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commit/galaxy-central: dan: Have data source tools display the provided 'name' parameter as the initial dataset name.
by commits-noreply＠bitbucket.org 22 Apr '13

22 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1e3d92ec22b2/ Changeset: 1e3d92ec22b2 User: dan Date: 2013-04-22 22:58:49 Summary: Have data source tools display the provided 'name' parameter as the initial dataset name. Affected #: 3 files diff -r ea0b7ca55aec1552718132227d80b0ae82ca2913 -r 1e3d92ec22b2794bfa2294edb74695c580791406 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -36,6 +36,7 @@ from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper from galaxy.jobs import ParallelismInfo from galaxy.tools.actions import DefaultToolAction +from galaxy.tools.actions.data_source import DataSourceToolAction from galaxy.tools.actions.data_manager import DataManagerToolAction from galaxy.tools.deps import DependencyManager from galaxy.tools.parameters import check_param, params_from_strings, params_to_strings @@ -3028,6 +3029,7 @@ allow the user to query and extract data from another web site. """ tool_type = 'data_source' + default_tool_action = DataSourceToolAction 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 ) ) diff -r ea0b7ca55aec1552718132227d80b0ae82ca2913 -r 1e3d92ec22b2794bfa2294edb74695c580791406 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -342,9 +342,10 @@ params['on_string'] = on_text data.name = fill_template( output.label, context=params ) else: - data.name = tool.name - if on_text: - data.name += ( " on " + on_text ) + if params is None: + params = make_dict_copy( incoming ) + 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 if output.actions: @@ -430,3 +431,9 @@ trans.app.job_queue.put( job.id, job.tool_id ) trans.log_event( "Added job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) return job, out_data + + def _get_default_data_name( self, dataset, tool, on_text=None, trans=None, incoming=None, history=None, params=None, job_params=None, **kwd ): + name = tool.name + if on_text: + name += ( " on " + on_text ) + return name diff -r ea0b7ca55aec1552718132227d80b0ae82ca2913 -r 1e3d92ec22b2794bfa2294edb74695c580791406 lib/galaxy/tools/actions/data_source.py --- /dev/null +++ b/lib/galaxy/tools/actions/data_source.py @@ -0,0 +1,12 @@ +from __init__ import DefaultToolAction + +import logging +log = logging.getLogger( __name__ ) + +class DataSourceToolAction( DefaultToolAction ): + """Tool action used for Data Source Tools""" + + def _get_default_data_name( self, dataset, tool, on_text=None, trans=None, incoming=None, history=None, params=None, job_params=None, **kwd ): + if incoming and 'name' in incoming: + return incoming[ 'name' ] + return super( DataSourceToolAction, self )._get_default_data_name( dataset, tool, on_text=on_text, trans=trans, incoming=incoming, history=history, params=params, job_params=job_params ) 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: Raise exceptions when tool dependency definition <install> and <set_environment> tags define an unsupported version attribute.
by commits-noreply＠bitbucket.org 22 Apr '13

22 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ea0b7ca55aec/ Changeset: ea0b7ca55aec User: greg Date: 2013-04-22 20:51:48 Summary: Raise exceptions when tool dependency definition <install> and <set_environment> tags define an unsupported version attribute. Affected #: 1 file diff -r 42632cc2a166e8933fe29496a6087309769b8987 -r ea0b7ca55aec1552718132227d80b0ae82ca2913 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -151,6 +151,8 @@ action_dict[ env_elem.tag ] = env_var_dicts actions.append( ( action_type, action_dict ) ) return tool_dependency, actions + else: + raise NotImplementedError( 'Only install version 1.0 is currently supported (i.e., change your tag to be <install version="1.0">).' ) return None, actions def install_and_build_package_via_fabric( app, tool_dependency, actions_dict ): @@ -299,6 +301,8 @@ sa_session.refresh( tool_dependency ) if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR: print package_name, 'version', package_version, 'installed in', install_dir + else: + raise NotImplementedError( 'Only install version 1.0 is currently supported (i.e., change your tag to be <install version="1.0">).' ) elif package_elem.tag == 'readme': # Nothing to be done. continue @@ -550,6 +554,8 @@ sa_session.add( tool_dependency ) sa_session.flush() print 'Environment variable ', env_var_name, 'set in', install_dir + else: + raise NotImplementedError( 'Only set_environment version 1.0 is currently supported (i.e., change your tag to be <set_environment version="1.0">).' ) def strip_path( fpath ): if not fpath: 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: Don't use paging on tool shed repository grids since generated urls filter out needed request params when using paging.
by commits-noreply＠bitbucket.org 22 Apr '13

22 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/42632cc2a166/ Changeset: 42632cc2a166 User: greg Date: 2013-04-22 19:37:28 Summary: Don't use paging on tool shed repository grids since generated urls filter out needed request params when using paging. Affected #: 1 file diff -r 1037ab5b4f761c104b01cf0aee9222d28a67034b -r 42632cc2a166e8933fe29496a6087309769b8987 lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -63,7 +63,7 @@ standard_filters = [] num_rows_per_page = 50 preserve_state = False - use_paging = True + use_paging = False class ValidCategoryGrid( CategoryGrid ): @@ -105,7 +105,7 @@ standard_filters = [] num_rows_per_page = 50 preserve_state = False - use_paging = True + use_paging = False class RepositoryGrid( grids.Grid ): @@ -310,6 +310,7 @@ allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ) ] + use_paging = False def build_initial_query( self, trans, **kwd ): category_id = kwd.get( 'id', None ) @@ -353,7 +354,7 @@ default_filter = dict( deleted="False" ) num_rows_per_page = 50 preserve_state = False - use_paging = True + use_paging = False def build_initial_query( self, trans, **kwd ): decoded_user_id = trans.security.decode_id( kwd[ 'user_id' ] ) @@ -395,6 +396,7 @@ allow_multiple=False, condition=( lambda item: not item.deleted and item.deprecated ), async_compatible=False ) ] + use_paging = False def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( model.Repository ) \ @@ -424,6 +426,7 @@ key="free-text-search", visible=False, filterable="standard" ) ) + use_paging = False def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( model.Repository ) \ @@ -462,7 +465,7 @@ async_compatible=False ) ] global_actions = [ grids.GridAction( "User preferences", dict( controller='user', action='index', cntrller='repository' ) ) - ] + ] class MyWritableRepositoriesGrid( RepositoryGrid ): @@ -499,6 +502,7 @@ allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ) ] + use_paging = False def build_initial_query( self, trans, **kwd ): # TODO: improve performance by adding a db table associating users with repositories for which they have write access. @@ -589,6 +593,7 @@ visible=False, filterable="standard" ) ) operations = [] + use_paging = False def build_initial_query( self, trans, **kwd ): if 'id' in kwd: @@ -665,7 +670,7 @@ default_filter = {} num_rows_per_page = 50 preserve_state = False - use_paging = True + use_paging = False def build_initial_query( self, trans, **kwd ): match_tuples = kwd.get( 'match_tuples', [] ) @@ -823,7 +828,7 @@ default_filter = dict( malicious="False" ) num_rows_per_page = 50 preserve_state = False - use_paging = True + use_paging = False def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( model.RepositoryMetadata ) \ 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: inithello: Tool shed functional tests for installation order with complex repository dependencies. Modified tests 0100 and 1100 to be less ambiguous regarding which repository contains what.
by commits-noreply＠bitbucket.org 22 Apr '13

22 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1037ab5b4f76/ Changeset: 1037ab5b4f76 User: inithello Date: 2013-04-22 18:53:43 Summary: Tool shed functional tests for installation order with complex repository dependencies. Modified tests 0100 and 1100 to be less ambiguous regarding which repository contains what. Affected #: 8 files diff -r a8139a367ed3de938f5d71336a06f1f768132469 -r 1037ab5b4f761c104b01cf0aee9222d28a67034b test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -800,8 +800,12 @@ self.check_for_strings( strings_displayed, strings_not_displayed ) # This section is tricky, due to the way twill handles form submission. The tool dependency checkbox needs to # be hacked in through tc.browser, putting the form field in kwd doesn't work. + form = tc.browser.get_form( 'select_tool_panel_section' ) + submit_button = 'select_tool_panel_section_button' + if form is None: + form = tc.browser.get_form( 'select_shed_tool_panel_config' ) + submit_button = 'select_shed_tool_panel_config_button' if 'install_tool_dependencies' in self.last_page(): - form = tc.browser.get_form( 'select_tool_panel_section' ) checkbox = form.find_control( id="install_tool_dependencies" ) checkbox.disabled = False if install_tool_dependencies: @@ -816,14 +820,10 @@ kwd[ 'shed_tool_conf' ] = self.shed_tool_conf if new_tool_panel_section: kwd[ 'new_tool_panel_section' ] = new_tool_panel_section - if includes_tools_for_display_in_tool_panel: - self.submit_form( 1, 'select_tool_panel_section_button', **kwd ) - self.check_for_strings( post_submit_strings_displayed, strings_not_displayed ) - else: - self.check_for_strings( strings_displayed=[ 'Choose the configuration file whose tool_path setting will be used for installing repositories' ] ) - args = dict( shed_tool_conf=self.shed_tool_conf ) - self.submit_form( 1, 'select_shed_tool_panel_config_button', **args ) - self.check_for_strings( post_submit_strings_displayed, strings_not_displayed ) + if not includes_tools_for_display_in_tool_panel: + self.check_for_strings( strings_displayed=[ 'Choose the configuration file' ] ) + self.submit_form( 1, submit_button, **kwd ) + self.check_for_strings( post_submit_strings_displayed, strings_not_displayed ) repository_ids = self.initiate_installation_process( new_tool_panel_section=new_tool_panel_section ) self.wait_for_repository_installation( repository_ids ) diff -r a8139a367ed3de938f5d71336a06f1f768132469 -r 1037ab5b4f761c104b01cf0aee9222d28a67034b test/tool_shed/functional/test_0100_complex_repository_dependencies.py --- a/test/tool_shed/functional/test_0100_complex_repository_dependencies.py +++ b/test/tool_shed/functional/test_0100_complex_repository_dependencies.py @@ -6,11 +6,11 @@ bwa_base_repository_name = 'bwa_base_repository_0100' bwa_base_repository_description = "BWA Base" -bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at bwa_tool_repository_0100" +bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at package_bwa_0_5_9_0100" -bwa_tool_repository_name = 'bwa_tool_repository_0100' -bwa_tool_repository_description = "BWA Tool" -bwa_tool_repository_long_description = "BWA repository with a package tool dependency defined for BWA 0.5.9." +bwa_package_repository_name = 'package_bwa_0_5_9_0100' +bwa_package_repository_description = "BWA Tool" +bwa_package_repository_long_description = "BWA repository with a package tool dependency defined for BWA 0.5.9." category_name = 'Test 0100 Complex Repository Dependencies' category_description = 'Test 0100 Complex Repository Dependencies' @@ -32,15 +32,15 @@ assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email admin_user_private_role = test_db_util.get_private_role( admin_user ) - def test_0005_create_bwa_tool_repository( self ): - '''Create and populate bwa_tool_repository_0100.''' + def test_0005_create_bwa_package_repository( self ): + '''Create and populate package_bwa_0_5_9_0100.''' category = self.create_category( name=category_name, description=category_description ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) - # Create a repository named bwa_tool_repository_0100 owned by user1. - repository = self.get_or_create_repository( name=bwa_tool_repository_name, - description=bwa_tool_repository_description, - long_description=bwa_tool_repository_long_description, + # Create a repository named package_bwa_0_5_9_0100 owned by user1. + repository = self.get_or_create_repository( name=bwa_package_repository_name, + description=bwa_package_repository_description, + long_description=bwa_package_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) @@ -53,7 +53,7 @@ commit_message='Uploaded tool_dependencies.xml.', strings_displayed=[ 'The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool' ], strings_not_displayed=[] ) - # Visit the manage repository page for bwa_tool_repository_0100. + # Visit the manage repository page for package_bwa_0_5_9_0100. self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'may not be', 'in this repository' ] ) def test_0010_create_bwa_base_repository( self ): @@ -85,10 +85,10 @@ xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) # The repository named bwa_base_repository_0100 is the dependent repository. base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) - # The tool_repository named bwa_tool_repository_0100 is the required repository. - tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + # The repository named package_bwa_0_5_9_0100 is the required repository. + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) url = 'http://http://this is not an url!' - name = 'bwa_tool_repository_0100' + name = 'package_bwa_0_5_9_0100' owner = 'user1' changeset_revision = self.get_repository_tip( tool_repository ) strings_displayed = [ 'Repository dependencies are currently supported only within the same tool shed' ] @@ -108,14 +108,14 @@ xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) - # The tool_repository named bwa_tool_repository_0100 is the required repository. - tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + # The repository named package_bwa_0_5_9_0100 is the required repository. + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) url = self.url name = 'invalid_repository!?' owner = 'user1' changeset_revision = self.get_repository_tip( tool_repository ) strings_displayed = [ 'because the name is invalid' ] - # Populate the dependent base_repository named bwa_tool_repository_0100 with an invalid tool_dependencies.xml file. + # Populate the dependent base_repository named package_bwa_0_5_9_0100 with an invalid tool_dependencies.xml file. repository_tuple = ( url, name, owner, changeset_revision ) self.create_repository_dependency( repository=base_repository, filepath=dependency_path, @@ -131,10 +131,10 @@ xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) - # The tool_repository named bwa_tool_repository_0100 is the required repository. - tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + # The repository named package_bwa_0_5_9_0100 is the required repository. + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) url = self.url - name = 'bwa_tool_repository_0100' + name = 'package_bwa_0_5_9_0100' owner = 'invalid_owner!?' changeset_revision = self.get_repository_tip( tool_repository ) strings_displayed = [ 'because the owner is invalid.' ] @@ -153,10 +153,10 @@ xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) - # The tool_repository named bwa_tool_repository_0100 is the