galaxy-commits May 2013

galaxy-commits@lists.galaxyproject.org

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218 discussions

commit/galaxy-central: dannon: Fix install_repository_tools script to appropriately handle a trailing slash in the URL.
by commits-noreply＠bitbucket.org 03 May '13

03 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/75e7383c5c79/ Changeset: 75e7383c5c79 User: dannon Date: 2013-05-03 21:46:53 Summary: Fix install_repository_tools script to appropriately handle a trailing slash in the URL. Affected #: 1 file diff -r 324d023bbf59aafb4be03cbb9842456aab0a1965 -r 75e7383c5c794e02503dc03e0d5daf3694323b7d scripts/api/install_repository_tools.py --- a/scripts/api/install_repository_tools.py +++ b/scripts/api/install_repository_tools.py @@ -34,7 +34,7 @@ data[ 'install_repository_dependencies' ] = options.install_repository_dependencies if options.install_tool_dependencies: data[ 'install_tool_dependencies' ] = options.install_tool_dependencies - submit( options.api, '%s%s' % ( options.local_url, '/api/tool_shed_repositories/new/install_repository_revision' ), data ) + submit( options.api, '%s%s' % ( options.local_url.strip('/'), '/api/tool_shed_repositories/new/install_repository_revision' ), data ) if __name__ == '__main__': parser = argparse.ArgumentParser( description='Installation of tool shed repositories via the Galaxy API.' ) 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: Explicitly uninstall all installed repositories after each set of tests has finished running. This prevents certain edge cases from interfering with subsequent tests.
by commits-noreply＠bitbucket.org 03 May '13

