History 3 is not marked as importable after make_accessible_via_link" + raise AssertionError( "History 3 is not marked as importable after make_accessible_via_link" ) # Try importing history3 #Importing your own history was enabled in 5248:dc9efb540f61. #self.import_history_via_url( self.security.encode_id( history3.id ), @@ -235,13 +236,13 @@ strings_displayed_after_submit=[ 'has been created.' ] ) global history3_clone1 history3_clone1 = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==regular_user1.id ) ) \ + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == regular_user1.id ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() assert history3_clone1 is not None, "Problem retrieving history3_clone1 from database" # Check list of histories to make sure shared history3 was cloned - strings_displayed=[ "Copy of '%s' shared by '%s'" % ( history3.name, admin_user.email ) ] + strings_displayed = [ "Copy of '%s' shared by '%s'" % ( history3.name, admin_user.email ) ] self.view_stored_active_histories( strings_displayed=strings_displayed ) def test_035_clone_current_history( self ): @@ -255,8 +256,8 @@ self.upload_file( '2.bed', dbkey='hg18' ) hda_2_bed = ( sa_session.query( galaxy.model.HistoryDatasetAssociation ) - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id == history3.id, + galaxy.model.HistoryDatasetAssociation.table.c.name == '2.bed' ) ) .first() ) assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database" self.delete_history_item( str( hda_2_bed.id ) ) @@ -264,8 +265,8 @@ self.upload_file( '3.bed', dbkey='hg18' ) hda_3_bed = ( sa_session.query( galaxy.model.HistoryDatasetAssociation ) - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='3.bed' ) ) + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id == history3.id, + galaxy.model.HistoryDatasetAssociation.table.c.name == '3.bed' ) ) .first() ) assert hda_3_bed is not None, "Problem retrieving hda_3_bed from database" self.delete_history_item( str( hda_3_bed.id ) ) @@ -276,8 +277,8 @@ strings_displayed_after_submit=['has been created.' ] ) global history3_clone2 history3_clone2 = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==admin_user.id ) ) \ + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == admin_user.id ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() assert history3_clone2 is not None, "Problem retrieving history3_clone2 from database" @@ -288,14 +289,14 @@ self.switch_history( id=self.security.encode_id( history3_clone2.id ), name=history3_clone2.name ) hda_2_bed = ( sa_session.query( galaxy.model.HistoryDatasetAssociation ) - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3_clone2.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id == history3_clone2.id, + galaxy.model.HistoryDatasetAssociation.table.c.name == '2.bed' ) ) .first() ) assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database" hda_3_bed = ( sa_session.query( galaxy.model.HistoryDatasetAssociation ) - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3_clone2.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='3.bed' ) ) + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id == history3_clone2.id, + galaxy.model.HistoryDatasetAssociation.table.c.name == '3.bed' ) ) .first() ) assert hda_3_bed is not None, "Problem retrieving hda_3_bed from database" @@ -315,15 +316,15 @@ global history3_clone3 history3_clone3 = ( sa_session.query( galaxy.model.History ) - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==admin_user.id ) ) + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == admin_user.id ) ) .order_by( desc( galaxy.model.History.table.c.create_time ) ) .first() ) assert history3_clone3 is not None, "Problem retrieving history3_clone3 from database" # Check list of histories to make sure shared history3 was cloned - self.view_stored_active_histories( strings_displayed = ["Copy of '%s'" % history3.name ] ) + self.view_stored_active_histories( strings_displayed=[ "Copy of '%s'" % history3.name ] ) # Switch to the cloned history to make sure ONLY activatable datasets were cloned self.switch_history( id=self.security.encode_id( history3_clone3.id ) ) @@ -332,7 +333,7 @@ try: self.check_history_for_exact_string( '"deleted": true', show_deleted=True ) #self.check_history_for_string( 'This dataset has been deleted.', show_deleted=True ) - raise AssertionError, "Deleted datasets incorrectly included in cloned history history3_clone3" + raise AssertionError( "Deleted datasets incorrectly included in cloned history history3_clone3" ) except: pass @@ -342,14 +343,14 @@ self.new_history() global history4 history4 = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==admin_user.id ) ) \ + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == admin_user.id ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() assert history4 is not None, "Problem retrieving history4 from database" self.rename_history( self.security.encode_id( history4.id ), history4.name, new_name=urllib.quote( 'history 4' ) ) sa_session.refresh( history4 ) - # Galaxy's new history sharing code does not yet support sharing multiple histories; when support for sharing multiple histories is added, + # Galaxy's new history sharing code does not yet support sharing multiple histories; when support for sharing multiple histories is added, # this test will be uncommented and updated. """ self.upload_file( '2.bed', dbkey='hg18' ) @@ -377,8 +378,8 @@ self.new_history() global history5 history5 = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==admin_user.id ) ) \ + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == admin_user.id ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() assert history5 is not None, "Problem retrieving history5 from database" @@ -405,14 +406,14 @@ history5_dataset1 = hda.dataset break assert history5_dataset1 is not None, "Problem retrieving history5_dataset1 from the database" - # The permissions on the dataset should be restricted from sharing with anyone due to the + # The permissions on the dataset should be restricted from sharing with anyone due to the # inherited history permissions dataset_permissions = [ a.action for a in history5_dataset1.actions ] dataset_permissions.sort() if dataset_permissions != history5_default_permissions: err_msg = "Dataset permissions for history5_dataset1 (%s) were not correctly inherited from history permissions (%s)" \ % ( str( dataset_permissions ), str( history5_default_permissions ) ) - raise AssertionError, err_msg + raise AssertionError( err_msg ) # Make sure when we logout and login, the history default permissions are preserved self.logout() self.login( email=admin_user.email ) @@ -420,7 +421,7 @@ current_history_permissions = [ dhp.action for dhp in history5.default_permissions ] current_history_permissions.sort() if current_history_permissions != history5_default_permissions: - raise AssertionError, "With logout and login, the history default permissions are not preserved" + raise AssertionError( "With logout and login, the history default permissions are not preserved" ) def test_050_sharing_restricted_history_by_making_datasets_public( self ): """Testing sharing a restricted history by making the datasets public""" @@ -440,8 +441,8 @@ strings_displayed_after_submit=[ 'has been created.' ] ) global history5_clone1 history5_clone1 = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==regular_user1.id ) ) \ + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == regular_user1.id ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() assert history5_clone1 is not None, "Problem retrieving history5_clone1 from database" @@ -462,21 +463,21 @@ 'The following datasets can be shared with %s by updating their permissions' % regular_user2.email ] self.share_current_history( regular_user2.email, strings_displayed_after_submit=strings_displayed_after_submit, - action='private' ) + action='private' ) # We should now have a new sharing role global sharing_role role_name = 'Sharing role for: %s, %s' % ( admin_user.email, regular_user2.email ) - sharing_role = sa_session.query( galaxy.model.Role ).filter( galaxy.model.Role.table.c.name==role_name ).first() + sharing_role = sa_session.query( galaxy.model.Role ).filter( galaxy.model.Role.table.c.name == role_name ).first() if not sharing_role: # May have created a sharing role in a previous functional test suite from the opposite direction. role_name = 'Sharing role for: %s, %s' % ( regular_user2.email, admin_user.email ) sharing_role = sa_session.query( galaxy.model.Role ) \ - .filter( and_( galaxy.model.Role.table.c.type==role_type, - galaxy.model.Role.table.c.name==role_name ) ) \ + .filter( and_( galaxy.model.Role.table.c.type == role_type, + galaxy.model.Role.table.c.name == role_name ) ) \ .first() if not sharing_role: raise AssertionError( "Privately sharing a dataset did not properly create a sharing role" ) - # The DATASET_ACCESS permission on 2.bed was originally associated with admin_user's private role. + # The DATASET_ACCESS permission on 2.bed was originally associated with admin_user's private role. # Since we created a new sharing role for 2.bed, the original permission should have been eliminated, # replaced with the sharing role. history5_dataset2 = None @@ -498,8 +499,8 @@ strings_displayed_after_submit=[ 'has been created.' ] ) global history5_clone2 history5_clone2 = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==regular_user2.id ) ) \ + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == regular_user2.id ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() assert history5_clone2 is not None, "Problem retrieving history5_clone2 from database" @@ -512,13 +513,13 @@ self.check_history_for_string( '2.bed' ) # Get both new hdas from the db that were created for the shared history hda_1_bed = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone2.