required repository. - tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + # The repository named package_bwa_0_5_9_0100 is the required repository. + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) url = self.url - name = 'bwa_tool_repository_0100' + name = 'package_bwa_0_5_9_0100' owner = 'user1' changeset_revision = '1234abcd' strings_displayed = [ 'because the changeset revision is invalid.' ] @@ -170,14 +170,14 @@ version='0.5.9' ) def test_0035_generate_complex_repository_dependency( self ): - '''Generate and upload a valid tool_dependencies.xml file that specifies bwa_tool_repository_0100.''' + '''Generate and upload a valid tool_dependencies.xml file that specifies package_bwa_0_5_9_0100.''' # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) - # The tool_repository named bwa_tool_repository_0100 is the required repository. - tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + # The repository named package_bwa_0_5_9_0100 is the required repository. + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex' ] ) url = self.url - name = 'bwa_tool_repository_0100' + name = 'package_bwa_0_5_9_0100' owner = 'user1' changeset_revision = self.get_repository_tip( tool_repository ) repository_tuple = ( url, name, owner, changeset_revision ) @@ -194,8 +194,8 @@ '''Generate and upload a new tool_dependencies.xml file that specifies an arbitrary file on the filesystem, and verify that bwa_base depends on the new changeset revision.''' # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) - # The tool_repository named bwa_tool_repository_0100 is the required repository. - tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + # The repository named package_bwa_0_5_9_0100 is the required repository. + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) previous_changeset = self.get_repository_tip( tool_repository ) old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'readme', 'tool_dependencies.xml' ) ) new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] ) @@ -220,12 +220,12 @@ self.display_manage_repository_page( tool_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) - # Visit the manage page of the bwa_tool_repository_0100 to confirm the valid tool dependency definition. + # Visit the manage page of the package_bwa_0_5_9_0100 to confirm the valid tool dependency definition. self.display_manage_repository_page( tool_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) # Visit the manage page of the bwa_base_repository_0100 to confirm the valid tool dependency definition - # and the updated changeset revision (updated tip) of the bwa_tool_repository_0100 repository is displayed + # and the updated changeset revision (updated tip) of the package_bwa_0_5_9_0100 repository is displayed # as the required repository revision. The original revision defined in the previously uploaded # tool_dependencies.xml file will be updated. self.display_manage_repository_page( base_repository, diff -r a8139a367ed3de938f5d71336a06f1f768132469 -r 1037ab5b4f761c104b01cf0aee9222d28a67034b test/tool_shed/functional/test_0170_complex_prior_installation_required.py --- /dev/null +++ b/test/tool_shed/functional/test_0170_complex_prior_installation_required.py @@ -0,0 +1,137 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +matplotlib_repository_name = 'package_matplotlib_1_2_0170' +matplotlib_repository_description = "Contains a tool dependency definition that downloads and compiles version 1.2.x of the the python matplotlib package." +matplotlib_repository_long_description = "This repository is intended to be defined as a complex repository dependency within a separate repository." + +numpy_repository_name = 'package_numpy_1_7_0170' +numpy_repository_description = "Contains a tool dependency definition that downloads and compiles version 1.7 of the the python numpy package." +numpy_repository_long_description = "This repository is intended to be defined as a complex repository dependency within a separate repository." + +category_name = 'Test 0170 Prior Installation Complex Dependencies' +category_description = 'Test 0170 Prior Installation Complex Dependencies' + +''' +1. Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170. +2. Create a complex repository dependency on package_numpy_1_7_0170, and upload this to package_matplotlib_1_2_0170. +3. Verify that package_matplotlib_1_2_0170 now depends on package_numpy_1_7_0170, and that the inherited tool dependency displays correctly. +''' + + +class TestComplexPriorInstallation( ShedTwillTestCase ): + '''Test features related to datatype converters.''' + + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + + def test_0005_create_matplotlib_repository( self ): + '''Create and populate the package_matplotlib_1_2_0170 repository.''' + ''' + This is step 1 - Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170. + ''' + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=matplotlib_repository_name, + description=matplotlib_repository_description, + long_description=matplotlib_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + filename='package_matplotlib/package_matplotlib_1_2.tar', + filepath=None, + valid_tools_only=False, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded matplotlib tool dependency tarball.', + strings_displayed=['orphan'], + strings_not_displayed=[] ) + + def test_0010_create_numpy_repository( self ): + '''Create and populate the package_numpy_1_7_0170 repository.''' + ''' + This is step 1 - Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170. + ''' + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=numpy_repository_name, + description=numpy_repository_description, + long_description=numpy_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + filename='package_numpy/package_numpy_1_7.tar', + filepath=None, + valid_tools_only=False, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded numpy tool dependency tarball.', + strings_displayed=['orphan'], + strings_not_displayed=[] ) + + def test_0015_create_complex_repository_dependency( self ): + '''Create a dependency on package_numpy_1_7_0170.''' + ''' + This is step 2 - Create a complex repository dependency on package_numpy_1_7_0170, and upload this to package_matplotlib_1_2_0170. + package_matplotlib_1_2_0170 should depend on package_numpy_1_7_0170, with prior_installation_required + set to True. When matplotlib is selected for installation, the result should be that numpy is compiled + and installed first. + ''' + numpy_repository = test_db_util.get_repository_by_name_and_owner( numpy_repository_name, common.test_user_1_name ) + matplotlib_repository = test_db_util.get_repository_by_name_and_owner( matplotlib_repository_name, common.test_user_1_name ) + # Generate the new dependency XML. Normally, the create_repository_dependency method would be used for this, but + # it replaces any existing tool or repository dependency XML file with the generated contents. This is undesirable + # in this case, because matplotlib already has an additional tool dependency definition that we don't want to + # overwrite. + new_xml = ' <package name="numpy" version="1.7">\n' + new_xml += ' <repository toolshed="%s" name="%s" owner="%s" changeset_revision="%s" prior_installation_required="True" />\n' + new_xml += ' </package>\n' + url = self.url + name = numpy_repository.name + owner = numpy_repository.user.username + changeset_revision = self.get_repository_tip( numpy_repository ) + processed_xml = new_xml % ( url, name, owner, changeset_revision ) + original_xml = file( self.get_filename( 'package_matplotlib/tool_dependencies.xml' ), 'r' ).read() + dependency_xml_path = self.generate_temp_path( 'test_0170', additional_paths=[ 'matplotlib' ] ) + new_xml_file = os.path.join( dependency_xml_path, 'tool_dependencies.xml' ) + file( new_xml_file, 'w' ).write( original_xml.replace( '', processed_xml ) ) + # Upload the generated complex repository dependency XML to the matplotlib repository. + self.upload_file( matplotlib_repository, + filename='tool_dependencies.xml', + filepath=dependency_xml_path, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded complex repository dependency on numpy 1.7.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0020_verify_generated_dependency( self ): + '''Verify that matplotlib now has a package tool dependency and a complex repository dependency.''' + ''' + This is step 3 - Verify that package_matplotlib_1_2_0170 now depends on package_numpy_1_7_0170, and that the inherited tool + dependency displays correctly. + 'Inhherited' in this case means that matplotlib should show a package tool dependency on numpy version 1.7, and a repository + dependency on the latest revision of package_numpy_1_7_0170. + ''' + numpy_repository = test_db_util.get_repository_by_name_and_owner( numpy_repository_name, common.test_user_1_name ) + matplotlib_repository = test_db_util.get_repository_by_name_and_owner( matplotlib_repository_name, common.test_user_1_name ) + changeset_revision = self.get_repository_tip( numpy_repository ) + self.check_repository_dependency( matplotlib_repository, depends_on_repository=numpy_repository ) + self.display_manage_repository_page( matplotlib_repository, strings_displayed=[ 'numpy', '1.7', 'package', changeset_revision ] ) + + \ No newline at end of file diff -r a8139a367ed3de938f5d71336a06f1f768132469 -r 1037ab5b4f761c104b01cf0aee9222d28a67034b test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py --- a/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py +++ b/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py @@ -3,11 +3,11 @@ bwa_base_repository_name = 'bwa_base_repository_0100' bwa_base_repository_description = "BWA Base" -bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at bwa_tool_repository_0100" +bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at package_bwa_0_5_9_0100" -bwa_tool_repository_name = 'bwa_tool_repository_0100' -bwa_tool_repository_description = "BWA Tool" -bwa_tool_repository_long_description = "BWA repository with a package tool dependency defined for BWA 0.5.9." +bwa_package_repository_name = 'package_bwa_0_5_9_0100' +bwa_package_repository_description = "BWA Tool" +bwa_package_repository_long_description = "BWA repository with a package tool dependency defined to compile and install BWA 0.5.9." category_name = 'Test 0100 Complex Repository Dependencies' category_description = 'Test 0100 Complex Repository Dependencies' @@ -30,15 +30,15 @@ assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email admin_user_private_role = test_db_util.get_private_role( admin_user ) - def test_0005_create_bwa_tool_repository( self ): + def test_0005_create_bwa_package_repository( self ): '''Create and populate bwa_tool_0100.''' global running_standalone category = self.create_category( name=category_name, description=category_description ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) - repository = self.get_or_create_repository( name=bwa_tool_repository_name, - description=bwa_tool_repository_description, - long_description=bwa_tool_repository_long_description, + repository = self.get_or_create_repository( name=bwa_package_repository_name, + description=bwa_package_repository_description, + long_description=bwa_package_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) @@ -73,7 +73,7 @@ owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) - tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) self.upload_file( repository, filename='bwa/complex/bwa_base.tar', filepath=None, @@ -91,7 +91,7 @@ dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) - tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) url = 'http://http://this is not an url!' name = tool_repository.name owner = tool_repository.user.username @@ -113,7 +113,7 @@ dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) - tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) url = self.url name = 'invalid_repository!?' owner = tool_repository.user.username @@ -135,7 +135,7 @@ dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) - tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) url = self.url name = tool_repository.name owner = 'invalid_owner!?' @@ -157,7 +157,7 @@ dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) - tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) url = self.url name = tool_repository.name owner = tool_repository.user.username @@ -173,11 +173,11 @@ version='0.5.9' ) def test_0035_generate_valid_complex_repository_dependency( self ): - '''Generate and upload a valid tool_dependencies.xml file that specifies bwa_tool_repository_0100.''' + '''Generate and upload a valid tool_dependencies.xml file that specifies package_bwa_0_5_9_0100.''' global running_standalone if running_standalone: base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) - tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) url = self.url @@ -199,7 +199,7 @@ global running_standalone if running_standalone: base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) - tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) previous_changeset = self.get_repository_tip( tool_repository ) old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'readme', 'tool_dependencies.xml' ) ) new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] ) @@ -225,7 +225,7 @@ self.galaxy_logout() self.galaxy_login( email=common.admin_email, username=common.admin_username ) base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) - tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) preview_strings_displayed = [ tool_repository.name, self.get_repository_tip( tool_repository ) ] self.install_repository( bwa_base_repository_name, common.test_user_1_name, @@ -238,19 +238,19 @@ def test_0050_verify_installed_repositories( self ): '''Verify that the installed repositories are displayed properly.''' base_repository = test_db_util.get_installed_repository_by_name_owner( bwa_base_repository_name, common.test_user_1_name ) - tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_tool_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_package_repository_name, common.test_user_1_name ) strings_displayed = [ 'bwa_base_repository_0100', 'user1', base_repository.installed_changeset_revision ] - strings_displayed.extend( [ 'bwa_tool_repository_0100', 'user1', tool_repository.installed_changeset_revision ] ) + strings_displayed.extend( [ 'package_bwa_0_5_9_0100', 'user1', tool_repository.installed_changeset_revision ] ) strings_displayed.append( self.url.replace( 'http://', '' ) ) self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=[] ) - strings_displayed = [ 'bwa_tool_repository_0100', 'user1', tool_repository.installed_changeset_revision ] + strings_displayed = [ 'package_bwa_0_5_9_0100', 'user1', tool_repository.installed_changeset_revision ] strings_not_displayed = [ 'Missing tool dependencies' ] self.display_installed_repository_manage_page( tool_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) strings_displayed = [ 'bwa_base_repository_0100', 'user1', - 'bwa_tool_repository_0100', + 'package_bwa_0_5_9_0100', base_repository.installed_changeset_revision, tool_repository.installed_changeset_revision ] strings_not_displayed = [ 'Missing tool dependencies' ] @@ -261,7 +261,7 @@ def test_0055_verify_complex_tool_dependency( self ): '''Verify that the generated env.sh contains the right data.''' base_repository = test_db_util.get_installed_repository_by_name_owner( bwa_base_repository_name, common.test_user_1_name ) - tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_tool_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_package_repository_name, common.test_user_1_name ) env_sh_path = os.path.join( self.galaxy_tool_dependency_dir, 'bwa', '0.5.9', @@ -274,17 +274,17 @@ if tool_repository.installed_changeset_revision not in contents: raise AssertionError( 'Installed changeset revision %s not found in env.sh.