03 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/324d023bbf59/ Changeset: 324d023bbf59 User: inithello Date: 2013-05-03 21:25:20 Summary: Explicitly uninstall all installed repositories after each set of tests has finished running. This prevents certain edge cases from interfering with subsequent tests. Affected #: 2 files diff -r e5577cd833abbd0ad072d55f4b56d1458105991b -r 324d023bbf59aafb4be03cbb9842456aab0a1965 test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py --- a/test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py +++ b/test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py @@ -3,8 +3,10 @@ from install_and_test_tool_shed_repositories.base.twilltestcase import InstallTestRepository log = logging.getLogger(__name__) + class InstallTestRepositories( InstallTestRepository ): """Abstract test case that installs and uninstalls a predefined list of repositories.""" + def do_installation( self, repository_info_dict ): self.logout() self.login( email='test(a)bx.psu.edu', username='test' ) @@ -73,7 +75,7 @@ return test_install_repository test_method = make_uninstall_method( repository_dict ) test_method.__doc__ = "Uninstall the repository %s." % repository_dict[ 'name' ] - namespace[ 'install_repository_%s' % repository_dict[ 'name' ] ] = test_method + namespace[ 'uninstall_repository_%s' % repository_dict[ 'name' ] ] = test_method # The new.classobj function returns a new class object, with name name, derived # from baseclasses (which should be a tuple of classes) and with namespace dict. new_class_obj = new.classobj( name, baseclasses, namespace ) diff -r e5577cd833abbd0ad072d55f4b56d1458105991b -r 324d023bbf59aafb4be03cbb9842456aab0a1965 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -179,19 +179,26 @@ return passed_tests return [] -def execute_uninstall_method( repository_dict ): - # Delete any configured tool functional tests from the test_toolbox.__dict__, otherwise nose will find them - # and try to re-run the tests after uninstalling the repository, which will cause false failure reports, - # since the test data has been deleted from disk by now. - tests_to_delete = [] - for key in test_toolbox.__dict__: - if key.startswith( 'TestForTool_' ): - log.info( 'Tool test found in test_toolbox, deleting: %s' % key ) - tests_to_delete.append( key ) - for key in tests_to_delete: - del test_toolbox.__dict__[ key ] - # Generate a test method to uninstall this repository through the embedded Galaxy application's web interface. - test_install_repositories.generate_uninstall_method( repository_dict ) +def execute_uninstall_method( app ): + # Clean out any generated tests. + remove_generated_tests( app ) + sa_session = app.model.context.current + repositories_to_uninstall = sa_session.query( app.model.ToolShedRepository ).all() + for repository in repositories_to_uninstall: + if repository.status == app.model.ToolShedRepository.states.UNINSTALLED: + continue + if repository.status not in [ app.model.ToolShedRepository.installation_status.UNINSTALLED, + app.model.ToolShedRepository.installation_status.ERROR, + app.model.ToolShedRepository.installation_status.INSTALLED ]: + repository.status = app.model.ToolShedRepository.installation_status.ERROR + sa_session.add( repository ) + sa_session.flush() + name = str( repository.name ) + owner = str( repository.owner ) + changeset_revision = str( repository.installed_changeset_revision ) + repository_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) + # Generate a test method to uninstall this repository through the embedded Galaxy application's web interface. + test_install_repositories.generate_uninstall_method( repository_dict ) # Set up nose to run the generated uninstall method as a functional test. test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) test_config.configure( sys.argv ) @@ -309,6 +316,25 @@ else: return update( tool_shed_api_key, '%s' % ( url_join( galaxy_tool_shed_url, 'api', 'repository_revisions', metadata_id ) ), params, return_formatted=False ) +def remove_generated_tests( app ): + # Delete any configured tool functional tests from the test_toolbox.__dict__, otherwise nose will find them + # and try to re-run the tests after uninstalling the repository, which will cause false failure reports, + # since the test data has been deleted from disk by now. + tests_to_delete = [] + global test_toolbox + for key in test_toolbox.__dict__: + if key.startswith( 'TestForTool_' ): + log.info( 'Tool test found in test_toolbox, deleting: %s' % key ) + # We can't delete this test just yet, we're still iterating over __dict__. + tests_to_delete.append( key ) + tool_id = key.replace( 'TestForTool_', '' ) + if tool_id in app.toolbox.tools_by_id: + # But we can remove the relevant tool from app.toolbox.tools_by_id. + del app.toolbox.tools_by_id[ tool_id ] + for key in tests_to_delete: + # Now delete the tests found in the previous loop. + del test_toolbox.__dict__[ key ] + def run_tests( test_config ): loader = nose.loader.TestLoader( config=test_config ) test_config.plugins.addPlugin( ReportResults() ) @@ -417,12 +443,12 @@ global_conf = { '__file__' : 'universe_wsgi.ini.sample' } if not database_connection.startswith( 'sqlite://' ): kwargs[ 'database_engine_option_max_overflow' ] = '20' + kwargs[ 'database_engine_option_pool_size' ] = '10' app = UniverseApplication( admin_users = 'test(a)bx.psu.edu', allow_user_creation = True, allow_user_deletion = True, allow_library_path_paste = True, database_connection = database_connection, - database_engine_option_pool_size = '10', datatype_converters_config_file = "datatype_converters_conf.xml.sample", file_path = galaxy_file_path, global_conf = global_conf, @@ -546,7 +572,14 @@ # it will record the result of the tests, and if any failed, the traceback and captured output of the tool that was run. # After all tests have completed, the repository is uninstalled, so that the previous test cases don't interfere with # the next repository's functional tests. + keep_skipping = True for repository_info_dict in detailed_repository_list: + if repository_info_dict[ 'name' ] == 'simsearch' and repository_info_dict[ 'changeset_revision' ] == '430f55978191': + keep_skipping = False + if keep_skipping: + continue + if repository_info_dict[ 'name' ] == 'sortmerna': + continue """ Each repository_info_dict looks something like: { @@ -575,10 +608,13 @@ metadata_revision_id = repository_info_dict.get( 'id', None ) # Add the URL for the tool shed we're installing from, so the automated installation methods go to the right place. repository_info_dict[ 'tool_shed_url' ] = galaxy_tool_shed_url - log.info( "Installing and testing revision %s of repository id %s..." % ( str( changeset_revision ), str( repository_id ) ) ) # Get the name and owner out of the repository info dict. - name = repository_info_dict[ 'name' ] - owner = repository_info_dict[ 'owner' ] + name = str( repository_info_dict[ 'name' ] ) + owner = str( repository_info_dict[ 'owner' ] ) + log.info( "Installing and testing revision %s of repository id %s (%s/%s)..." % \ + ( str( changeset_revision ), str( repository_id ), owner, name ) ) + # Explicitly clear tests from twill's test environment. + remove_generated_tests( app ) # Use the repository information dict to generate an install method that will install the repository into the embedded # Galaxy application, with tool dependencies and repository dependencies, if any. test_install_repositories.generate_install_method( repository_info_dict ) @@ -661,7 +697,7 @@ register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, passed_tests=False ) # Run the cleanup method. This removes tool functional test methods from the test_toolbox module and uninstalls the # repository using Twill. - execute_uninstall_method( repository_info_dict ) + execute_uninstall_method( app ) # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. test_toolbox.toolbox = app.toolbox repositories_failed.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) @@ -675,6 +711,8 @@ os.environ[ 'GALAXY_TOOL_SHED_TEST_FILE' ] = galaxy_shed_tools_dict os.environ[ 'GALAXY_TEST_HOST' ] = galaxy_test_host os.environ[ 'GALAXY_TEST_PORT' ] = galaxy_test_port + # Explicitly clear tests from twill's test environment. + remove_generated_tests( app ) # Set the module-level variable 'toolbox', so that test.functional.test_toolbox will generate the appropriate test methods. test_toolbox.toolbox = app.toolbox # Generate the test methods for this installed repository. We need to pass in True here, or it will look @@ -751,14 +789,23 @@ register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, passed_tests=False ) log.debug( 'Revision %s of repository %s installed successfully, but did not pass functional tests.' % \ ( changeset_revision, name ) ) - # Run the cleanup method. This removes tool functional test methods from the test_toolbox module and uninstalls the + # Run the uninstall method. This removes tool functional test methods from the test_toolbox module and uninstalls the # repository using Twill. - success = execute_uninstall_method( repository_info_dict ) + log.debug( 'Uninstalling changeset revision %s of repository %s' % \ + ( repository_info_dict[ 'changeset_revision' ], repository_info_dict[ 'name' ] ) ) + success = execute_uninstall_method( app ) + if not success: + log.error( 'Repository %s failed to uninstall.' ) # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. test_toolbox.toolbox = app.toolbox else: + # Even if the repository failed to install, execute the uninstall method, in case a dependency did succeed. + log.debug( 'Uninstalling repository %s' % repository_info_dict[ 'name' ] ) + success = execute_uninstall_method( app ) + if not success: + log.error( 'Repository %s failed to uninstall.' ) repositories_failed_install.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) - log.debug( 'Repository %s failed to install correctly.' % name ) + log.debug( 'Repository %s failed to install correctly.' % repository_info_dict[ 'name' ] ) except: log.exception( "Failure running tests" ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Make sure dependent eggs are loaded for sqlalchemy-migrate, regardless of entry point. This is a hack, and dependency management should/will eventually handle it.
by commits-noreply＠bitbucket.org 03 May '13