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='1.bed' ) ) \ + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id == history5_clone2.id, + galaxy.model.HistoryDatasetAssociation.table.c.name == '1.bed' ) ) \ .first() assert hda_1_bed is not None, "Problem retrieving hda_1_bed from database" hda_2_bed = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone2.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) \ + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id == history5_clone2.id, + galaxy.model.HistoryDatasetAssociation.table.c.name == '2.bed' ) ) \ .first() assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database" # Make sure 1.bed is accessible since it is public @@ -549,7 +550,7 @@ self.visit_page( "root/history_options" ) try: self.check_page_for_string( 'List</a> histories shared with you by others' ) - raise AssertionError, "history5 still shared with regular_user2 after unsharing it with that user." + raise AssertionError( "history5 still shared with regular_user2 after unsharing it with that user." ) except: pass @@ -558,7 +559,8 @@ email = '%s,%s' % ( regular_user2.email, regular_user3.email ) strings_displayed_after_submit = [ 'The following datasets can be shared with %s with no changes' % email, - 'The following datasets can be shared with %s by updating their permissions' % email ] + 'The following datasets can be shared with %s by updating their permissions' % email + ] # history5 will be shared with regular_user1, regular_user2 and regular_user3 self.share_current_history( email, @@ -576,8 +578,8 @@ global history5_clone3 history5_clone3 = ( sa_session.query( galaxy.model.History ) - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==regular_user2.id ) ) + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == regular_user2.id ) ) .order_by( desc( galaxy.model.History.table.c.create_time ) ) .first() ) assert history5_clone3 is not None, "Problem retrieving history5_clone3 from database" @@ -592,14 +594,14 @@ # Get both new hdas from the db that were created for the shared history hda_1_bed = ( sa_session.query( galaxy.model.HistoryDatasetAssociation ) - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone3.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='1.bed' ) ) + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id == history5_clone3.id, + galaxy.model.HistoryDatasetAssociation.table.c.name == '1.bed' ) ) .first() ) assert hda_1_bed is not None, "Problem retrieving hda_1_bed from database" hda_2_bed = ( sa_session.query( galaxy.model.HistoryDatasetAssociation ) - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone3.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id == history5_clone3.id, + galaxy.model.HistoryDatasetAssociation.table.c.name == '2.bed' ) ) .first() ) assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database" @@ -622,8 +624,8 @@ global history5_clone4 history5_clone4 = ( sa_session.query( galaxy.model.History ) - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==regular_user3.id ) ) + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == regular_user3.id ) ) .order_by( desc( galaxy.model.History.table.c.create_time ) ) .first() ) assert history5_clone4 is not None, "Problem retrieving history5_clone4 from database" @@ -638,14 +640,14 @@ # Get both new hdas from the db that were created for the shared history hda_1_bed = ( sa_session.query( galaxy.model.HistoryDatasetAssociation ) - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone4.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='1.bed' ) ) + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id == history5_clone4.id, + galaxy.model.HistoryDatasetAssociation.table.c.name == '1.bed' ) ) .first() ) assert hda_1_bed is not None, "Problem retrieving hda_1_bed from database" hda_2_bed = ( sa_session.query( galaxy.model.HistoryDatasetAssociation ) - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone4.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id == history5_clone4.id, + galaxy.model.HistoryDatasetAssociation.table.c.name == '2.bed' ) ) .first() ) assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database" # Make sure 1.bed is accessible since it is public @@ -653,7 +655,7 @@ # Make sure 2.bed is not accessible since it is protected try: self.display_history_item( str( hda_2_bed.id ), strings_displayed=[ 'chr1' ] ) - raise AssertionError, "History item 2.bed is accessible by user %s when is should not be" % regular_user3.email + raise AssertionError( "History item 2.bed is accessible by user %s when is should not be" % regular_user3.email ) except: pass @@ -696,7 +698,7 @@ self.visit_page( "root/history_options" ) try: self.check_page_for_string( 'List</a> histories shared with you by others' ) - raise AssertionError, "history5 still shared with regular_user2 after unshaing it with that user." + raise AssertionError( "history5 still shared with regular_user2 after unshaing it with that user." ) except: pass @@ -705,7 +707,7 @@ self.visit_page( "root/history_options" ) try: self.check_page_for_string( 'List</a> histories shared with you by others' ) - raise AssertionError, "history5 still shared with regular_user3 after unshaing it with that user." + raise AssertionError( "history5 still shared with regular_user3 after unshaing it with that user." ) except: pass self.logout() @@ -725,8 +727,8 @@ self.new_history( name=urllib.quote( 'show hide deleted datasets' ) ) latest_history = ( sa_session.query( galaxy.model.History ) - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==admin_user.id ) ) + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == admin_user.id ) ) .order_by( desc( galaxy.model.History.table.c.create_time ) ) .first() ) assert latest_history is not None, "Problem retrieving latest_history from database" @@ -769,8 +771,8 @@ # Deleting the current history in the last method created a new history latest_history = ( sa_session.query( galaxy.model.History ) - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==admin_user.id ) ) + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == admin_user.id ) ) .order_by( desc( galaxy.model.History.table.c.create_time ) ) .first() ) assert latest_history is not None, "Problem retrieving latest_history from database" @@ -786,14 +788,14 @@ self.visit_url( "%s/history/?show_deleted=False" % self.url ) self.check_page_for_string( '1.bed' ) self.check_page_for_string( 'hg15' ) - self.assertEqual ( len( self.get_history_as_data_list() ), 1 ) + self.assertEqual( len( self.get_history_as_data_list() ), 1 ) # Delete the history item self.delete_history_item( str( latest_hda.id ), strings_displayed=[ "Your history is empty" ] ) - self.assertEqual ( len( self.get_history_as_data_list() ), 0 ) + self.assertEqual( len( self.get_history_as_data_list() ), 0 ) # Try deleting an invalid hid try: self.delete_history_item( 'XXX' ) - raise AssertionError, "Inproperly able to delete hda_id 'XXX' which is not an integer" + raise AssertionError( "Inproperly able to delete hda_id 'XXX' which is not an integer" ) except: pass # Undelete the history item @@ -809,8 +811,8 @@ # logged in as admin_user self.new_history( name=urllib.quote( 'copy history items' ) ) history6 = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==admin_user.id ) ) \ + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == admin_user.id ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() assert history6 is not None, "Problem retrieving history6 from database" @@ -820,7 +822,7 @@ .first() assert hda1 is not None, "Problem retrieving hda1 from database" # We'll just test copying 1 hda - source_dataset_ids=self.security.encode_id( hda1.id ) + source_dataset_ids = self.security.encode_id( hda1.id ) # The valid list of target histories is only the user's active histories all_target_history_ids = [ self.security.encode_id( hda.id ) for hda in admin_user.active_histories ] # Since history1 and history2 have been deleted, they should not be displayed in the list of target histories @@ -834,12 +836,12 @@ deleted_history_ids=deleted_history_ids ) sa_session.refresh( history6 ) if len( history6.datasets ) != 2: - raise AssertionError, "Copying hda1 to the current history failed, history 6 has %d datasets, but should have 2" % len( history6.datasets ) + raise AssertionError( "Copying hda1 to the current history failed, history 6 has %d datasets, but should have 2" % len( history6.datasets ) ) # Test copying 1 hda to another history self.new_history( name=urllib.quote( 'copy history items - 2' ) ) history7 = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==admin_user.id ) ) \ + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == admin_user.id ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() assert history7 is not None, "Problem retrieving history7 from database" @@ -848,7 +850,7 @@ target_history_id = self.security.encode_id( history7.id ) all_target_history_ids = [ self.security.encode_id( hda.id ) for hda in admin_user.active_histories ] # Test copying to the a history that is not the current history - target_history_ids=[ self.security.encode_id( history7.id ) ] + self.security.encode_id( history7.id ) self.copy_history_item( source_dataset_id=source_dataset_ids, target_history_id=target_history_id, all_target_history_ids=all_target_history_ids, diff -r 494b51bda9c1a319672e92cce4ec17386cd65390 -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a test/functional/test_library_features.py --- a/test/functional/test_library_features.py +++ b/test/functional/test_library_features.py @@ -1,6 +1,8 @@ from base.twilltestcase import * from base.test_db_util import * + +# TODO: Functional tests start failing at 070, fix or eliminate rest of tests. class TestLibraryFeatures( TwillTestCase ): def test_000_initiate_users( self ): """Ensuring all required user accounts exist""" diff -r 494b51bda9c1a319672e92cce4ec17386cd65390 -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a test/functional/test_library_security.py --- a/test/functional/test_library_security.py +++ b/test/functional/test_library_security.py @@ -1,6 +1,8 @@ from base.twilltestcase import * from base.test_db_util import * + +# TODO: Functional tests start failing at 050, fix or eliminate rest of tests. class TestLibrarySecurity( TwillTestCase ): def test_000_initiate_users( self ): """Ensuring all required user accounts exist""" diff -r 494b51bda9c1a319672e92cce4ec17386cd65390 -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a test/functional/test_library_templates.py --- a/test/functional/test_library_templates.py +++ b/test/functional/test_library_templates.py @@ -1,7 +1,35 @@ -from base.twilltestcase import * -from base.test_db_util import * +from base.twilltestcase import TwillTestCase +from base.test_db_util import ( + get_user, + get_private_role, + get_form, + get_library, + get_folder, + get_user_address, + get_latest_ldda_by_name, + get_latest_hda, + mark_obj_deleted, + refresh +) +import galaxy.model + +AddressField_form = None +CheckboxField_form = None +SelectField_form = None +TextArea_form = None +TextField_form = None +WorkflowField_form = None +address_field_name = checkbox_field_name = select_field_name = None +workflow_field_name = textfield_name = textarea_name = None +user_address1 = user_address2 = None +ldda1 = library1 = library2 = library3 = library4 = library5 = library6 = None +folder1 = folder2 = folder3 = folder4 = folder5 = folder6 = None +admin_user = None +regular_user1 = regular_user2 = regular_user3 = None + class TestLibraryFeatures( TwillTestCase ): + def test_000_initiate_users( self ): """Ensuring all required user accounts exist""" self.logout() @@ -32,6 +60,7 @@ assert admin_user is not None, 'Problem retrieving user with email "test(a)bx.psu.edu" from the database' global admin_user_private_role admin_user_private_role = get_private_role( admin_user ) + def test_005_create_library_templates( self ): """Testing creating several LibraryInformationTemplate form definitions""" # Logged in as admin_user @@ -109,6 +138,7 @@ library5 = get_library( 'library5', 'library5 description', 'library5 synopsis' ) global library6 library6 = get_library( 'library6', 'library6 description', 'library6 synopsis' ) + def test_015_add_template_to_library1( self ): """Testing add an inheritable template containing an AddressField to library1""" # Logged in as admin_user @@ -119,6 +149,7 @@ form_id=self.security.encode_id( AddressField_form.id ), form_name=AddressField_form.name, library_id=self.security.encode_id( library1.id ) ) + def test_020_add_folder_to_library1( self ): """Testing adding a folder to library1""" # Logged in as admin_user @@ -133,6 +164,7 @@ description=description ) global folder1 folder1 = get_folder( folder.id, name, description ) + def test_025_check_library1( self ): """Checking library1 and its root folder""" # Logged in as admin_user @@ -146,6 +178,7 @@ template_refresh_field_name=address_field_name, strings_displayed=[ AddressField_form.name, 'This is an inherited template and is not required to be used with this folder' ] ) + def test_030_add_dataset_to_folder1( self ): """Testing adding a ldda1 to folder1, and adding a new UserAddress on the upload form.""" # Logged in as admin_user @@ -189,6 +222,7 @@ self.security.encode_id( ldda1.id ), ldda1.name, strings_displayed=[ 'Dick' ] ) + def test_035_edit_contents_of_ldda1_tempplate( self ): """Testing editing the contents of ldda1 AddressField template by adding a new user_address""" short_desc = 'Home' @@ -212,6 +246,7 @@ global user_address2 user_address2 = get_user_address( admin_user, short_desc ) assert user_address2 is not None, 'Problem retrieving user_address2 from the database' + def test_040_edit_contents_of_folder1_template( self ): """Testing editing the contents of folder1 AddressField template""" # Make sure the template and contents were inherited to folder1 @@ -223,6 +258,7 @@ strings_displayed=[ AddressField_form.name, 'This is an inherited template and is not required to be used with this folder' ], strings_displayed_after_submit=[ 'Richard' ] ) + def test_045_add_dataset_to_folder1( self ): """Testing adding another ldda to folder1""" # The upload form should now inherit user_address2 on the upload form @@ -245,6 +281,7 @@ ldda_name=ldda1.name, template_refresh_field_name=address_field_name, strings_displayed=[ user_address2.desc ] ) + def test_050_add_template_to_library2( self ): """ Testing add an inheritable template containing an CheckboxField to library2""" # Add a template containing an CheckboxField to library1 @@ -257,7 +294,8 @@ # Check the CheckboxField to make sure the template contents are inherited self.library_info( 'library_admin', self.security.encode_id( library2.id ), - template_fields = [ ( checkbox_field_name, '1' ) ] ) + template_fields=[ ( checkbox_field_name, '1' ) ] ) + def test_055_add_folder2_to_library2( self ): """Testing adding a folder to library2""" # Logged in as admin_user @@ -272,12 +310,14 @@ description=description ) global folder2 folder2 = get_folder( folder.id, name, description ) + def test_060_check_library2( self ): """Checking library2 and its root folder""" # Logged in as admin_user self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library2.id ), strings_displayed=[ folder2.name, folder2.description ] ) + def test_065_save_folder2_inherited_template( self ): """Saving the inherited template for folder2""" # Logged in as admin_user @@ -288,6 +328,7 @@ template_fields=[ ( checkbox_field_name, '1' ) ], strings_displayed=[ CheckboxField_form.name, 'This is an inherited template and is not required to be used with this folder' ] ) + def test_070_add_ldda_to_folder2( self ): """ Testing adding a new library dataset to library2's folder, making sure the CheckboxField is @@ -316,6 +357,7 @@ self.security.encode_id( ldda.id ), ldda.name, strings_displayed=[ 'CheckboxField', 'checked' ] ) + def test_080_add_template_to_library3( self ): """ Testing add an inheritable template