\nContents of env.sh: %s' % \ ( tool_repository.installed_changeset_revision, contents ) ) - if 'bwa_tool_repository_0100' not in contents: - raise AssertionError( 'Repository name bwa_tool_repository_0100 not found in env.sh.\nContents of env.sh: %s' % contents ) + if 'package_bwa_0_5_9_0100' not in contents: + raise AssertionError( 'Repository name package_bwa_0_5_9_0100 not found in env.sh.\nContents of env.sh: %s' % contents ) def test_0060_verify_tool_dependency_uninstallation( self ): - '''Uninstall the bwa_tool_repository_0100 repository.''' + '''Uninstall the package_bwa_0_5_9_0100 repository.''' ''' Uninstall the repository that defines an orphan tool dependency on BWA 0.5.9, and verify that this results in the compiled binary package also being removed. ''' base_repository = test_db_util.get_installed_repository_by_name_owner( bwa_base_repository_name, common.test_user_1_name ) - tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_tool_repository_name, common.test_user_1_name ) + tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_package_repository_name, common.test_user_1_name ) self.uninstall_repository( tool_repository, remove_from_disk=True ) env_sh_path = os.path.join( self.galaxy_tool_dependency_dir, 'bwa', diff -r a8139a367ed3de938f5d71336a06f1f768132469 -r 1037ab5b4f761c104b01cf0aee9222d28a67034b test/tool_shed/functional/test_1170_complex_prior_installation_required.py --- /dev/null +++ b/test/tool_shed/functional/test_1170_complex_prior_installation_required.py @@ -0,0 +1,181 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +matplotlib_repository_name = 'package_matplotlib_1_2_0170' +matplotlib_repository_description = "Contains a tool dependency definition that downloads and compiles version 1.2.x of the the python matplotlib package." +matplotlib_repository_long_description = "This repository is intended to be defined as a complex repository dependency within a separate repository." + +numpy_repository_name = 'package_numpy_1_7_0170' +numpy_repository_description = "Contains a tool dependency definition that downloads and compiles version 1.7 of the the python numpy package." +numpy_repository_long_description = "This repository is intended to be defined as a complex repository dependency within a separate repository." + +category_name = 'Test 0170 Prior Installation Complex Dependencies' +category_description = 'Test 0170 Prior Installation Complex Dependencies' + +''' +1. Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170. +2. Create a complex repository dependency on package_numpy_1_7_0170, and upload this to package_matplotlib_1_2_0170. +3. Verify that package_matplotlib_1_2_0170 now depends on package_numpy_1_7_0170, and that the inherited tool dependency displays correctly. +4. Install package_matplotlib_1_2_0170 with repository dependencies. +5. Verify that the prior_installation_required attribute resulted in package_numpy_1_7_0170 being installed first. +''' + +running_standalone = False + + +class TestComplexPriorInstallation( ShedTwillTestCase ): + '''Test features related to datatype converters.''' + + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + + def test_0005_create_matplotlib_repository( self ): + '''Create and populate the package_matplotlib_1_2_0170 repository.''' + ''' + This is step 1 - Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170. + ''' + global running_standalone + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=matplotlib_repository_name, + description=matplotlib_repository_description, + long_description=matplotlib_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + running_standalone = True + self.upload_file( repository, + filename='package_matplotlib/package_matplotlib_1_2.tar', + filepath=None, + valid_tools_only=False, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded matplotlib tool dependency tarball.', + strings_displayed=['orphan'], + strings_not_displayed=[] ) + + def test_0010_create_numpy_repository( self ): + '''Create and populate the package_numpy_1_7_0170 repository.''' + ''' + This is step 1 - Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170. + ''' + global running_standalone + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + if running_standalone: + repository = self.get_or_create_repository( name=numpy_repository_name, + description=numpy_repository_description, + long_description=numpy_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + filename='package_numpy/package_numpy_1_7.tar', + filepath=None, + valid_tools_only=False, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded numpy tool dependency tarball.', + strings_displayed=['orphan'], + strings_not_displayed=[] ) + + def test_0015_create_complex_repository_dependency( self ): + '''Create a dependency on package_numpy_1_7_0170.''' + ''' + This is step 2 - Create a complex repository dependency on package_numpy_1_7_0170, and upload this to package_matplotlib_1_2_0170. + package_matplotlib_1_2_0170 should depend on package_numpy_1_7_0170, with prior_installation_required + set to True. When matplotlib is selected for installation, the result should be that numpy is compiled + and installed first. + ''' + global running_standalone + numpy_repository = test_db_util.get_repository_by_name_and_owner( numpy_repository_name, common.test_user_1_name ) + matplotlib_repository = test_db_util.get_repository_by_name_and_owner( matplotlib_repository_name, common.test_user_1_name ) + # Generate the new dependency XML. Normally, the create_repository_dependency method would be used for this, but + # it replaces any existing tool or repository dependency XML file with the generated contents. This is undesirable + # in this case, because matplotlib already has an additional tool dependency definition that we don't want to + # overwrite. + new_xml = ' <package name="numpy" version="1.7">\n' + new_xml += ' <repository toolshed="%s" name="%s" owner="%s" changeset_revision="%s" prior_installation_required="True" />\n' + new_xml += ' </package>\n' + url = self.url + name = numpy_repository.name + owner = numpy_repository.user.username + if running_standalone: + changeset_revision = self.get_repository_tip( numpy_repository ) + processed_xml = new_xml % ( url, name, owner, changeset_revision ) + original_xml = file( self.get_filename( 'package_matplotlib/tool_dependencies.xml' ), 'r' ).read() + dependency_xml_path = self.generate_temp_path( 'test_0170', additional_paths=[ 'matplotlib' ] ) + new_xml_file = os.path.join( dependency_xml_path, 'tool_dependencies.xml' ) + file( new_xml_file, 'w' ).write( original_xml.replace( '', processed_xml ) ) + # Upload the generated complex repository dependency XML to the matplotlib repository. + self.upload_file( matplotlib_repository, + filename='tool_dependencies.xml', + filepath=dependency_xml_path, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded complex repository dependency on numpy 1.7.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0020_verify_generated_dependency( self ): + '''Verify that matplotlib now has a package tool dependency and a complex repository dependency.''' + ''' + This is step 3 - Verify that package_matplotlib_1_2_0170 now depends on package_numpy_1_7_0170, and that the inherited tool + dependency displays correctly. + 'Inhherited' in this case means that matplotlib should show a package tool dependency on numpy version 1.7, and a repository + dependency on the latest revision of package_numpy_1_7_0170. + ''' + numpy_repository = test_db_util.get_repository_by_name_and_owner( numpy_repository_name, common.test_user_1_name ) + matplotlib_repository = test_db_util.get_repository_by_name_and_owner( matplotlib_repository_name, common.test_user_1_name ) + changeset_revision = self.get_repository_tip( numpy_repository ) + self.check_repository_dependency( matplotlib_repository, depends_on_repository=numpy_repository ) + self.display_manage_repository_page( matplotlib_repository, strings_displayed=[ 'numpy', '1.7', 'package', changeset_revision ] ) + + def test_0025_install_matplotlib_repository( self ): + '''Install the package_matplotlib_1_2_0170 repository.''' + ''' + This is step 4 - Install package_matplotlib_1_2_0170 with repository dependencies. + ''' + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + matplotlib_repository = test_db_util.get_repository_by_name_and_owner( matplotlib_repository_name, common.test_user_1_name ) + preview_strings_displayed = [ 'package_matplotlib_1_2_0170', self.get_repository_tip( matplotlib_repository ) ] + strings_displayed = [ 'Choose the tool panel section' ] + self.install_repository( matplotlib_repository_name, + common.test_user_1_name, + category_name, + install_tool_dependencies=False, + install_repository_dependencies=True, + preview_strings_displayed=preview_strings_displayed, + strings_displayed=[], + strings_not_displayed=[], + post_submit_strings_displayed=[ 'package_matplotlib_1_2_0170', 'new' ], + includes_tools_for_display_in_tool_panel=False ) + + def test_0030_verify_installation_order( self ): + '''Verify that the numpy repository was installed before the matplotlib repository.''' + ''' + This is step 5 - Verify that the prior_installation_required attribute resulted in package_numpy_1_7_0170 being installed first. + In the previous step, package_matplotlib_1_2_0170 was selected for installation, but package_numpy_1_7_0170 had the + prior_installation_required attribute set. Confirm that this resulted in package_numpy_1_7_0170 being installed before + package_matplotlib_1_2_0170. + ''' + matplotlib_repository = test_db_util.get_installed_repository_by_name_owner( matplotlib_repository_name, common.test_user_1_name ) + numpy_repository = test_db_util.get_installed_repository_by_name_owner( numpy_repository_name, common.test_user_1_name ) + assert matplotlib_repository.update_time > numpy_repository.update_time, \ + 'Error: package_numpy_1_7_0170 shows a later update time than package_matplotlib_1_2_0170' + \ No newline at end of file diff -r a8139a367ed3de938f5d71336a06f1f768132469 -r 1037ab5b4f761c104b01cf0aee9222d28a67034b test/tool_shed/test_data/package_matplotlib/package_matplotlib_1_2.tar Binary file test/tool_shed/test_data/package_matplotlib/package_matplotlib_1_2.tar has changed diff -r a8139a367ed3de938f5d71336a06f1f768132469 -r 1037ab5b4f761c104b01cf0aee9222d28a67034b test/tool_shed/test_data/package_matplotlib/tool_dependencies.xml --- /dev/null +++ b/test/tool_shed/test_data/package_matplotlib/tool_dependencies.xml @@ -0,0 +1,25 @@ +<tool_dependency> + + <package name="matplotlib" version="1.2.1"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-…</action> + <action type="shell_command">wget http://downloads.sourceforge.net/project/freetype/freetype2/2.4.11/freetype…</action> + <action type="shell_command">tar xfvj freetype-2.4.11.tar.bz2 && + cd freetype-2.4.11 && + ./configure --prefix=$INSTALL_DIR/freetype/build && + make && + make install</action> + <action type="make_directory">$INSTALL_DIR/lib/python</action> + <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && + export CPLUS_INCLUDE_PATH=$INSTALL_DIR/freetype/build/include:$INSTALL_DIR/freetype/build/include/freetype2/ && + export LIBRARY_PATH=$INSTALL_DIR/freetype/build/lib/ && + python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> + <action type="set_environment"> + <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> + </action> + </actions> + </install> + <readme>Compiling matplotlib requires a C compiler (typically gcc), freetype2, numpy and libpng.</readme> + </package> +</tool_dependency> diff -r a8139a367ed3de938f5d71336a06f1f768132469 -r 1037ab5b4f761c104b01cf0aee9222d28a67034b test/tool_shed/test_data/package_numpy/package_numpy_1_7.tar Binary file test/tool_shed/test_data/package_numpy/package_numpy_1_7.tar has changed Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Abbreviate not applicable in tool shed grids.
by commits-noreply＠bitbucket.org 22 Apr '13

22 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a8139a367ed3/ Changeset: a8139a367ed3 User: greg Date: 2013-04-22 16:52:29 Summary: Abbreviate not applicable in tool shed grids. Affected #: 1 file diff -r 77f32521f235ace1773e54389d7b536a9f5235a5 -r a8139a367ed3de938f5d71336a06f1f768132469 lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -154,9 +154,9 @@ return 'yes' else: return 'no' - return 'not applicable' + return 'n/a' except: - return 'not applicable' + return 'n/a' class DescriptionColumn( grids.TextColumn ): @@ -748,9 +748,9 @@ return 'yes' else: return 'no' - return 'not applicable' + return 'n/a' except: - return 'not applicable' + return 'n/a' class DoNotTestColumn( grids.BooleanColumn ): 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: Handle repositories whith no metadata revisions when displaying the verified tool column in the tool shed.
by commits-noreply＠bitbucket.org 22 Apr '13

22 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/77f32521f235/ Changeset: 77f32521f235 User: greg Date: 2013-04-22 16:50:10 Summary: Handle repositories whith no metadata revisions when displaying the verified tool column in the tool shed. Affected #: 1 file diff -r 5138b63cc96435ea72415796aa3daabfbfe2f23f -r 77f32521f235ace1773e54389d7b536a9f5235a5 lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -147,13 +147,16 @@ def get_value( self, trans, grid, repository ): # This column will display the value associated with the currently displayed metadata revision. - displayed_metadata_revision = repository.metadata_revisions[ -1 ] - if displayed_metadata_revision.includes_tools: - if displayed_metadata_revision.tools_functionally_correct: - return 'yes' - else: - return 'no' - return 'not applicable' + try: + displayed_metadata_revision = repository.metadata_revisions[ -1 ] + if displayed_metadata_revision.includes_tools: + if displayed_metadata_revision.tools_functionally_correct: + return 'yes' + else: + return 'no' + return 'not applicable' + except: + return 'not applicable' class DescriptionColumn( grids.TextColumn ): @@ -735,13 +738,19 @@ class ToolsFunctionallyCorrectColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.includes_tools: - if repository_metadata.tools_functionally_correct: - return 'yes' - else: - return 'no' - return 'not applicable' + + def get_value( self, trans, grid, repository ): + # This column will display the value associated with the currently displayed metadata revision. + try: + displayed_metadata_revision = repository.metadata_revisions[ -1 ] + if displayed_metadata_revision.includes_tools: + if displayed_metadata_revision.tools_functionally_correct: + return 'yes' + else: + return 'no' + return 'not applicable' + except: + return 'not applicable' class DoNotTestColumn( grids.BooleanColumn ): 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: Clean up the main repositories by category grid and add a tools verified column.
by commits-noreply＠bitbucket.org 22 Apr '13

22 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5138b63cc964/ Changeset: 5138b63cc964 User: greg Date: 2013-04-22 16:44:20 Summary: Clean up the main repositories by category grid and add a tools verified column. Affected #: 2 files diff -r cac1c2a9247bf1f2c7f78275a6d11bf209867fb2 -r 5138b63cc96435ea72415796aa3daabfbfe2f23f 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 @@ -61,6 +61,7 @@ my_writable_repositories_grid = repository_grids.MyWritableRepositoriesGrid() repositories_by_user_grid = repository_grids.RepositoriesByUserGrid() repositories_i_own_grid = repository_grids.RepositoriesIOwnGrid() + repositories_in_category_grid = repository_grids.RepositoriesInCategoryGrid() repository_dependencies_grid = repository_grids.RepositoryDependenciesGrid() repository_grid = repository_grids.RepositoryGrid() # The repository_metadata_grid is not currently displayed, but is sub-classed by several grids. @@ -202,13 +203,14 @@ elif operation == "my_writable_repositories": return self.my_writable_repositories_grid( trans, **kwd ) elif operation == "repositories_by_category": - # Eliminate the current filters if any exist. - for k, v in kwd.items(): - if k.startswith( 'f-' ): - del kwd[ k ] category_id = kwd.get( 'id', None ) - category = suc.get_category( trans, category_id ) - kwd[ 'f-Category.name' ] = category.name + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories_in_category', + id=category_id, + message=message, + status=status ) ) elif operation == "receive email alerts": if trans.user: if kwd[ 'id' ]: @@ -244,7 +246,7 @@ **kwd ) ) user_id = kwd.get( 'user_id', None ) if user_id is None: - # The received id is the repository id, so we need to get the id of the user that uploaded the repository. + # The received id is the repository id, so we need to get the id of the user that owns the repository. repository_id = kwd.get( 'id', None ) if repository_id: repository = suc.get_repository_in_tool_shed( trans, repository_id ) @@ -263,6 +265,40 @@ return self.repositories_by_user_grid( trans, **kwd ) @web.expose + def browse_repositories_in_category( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd[ 'operation' ].lower() + if operation == "view_or_manage_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='view_or_manage_repository', + **kwd ) ) + if operation == 'repositories_by_user': + user_id = kwd.get( 'user_id', None ) + if user_id is None: + # The received id is the repository id, so we need to get the id of the user that owns the repository. + repository_id = kwd.get( 'id', None ) + if repository_id: + repository = suc.get_repository_in_tool_shed( trans, repository_id ) + user_id = trans.security.encode_id( repository.user.id ) + user = suc.get_user( trans, user_id ) + self.repositories_by_user_grid.title = "Repositories owned by %s" % user.username + kwd[ 'user_id' ] = user_id + return self.repositories_by_user_grid( trans, **kwd ) + selected_changeset_revision, repository = self.__get_repository_from_refresh_on_change( trans, **kwd ) + if repository: + # The user selected a repository revision which results in a refresh_on_change. + return trans.response.send_redirect( web.url_for( controller='repository', + action='view_or_manage_repository', + id=trans.security.encode_id( repository.id ), + changeset_revision=selected_changeset_revision ) ) + category_id = kwd.get( 'id', None ) + if category_id: + category = suc.get_category( trans, category_id ) + if category: + self.repositories_in_category_grid.title = 'Category %s' % str( category.name ) + return self.repositories_in_category_grid( trans, **kwd ) + + @web.expose def browse_repository( self, trans, id, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) diff -r cac1c2a9247bf1f2c7f78275a6d11bf209867fb2 -r 5138b63cc96435ea72415796aa3daabfbfe2f23f lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -143,6 +143,19 @@ return escape_html( repository.revision( trans.app ) ) + class ToolsFunctionallyCorrectColumn( grids.BooleanColumn ): + + def get_value( self, trans, grid, repository ): + # This column will display the value associated with the currently displayed metadata revision. + displayed_metadata_revision = repository.metadata_revisions[ -1 ] + if displayed_metadata_revision.includes_tools: + if displayed_metadata_revision.tools_functionally_correct: + return 'yes' + else: + return 'no' + return 'not applicable' + + class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): @@ -261,6 +274,60 @@ .outerjoin( model.Category.table ) +class RepositoriesInCategoryGrid( RepositoryGrid ): + title = "Category" + + columns = [ + RepositoryGrid.NameColumn( "Name", + key="name", + link=( lambda item: dict( controller="repository", operation="view_or_manage_repository", id=item.id ) ), + attach_popup=False ), + RepositoryGrid.DescriptionColumn( "Synopsis", + key="description", + attach_popup=False ), + RepositoryGrid.MetadataRevisionColumn( "Metadata Revisions" ), + RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools Verified" ), + RepositoryGrid.UserColumn( "Owner", + model_class=model.User, + link=( lambda item: dict( controller="repository", operation="repositories_by_user", id=item.id ) ), + attach_popup=False, + key="User.username" ), + # Columns that are valid for filtering but are not visible. + RepositoryGrid.EmailColumn( "Email", + model_class=model.User, + key="email", + visible=False ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name, description", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + operations = [ grids.GridOperation( "Receive email alerts", + allow_multiple=False, + condition=( lambda item: not item.deleted ), + async_compatible=False ) ] + + def build_initial_query( self, trans, **kwd ): + category_id = kwd.get( 'id', None ) + if category_id: + category = suc.get_category( trans, category_id ) + if category: + return trans.sa_session.query( model.Repository ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ + .join( model.User.table ) \ + .outerjoin( model.RepositoryCategoryAssociation.table ) \ + .outerjoin( model.Category.table ) \ + .filter( model.Category.table.c.name == category.name ) + return trans.sa_session.query( model.Repository ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ + .join( model.User.table ) \ + .outerjoin( model.RepositoryCategoryAssociation.table ) \ + .outerjoin( model.Category.table ) + + class RepositoriesByUserGrid( RepositoryGrid ): title = "Repositories by user" columns = [ @@ -268,11 +335,11 @@ key="name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False ), - RepositoryGrid.MetadataRevisionColumn( "Metadata Revisions" ), - RepositoryGrid.TipRevisionColumn( "Tip Revision" ), RepositoryGrid.DescriptionColumn( "Synopsis", key="description", attach_popup=False ), + RepositoryGrid.MetadataRevisionColumn( "Metadata Revisions" ), + RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools Verified" ), RepositoryGrid.CategoryColumn( "Category", model_class=model.Category, key="Category.name", @@ -304,7 +371,7 @@ link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=True ), RepositoryGrid.MetadataRevisionColumn( "Metadata Revisions" ), - RepositoryGrid.TipRevisionColumn( "Tip Revision" ), + RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools Verified" ), RepositoryGrid.CategoryColumn( "Category", model_class=model.Category, key="Category.name", @@ -343,7 +410,7 @@ link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=True ), RepositoriesIOwnGrid.MetadataRevisionColumn( "Metadata Revisions" ), - RepositoriesIOwnGrid.TipRevisionColumn( "Tip Revision" ), + RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools Verified" ), RepositoriesIOwnGrid.CategoryColumn( "Category", model_class=model.Category, key="Category.name", @@ -403,7 +470,7 @@ link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=True ), RepositoryGrid.MetadataRevisionColumn( "Metadata Revisions" ), - RepositoryGrid.TipRevisionColumn( "Tip Revision" ), + RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools Verified" ), RepositoryGrid.UserColumn( "Owner", model_class=model.User, link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), @@ -480,7 +547,7 @@ return query.filter( model.Category.name == column_filter ) - class RevisionColumn( grids.GridColumn ): + class InstallableRevisionColumn( grids.GridColumn ): def __init__( self, col_name ): grids.GridColumn.__init__( self, col_name ) @@ -502,7 +569,8 @@ RepositoryGrid.DescriptionColumn( "Synopsis", key="description", attach_popup=False ), - RevisionColumn( "Installable Revisions" ), + InstallableRevisionColumn( "Installable Revisions" ), + RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools Verified" ), RepositoryGrid.UserColumn( "Owner", model_class=model.User, attach_popup=False ), @@ -668,9 +736,12 @@ class ToolsFunctionallyCorrectColumn( grids.BooleanColumn ): def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.tools_functionally_correct: - return 'yes' - return '' + if repository_metadata.includes_tools: + if repository_metadata.tools_functionally_correct: + return 'yes' + else: + return 'no' + return 'not applicable' class DoNotTestColumn( grids.BooleanColumn ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 Apr '13

20 Apr '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cac1c2a9247b/ Changeset: cac1c2a9247b User: jgoecks Date: 2013-04-20 21:04:07 Summary: (a) Fetch sample names before drawing variant track and (b) update dataset metadata when changed. Affected #: 2 files diff -r 9b46c246c9cffbf9cbaaf1398e3d1cf51a3c42f6 -r cac1c2a9247bf1f2c7f78275a6d11bf209867fb2 static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -20,8 +20,15 @@ }, initialize: function() { - // -- Create and initialize metadata. -- + // Set metadata. + // FIXME: pass back a metadata dict and then Backbone-relational + // can be used unpack metadata automatically. + this._set_metadata(); + // Update metadata on change. + this.on('change', this._set_metadata, this); + }, + _set_metadata: function() { var metadata = new DatasetMetadata(); // Move metadata from dataset attributes to metadata object. @@ -34,7 +41,8 @@ } }, this); - this.set('metadata', metadata); + // Because this is an internal change, silence it. + this.set('metadata', metadata, { 'silent': true }); }, /** diff -r 9b46c246c9cffbf9cbaaf1398e3d1cf51a3c42f6 -r cac1c2a9247bf1f2c7f78275a6d11bf209867fb2 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -4263,6 +4263,15 @@ }, /** + * Additional initialization required before drawing track for the first time. + */ + predraw_init: function() { + if (!this.dataset.get_metadata('sample_names')) { + return this.dataset.fetch(); + } + }, + + /** * Actions to be taken after draw has been completed. Draw is completed when all tiles have been * drawn/fetched and shown. */ https://bitbucket.org/galaxy/galaxy-central/commits/9b46c246c9cf/ Changeset: 9b46c246c9cf User: jgoecks Date: 2013-04-20 20:28:11 Summary: Trackster: refactor variant sample labels and fix line-height issues. Affected #: 1 file diff -r 71fdd146b95ce53735003afa282f51fa188398ad -r 9b46c246c9cffbf9cbaaf1398e3d1cf51a3c42f6 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -4271,45 +4271,44 @@ // Add summary/sample labels if needed and not already included. if ( !(tiles[0] instanceof SummaryTreeTile) && this.prefs.show_labels) { + var font_size; + // Add and/or style labels. if (this.container_div.find('.yaxislabel.variant').length === 0) { // Add summary and sample labels. - // FIXME: label attributes could be cleaner by using CSS classes. - - // Add summary label. - var summary_div_font_size = 10, - summary_div = $("<div/>").text('Summary').addClass('yaxislabel variant top').css({ - 'font-size': summary_div_font_size + 'px' - }); - this.container_div.prepend(summary_div); - - // Adjust summary label to middle of summary. - var base_offset = summary_div.position().top; - summary_div.css('top', base_offset + (this.prefs.summary_height - summary_div_font_size) / 2 + 'px'); - + // Add summary label to middle of summary area. + font_size = this.prefs.summary_height / 2; + this.tiles_div.prepend( + $("<div/>").text('Summary').addClass('yaxislabel variant top').css({ + 'font-size': font_size + 'px', + 'top': (this.prefs.summary_height - font_size) / 2 + 'px' + }) + ); + // Show sample labels. if (this.prefs.show_sample_data) { - var samples_div_html = ''; - _.each(this.dataset.get('metadata').get('sample_names'), function(name) { - samples_div_html += (name + '<br>'); - }); + var samples_div_html = this.dataset.get('metadata').get('sample_names').join('<br/>'); - var samples_div = $("<div/>").html(samples_div_html).addClass('yaxislabel variant top sample').css({ - // +2 for padding - 'top': base_offset + this.prefs.summary_height + 2, - }); - this.container_div.prepend(samples_div); + this.tiles_div.prepend( + $("<div/>").html(samples_div_html).addClass('yaxislabel variant top sample').css({ + // +2 for padding + 'top': this.prefs.summary_height + 2, + }) + ); } } // Style labels. // Match sample font size to mode. - $(this.container_div).find('.sample').css('font-size', (this.mode === 'Squish' ? 5 : 10) + 'px'); + font_size = (this.mode === 'Squish' ? 5 : 10) + 'px'; + $(this.tiles_div).find('.sample').css({ + 'font-size': font_size, + 'line-height': font_size + }); // Color labels to preference color. - $(this.container_div).find('.yaxislabel').css('color', this.prefs.label_color); - + $(this.tiles_div).find('.yaxislabel').css('color', this.prefs.label_color); } else { // Remove all labels. 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 20 Apr '13

20 Apr '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/71fdd146b95c/ Changeset: 71fdd146b95c User: jgoecks Date: 2013-04-20 17:05:42 Summary: Visual analysis enhancements: (a) do not manually convert to json because it is not necessary and (b) gracefully handle missing sample names. Affected #: 2 files diff -r 034b2d6118caa1dc6808f1570e92d927973a87ed -r 71fdd146b95ce53735003afa282f51fa188398ad lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -193,7 +193,7 @@ original_dataset = self.get_dataset( trans, payload[ 'target_dataset_id' ], check_ownership=False, check_accessible=True ) msg = self.check_dataset_state( trans, original_dataset ) if msg: - return to_json_string( msg ) + return msg # # Set tool parameters--except non-hidden dataset parameters--using combination of @@ -223,7 +223,8 @@ for jida in original_job.input_datasets: input_dataset = jida.dataset data_provider = data_provider_registry.get_data_provider( trans, original_dataset=input_dataset, source='data' ) - if data_provider and not data_provider.converted_dataset: + if data_provider and ( not data_provider.converted_dataset + or data_provider.converted_dataset.state != trans.app.model.Dataset.states.OK ): # Can convert but no converted dataset yet, so return message about why. data_sources = input_dataset.datatype.data_sources msg = input_dataset.convert_dataset( trans, data_sources[ 'data' ] ) @@ -233,7 +234,7 @@ # Return any messages generated during conversions. return_message = self._get_highest_priority_msg( messages_list ) if return_message: - return to_json_string( return_message ) + return return_message # # Set target history (the history that tool will use for inputs/outputs). @@ -371,7 +372,7 @@ # Add dataset to tool's parameters. if not set_param_value( tool_params, jida.name, subset_dataset ): - return to_json_string( { "error" : True, "message" : "error setting parameter %s" % jida.name } ) + return { "error" : True, "message" : "error setting parameter %s" % jida.name } # # Execute tool and handle outputs. @@ -382,7 +383,7 @@ job_params={ "source" : "trackster" } ) except Exception, e: # Lots of things can go wrong when trying to execute tool. - return to_json_string( { "error" : True, "message" : e.__class__.__name__ + ": " + str(e) } ) + return { "error" : True, "message" : e.__class__.__name__ + ": " + str(e) } if run_on_regions: for output in subset_job_outputs.values(): output.visible = False diff -r 034b2d6118caa1dc6808f1570e92d927973a87ed -r 71fdd146b95ce53735003afa282f51fa188398ad static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1821,7 +1821,7 @@ // Start with this status message. //new_track.container_div.addClass("pending"); - //new_track.content_div.text("Converting input data so that it can be used quickly with tool."); + //new_track.content_div.html(DATA_PENDING); $.when(ss_deferred.go()).then(function(response) { if (response === "no converter") { @@ -4234,7 +4234,23 @@ } else { var dummy_painter = new (this.painter)(null, null, null, this.prefs, mode); - return dummy_painter.get_required_height(this.dataset.get_metadata('sample_names').length); + // HACK: sample_names is not be defined when dataset definition is fetched before + // dataset is complete (as is done when running tools). In that case, fall back on + // # of samples in data. This can be fixed by re-requesting dataset definition + // in init. + var num_samples = ( this.dataset.get_metadata('sample_names') ? this.dataset.get_metadata('sample_names').length : 0); + if (num_samples === 0 && result.data.length !== 0) { + // Sample data is separated by commas, so this computes # of samples: + num_samples = result.data[0][7].match(/,/g); + if ( num_samples === null ) { + num_samples = 1; + } + else { + num_samples = num_samples.length + 1; + } + } + + return dummy_painter.get_required_height(num_samples); } }, https://bitbucket.org/galaxy/galaxy-central/commits/034b2d6118ca/ Changeset: 034b2d6118ca User: jgoecks Date: 2013-04-20 16:08:29 Summary: Remove debugging statement Affected #: 1 file diff -r 1fa1583641474f160ca1569ec91faf8f3d7093c8 -r 034b2d6118caa1dc6808f1570e92d927973a87ed lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -796,7 +796,6 @@ # Search for and yield other data lines. for data_line in source: if line_in_region( data_line, chrom, start, end ): - print chrom, start, end, ">>>", data_line, yield data_line return line_filter_iter() https://bitbucket.org/galaxy/galaxy-central/commits/1fa158364147/ Changeset: 1fa158364147 User: jgoecks Date: 2013-04-20 16:06:26 Summary: Use tabix rather than interval index for pileup data indexing. Affected #: 2 files diff -r 8d72c9adccf92f8a1971ec7d9b622de43cbd6f48 -r 1fa1583641474f160ca1569ec91faf8f3d7093c8 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -160,7 +160,8 @@ </datatype><datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf"/><datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true"> - <converter file="pileup_to_interval_index_converter.xml" target_datatype="interval_index"/> + <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/></datatype><datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/><datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" /> diff -r 8d72c9adccf92f8a1971ec7d9b622de43cbd6f48 -r 1fa1583641474f160ca1569ec91faf8f3d7093c8 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -474,11 +474,12 @@ """Tab delimited data in pileup (6- or 10-column) format""" file_ext = "pileup" line_class = "genomic coordinate" - data_sources = { "data": "interval_index" } + data_sources = { "data": "tabix" } """Add metadata elements""" MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter ) MetadataElement( name="startCol", default=2, desc="Start column", param=metadata.ColumnParameter ) + MetadataElement( name="endCol", default=2, desc="End column", param=metadata.ColumnParameter ) MetadataElement( name="baseCol", default=3, desc="Reference base column", param=metadata.ColumnParameter ) def init_meta( self, dataset, copy_from=None ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Refactor repository dependency generation. Add functional tests for the recently introduced feature to determine installation order of dependencies.