containing an SelectField to library3""" # Logged in as admin_user @@ -330,6 +372,7 @@ self.library_info( 'library_admin', self.security.encode_id( library3.id ), template_fields=[ ( select_field_name, 'Option1' ) ] ) + def test_085_add_folder3_to_library3( self ): """Testing adding a folder to library3""" # Logged in as admin_user @@ -344,12 +387,14 @@ description=description ) global folder3 folder3 = get_folder( folder.id, name, description ) + def test_090_check_library3( self ): """Checking library3 and its root folder""" # Logged in as admin_user self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library3.id ), strings_displayed=[ folder3.name, folder3.description ] ) + def test_095_save_folder3_inherited_template( self ): """Saving the inherited template for folder3""" # Logged in as admin_user @@ -361,6 +406,7 @@ strings_displayed=[ SelectField_form.name, 'This is an inherited template and is not required to be used with this folder', 'Option1' ] ) + def test_100_add_ldda_to_folder3( self ): """ Testing adding a new library dataset to library3's folder, making sure the SelectField setting is correct on the upload form. @@ -411,6 +457,7 @@ self.security.encode_id( ldda.id ), ldda.name, strings_displayed=[ 'SelectField', 'Option1' ] ) + def test_105_add_template_to_library4( self ): """ Testing add an inheritable template containing an TextArea to library4""" # Logged in as admin_user @@ -425,6 +472,7 @@ self.library_info( 'library_admin', self.security.encode_id( library4.id ), template_fields=[ ( textarea_name, 'This text should be inherited' ) ] ) + def test_110_add_folder4_to_library4( self ): """Testing adding a folder to library4""" # Logged in as admin_user @@ -439,6 +487,7 @@ description=description ) global folder4 folder4 = get_folder( folder.id, name, description ) + def test_115_save_folder4_inherited_template( self ): """Saving the inherited template for folder4""" # Logged in as admin_user @@ -450,6 +499,7 @@ strings_displayed=[ TextArea_form.name, 'This is an inherited template and is not required to be used with this folder', 'This text should be inherited' ] ) + def test_120_add_ldda_to_folder4( self ): """ Testing adding a new library dataset to library4's folder, making sure the TextArea setting is correct on the upload form. @@ -477,6 +527,7 @@ self.security.encode_id( ldda.id ), ldda.name, strings_displayed=[ 'TextArea', 'This text should be inherited' ] ) + def test_125_add_template_to_library5( self ): """ Testing add an inheritable template containing an TextField to library5""" # Add an inheritable template to library5 @@ -490,6 +541,7 @@ self.library_info( 'library_admin', self.security.encode_id( library5.id ), template_fields=[ ( textfield_name, 'This text should be inherited' ) ] ) + def test_130_add_folder5_to_library5( self ): """Testing adding a folder to library5""" # Logged in as admin_user @@ -504,6 +556,7 @@ description=description ) global folder5 folder5 = get_folder( folder.id, name, description ) + def test_135_save_folder5_inherited_template( self ): """Saving the inherited template for folder5""" # Logged in as admin_user @@ -515,6 +568,7 @@ strings_displayed=[ TextField_form.name, 'This is an inherited template and is not required to be used with this folder', 'This text should be inherited' ] ) + def test_140_add_ldda_to_folder5( self ): """ Testing adding a new library dataset to library5's folder, making sure the TextField setting is correct on the upload form. @@ -542,6 +596,7 @@ self.security.encode_id( ldda.id ), ldda.name, strings_displayed=[ 'TextField', 'This text should be inherited' ] ) + def test_145_edit_library5_template_layout( self ): """Test editing the layout of library5's template""" # Currently there is only a TextField, and we'll add a TextArea. @@ -553,6 +608,7 @@ field_label_1=TextArea_form.name, field_helptext_1='%s help' % TextArea_form.name, field_default_1='%s default' % TextArea_form.name ) + def test_150_add_ldda_to_library5( self ): """ Testing adding a new library dataset to library5's folder, making sure the TextField and new TextArea settings are correct on the upload form. @@ -584,6 +640,7 @@ strings_displayed=[ 'TextField', 'This text should be inherited', 'TextArea' ] ) + def test_155_add_template_to_library6( self ): """ Testing add an inheritable template containing an WorkflowField to library6""" # Add an inheritable template to library6 @@ -594,6 +651,7 @@ form_id=self.security.encode_id( WorkflowField_form.id ), form_name=WorkflowField_form.name, library_id=self.security.encode_id( library6.id ) ) + def test_160_add_folder6_to_library6( self ): """Testing adding a folder to library6""" # Logged in as admin_user @@ -608,6 +666,7 @@ description=description ) global folder6 folder6 = get_folder( folder.id, name, description ) + def test_165_save_folder6_inherited_template( self ): """Saving the inherited template for folder6""" # Logged in as admin_user @@ -619,6 +678,7 @@ strings_displayed=[ WorkflowField_form.name, 'This is an inherited template and is not required to be used with this folder', 'none' ] ) + def test_170_add_ldda_to_folder6( self ): """ Testing adding a new library dataset to library6's folder, making sure the WorkflowField setting is correct on the upload form. @@ -646,6 +706,7 @@ self.security.encode_id( ldda.id ), ldda.name, strings_displayed=[ 'WorkflowField', 'none' ] ) + def test_999_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to pass""" # Logged in as admin_user diff -r 494b51bda9c1a319672e92cce4ec17386cd65390 -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a test/functional/test_metadata_editing.py --- a/test/functional/test_metadata_editing.py +++ b/test/functional/test_metadata_editing.py @@ -1,21 +1,26 @@ +from base.twilltestcase import TwillTestCase +from functional import database_contexts import galaxy.model -from galaxy.model.orm import * -from base.test_db_util import sa_session -from base.twilltestcase import TwillTestCase +from galaxy.model.orm import ( + and_, + desc, +) + class TestMetadataEdit( TwillTestCase ): def test_00_metadata_edit( self ): """test_metadata_edit: Testing metadata editing""" + sa_session = database_contexts.galaxy_context self.logout() self.login( email='test(a)bx.psu.edu', username='admin-user' ) admin_user = sa_session.query( galaxy.model.User ) \ - .filter( galaxy.model.User.table.c.email=='test(a)bx.psu.edu' ) \ + .filter( galaxy.model.User.table.c.email == 'test(a)bx.psu.edu' ) \ .one() self.new_history( name='Test Metadata Edit' ) history1 = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==admin_user.id ) ) \ + .filter( and_( galaxy.model.History.table.c.deleted == False, + galaxy.model.History.table.c.user_id == admin_user.id ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() self.upload_file( '1.bed' ) diff -r 494b51bda9c1a319672e92cce4ec17386cd65390 -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a test/functional/test_sample_tracking.py --- a/test/functional/test_sample_tracking.py +++ b/test/functional/test_sample_tracking.py @@ -3,6 +3,8 @@ from base.twilltestcase import * from base.test_db_util import * + +# TODO: Functional tests start failing at 025, fix or eliminate rest of tests. class TestFormsAndSampleTracking( TwillTestCase ): # ====== Setup Users, Groups & Roles required for this test suite ========= def test_000_initiate_users( self ): diff -r 494b51bda9c1a319672e92cce4ec17386cd65390 -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a test/functional/test_tags.py --- a/test/functional/test_tags.py +++ b/test/functional/test_tags.py @@ -1,7 +1,17 @@ -from base.twilltestcase import * -from base.test_db_util import * +from base.twilltestcase import TwillTestCase +from base.test_db_util import ( + get_user, + get_private_role, + get_latest_history_for_user, + get_latest_hda, +) + +history1 = None +admin_user = None + class TestTags( TwillTestCase ): + # TODO: Add more functional test coverage for tags def test_000_initiate_users( self ): """Ensuring all required user accounts exist""" diff -r 494b51bda9c1a319672e92cce4ec17386cd65390 -r c7986c31fd7447f7d1e2a85bdfa43be6bc4b3b8a test/functional/test_user_info.py --- a/test/functional/test_user_info.py +++ b/test/functional/test_user_info.py @@ -1,6 +1,8 @@ from base.twilltestcase import * from base.test_db_util import * + +# TODO: Functional tests start failing at 020, fix or eliminate rest of tests. class TestUserInfo( TwillTestCase ): def test_000_initiate_users( self ): """Ensuring all required user accounts exist""" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Code duplication reduction in Tool.