by commits-noreply＠bitbucket.org 19 Apr '13

19 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8d72c9adccf9/ Changeset: 8d72c9adccf9 User: inithello Date: 2013-04-19 21:59:09 Summary: Refactor repository dependency generation. Add functional tests for the recently introduced feature to determine installation order of dependencies. Affected #: 31 files diff -r 2c50935e70c8a483bcd09b358765408543a153fb -r 8d72c9adccf92f8a1971ec7d9b622de43cbd6f48 test/tool_shed/base/common.py --- a/test/tool_shed/base/common.py +++ b/test/tool_shed/base/common.py @@ -32,7 +32,7 @@ </repositories> ''' -new_repository_dependencies_line = ''' <repository toolshed="${toolshed_url}" name="${repository_name}" owner="${owner}" changeset_revision="${changeset_revision}" />''' +new_repository_dependencies_line = ''' <repository toolshed="${toolshed_url}" name="${repository_name}" owner="${owner}" changeset_revision="${changeset_revision}"${prior_installation_required} />''' # Set a 3 minute timeout for repository installation. This should be sufficient, since we're not installing tool dependencies. repository_installation_timeout = 180 \ No newline at end of file diff -r 2c50935e70c8a483bcd09b358765408543a153fb -r 8d72c9adccf92f8a1971ec7d9b622de43cbd6f48 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -254,29 +254,37 @@ else: return '%s=%s' % ( field_name, field_value ) - def create_repository_complex_dependency( self, repository, xml_filename, depends_on={} ): - self.generate_repository_dependency_xml( depends_on[ 'repositories' ], - xml_filename, - complex=True, - package=depends_on[ 'package' ], - version=depends_on[ 'version' ] ) + def create_repository_dependency( self, + repository=None, + repository_tuples=[], + filepath=None, + prior_installation_required=False, + complex=False, + package=None, + version=None, + strings_displayed=[], + strings_not_displayed=[] ): + repository_names = [] + if complex: + filename = 'tool_dependencies.xml' + self.generate_complex_dependency_xml( filename=filename, filepath=filepath, repository_tuples=repository_tuples, package=package, version=version ) + else: + for toolshed_url, name, owner, changeset_revision in repository_tuples: + repository_names.append( name ) + dependency_description = '%s depends on %s.' % ( repository.name, ', '.join( repository_names ) ) + filename = 'repository_dependencies.xml' + self.generate_simple_dependency_xml( repository_tuples=repository_tuples, + filename=filename, + filepath=filepath, + dependency_description=dependency_description, + prior_installation_required=prior_installation_required ) self.upload_file( repository, - 'tool_dependencies.xml', - filepath=os.path.split( xml_filename )[0], - commit_message='Uploaded dependency on %s.' % ', '.join( repo.name for repo in depends_on[ 'repositories' ] ) ) - - def create_repository_dependency( self, repository=None, depends_on=[], filepath=None ): - dependency_description = '%s depends on %s.' % ( repository.name, ', '.join( repo.name for repo in depends_on ) ) - self.generate_repository_dependency_xml( depends_on, - self.get_filename( 'repository_dependencies.xml', filepath=filepath ), - dependency_description=dependency_description ) - self.upload_file( repository, - 'repository_dependencies.xml', + filename=filename, filepath=filepath, - valid_tools_only=True, + valid_tools_only=False, uncompress_file=False, remove_repo_files_not_in_tar=False, - commit_message='Uploaded dependency on %s.' % ', '.join( repo.name for repo in depends_on ), + commit_message='Uploaded dependency on %s.' % ', '.join( repository_names ), strings_displayed=[], strings_not_displayed=[] ) @@ -512,53 +520,55 @@ self.check_page_for_string( "You have been logged out" ) self.home() - def generate_invalid_dependency_xml( self, xml_filename, url, name, owner, changeset_revision, complex=True, package=None, version=None, description=None ): - file_path = os.path.split( xml_filename )[0] + def generate_complex_dependency_xml( self, filename, filepath, repository_tuples, package, version ): + file_path = os.path.join( filepath, filename ) dependency_entries = [] template = string.Template( common.new_repository_dependencies_line ) - dependency_entries.append( template.safe_substitute( toolshed_url=url, - owner=owner, - repository_name=name, - changeset_revision=changeset_revision ) ) - if not os.path.exists( file_path ): - os.makedirs( file_path ) - if complex: - dependency_template = string.Template( common.complex_repository_dependency_template ) - repository_dependency_xml = dependency_template.safe_substitute( package=package, version=version, dependency_lines='\n'.join( dependency_entries ) ) + for toolshed_url, name, owner, changeset_revision in repository_tuples: + dependency_entries.append( template.safe_substitute( toolshed_url=toolshed_url, + owner=owner, + repository_name=name, + changeset_revision=changeset_revision, + prior_installation_required='' ) ) + if not os.path.exists( filepath ): + os.makedirs( filepath ) + dependency_template = string.Template( common.complex_repository_dependency_template ) + repository_dependency_xml = dependency_template.safe_substitute( package=package, version=version, dependency_lines='\n'.join( dependency_entries ) ) + # Save the generated xml to the specified location. + file( file_path, 'w' ).write( repository_dependency_xml ) + + def generate_simple_dependency_xml( self, + repository_tuples, + filename, + filepath, + dependency_description='', + complex=False, + package=None, + version=None, + prior_installation_required=False ): + if not os.path.exists( filepath ): + os.makedirs( filepath ) + dependency_entries = [] + if prior_installation_required: + prior_installation_value = ' prior_installation_required="True"' else: - if not description: - description = ' description=""' - else: - description = ' description="%s"' % description - template_parser = string.Template( common.new_repository_dependencies_xml ) - repository_dependency_xml = template_parser.safe_substitute( description=description, dependency_lines='\n'.join( dependency_entries ) ) - # Save the generated xml to the specified location. - file( xml_filename, 'w' ).write( repository_dependency_xml ) - - def generate_repository_dependency_xml( self, repositories, xml_filename, dependency_description='', complex=False, package=None, version=None ): - file_path = os.path.split( xml_filename )[0] - if not os.path.exists( file_path ): - os.makedirs( file_path ) - dependency_entries = [] - for repository in repositories: - changeset_revision = self.get_repository_tip( repository ) + prior_installation_value = '' + for toolshed_url, name, owner, changeset_revision in repository_tuples: template = string.Template( common.new_repository_dependencies_line ) - dependency_entries.append( template.safe_substitute( toolshed_url=self.url, - owner=repository.user.username, - repository_name=repository.name, - changeset_revision=changeset_revision ) ) + dependency_entries.append( template.safe_substitute( toolshed_url=toolshed_url, + owner=owner, + repository_name=name, + changeset_revision=changeset_revision, + prior_installation_required=prior_installation_value ) ) if dependency_description: description = ' description="%s"' % dependency_description else: description = dependency_description - if complex: - dependency_template = string.Template( common.complex_repository_dependency_template ) - repository_dependency_xml = dependency_template.safe_substitute( package=package, version=version, dependency_lines='\n'.join( dependency_entries ) ) - else: - template_parser = string.Template( common.new_repository_dependencies_xml ) - repository_dependency_xml = template_parser.safe_substitute( description=description, dependency_lines='\n'.join( dependency_entries ) ) + template_parser = string.Template( common.new_repository_dependencies_xml ) + repository_dependency_xml = template_parser.safe_substitute( description=description, dependency_lines='\n'.join( dependency_entries ) ) # Save the generated xml to the specified location. - file( xml_filename, 'w' ).write( repository_dependency_xml ) + full_path = os.path.join( filepath, filename ) + file( full_path, 'w' ).write( repository_dependency_xml ) def generate_temp_path( self, test_script_path, additional_paths=[] ): temp_path = os.path.join( self.tool_shed_test_tmp_dir, test_script_path, os.sep.join( additional_paths ) ) diff -r 2c50935e70c8a483bcd09b358765408543a153fb -r 8d72c9adccf92f8a1971ec7d9b622de43cbd6f48 test/tool_shed/functional/test_0020_basic_repository_dependencies.py --- a/test/tool_shed/functional/test_0020_basic_repository_dependencies.py +++ b/test/tool_shed/functional/test_0020_basic_repository_dependencies.py @@ -9,8 +9,10 @@ emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0020' emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0020' + class TestBasicRepositoryDependencies( ShedTwillTestCase ): '''Testing emboss 5 with repository dependencies.''' + def test_0000_initiate_users( self ): """Create necessary user accounts and login as an admin user.""" self.logout() @@ -23,9 +25,11 @@ admin_user = test_db_util.get_user( common.admin_email ) assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_category( self ): """Create a category for this test suite""" self.create_category( name='Test 0020 Basic Repository Dependencies', description='Testing basic repository dependency features.' ) + def test_0010_create_emboss_datatypes_repository_and_upload_tarball( self ): '''Create and populate the emboss_datatypes repository.''' self.logout() @@ -46,10 +50,12 @@ commit_message='Uploaded datatypes_conf.xml.', strings_displayed=[], strings_not_displayed=[] ) + def test_0015_verify_datatypes_in_datatypes_repository( self ): '''Verify that the emboss_datatypes repository contains datatype entries.''' repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) self.display_manage_repository_page( repository, strings_displayed=[ 'Datatypes', 'equicktandem', 'hennig86', 'vectorstrip' ] ) + def test_0020_create_emboss_5_repository_and_upload_files( self ): '''Create and populate the emboss_5_0020 repository.''' category = test_db_util.get_category_by_name( 'Test 0020 Basic Repository Dependencies' ) @@ -68,22 +74,15 @@ commit_message='Uploaded emboss.tar', strings_displayed=[], strings_not_displayed=[] ) + def test_0025_generate_and_upload_repository_dependencies_xml( self ): '''Generate and upload the repository_dependencies.xml file''' repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0020', additional_paths=[ 'emboss', '5' ] ) - self.generate_repository_dependency_xml( [ datatypes_repository ], - self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) ) - self.upload_file( repository, - filename='repository_dependencies.xml', - filepath=repository_dependencies_path, - valid_tools_only=True, - uncompress_file=False, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded repository_dependencies.xml.', - strings_displayed=[], - strings_not_displayed=[] ) + repository_tuple = ( self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip( datatypes_repository ) ) + self.create_repository_dependency( repository=repository, repository_tuples=[ repository_tuple ], filepath=repository_dependencies_path ) + def test_0030_verify_emboss_5_dependencies( self ): '''Verify that the emboss_5 repository now depends on the emboss_datatypes repository with correct name, owner, and changeset revision.''' repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) @@ -98,6 +97,7 @@ changeset_revision, 'Repository dependencies' ] self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + def test_0040_verify_repository_metadata( self ): '''Verify that resetting the metadata does not change it.''' emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) diff -r 2c50935e70c8a483bcd09b358765408543a153fb -r 8d72c9adccf92f8a1971ec7d9b622de43cbd6f48 test/tool_shed/functional/test_0030_repository_dependency_revisions.py --- a/test/tool_shed/functional/test_0030_repository_dependency_revisions.py +++ b/test/tool_shed/functional/test_0030_repository_dependency_revisions.py @@ -1,7 +1,6 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import tool_shed.base.test_db_util as test_db_util -import logging -log = logging.getLogger(__name__) + datatypes_repository_name = 'emboss_datatypes_0030' datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools." datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This repository contains no tools." @@ -12,8 +11,10 @@ emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0030' emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0030' + class TestRepositoryDependencyRevisions( ShedTwillTestCase ): '''Test dependencies on different revisions of a repository.''' + def test_0000_initiate_users( self ): """Create necessary user accounts.""" self.logout() @@ -26,9 +27,11 @@ admin_user = test_db_util.get_user( common.admin_email ) assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_category( self ): """Create a category for this test suite""" self.create_category( name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.' ) + def test_0010_create_emboss_5_repository( self ): '''Create and populate the emboss_5_0030 repository.''' self.logout() @@ -48,6 +51,7 @@ commit_message='Uploaded tool tarball.', strings_displayed=[], strings_not_displayed=[] ) + def test_0015_create_emboss_6_repository( self ): '''Create and populate the emboss_6_0030 repository.''' self.logout() @@ -67,6 +71,7 @@ commit_message='Uploaded tool tarball.', strings_displayed=[], strings_not_displayed=[] ) + def test_0020_create_emboss_datatypes_repository( self ): '''Create and populate the emboss_datatypes_0030 repository.''' self.logout() @@ -86,6 +91,7 @@ commit_message='Uploaded datatypes_conf.xml.', strings_displayed=[], strings_not_displayed=[] ) + def test_0025_create_emboss_repository( self ): '''Create and populate the emboss_0030 repository.''' self.logout() @@ -105,69 +111,39 @@ commit_message='Uploaded the tool tarball.', strings_displayed=[], strings_not_displayed=[] ) + def test_0030_generate_repository_dependencies_for_emboss_5( self ): '''Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_5 repository.''' datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) - repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss' ] ) - self.generate_repository_dependency_xml( [ datatypes_repository ], - self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) ) emboss_5_repository = test_db_util.get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name ) - self.upload_file( emboss_5_repository, - filename='repository_dependencies.xml', - filepath=repository_dependencies_path, - valid_tools_only=True, - uncompress_file=False, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded repository_dependencies.xml.', - strings_displayed=[], - strings_not_displayed=[] ) + repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss5' ] ) + datatypes_tuple = ( self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip( datatypes_repository ) ) + self.create_repository_dependency( repository=emboss_5_repository, repository_tuples=[ datatypes_tuple ], filepath=repository_dependencies_path ) + def test_0035_generate_repository_dependencies_for_emboss_6( self ): '''Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_6 repository.''' emboss_6_repository = test_db_util.get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name ) - repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss' ] ) - self.upload_file( emboss_6_repository, - filename='repository_dependencies.xml', - filepath=repository_dependencies_path, - valid_tools_only=True, - uncompress_file=False, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded repository_dependencies.xml.', - strings_displayed=[], - strings_not_displayed=[] ) + datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss6' ] ) + datatypes_tuple = ( self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip( datatypes_repository ) ) + self.create_repository_dependency( repository=emboss_6_repository, repository_tuples=[ datatypes_tuple ], filepath=repository_dependencies_path ) + def test_0040_generate_repository_dependency_on_emboss_5( self ): '''Create and upload repository_dependencies.xml for the emboss_5_0030 repository.''' emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) emboss_5_repository = test_db_util.get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss', '5' ] ) - self.generate_repository_dependency_xml( [ emboss_5_repository ], - self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), - dependency_description='Emboss requires the Emboss 5 repository.' ) - self.upload_file( emboss_repository, - filename='repository_dependencies.xml', - filepath=repository_dependencies_path, - valid_tools_only=True, - uncompress_file=False, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded repository_dependencies.xml.', - strings_displayed=[], - strings_not_displayed=[] ) + emboss_tuple = ( self.url, emboss_5_repository.name, emboss_5_repository.user.username, self.get_repository_tip( emboss_5_repository ) ) + self.create_repository_dependency( repository=emboss_repository, repository_tuples=[ emboss_tuple ], filepath=repository_dependencies_path ) + def test_0045_generate_repository_dependency_on_emboss_6( self ): '''Create and upload repository_dependencies.xml for the emboss_6_0030 repository.''' emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) emboss_6_repository = test_db_util.get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name ) - repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss', '6' ] ) - self.generate_repository_dependency_xml( [ emboss_6_repository ], - self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), - dependency_description='Emboss requires the Emboss 6 repository.' ) - self.upload_file( emboss_repository, - filename='repository_dependencies.xml', - filepath=repository_dependencies_path, - valid_tools_only=True, - uncompress_file=False, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded repository_dependencies.xml.', - strings_displayed=[], - strings_not_displayed=[] ) + repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss', '5' ] ) + emboss_tuple = ( self.url, emboss_6_repository.name, emboss_6_repository.user.username, self.get_repository_tip( emboss_6_repository ) ) + self.create_repository_dependency( repository=emboss_repository, repository_tuples=[ emboss_tuple ], filepath=repository_dependencies_path ) + def test_0050_verify_repository_dependency_revisions( self ): '''Verify that different metadata revisions of the emboss repository have different repository dependencies.''' repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) @@ -178,7 +154,7 @@ # Iterate through all metadata revisions and check for repository dependencies. for metadata, changeset_revision in repository_metadata: # Add the dependency description and datatypes repository details to the strings to check. - strings_displayed = [ 'Emboss requires the Emboss', 'emboss_datatypes_0030', 'user1', datatypes_tip ] + strings_displayed = [ 'emboss_datatypes_0030', 'user1', datatypes_tip ] strings_displayed.extend( [ 'Tool dependencies', 'emboss', '5.0.0', 'package' ] ) self.display_manage_repository_page( repository, changeset_revision=changeset_revision, diff -r 2c50935e70c8a483bcd09b358765408543a153fb -r 8d72c9adccf92f8a1971ec7d9b622de43cbd6f48 test/tool_shed/functional/test_0040_repository_circular_dependencies.py --- a/test/tool_shed/functional/test_0040_repository_circular_dependencies.py +++ b/test/tool_shed/functional/test_0040_repository_circular_dependencies.py @@ -9,8 +9,10 @@ filtering_repository_description = "Galaxy's filtering tool for test 0040" filtering_repository_long_description = "Long description of Galaxy's filtering tool for test 0040" + class TestRepositoryCircularDependencies( ShedTwillTestCase ): '''Verify that the code correctly displays repositories with circular repository dependencies.''' + def test_0000_initiate_users( self ): """Create necessary user accounts.""" self.logout() @@ -23,9 +25,11 @@ admin_user = test_db_util.get_user( common.admin_email ) assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_category( self ): """Create a category for this test suite""" self.create_category( name='test_0040_repository_circular_dependencies', description='Testing handling of circular repository dependencies.' ) + def test_0010_create_freebayes_repository( self ): '''Create and populate freebayes_0040.''' self.logout() @@ -45,6 +49,7 @@ commit_message='Uploaded the tool tarball.', strings_displayed=[], strings_not_displayed=[] ) + def test_0015_create_filtering_repository( self ): '''Create and populate filtering_0040.''' self.logout() @@ -64,6 +69,7 @@ commit_message='Uploaded the tool tarball for filtering 1.1.0.', strings_displayed=[], strings_not_displayed=[] ) + def test_0020_create_dependency_on_freebayes( self ): '''Upload a repository_dependencies.xml file that specifies the current revision of freebayes to the filtering_0040 repository.''' # The dependency structure should look like: @@ -73,18 +79,9 @@ repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0040', additional_paths=[ 'filtering' ] ) - self.generate_repository_dependency_xml( [ repository ], - self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), - dependency_description='Filtering 1.1.0 depends on the freebayes repository.' ) - self.upload_file( filtering_repository, - filename='repository_dependencies.xml', - filepath=repository_dependencies_path, - valid_tools_only=True, - uncompress_file=False, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded dependency on freebayes.', - strings_displayed=[], - strings_not_displayed=[] ) + repository_tuple = ( self.url, repository.name, repository.user.username, self.get_repository_tip( repository ) ) + self.create_repository_dependency( repository=filtering_repository, repository_tuples=[ repository_tuple ], filepath=repository_dependencies_path ) + def test_0025_create_dependency_on_filtering( self ): '''Upload a repository_dependencies.xml file that specifies the current revision of filtering to the freebayes_0040 repository.''' # The dependency structure should look like: @@ -94,18 +91,9 @@ repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0040', additional_paths=[ 'freebayes' ] ) - self.generate_repository_dependency_xml( [ repository ], - self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), - dependency_description='Freebayes depends on the filtering repository.' ) - self.upload_file( freebayes_repository, - filename='repository_dependencies.xml', - filepath=repository_dependencies_path, - valid_tools_only=True, - uncompress_file=False, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded dependency on filtering.', - strings_displayed=[], - strings_not_displayed=[] ) + repository_tuple = ( self.url, repository.name, repository.user.username, self.get_repository_tip( repository ) ) + self.create_repository_dependency( repository=freebayes_repository, repository_tuples=[ repository_tuple ], filepath=repository_dependencies_path ) + def test_0030_verify_repository_dependencies( self ): '''Verify that each repository can depend on the other without causing an infinite loop.''' filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) @@ -117,12 +105,14 @@ # In this case, the displayed dependency will specify the tip revision, but this will not always be the case. self.check_repository_dependency( filtering_repository, freebayes_repository, self.get_repository_tip( freebayes_repository ) ) self.check_repository_dependency( freebayes_repository, filtering_repository, self.get_repository_tip( filtering_repository ) ) + def test_0035_verify_repository_metadata( self ): '''Verify that resetting the metadata does not change it.''' freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) for repository in [ freebayes_repository, filtering_repository ]: self.verify_unchanged_repository_metadata( repository ) + def test_0040_verify_tool_dependencies( self ): '''Verify that freebayes displays tool dependencies.''' repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) diff -r 2c50935e70c8a483bcd09b358765408543a153fb -r 8d72c9adccf92f8a1971ec7d9b622de43cbd6f48 test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py --- a/test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py +++ b/test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py @@ -32,8 +32,10 @@ category_name = 'Test 0050 Circular Dependencies 5 Levels' category_description = 'Test circular dependency features' + class TestRepositoryCircularDependenciesToNLevels( ShedTwillTestCase ): '''Verify that the code correctly handles circular dependencies down to n levels.''' + def test_0000_initiate_users( self ): """Create necessary user accounts.""" self.logout() @@ -46,6 +48,7 @@ admin_user = test_db_util.get_user( common.admin_email ) assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_convert_repository( self ): '''Create and populate convert_chars_0050.''' category = self.create_category( name=category_name, description=category_description ) @@ -66,6 +69,7 @@ commit_message='Uploaded convert_chars tarball.', strings_displayed=[], strings_not_displayed=[] ) + def test_0010_create_column_repository( self ): '''Create and populate convert_chars_0050.''' category = self.create_category( name=category_name, description=category_description ) @@ -84,6 +88,7 @@ commit_message='Uploaded column_maker tarball.', strings_displayed=[], strings_not_displayed=[] ) + def test_0015_create_emboss_datatypes_repository( self ): '''Create and populate emboss_datatypes_0050.''' category = self.create_category( name=category_name, description=category_description ) @@ -104,6 +109,7 @@ commit_message='Uploaded datatypes_conf.xml.', strings_displayed=[], strings_not_displayed=[] ) + def test_0020_create_emboss_repository( self ): '''Create and populate emboss_0050.''' category = self.create_category( name=category_name, description=category_description ) @@ -122,20 +128,7 @@ commit_message='Uploaded emboss tarball.', strings_displayed=[], strings_not_displayed=[] ) - datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) - repository_dependencies_path = self.generate_temp_path( 'test_0050', additional_paths=[ 'emboss' ] ) - self.generate_repository_dependency_xml( [ datatypes_repository ], - self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), - dependency_description='Emboss depends on the emboss_datatypes repository.' ) - self.upload_file( repository, - filename='repository_dependencies.xml', - filepath=repository_dependencies_path, - valid_tools_only=True, - uncompress_file=False, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded dependency on emboss_datatypes.', - strings_displayed=[], - strings_not_displayed=[] ) + def test_0025_create_filtering_repository( self ): '''Create and populate filtering_0050.''' category = self.create_category( name=category_name, description=category_description ) @@ -154,20 +147,7 @@ commit_message='Uploaded filtering 1.1.0 tarball.', strings_displayed=[], strings_not_displayed=[] ) - emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) - repository_dependencies_path = self.generate_temp_path( 'test_0050', additional_paths=[ 'filtering' ] ) - self.generate_repository_dependency_xml( [ emboss_repository ], - self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), - dependency_description='Filtering depends on the emboss repository.' ) - self.upload_file( filtering_repository, - filename='repository_dependencies.xml', - filepath=repository_dependencies_path, - valid_tools_only=True, - uncompress_file=False, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded dependency on emboss.', - strings_displayed=[], - strings_not_displayed=[] ) + def test_0030_create_freebayes_repository( self ): '''Create and populate freebayes_0050.''' category = self.create_category( name=category_name, description=category_description ) @@ -186,6 +166,7 @@ commit_message='Uploaded freebayes tarball.', strings_displayed=[], strings_not_displayed=[] ) + def test_0035_create_bismark_repository( self ): '''Create and populate bismark_0050.''' category = self.create_category( name=category_name, description=category_description ) @@ -204,10 +185,11 @@ commit_message='Uploaded bismark tarball.', strings_displayed=[], strings_not_displayed=[] ) + def test_0040_create_and_upload_dependency_definitions( self ): column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) - emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) + datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) @@ -219,14 +201,21 @@ # emboss_datatypes depends on bismark # freebayes depends on freebayes, emboss, emboss_datatypes, and column_maker # filtering depends on emboss - self.create_repository_dependency( convert_repository, depends_on=[ column_repository ], filepath=dependency_xml_path ) - self.create_repository_dependency( column_repository, depends_on=[ convert_repository ], filepath=dependency_xml_path ) - self.create_repository_dependency( emboss_datatypes_repository, depends_on=[ bismark_repository ], filepath=dependency_xml_path ) - self.create_repository_dependency( emboss_repository, depends_on=[ emboss_datatypes_repository ], filepath=dependency_xml_path ) - self.create_repository_dependency( freebayes_repository, - depends_on=[ freebayes_repository, emboss_datatypes_repository, emboss_repository, column_repository ], + column_tuple = ( self.url, column_repository.name, column_repository.user.username, self.get_repository_tip( column_repository ) ) + convert_tuple = ( self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip( convert_repository ) ) + freebayes_tuple = ( self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip( freebayes_repository ) ) + emboss_tuple = ( self.url, emboss_repository.name, emboss_repository.user.username, self.get_repository_tip( emboss_repository ) ) + datatypes_tuple = ( self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip( datatypes_repository ) ) + bismark_tuple = ( self.url, bismark_repository.name, bismark_repository.user.username, self.get_repository_tip( bismark_repository ) ) + self.create_repository_dependency( repository=convert_repository, repository_tuples=[ column_tuple ], filepath=dependency_xml_path ) + self.create_repository_dependency( repository=column_repository, repository_tuples=[ convert_tuple ], filepath=dependency_xml_path ) + self.create_repository_dependency( repository=datatypes_repository, repository_tuples=[ bismark_tuple ], filepath=dependency_xml_path ) + self.create_repository_dependency( repository=emboss_repository, repository_tuples=[ datatypes_tuple ], filepath=dependency_xml_path ) + self.create_repository_dependency( repository=freebayes_repository, + repository_tuples=[ freebayes_tuple, datatypes_tuple, emboss_tuple, column_tuple ], filepath=dependency_xml_path ) - self.create_repository_dependency( filtering_repository, depends_on=[ emboss_repository ], filepath=dependency_xml_path ) + self.create_repository_dependency( repository=filtering_repository, repository_tuples=[ emboss_tuple ], filepath=dependency_xml_path ) + def test_0045_verify_repository_dependencies( self ): '''Verify that the generated dependency circle does not cause an infinite loop. Expected structure: @@ -264,6 +253,7 @@ strings_displayed = [ 'freebayes_0050 depends on freebayes_0050, emboss_datatypes_0050, emboss_0050, column_maker_0050.' ] self.display_manage_repository_page( freebayes_repository, strings_displayed=strings_displayed ) + def test_0050_verify_tool_dependencies( self ): '''Check that freebayes and emboss display tool dependencies.''' freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) @@ -271,6 +261,7 @@ self.display_manage_repository_page( freebayes_repository, strings_displayed=[ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Tool dependencies', 'package' ] ) self.display_manage_repository_page( emboss_repository, strings_displayed=[ 'Tool dependencies', 'emboss', '5.0.0', 'package' ] ) + def test_0055_verify_repository_metadata( self ): '''Verify that resetting the metadata does not change it.''' emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) diff -r 2c50935e70c8a483bcd09b358765408543a153fb -r 8d72c9adccf92f8a1971ec7d9b622de43cbd6f48 test/tool_shed/functional/test_0080_advanced_circular_dependencies.py --- a/test/tool_shed/functional/test_0080_advanced_circular_dependencies.py +++ b/test/tool_shed/functional/test_0080_advanced_circular_dependencies.py @@ -12,8 +12,10 @@ category_name = 'Test 0080 Advanced Circular Dependencies' category_description = 'Test circular dependency features' + class TestRepositoryCircularDependencies( ShedTwillTestCase ): '''Verify that the code correctly handles circular dependencies.''' + def test_0000_initiate_users( self ): """Create necessary user accounts.""" self.logout() @@ -26,6 +28,7 @@ admin_user = test_db_util.get_user( common.admin_email ) assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_column_repository( self ): """Create and populate the column_maker repository.""" category = self.create_category( name=category_name, description=category_description ) @@ -46,6 +49,7 @@ commit_message='Uploaded column_maker tarball.', strings_displayed=[], strings_not_displayed=[] ) + def test_0005_create_convert_repository( self ): """Create and populate the convert_chars repository.""" self.logout() @@ -68,46 +72,30 @@ commit_message='Uploaded convert_chars tarball.', strings_displayed=[], strings_not_displayed=[] ) + def test_0020_create_repository_dependencies( self ): - '''Upload a repository_dependencies.xml file that specifies the current revision of freebayes to the filtering_0040 repository.''' + '''Upload a repository_dependencies.xml file that specifies the current revision of convert_chars_0080 to the column_maker_0080 repository.''' convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0080', additional_paths=[ 'convert' ] ) - self.generate_repository_dependency_xml( [ convert_repository ], - self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), - dependency_description='Column maker depends on the convert repository.' ) - self.upload_file( column_repository, - filename='repository_dependencies.xml', - filepath=repository_dependencies_path, - valid_tools_only=True, - uncompress_file=True, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded dependency on convert_chars.', - strings_displayed=[], - strings_not_displayed=[] ) + repository_tuple = ( self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip( convert_repository ) ) + self.create_repository_dependency( repository=column_repository, repository_tuples=[ repository_tuple ], filepath=repository_dependencies_path ) + def test_0025_create_dependency_on_filtering( self ): '''Upload a repository_dependencies.xml file that specifies the current revision of filtering to the freebayes_0040 repository.''' convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0080', additional_paths=[ 'convert' ] ) - self.generate_repository_dependency_xml( [ column_repository ], - self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), - dependency_description='Convert chars depends on the column_maker