by commits-noreply＠bitbucket.org 11 Jan '14

11 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c8c00d106c7a/ Changeset: c8c00d106c7a User: jmchilton Date: 2014-01-11 04:23:07 Summary: Code duplication reduction in Tool. Affected #: 1 file diff -r 9f55b4b37d35b8366f42ab430ac4213554d83311 -r c8c00d106c7a6883feaacca809b42fd7c107fe2a lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1834,7 +1834,7 @@ # external data source tools). if "runtool_btn" not in incoming and "URL" not in incoming: if not self.display_interface: - return 'message.mako', dict( status='info', message="The interface for this tool cannot be displayed", refresh_frames=['everything'] ) + return self.__no_display_interface_response() if len(incoming): self.update_state( trans, self.inputs_by_page[state.page], state.inputs, incoming, old_errors=old_errors or {}, source=source ) return "tool_form.mako", dict( errors={}, tool_state=state, param_values={}, incoming={} ) @@ -1894,7 +1894,7 @@ pass # Just a refresh, render the form with updated state and errors. if not self.display_interface: - return 'message.mako', dict( status='info', message="The interface for this tool cannot be displayed", refresh_frames=['everything'] ) + return self.__no_display_interface_response() return 'tool_form.mako', dict( errors=errors, tool_state=state ) def __handle_page_advance( self, trans, state, errors ): @@ -1902,9 +1902,12 @@ # Fill in the default values for the next page self.fill_in_new_state( trans, self.inputs_by_page[ state.page ], state.inputs ) if not self.display_interface: - return 'message.mako', dict( status='info', message="The interface for this tool cannot be displayed", refresh_frames=['everything'] ) + return self.__no_display_interface_response() return 'tool_form.mako', dict( errors=errors, tool_state=state ) + def __no_display_interface_response( self ): + return 'message.mako', dict( status='info', message="The interface for this tool cannot be displayed", refresh_frames=['everything'] ) + def __fetch_state( self, trans, incoming, history, all_pages ): # Get the state or create if not found if "tool_state" in incoming: 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: PEP-8 fixes for tools/actions/__init__.py
by commits-noreply＠bitbucket.org 11 Jan '14

11 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9f55b4b37d35/ Changeset: 9f55b4b37d35 User: jmchilton Date: 2014-01-11 04:17:39 Summary: PEP-8 fixes for tools/actions/__init__.py Affected #: 1 file diff -r 582d1e318dd3b604f2371a861f35c6fae1a2d36d -r 9f55b4b37d35b8366f42ab430ac4213554d83311 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -3,7 +3,8 @@ from galaxy.exceptions import ObjectInvalid from galaxy.model import LibraryDatasetDatasetAssociation -from galaxy.tools.parameters import DataToolParameter, SelectToolParameter +from galaxy.tools.parameters import DataToolParameter +from galaxy.tools.parameters import SelectToolParameter from galaxy.tools.parameters.grouping import Conditional, Repeat from galaxy.util.json import from_json_string from galaxy.util.json import to_json_string @@ -15,6 +16,7 @@ import logging log = logging.getLogger( __name__ ) + class ToolAction( object ): """ The actions to be taken when a tool is run (after parameters have @@ -23,6 +25,7 @@ def execute( self, tool, trans, incoming={}, set_output_hid=True ): raise TypeError("Abstract method") + class DefaultToolAction( object ): """Default tool action is to run an external command""" @@ -33,8 +36,10 @@ of the DataToolParameter type. """ input_datasets = dict() - def visitor( prefix, input, value, parent = None ): - def process_dataset( data, formats = None ): + + def visitor( prefix, input, value, parent=None ): + + def process_dataset( data, formats=None ): if not data: return data if formats is None: @@ -48,11 +53,11 @@ data = converted_dataset else: #run converter here - new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output = True, visible = False ).values()[0] + new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output=True, visible=False ).values()[0] new_data.hid = data.hid new_data.name = data.name trans.sa_session.add( new_data ) - assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = data, file_type = target_ext, dataset = new_data, metadata_safe = False ) + assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent=data, file_type=target_ext, dataset=new_data, metadata_safe=False ) trans.sa_session.add( assoc ) trans.sa_session.flush() data = new_data @@ -77,17 +82,17 @@ input_datasets[ prefix + conversion_name + str( i + 1 ) ] = new_data conversions.append( ( conversion_name, new_data ) ) else: - raise Exception, 'A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_datasets[ prefix + input.name + str( i + 1 ) ].extension, conversion_extensions ) + raise Exception('A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_datasets[ prefix + input.name + str( i + 1 ) ].extension, conversion_extensions ) ) if parent: parent[input.name][i] = input_datasets[ prefix + input.name + str( i + 1 ) ] for conversion_name, conversion_data in conversions: #allow explicit conversion to be stored in job_parameter table - parent[ conversion_name ][i] = conversion_data.id #a more robust way to determine JSONable value is desired + parent[ conversion_name ][i] = conversion_data.id # a more robust way to determine JSONable value is desired else: param_values[input.name][i] = input_datasets[ prefix + input.name + str( i + 1 ) ] for conversion_name, conversion_data in conversions: #allow explicit conversion to be stored in job_parameter table - param_values[ conversion_name ][i] = conversion_data.id #a more robust way to determine JSONable value is desired + param_values[ conversion_name ][i] = conversion_data.id # a more robust way to determine JSONable value is desired else: input_datasets[ prefix + input.name ] = process_dataset( value ) conversions = [] @@ -97,14 +102,14 @@ input_datasets[ prefix + conversion_name ] = new_data conversions.append( ( conversion_name, new_data ) ) else: - raise Exception, 'A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_datasets[ prefix + input.name ].extension, conversion_extensions ) + raise Exception( 'A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_datasets[ prefix + input.name ].extension, conversion_extensions ) ) target_dict = parent if not target_dict: target_dict = param_values target_dict[ input.name ] = input_datasets[ prefix + input.name ] for conversion_name, conversion_data in conversions: #allow explicit conversion to be stored in job_parameter table - target_dict[ conversion_name ] = conversion_data.id #a more robust way to determine JSONable value is desired + target_dict[ conversion_name ] = conversion_data.id # a more robust way to determine JSONable value is desired tool.visit_inputs( param_values, visitor ) return input_datasets @@ -130,6 +135,7 @@ else: copy_from_dict[ key ] = value return copy_from_dict + def make_list_copy( from_list ): new_list = [] for value in from_list: @@ -140,32 +146,33 @@ else: new_list.append( value ) return new_list - def wrap_values( inputs, input_values, skip_missing_values = False ): + + def wrap_values( inputs, input_values, skip_missing_values=False ): # Wrap tool inputs as necessary for input in inputs.itervalues(): if input.name not in input_values and skip_missing_values: continue if isinstance( input, Repeat ): for d in input_values[ input.name ]: - wrap_values( input.inputs, d, skip_missing_values = skip_missing_values ) + wrap_values( input.inputs, d, skip_missing_values=skip_missing_values ) elif isinstance( input, Conditional ): values = input_values[ input.name ] current = values[ "__current_case__" ] - wrap_values( input.cases[current].inputs, values, skip_missing_values = skip_missing_values ) + wrap_values( input.cases[current].inputs, values, skip_missing_values=skip_missing_values ) elif isinstance( input, DataToolParameter ) and input.multiple: input_values[ input.name ] = \ galaxy.tools.DatasetListWrapper( input_values[ input.name ], - datatypes_registry = trans.app.datatypes_registry, - tool = tool, - name = input.name ) + datatypes_registry=trans.app.datatypes_registry, + tool=tool, + name=input.name ) elif isinstance( input, DataToolParameter ): input_values[ input.name ] = \ galaxy.tools.DatasetFilenameWrapper( input_values[ input.name ], - datatypes_registry = trans.app.datatypes_registry, - tool = tool, - name = input.name ) + datatypes_registry=trans.app.datatypes_registry, + tool=tool, + name=input.name ) elif isinstance( input, SelectToolParameter ): - input_values[ input.name ] = galaxy.tools.SelectToolParameterWrapper( input, input_values[ input.name ], tool.app, other_values = incoming ) + input_values[ input.name ] = galaxy.tools.SelectToolParameterWrapper( input, input_values[ input.name ], tool.app, other_values=incoming ) else: input_values[ input.name ] = galaxy.tools.InputValueWrapper( input, input_values[ input.name ], incoming ) @@ -183,7 +190,7 @@ input_dbkey = incoming.get( "dbkey", "?" ) for name, data in inp_data.items(): if not data: - data = NoneDataset( datatypes_registry = trans.app.datatypes_registry ) + data = NoneDataset( datatypes_registry=trans.app.datatypes_registry ) continue # Convert LDDA to an HDA. @@ -191,7 +198,7 @@ data = data.to_history_dataset_association( None ) inp_data[name] = data - else: # HDA + else: # HDA if data.hid: input_names.append( 'data %s' % data.hid ) input_ext = data.ext @@ -212,9 +219,9 @@ if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ): # Custom build. custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ] - # HACK: the attempt to get chrom_info below will trigger the + # HACK: the attempt to get chrom_info below will trigger the # fasta-to-len converter if the dataset is not available or, - # which will in turn create a recursive loop when + # which will in turn create a recursive loop when # running the fasta-to-len tool. So, use a hack in the second # condition below to avoid getting chrom_info when running the # fasta-to-len converter. @@ -248,7 +255,7 @@ on_text = "" # Add the dbkey to the incoming parameters incoming[ "dbkey" ] = input_dbkey - params = None #wrapped params are used by change_format action and by output.label; only perform this wrapping once, as needed + params = None # wrapped params are used by change_format action and by output.label; only perform this wrapping once, as needed # Keep track of parent / child relationships, we'll create all the # datasets first, then create the associations parent_to_child_pairs = [] @@ -258,10 +265,10 @@ for filter in output.filters: try: if not eval( filter.text.strip(), globals(), incoming ): - break #do not create this dataset + break # do not create this dataset except Exception, e: log.debug( 'Dataset output filter failed: %s' % e ) - else: #all filters passed + else: # all filters passed if output.parent: parent_to_child_pairs.append( ( output.parent, name ) ) child_dataset_names.add( name ) @@ -291,7 +298,7 @@ if output.change_format: if params is None: params = make_dict_copy( incoming ) - wrap_values( tool.inputs, params, skip_missing_values = not tool.check_values ) + wrap_values( tool.inputs, params, skip_missing_values=not tool.check_values ) for change_elem in output.change_format: for when_elem in change_elem.findall( 'when' ): check = when_elem.get( 'input', None ) @@ -300,9 +307,9 @@ if '$' not in check: #allow a simple name or more complex specifications check = '${%s}' % check - if str( fill_template( check, context = params ) ) == when_elem.get( 'value', None ): + if str( fill_template( check, context=params ) ) == when_elem.get( 'value', None ): ext = when_elem.get( 'format', ext ) - except: #bad tag input value; possibly referencing a param within a different conditional when block or other nonexistent grouping construct + except: # bad tag input value; possibly referencing a param within a different conditional when block or other nonexistent grouping construct continue else: check = when_elem.get( 'input_dataset', None ) @@ -348,7 +355,7 @@ # <outputs> # <data format="input" name="output" label="Blat on ${<input_param>.name}" /> # </outputs> - wrap_values( tool.inputs, params, skip_missing_values = not tool.check_values ) + wrap_values( tool.inputs, params, skip_missing_values=not tool.check_values ) #tool (only needing to be set once) and on_string (set differently for each label) are overwritten for each output dataset label being determined params['tool'] = tool params['on_string'] = on_text @@ -356,7 +363,7 @@ else: if params is None: params = make_dict_copy( incoming ) - wrap_values( tool.inputs, params, skip_missing_values = not tool.check_values ) + wrap_values( tool.inputs, params, skip_missing_values=not tool.check_values ) data.name = self._get_default_data_name( data, tool, on_text=on_text, trans=trans, incoming=incoming, history=history, params=params, job_params=job_params ) # Store output out_data[ name ] = data @@ -369,10 +376,10 @@ trans.sa_session.flush() # Add all the top-level (non-child) datasets to the history unless otherwise specified for name in out_data.keys(): - if name not in child_dataset_names and name not in incoming: #don't add children; or already existing datasets, i.e. async created + if name not in child_dataset_names and name not in incoming: # don't add children; or already existing datasets, i.e. async created data = out_data[ name ] if set_output_history: - history.add_dataset( data, set_hid = set_output_hid ) + history.add_dataset( data, set_hid=set_output_hid ) trans.sa_session.add( data ) trans.sa_session.flush() # Add all the children to their parents Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix message rendering for repositories with multiple heads.
by commits-noreply＠bitbucket.org 10 Jan '14

10 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/582d1e318dd3/ Changeset: 582d1e318dd3 User: greg Date: 2014-01-10 22:36:45 Summary: Fix message rendering for repositories with multiple heads. Affected #: 2 files diff -r 56b61e7d5bbcea1dff823cf78229289480ee15e7 -r 582d1e318dd3b604f2371a861f35c6fae1a2d36d templates/webapps/tool_shed/repository/manage_repository.mako --- a/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/templates/webapps/tool_shed/repository/manage_repository.mako @@ -125,7 +125,7 @@ from tool_shed.util.shed_util_common import get_revision_label_from_ctx heads_str = '' for ctx in heads: - heads_str += get_revision_label_from_ctx( ctx ) + heads_str += '%s<br/>' % get_revision_label_from_ctx( ctx ) %> Contact the administrator of this Tool Shed as soon as possible and let them know that this repository has the following multiple heads which must be merged.<br/> diff -r 56b61e7d5bbcea1dff823cf78229289480ee15e7 -r 582d1e318dd3b604f2371a861f35c6fae1a2d36d templates/webapps/tool_shed/repository/view_repository.mako --- a/templates/webapps/tool_shed/repository/view_repository.mako +++ b/templates/webapps/tool_shed/repository/view_repository.mako @@ -72,7 +72,7 @@ from tool_shed.util.shed_util_common import get_revision_label_from_ctx heads_str = '' for ctx in heads: - heads_str += get_revision_label_from_ctx( ctx ) + heads_str += '%s<br/>' % get_revision_label_from_ctx( ctx ) %> Contact the administrator of this Tool Shed as soon as possible and let them know that this repository has the following multiple heads which must be merged.<br/> 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: Add tool shed features for displaying repository heads and alerting users if a repository has multiple heads that require merging.
by commits-noreply＠bitbucket.org 10 Jan '14

10 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/56b61e7d5bbc/ Changeset: 56b61e7d5bbc User: greg Date: 2014-01-10 22:30:45 Summary: Add tool shed features for displaying repository heads and alerting users if a repository has multiple heads that require merging. Affected #: 6 files diff -r 4ab2017348e25958bcd8babd8e110f574dff24df -r 56b61e7d5bbcea1dff823cf78229289480ee15e7 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 @@ -2255,6 +2255,7 @@ categories = suc.get_categories( trans ) selected_categories = [ rca.category_id for rca in repository.categories ] containers_dict = container_util.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) + heads = suc.get_repository_heads( repo ) return trans.fill_template( '/webapps/tool_shed/repository/manage_repository.mako', repo_name=repo_name, description=description, @@ -2262,6 +2263,7 @@ current_allow_push_list=current_allow_push_list, allow_push_select_field=allow_push_select_field, repo=repo, + heads=heads, repository=repository, containers_dict=containers_dict, repository_metadata=repository_metadata, @@ -3043,8 +3045,10 @@ status = 'error' containers_dict = container_util.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) + heads = suc.get_repository_heads( repo ) return trans.fill_template( '/webapps/tool_shed/repository/view_repository.mako', repo=repo, + heads=heads, repository=repository, repository_metadata=repository_metadata, metadata=metadata, diff -r 4ab2017348e25958bcd8babd8e110f574dff24df -r 56b61e7d5bbcea1dff823cf78229289480ee15e7 lib/tool_shed/grids/admin_grids.py --- a/lib/tool_shed/grids/admin_grids.py +++ b/lib/tool_shed/grids/admin_grids.py @@ -365,6 +365,7 @@ key="name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=True ), + RepositoryGrid.HeadsColumn( "Heads" ), RepositoryGrid.UserColumn( "Owner", model_class=model.User, link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), diff -r 4ab2017348e25958bcd8babd8e110f574dff24df -r 56b61e7d5bbcea1dff823cf78229289480ee15e7 lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -89,6 +89,29 @@ return escape_html( type_class.label ) + class HeadsColumn( grids.GridColumn ): + + def __init__( self, col_name ): + grids.GridColumn.__init__( self, col_name ) + + def get_value( self, trans, grid, repository ): + """Display the current repository heads.""" + repo_dir = repository.repo_path( trans.app ) + repo = hg.repository( suc.get_configured_ui(), repo_dir ) + heads = suc.get_repository_heads( repo ) + multiple_heads = len( heads ) > 1 + if multiple_heads: + heads_str = '<font color="red">' + else: + heads_str = '' + for ctx in heads: + heads_str += '%s<br/>' % suc.get_revision_label_from_ctx( ctx ) + heads_str.rstrip( '<br/>' ) + if multiple_heads: + heads_str += '</font>' + return heads_str + + class MetadataRevisionColumn( grids.GridColumn ): def __init__( self, col_name ): diff -r 4ab2017348e25958bcd8babd8e110f574dff24df -r 56b61e7d5bbcea1dff823cf78229289480ee15e7 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1108,6 +1108,11 @@ # This should never be reached - raise an exception? return v, None +def get_repository_heads( repo ): + """Return current repository heads, which are changesets with no child changesets.""" + heads = [ repo[ h ] for h in repo.heads( None ) ] + return heads + def get_repository_ids_requiring_prior_import_or_install( trans, tsr_ids, repository_dependencies ): """ This method is used in the Tool Shed when exporting a repository and it's dependencies, and in Galaxy when a repository and it's dependencies @@ -1213,18 +1218,20 @@ repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx: - return '%s:%s <i><font color="#666666">(%s)</font></i>' % \ - ( str( ctx.rev() ), changeset_revision, str( get_readable_ctx_date( ctx ) ) ) + return get_revision_label_from_ctx( ctx ) else: return "-1:%s" % changeset_revision +def get_revision_label_from_ctx( ctx ): + return '%s:%s <i><font color="#666666">(%s)</font></i>' % \ + ( str( ctx.rev() ), str( ctx ), str( get_readable_ctx_date( ctx ) ) ) + def get_rev_label_from_changeset_revision( repo, changeset_revision ): """Given a changeset revision hash, return two strings, the changeset rev and the changeset revision hash.""" ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx: rev = '%04d' % ctx.rev() - label = '%s:%s <i><font color="#666666">(%s)</font></i>' % \ - ( str( ctx.rev() ), changeset_revision, str( get_readable_ctx_date( ctx ) ) ) + label = get_revision_label_from_ctx( ctx ) else: rev = '-1' label = "-1:%s" % changeset_revision diff -r 4ab2017348e25958bcd8babd8e110f574dff24df -r 56b61e7d5bbcea1dff823cf78229289480ee15e7 templates/webapps/tool_shed/repository/manage_repository.mako --- a/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/templates/webapps/tool_shed/repository/manage_repository.mako @@ -83,6 +83,10 @@ can_render_skip_tool_test_section = True else: can_render_skip_tool_test_section = False + if heads: + multiple_heads = len( heads ) > 1 + else: + multiple_heads = False %><%! @@ -115,6 +119,18 @@ <div class="warningmessage"> This repository has been marked as deprecated, so some tool shed features may be restricted. </div> +%elif multiple_heads: + <div class="warningmessage"> + <% + from tool_shed.util.shed_util_common import get_revision_label_from_ctx + heads_str = '' + for ctx in heads: + heads_str += get_revision_label_from_ctx( ctx ) + %> + Contact the administrator of this Tool Shed as soon as possible and let them know that + this repository has the following multiple heads which must be merged.<br/> + ${heads_str} + </div> %endif %if len( changeset_revision_select_field.options ) > 1: diff -r 4ab2017348e25958bcd8babd8e110f574dff24df -r 56b61e7d5bbcea1dff823cf78229289480ee15e7 templates/webapps/tool_shed/repository/view_repository.mako --- a/templates/webapps/tool_shed/repository/view_repository.mako +++ b/templates/webapps/tool_shed/repository/view_repository.mako @@ -25,6 +25,11 @@ tip_str = '' sharable_link_label = 'Sharable link to this repository revision:' sharable_link_changeset_revision = changeset_revision + + if heads: + multiple_heads = len( heads ) > 1 + else: + multiple_heads = False %><%! @@ -61,6 +66,18 @@ <div class="warningmessage"> This repository has been marked as deprecated, so some tool shed features may be restricted. </div> +%elif multiple_heads: + <div class="warningmessage"> + <% + from tool_shed.util.shed_util_common import get_revision_label_from_ctx + heads_str = '' + for ctx in heads: + heads_str += get_revision_label_from_ctx( ctx ) + %> + Contact the administrator of this Tool Shed as soon as possible and let them know that + this repository has the following multiple heads which must be merged.<br/> + ${heads_str} + </div> %endif %if len( changeset_revision_select_field.options ) > 1: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: PEP-8 fixes for pages API.