repository.' ) - self.upload_file( convert_repository, - filename='repository_dependencies.xml', - filepath=repository_dependencies_path, - valid_tools_only=True, - uncompress_file=True, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded dependency on column_maker.', - strings_displayed=[], - strings_not_displayed=[] ) + repository_tuple = ( self.url, column_repository.name, column_repository.user.username, self.get_repository_tip( column_repository ) ) + self.create_repository_dependency( repository=convert_repository, repository_tuples=[ repository_tuple ], filepath=repository_dependencies_path ) + def test_0030_verify_repository_dependencies( self ): '''Verify that each repository can depend on the other without causing an infinite loop.''' convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) self.check_repository_dependency( convert_repository, column_repository, self.get_repository_tip( column_repository ) ) self.check_repository_dependency( column_repository, convert_repository, self.get_repository_tip( convert_repository ) ) + def test_0035_verify_repository_metadata( self ): '''Verify that resetting the metadata does not change it.''' column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) diff -r 2c50935e70c8a483bcd09b358765408543a153fb -r 8d72c9adccf92f8a1971ec7d9b622de43cbd6f48 test/tool_shed/functional/test_0090_tool_search.py --- a/test/tool_shed/functional/test_0090_tool_search.py +++ b/test/tool_shed/functional/test_0090_tool_search.py @@ -28,8 +28,10 @@ category_name = 'Test 0090 Tool Search And Installation' category_description = 'Test 0090 Tool Search And Installation' + class TestRepositoryCircularDependenciesAgain( ShedTwillTestCase ): '''Test more features related to repository dependencies.''' + def test_0000_initiate_users( self ): """Create necessary user accounts.""" self.logout() @@ -42,6 +44,7 @@ admin_user = test_db_util.get_user( common.admin_email ) assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_bwa_base_repository( self ): '''Create and populate bwa_base_0090.''' category = self.create_category( name=category_name, description=category_description ) @@ -62,6 +65,7 @@ commit_message='Uploaded BWA tarball.', strings_displayed=[], strings_not_displayed=[] ) + def test_0010_create_bwa_color_repository( self ): '''Create and populate bwa_color_0090.''' category = self.create_category( name=category_name, description=category_description ) @@ -82,6 +86,7 @@ commit_message='Uploaded BWA color tarball.', strings_displayed=[], strings_not_displayed=[] ) + def test_0015_create_emboss_datatypes_repository( self ): '''Create and populate emboss_datatypes_0090.''' category = self.create_category( name=category_name, description=category_description ) @@ -102,6 +107,7 @@ commit_message='Uploaded datatypes_conf.xml.', strings_displayed=[], strings_not_displayed=[] ) + def test_0020_create_emboss_repository( self ): '''Create and populate emboss_0090.''' category = self.create_category( name=category_name, description=category_description ) @@ -120,20 +126,7 @@ commit_message='Uploaded emboss tarball.', strings_displayed=[], strings_not_displayed=[] ) - datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) - repository_dependencies_path = self.generate_temp_path( 'test_0090', additional_paths=[ 'emboss' ] ) - self.generate_repository_dependency_xml( [ datatypes_repository ], - self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), - dependency_description='Emboss depends on the emboss_datatypes repository.' ) - self.upload_file( repository, - filename='repository_dependencies.xml', - filepath=repository_dependencies_path, - valid_tools_only=True, - uncompress_file=True, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded dependency on emboss_datatypes.', - strings_displayed=[], - strings_not_displayed=[] ) + def test_0025_create_filtering_repository( self ): '''Create and populate filtering_0090.''' category = self.create_category( name=category_name, description=category_description ) @@ -152,20 +145,7 @@ commit_message='Uploaded filtering 1.1.0 tarball.', strings_displayed=[], strings_not_displayed=[] ) - emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) - repository_dependencies_path = self.generate_temp_path( 'test_0090', additional_paths=[ 'filtering' ] ) - self.generate_repository_dependency_xml( [ emboss_repository ], - self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), - dependency_description='Filtering depends on the emboss repository.' ) - self.upload_file( filtering_repository, - filename='repository_dependencies.xml', - filepath=repository_dependencies_path, - valid_tools_only=True, - uncompress_file=False, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded dependency on emboss.', - strings_displayed=[], - strings_not_displayed=[] ) + def test_0030_create_freebayes_repository( self ): '''Create and populate freebayes_0090.''' category = self.create_category( name=category_name, description=category_description ) @@ -184,19 +164,25 @@ commit_message='Uploaded freebayes tarball.', strings_displayed=[], strings_not_displayed=[] ) + def test_0035_create_and_upload_dependency_definitions( self ): '''Create and upload repository dependency definitions.''' bwa_color_repository = test_db_util.get_repository_by_name_and_owner( bwa_color_repository_name, common.test_user_1_name ) bwa_base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) - emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) + datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) dependency_xml_path = self.generate_temp_path( 'test_0090', additional_paths=[ 'freebayes' ] ) - self.create_repository_dependency( emboss_repository, depends_on=[ emboss_datatypes_repository ], filepath=dependency_xml_path ) - self.create_repository_dependency( filtering_repository, depends_on=[ freebayes_repository ], filepath=dependency_xml_path ) - self.create_repository_dependency( bwa_base_repository, depends_on=[ emboss_repository ], filepath=dependency_xml_path ) - self.create_repository_dependency( bwa_color_repository, depends_on=[ filtering_repository ], filepath=dependency_xml_path ) + freebayes_tuple = ( self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip( freebayes_repository ) ) + emboss_tuple = ( self.url, emboss_repository.name, emboss_repository.user.username, self.get_repository_tip( emboss_repository ) ) + datatypes_tuple = ( self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip( datatypes_repository ) ) + filtering_tuple = ( self.url, filtering_repository.name, filtering_repository.user.username, self.get_repository_tip( filtering_repository ) ) + self.create_repository_dependency( repository=emboss_repository, repository_tuples=[ datatypes_tuple ], filepath=dependency_xml_path ) + self.create_repository_dependency( repository=filtering_repository, repository_tuples=[ freebayes_tuple ], filepath=dependency_xml_path ) + self.create_repository_dependency( repository=bwa_base_repository, repository_tuples=[ emboss_tuple ], filepath=dependency_xml_path ) + self.create_repository_dependency( repository=bwa_color_repository, repository_tuples=[ filtering_tuple ], filepath=dependency_xml_path ) + def test_0040_verify_repository_dependencies( self ): '''Verify the generated dependency structure.''' bwa_color_repository = test_db_util.get_repository_by_name_and_owner( bwa_color_repository_name, common.test_user_1_name ) diff -r 2c50935e70c8a483bcd09b358765408543a153fb -r 8d72c9adccf92f8a1971ec7d9b622de43cbd6f48 test/tool_shed/functional/test_0100_complex_repository_dependencies.py --- a/test/tool_shed/functional/test_0100_complex_repository_dependencies.py +++ b/test/tool_shed/functional/test_0100_complex_repository_dependencies.py @@ -1,6 +1,9 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import tool_shed.base.test_db_util as test_db_util +import logging +log = logging.getLogger( __name__ ) + bwa_base_repository_name = 'bwa_base_repository_0100' bwa_base_repository_description = "BWA Base" bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at bwa_tool_repository_0100" @@ -12,8 +15,10 @@ category_name = 'Test 0100 Complex Repository Dependencies' category_description = 'Test 0100 Complex Repository Dependencies' + class TestComplexRepositoryDependencies( ShedTwillTestCase ): '''Test features related to complex repository dependencies.''' + def test_0000_initiate_users( self ): """Create necessary user accounts.""" self.logout() @@ -26,6 +31,7 @@ admin_user = test_db_util.get_user( common.admin_email ) assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_bwa_tool_repository( self ): '''Create and populate bwa_tool_repository_0100.''' category = self.create_category( name=category_name, description=category_description ) @@ -49,6 +55,7 @@ strings_not_displayed=[] ) # Visit the manage repository page for bwa_tool_repository_0100. self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'may not be', 'in this repository' ] ) + def test_0010_create_bwa_base_repository( self ): '''Create and populate bwa_base_0100.''' category = self.create_category( name=category_name, description=category_description ) @@ -71,30 +78,30 @@ commit_message='Uploaded bwa_base.tar with tool wrapper XML, but without tool dependency XML.', strings_displayed=[], strings_not_displayed=[] ) + def test_0015_generate_complex_repository_dependency_invalid_shed_url( self ): '''Generate and upload a complex repository definition that specifies an invalid tool shed URL.''' dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) # The repository named bwa_base_repository_0100 is the dependent repository. - repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) # The tool_repository named bwa_tool_repository_0100 is the required repository. tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) url = 'http://http://this is not an url!' name = 'bwa_tool_repository_0100' owner = 'user1' changeset_revision = self.get_repository_tip( tool_repository ) - self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) strings_displayed = [ 'Repository dependencies are currently supported only within the same tool shed' ] # Populate the dependent repository named bwa_base_repository_0100 with an invalid tool_dependencies.xml file. - self.upload_file( repository, - filename='tool_dependencies.xml', - filepath=dependency_path, - valid_tools_only=False, - uncompress_file=False, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded dependency on bwa_tool_0100 with invalid url.', - strings_displayed=strings_displayed, - strings_not_displayed=[] ) + repository_tuple = ( url, name, owner, changeset_revision ) + self.create_repository_dependency( repository=base_repository, + filepath=dependency_path, + repository_tuples=[ repository_tuple ], + strings_displayed=strings_displayed, + complex=True, + package='bwa', + version='0.5.9' ) + def test_0020_generate_complex_repository_dependency_invalid_repository_name( self ): '''Generate and upload a complex repository definition that specifies an invalid repository name.''' dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] ) @@ -107,18 +114,17 @@ name = 'invalid_repository!?' owner = 'user1' changeset_revision = self.get_repository_tip( tool_repository ) - self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) strings_displayed = [ 'because the name is invalid' ] - # # Populate the dependent base_repository named bwa_tool_repository_0100 with an invalid tool_dependencies.xml file. - self.upload_file( base_repository, - filename='tool_dependencies.xml', - filepath=dependency_path, - valid_tools_only=False, - uncompress_file=False, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded dependency on bwa_tool_0100 with invalid repository name.', - strings_displayed=strings_displayed, - strings_not_displayed=[] ) + # Populate the dependent base_repository named bwa_tool_repository_0100 with an invalid tool_dependencies.xml file. + repository_tuple = ( url, name, owner, changeset_revision ) + self.create_repository_dependency( repository=base_repository, + filepath=dependency_path, + repository_tuples=[ repository_tuple ], + strings_displayed=strings_displayed, + complex=True, + package='bwa', + version='0.5.9' ) + def test_0025_generate_complex_repository_dependency_invalid_owner_name( self ): '''Generate and upload a complex repository definition that specifies an invalid owner.''' dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] ) @@ -131,17 +137,16 @@ name = 'bwa_tool_repository_0100' owner = 'invalid_owner!?' changeset_revision = self.get_repository_tip( tool_repository ) - self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) - strings_displayed = [ 'because the owner is invalid.' ] - self.upload_file( base_repository, - filename='tool_dependencies.xml', - filepath=dependency_path, - valid_tools_only=False, - uncompress_file=False, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded dependency on bwa_tool_0100 with invalid owner.', - strings_displayed=strings_displayed, - strings_not_displayed=[] ) + strings_displayed = [ 'because the owner is invalid.' ] + repository_tuple = ( url, name, owner, changeset_revision ) + self.create_repository_dependency( repository=base_repository, + filepath=dependency_path, + repository_tuples=[ repository_tuple ], + strings_displayed=strings_displayed, + complex=True, + package='bwa', + version='0.5.9' ) + def test_0030_generate_complex_repository_dependency_invalid_changeset_revision( self ): '''Generate and upload a complex repository definition that specifies an invalid changeset revision.''' dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] ) @@ -154,17 +159,16 @@ name = 'bwa_tool_repository_0100' owner = 'user1' changeset_revision = '1234abcd' - self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) strings_displayed = [ 'because the changeset revision is invalid.' ] - self.upload_file( base_repository, - filename='tool_dependencies.xml', - filepath=dependency_path, - valid_tools_only=False, - uncompress_file=False, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded dependency on bwa_tool_0100 with invalid changeset revision.', - strings_displayed=strings_displayed, - strings_not_displayed=[] ) + repository_tuple = ( url, name, owner, changeset_revision ) + self.create_repository_dependency( repository=base_repository, + filepath=dependency_path, + repository_tuples=[ repository_tuple ], + strings_displayed=strings_displayed, + complex=True, + package='bwa', + version='0.5.9' ) + def test_0035_generate_complex_repository_dependency( self ): '''Generate and upload a valid tool_dependencies.xml file that specifies bwa_tool_repository_0100.''' # The base_repository named bwa_base_repository_0100 is the dependent repository. @@ -172,25 +176,20 @@ # The tool_repository named bwa_tool_repository_0100 is the required repository. tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex' ] ) - xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) url = self.url name = 'bwa_tool_repository_0100' owner = 'user1' changeset_revision = self.get_repository_tip( tool_repository ) - self.generate_repository_dependency_xml( [ tool_repository ], xml_filename, complex=True, package='bwa', version='0.5.9' ) - # Upload the valid tool_dependencies.xml file to bwa_base_repository_0100 that specifies bwa_tool_repository_0100 - # as a repository dependency via a complex repository dependency definition. - self.upload_file( base_repository, - filename='tool_dependencies.xml', - filepath=dependency_path, - valid_tools_only=True, - uncompress_file=False, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded valid complex dependency on bwa_tool_0100.', - strings_displayed=[], - strings_not_displayed=[] ) - self.check_repository_dependency( base_repository, tool_repository ) - self.display_manage_repository_page( base_repository, strings_displayed=[ 'bwa', '0.5.9', 'package' ] ) + repository_tuple = ( url, name, owner, changeset_revision ) + self.create_repository_dependency( repository=base_repository, + filepath=dependency_path, + repository_tuples=[ repository_tuple ], + complex=True, + package='bwa', + version='0.5.9' ) + self.check_repository_dependency( base_repository, depends_on_repository=tool_repository ) + self.display_manage_repository_page( base_repository, strings_displayed=[ 'bwa', '0.5.9', 'package', changeset_revision ] ) + def test_0040_generate_tool_dependency( self ): '''Generate and upload a new tool_dependencies.xml file that specifies an arbitrary file on the filesystem, and verify that bwa_base depends on the new changeset revision.''' # The base_repository named bwa_base_repository_0100 is the dependent repository. diff -r 2c50935e70c8a483bcd09b358765408543a153fb -r 8d72c9adccf92f8a1971ec7d9b622de43cbd6f48 test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py --- a/test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py +++ b/test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py @@ -12,8 +12,10 @@ category_name = 'Test 0110 Invalid Repository Dependencies' category_desc = 'Test 0110 Invalid Repository Dependencies' + class TestBasicRepositoryDependencies( ShedTwillTestCase ): '''Testing emboss 5 with repository dependencies.''' + def test_0000_initiate_users( self ): """Create necessary user accounts and login as an admin user.""" self.logout() @@ -26,9 +28,11 @@ admin_user = test_db_util.get_user( common.admin_email ) assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_category( self ): """Create a category for this test suite""" self.create_category( name=category_name, description=category_desc ) + def test_0010_create_emboss_datatypes_repository_and_upload_tarball( self ): '''Create and populate the emboss_datatypes repository.''' self.logout() @@ -49,10 +53,12 @@ commit_message='Uploaded