by commits-noreply＠bitbucket.org 10 Jan '14

10 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4ab2017348e2/ Changeset: 4ab2017348e2 User: jmchilton Date: 2014-01-10 22:08:30 Summary: PEP-8 fixes for pages API. Affected #: 2 files diff -r 43a964de0758ea9deffb88fd2c59441a13cae14b -r 4ab2017348e25958bcd8babd8e110f574dff24df lib/galaxy/webapps/galaxy/api/page_revisions.py --- a/lib/galaxy/webapps/galaxy/api/page_revisions.py +++ b/lib/galaxy/webapps/galaxy/api/page_revisions.py @@ -4,13 +4,12 @@ import logging from galaxy import web from galaxy.web.base.controller import SharableItemSecurityMixin, BaseAPIController, SharableMixin -from galaxy.model.search import GalaxySearchEngine from galaxy.model.item_attrs import UsesAnnotations -from galaxy.exceptions import ItemAccessibilityException from galaxy.util.sanitize_html import sanitize_html log = logging.getLogger( __name__ ) + class PageRevisionsController( BaseAPIController, SharableItemSecurityMixin, UsesAnnotations, SharableMixin ): @web.expose_api @@ -32,7 +31,6 @@ out.append( self.encode_all_ids( trans, page.to_dict(), True) ) return out - @web.expose_api def create( self, trans, page_id, payload, **kwd ): """ @@ -46,11 +44,10 @@ 'content' = New content of the page :rtype: dictionary - :returns: Dictionary with 'success' or 'error' element to indicate the result of the request + :returns: Dictionary with 'success' or 'error' element to indicate the result of the request """ - user = trans.get_user() error_str = "" - + if not page_id: error_str = "page_id is required" elif not payload.get("content", None): @@ -61,7 +58,7 @@ page = trans.sa_session.query( trans.app.model.Page ).get( trans.security.decode_id(page_id) ) if page is None: return { "error" : "page not found"} - + if not self.security_check( trans, page, True, True ): return { "error" : "page not found"} @@ -82,6 +79,6 @@ session = trans.sa_session session.flush() - return {"success" : "revision posted"} - - return { "error" : error_str } + return { "success" : "revision posted" } + + return { "error" : error_str } diff -r 43a964de0758ea9deffb88fd2c59441a13cae14b -r 4ab2017348e25958bcd8babd8e110f574dff24df lib/galaxy/webapps/galaxy/api/pages.py --- a/lib/galaxy/webapps/galaxy/api/pages.py +++ b/lib/galaxy/webapps/galaxy/api/pages.py @@ -4,13 +4,12 @@ import logging from galaxy import web from galaxy.web.base.controller import SharableItemSecurityMixin, BaseAPIController, SharableMixin -from galaxy.model.search import GalaxySearchEngine from galaxy.model.item_attrs import UsesAnnotations -from galaxy.exceptions import ItemAccessibilityException from galaxy.util.sanitize_html import sanitize_html log = logging.getLogger( __name__ ) + class PagesController( BaseAPIController, SharableItemSecurityMixin, UsesAnnotations, SharableMixin ): @web.expose_api @@ -26,7 +25,7 @@ :returns: dictionaries containing summary or detailed Page information """ out = [] - + if trans.user_is_admin(): r = trans.sa_session.query( trans.app.model.Page ) if not deleted: @@ -48,7 +47,6 @@ return out - @web.expose_api def create( self, trans, payload, **kwd ): """ @@ -67,7 +65,7 @@ """ user = trans.get_user() error_str = "" - + if not payload.get("title", None): error_str = "Page name is required" elif not payload.get("slug", None): @@ -85,7 +83,7 @@ page = trans.app.model.Page() page.title = payload['title'] page.slug = payload['slug'] - page_annotation = sanitize_html( payload.get("annotation",""), 'utf-8', 'text/html' ) + page_annotation = sanitize_html( payload.get( "annotation", "" ), 'utf-8', 'text/html' ) self.add_item_annotation( trans.sa_session, trans.get_user(), page, page_annotation ) page.user = user # And the first (empty) page revision @@ -99,11 +97,10 @@ session.add( page ) session.flush() - rval = self.encode_all_ids( trans, page.to_dict(), True) + rval = self.encode_all_ids( trans, page.to_dict(), True ) return rval - - return { "error" : error_str } + return { "error" : error_str } @web.expose_api def delete( self, trans, id, **kwd ): @@ -115,9 +112,9 @@ :param id: ID of page to be deleted :rtype: dict - :returns: Dictionary with 'success' or 'error' element to indicate the result of the request + :returns: Dictionary with 'success' or 'error' element to indicate the result of the request """ - page_id = id; + page_id = id try: page = trans.sa_session.query(self.app.model.Page).get(trans.security.decode_id(page_id)) except Exception, e: @@ -130,7 +127,7 @@ #Mark a workflow as deleted page.deleted = True trans.sa_session.flush() - return {"success" : "Deleted", "id" : page_id} + return { "success" : "Deleted", "id" : page_id } @web.expose_api def show( self, trans, id, **kwd ): @@ -146,6 +143,6 @@ """ page = trans.sa_session.query( trans.app.model.Page ).get( trans.security.decode_id( id ) ) self.security_check( trans, page, check_ownership=False, check_accessible=True) - rval = self.encode_all_ids( trans, page.to_dict(), True) + rval = self.encode_all_ids( trans, page.to_dict(), True ) rval['content'] = page.latest_revision.content - return rval \ No newline at end of file + return rval Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Library_contents API: Fix permissions and dataset ref on LD delete
by commits-noreply＠bitbucket.org 10 Jan '14

10 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/43a964de0758/ Changeset: 43a964de0758 User: carlfeberhard Date: 2014-01-10 22:03:04 Summary: Library_contents API: Fix permissions and dataset ref on LD delete Affected #: 1 file diff -r ad9661041105bbffe4772ee9bedbcf174c53eac3 -r 43a964de0758ea9deffb88fd2c59441a13cae14b lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -324,8 +324,7 @@ """ delete( self, trans, library_id, id, **kwd ) * DELETE /api/libraries/{library_id}/contents/{id} - delete the HDA with the given ``id`` - + delete the LibraryDataset with the given ``id`` :type id: str :param id: the encoded id of the library dataset to delete @@ -333,7 +332,7 @@ :param kwd: (optional) dictionary structure containing: * payload: a dictionary itself containing: - * purge: if True, purge the HDA + * purge: if True, purge the LD :rtype: dict :returns: an error object if an error occurred or a dictionary containing: @@ -345,21 +344,34 @@ purge = False if kwd.get( 'payload', None ): purge = util.string_as_bool( kwd['payload'].get( 'purge', False ) ) + rval = { 'id' : id } try: - hda = self.get_library_dataset( trans, id, check_ownership=False, check_accessible=True ) - hda.deleted = True + ld = self.get_library_dataset( trans, id, check_ownership=False, check_accessible=True ) + user_is_admin = trans.user_is_admin() + can_modify = trans.app.security_agent.can_modify_library_item( trans.user.all_roles(), ld ) + print 'is_admin: %s, can_modify: %s' % ( user_is_admin, can_modify ) + if not ( user_is_admin or can_modify ): + trans.response.status = 403 + rval.update({ 'error': 'Unauthorized to delete or purge this library dataset' }) + return rval + + ld.deleted = True if purge: - if not trans.app.config.allow_user_dataset_purge: - raise exceptions.httpexceptions.HTTPForbidden( - detail='This instance does not allow user dataset purging' ) - hda.purged = True - trans.sa_session.add( hda ) + ld.purged = True + trans.sa_session.add( ld ) trans.sa_session.flush() - if hda.dataset.user_can_purge: + + #TODO: had to change this up a bit from Dataset.user_can_purge + dataset = ld.library_dataset_dataset_association.dataset + no_history_assoc = len( dataset.history_associations ) == len( dataset.purged_history_associations ) + no_library_assoc = dataset.library_associations == [ ld.library_dataset_dataset_association ] + can_purge_dataset = not dataset.purged and no_history_assoc and no_library_assoc + + if can_purge_dataset: try: - hda.dataset.full_delete() - trans.sa_session.add( hda.dataset ) + ld.library_dataset_dataset_association.dataset.full_delete() + trans.sa_session.add( ld.dataset ) except: pass # flush now to preserve deleted state in case of later interruption @@ -367,8 +379,9 @@ rval[ 'purged' ] = True trans.sa_session.flush() rval[ 'deleted' ] = True + except exceptions.httpexceptions.HTTPInternalServerError, http_server_err: - log.exception( 'HDA API, delete: uncaught HTTPInternalServerError: %s, %s\n%s', + log.exception( 'Library_contents API, delete: uncaught HTTPInternalServerError: %s, %s\n%s', id, str( kwd ), str( http_server_err ) ) raise except exceptions.httpexceptions.HTTPException: 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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