datatypes_conf.xml.', strings_displayed=[], strings_not_displayed=[] ) + def test_0015_verify_datatypes_in_datatypes_repository( self ): '''Verify that the emboss_datatypes repository contains datatype entries.''' repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) self.display_manage_repository_page( repository, strings_displayed=[ 'Datatypes', 'equicktandem', 'hennig86', 'vectorstrip' ] ) + def test_0020_create_emboss_5_repository_and_upload_files( self ): '''Create and populate the emboss_5_0110 repository.''' category = test_db_util.get_category_by_name( category_name ) @@ -71,27 +77,25 @@ commit_message='Uploaded emboss tool tarball.', strings_displayed=[], strings_not_displayed=[] ) + def test_0025_generate_repository_dependency_with_invalid_url( self ): '''Generate a repository dependency for emboss 5 with an invalid URL.''' dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple' ] ) xml_filename = self.get_filename( 'repository_dependencies.xml', filepath=dependency_path ) - repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) url = 'http://http://this is not an url!' - name = repository.name - owner = repository.user.username - changeset_revision = self.get_repository_tip( repository ) - self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' ) + name = datatypes_repository.name + owner = datatypes_repository.user.username + changeset_revision = self.get_repository_tip( datatypes_repository ) strings_displayed = [ 'Repository dependencies are currently supported only within the same tool shed' ] - self.upload_file( emboss_repository, - filename='repository_dependencies.xml', - filepath=dependency_path, - valid_tools_only=False, - uncompress_file=False, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid url.', - strings_displayed=strings_displayed, - strings_not_displayed=[] ) + repository_tuple = ( url, name, owner, changeset_revision ) + self.create_repository_dependency( repository=emboss_repository, + filepath=dependency_path, + repository_tuples=[ repository_tuple ], + strings_displayed=strings_displayed, + complex=False ) + def test_0030_generate_repository_dependency_with_invalid_name( self ): '''Generate a repository dependency for emboss 5 with an invalid name.''' dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple' ] ) @@ -102,17 +106,14 @@ name = '!?invalid?!' owner = repository.user.username changeset_revision = self.get_repository_tip( repository ) - self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' ) strings_displayed = [ 'because the name is invalid.' ] - self.upload_file( emboss_repository, - filename='repository_dependencies.xml', - filepath=dependency_path, - valid_tools_only=False, - uncompress_file=False, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid name.', - strings_displayed=strings_displayed, - strings_not_displayed=[] ) + repository_tuple = ( url, name, owner, changeset_revision ) + self.create_repository_dependency( repository=emboss_repository, + filepath=dependency_path, + repository_tuples=[ repository_tuple ], + strings_displayed=strings_displayed, + complex=False ) + def test_0035_generate_repository_dependency_with_invalid_owner( self ): '''Generate a repository dependency for emboss 5 with an invalid owner.''' dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple' ] ) @@ -123,17 +124,14 @@ name = repository.name owner = '!?invalid?!' changeset_revision = self.get_repository_tip( repository ) - self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' ) strings_displayed = [ 'because the owner is invalid.' ] - self.upload_file( emboss_repository, - filename='repository_dependencies.xml', - filepath=dependency_path, - valid_tools_only=False, - uncompress_file=False, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid owner.', - strings_displayed=strings_displayed, - strings_not_displayed=[] ) + repository_tuple = ( url, name, owner, changeset_revision ) + self.create_repository_dependency( repository=emboss_repository, + filepath=dependency_path, + repository_tuples=[ repository_tuple ], + strings_displayed=strings_displayed, + complex=False ) + def test_0040_generate_repository_dependency_with_invalid_changeset_revision( self ): '''Generate a repository dependency for emboss 5 with an invalid changeset revision.''' dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple', 'invalid' ] ) @@ -144,14 +142,10 @@ name = repository.name owner = repository.user.username changeset_revision = '!?invalid?!' - self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' ) strings_displayed = [ 'because the changeset revision is invalid.' ] - self.upload_file( emboss_repository, - filename='repository_dependencies.xml', - filepath=dependency_path, - valid_tools_only=False, - uncompress_file=False, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid changeset revision.', - strings_displayed=strings_displayed, - strings_not_displayed=[] ) + repository_tuple = ( url, name, owner, changeset_revision ) + self.create_repository_dependency( repository=emboss_repository, + filepath=dependency_path, + repository_tuples=[ repository_tuple ], + strings_displayed=strings_displayed, + complex=False ) diff -r 2c50935e70c8a483bcd09b358765408543a153fb -r 8d72c9adccf92f8a1971ec7d9b622de43cbd6f48 test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py --- a/test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py +++ b/test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py @@ -23,7 +23,9 @@ base_datatypes_count = 0 repository_datatypes_count = 0 + class TestRepositoryMultipleOwners( ShedTwillTestCase ): + def test_0000_initiate_users( self ): """Create necessary user accounts and login as an admin user.""" """ @@ -45,6 +47,7 @@ admin_user = test_db_util.get_user( common.admin_email ) assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_datatypes_repository( self ): """Create and populate the blast_datatypes_0120 repository""" """ @@ -71,6 +74,7 @@ commit_message='Uploaded blast_datatypes tarball.', strings_displayed=[], strings_not_displayed=[] ) + def test_0010_verify_datatypes_repository( self ): '''Verify the blast_datatypes_0120 repository.''' ''' @@ -83,6 +87,7 @@ strings_displayed = [ 'BlastXml', 'BlastNucDb', 'BlastProtDb', 'application/xml', 'text/html', 'blastxml', 'blastdbn', 'blastdbp'] self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) repository_datatypes_count = int( self.get_repository_datatypes_count( repository ) ) + def test_0015_create_tool_repository( self ): """Create and populate the blastxml_to_top_descr_0120 repository""" """ @@ -109,6 +114,7 @@ commit_message='Uploaded blastxml_to_top_descr tarball.', strings_displayed=[], strings_not_displayed=[] ) + def test_0020_verify_tool_repository( self ): '''Verify the blastxml_to_top_descr_0120 repository.''' ''' @@ -119,6 +125,7 @@ strings_displayed = [ 'blastxml_to_top_descr_0120', 'BLAST top hit descriptions', 'Make a table from BLAST XML' ] strings_displayed.extend( [ '0.0.1', 'Valid tools'] ) self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + def test_0025_create_repository_dependency( self ): '''Create a repository dependency on blast_datatypes_0120.''' ''' @@ -128,7 +135,9 @@ datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_2_name ) tool_repository = test_db_util.get_repository_by_name_and_owner( tool_repository_name, common.test_user_1_name ) dependency_xml_path = self.generate_temp_path( 'test_0120', additional_paths=[ 'dependencies' ] ) - self.create_repository_dependency( repository=tool_repository, depends_on=[ datatypes_repository ], filepath=dependency_xml_path ) + datatypes_tuple = ( self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip( datatypes_repository ) ) + self.create_repository_dependency( repository=tool_repository, repository_tuples=[ datatypes_tuple ], filepath=dependency_xml_path ) + def test_0040_verify_repository_dependency( self ): '''Verify the created repository dependency.''' ''' diff -r 2c50935e70c8a483bcd09b358765408543a153fb -r 8d72c9adccf92f8a1971ec7d9b622de43cbd6f48 test/tool_shed/functional/test_0150_prior_installation_required.py --- /dev/null +++ b/test/tool_shed/functional/test_0150_prior_installation_required.py @@ -0,0 +1,109 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +column_repository_name = 'column_maker_0150' +column_repository_description = "Add column" +column_repository_long_description = "Compute an expression on every row" + +convert_repository_name = 'convert_chars_0150' +convert_repository_description = "Convert delimiters" +convert_repository_long_description = "Convert delimiters to tab" + +category_name = 'Test 0150 Simple Prior Installation' +category_description = 'Test 0150 Simple Prior Installation' + +''' +Create column_maker and convert_chars. + +Column maker repository dependency: +<repository toolshed="self.url" name="convert_chars" owner="test" changeset_revision="c3041382815c" prior_installation_required="True" /> + +Verify display. + +Galaxy side: + +Install column_maker. +Verify that convert_chars was installed first, contrary to the ordering that would be present without prior_installation_required. +''' + + +class TestSimplePriorInstallation( ShedTwillTestCase ): + '''Test features related to datatype converters.''' + + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + + def test_0005_create_convert_repository( self ): + '''Create and populate convert_chars_0150.''' + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=convert_repository_name, + description=convert_repository_description, + long_description=convert_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + filename='convert_chars/convert_chars.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded convert_chars tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0010_create_column_repository( self ): + '''Create and populate convert_chars_0150.''' + category = self.create_category( name=category_name, description=category_description ) + repository = self.get_or_create_repository( name=column_repository_name, + description=column_repository_description, + long_description=column_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + filename='column_maker/column_maker.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded column_maker tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0015_create_repository_dependency( self ): + '''Create a repository dependency specifying convert_chars.''' + ''' + Column maker repository dependency: + <repository toolshed="self.url" name="convert_chars" owner="test" changeset_revision="<tip>" prior_installation_required="True" /> + ''' + column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) + convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) + dependency_xml_path = self.generate_temp_path( 'test_0150', additional_paths=[ 'column' ] ) + convert_tuple = ( self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip( convert_repository ) ) + self.create_repository_dependency( repository=column_repository, + repository_tuples=[ convert_tuple ], + filepath=dependency_xml_path, + prior_installation_required=True ) + + def test_0020_verify_repository_dependency( self ): + '''Verify that the previously generated repositiory dependency displays correctly.''' + column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) + convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) + self.check_repository_dependency( repository=column_repository, + depends_on_repository=convert_repository, + depends_on_changeset_revision=None, + changeset_revision=None ) + diff -r 2c50935e70c8a483bcd09b358765408543a153fb -r 8d72c9adccf92f8a1971ec7d9b622de43cbd6f48 test/tool_shed/functional/test_0160_circular_prior_installation_required.py --- /dev/null +++ b/test/tool_shed/functional/test_0160_circular_prior_installation_required.py @@ -0,0 +1,161 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +filter_repository_name = 'filtering_0160' +filter_repository_description = "Galaxy's filtering tool for test 0160" +filter_repository_long_description = "Long description of Galaxy's filtering tool for test 0160" + +column_repository_name = 'column_maker_0160' +column_repository_description = "Add column" +column_repository_long_description = "Compute an expression on every row" + +convert_repository_name = 'convert_chars_0160' +convert_repository_description = "Convert delimiters" +convert_repository_long_description = "Convert delimiters to tab" + +category_name = 'Test 0160 Simple Prior Installation' +category_description = 'Test 0160 Simple Prior Installation' + +''' +Create column_maker and convert_chars. + +Column maker repository dependency: +<repository toolshed="self.url" name="convert_chars" owner="test" changeset_revision="c3041382815c" prior_installation_required="True" /> + +Verify display. +''' + + +class TestSimplePriorInstallation( ShedTwillTestCase ): + '''Test features related to datatype converters.''' + + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + + def test_0005_create_convert_repository( self ): + '''Create and populate convert_chars_0160.''' + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=convert_repository_name, + description=convert_repository_description, + long_description=convert_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + filename='convert_chars/convert_chars.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded convert_chars tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0010_create_column_repository( self ): + '''Create and populate convert_chars_0160.''' + category = self.create_category( name=category_name, description=category_description ) + repository = self.get_or_create_repository( name=column_repository_name, + description=column_repository_description, + long_description=column_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + filename='column_maker/column_maker.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded column_maker tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0015_create_filtering_repository( self ): + '''Create and populate filtering_0160.''' + category = self.create_category( name=category_name, description=category_description ) + repository = self.get_or_create_repository( name=filter_repository_name, + description=filter_repository_description, + long_description=filter_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + filename='filtering/filtering_1.1.0.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded filtering 1.1.0 tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0020_create_repository_dependency( self ): + '''Create a repository dependency specifying convert_chars.''' + ''' + Each of the three repositories should depend on the other two, to make this as circular as possible. + ''' + filter_repository = test_db_util.get_repository_by_name_and_owner( filter_repository_name, common.test_user_1_name ) + column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) + convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) + dependency_xml_path = self.generate_temp_path( 'test_0160', additional_paths=[ 'column' ] ) + filter_revision = self.get_repository_tip( filter_repository ) + column_revision = self.get_repository_tip( column_repository ) + convert_revision = self.get_repository_tip( convert_repository ) + column_tuple = ( self.url, column_repository.name, column_repository.user.username, column_revision ) + convert_tuple = ( self.url, convert_repository.name, convert_repository.user.username, convert_revision ) + filter_tuple = ( self.url, filter_repository.name, filter_repository.user.username, filter_revision ) + self.create_repository_dependency( repository=column_repository, + repository_tuples=[ convert_tuple, filter_tuple], + filepath=dependency_xml_path, + prior_installation_required=False ) + self.create_repository_dependency( repository=convert_repository, + repository_tuples=[ column_tuple, filter_tuple ], + filepath=dependency_xml_path, + prior_installation_required=False ) + self.create_repository_dependency( repository=filter_repository, + repository_tuples=[ convert_tuple, column_tuple ], + filepath=dependency_xml_path, + prior_installation_required=True ) + + def test_0025_verify_repository_dependency( self ): + '''Verify that the previously generated repositiory dependency displays correctly.''' + filter_repository = test_db_util.get_repository_by_name_and_owner( filter_repository_name, common.test_user_1_name ) + column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) + convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) + self.check_repository_dependency( repository=column_repository, + depends_on_repository=convert_repository, + depends_on_changeset_revision=None, + changeset_revision=None ) + self.check_repository_dependency( repository=column_repository, + depends_on_repository=filter_repository, + depends_on_changeset_revision=None, + changeset_revision=None ) + self.check_repository_dependency( repository=convert_repository, + depends_on_repository=column_repository, + depends_on_changeset_revision=None, + changeset_revision=None ) + self.check_repository_dependency( repository=convert_repository, + depends_on_repository=filter_repository, + depends_on_changeset_revision=None, + changeset_revision=None ) + self.check_repository_dependency( repository=filter_repository, + depends_on_repository=column_repository, + depends_on_changeset_revision=None, + changeset_revision=None ) + self.check_repository_dependency( repository=filter_repository, + depends_on_repository=convert_repository, + depends_on_changeset_revision=None, + changeset_revision=None ) + 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.

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