03 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e5577cd833ab/ Changeset: e5577cd833ab User: dannon Date: 2013-05-03 18:55:55 Summary: Make sure dependent eggs are loaded for sqlalchemy-migrate, regardless of entry point. This is a hack, and dependency management should/will eventually handle it. Affected #: 4 files diff -r 5aec1f220d4f1bccc9ac3f2b014d2727e0f0f907 -r e5577cd833abbd0ad072d55f4b56d1458105991b lib/galaxy/webapps/tool_shed/model/migrate/check.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/check.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/check.py @@ -3,6 +3,7 @@ from galaxy import eggs import pkg_resources +pkg_resources.require( "SQLAlchemy" ) pkg_resources.require( "decorator" ) pkg_resources.require( "sqlalchemy-migrate" ) pkg_resources.require( "Tempita" ) diff -r 5aec1f220d4f1bccc9ac3f2b014d2727e0f0f907 -r e5577cd833abbd0ad072d55f4b56d1458105991b lib/tool_shed/galaxy_install/migrate/check.py --- a/lib/tool_shed/galaxy_install/migrate/check.py +++ b/lib/tool_shed/galaxy_install/migrate/check.py @@ -1,7 +1,9 @@ import sys, os, logging, subprocess from galaxy import eggs import pkg_resources +pkg_resources.require( "SQLAlchemy" ) pkg_resources.require( "decorator" ) +pkg_resources.require( "Tempita " ) pkg_resources.require( "sqlalchemy-migrate" ) from migrate.versioning import repository, schema diff -r 5aec1f220d4f1bccc9ac3f2b014d2727e0f0f907 -r e5577cd833abbd0ad072d55f4b56d1458105991b scripts/db_shell.py --- a/scripts/db_shell.py +++ b/scripts/db_shell.py @@ -20,6 +20,7 @@ import pkg_resources pkg_resources.require( "decorator" ) +pkg_resources.require( "Tempita" ) pkg_resources.require( "sqlalchemy-migrate" ) pkg_resources.require( "SQLAlchemy" ) diff -r 5aec1f220d4f1bccc9ac3f2b014d2727e0f0f907 -r e5577cd833abbd0ad072d55f4b56d1458105991b scripts/manage_tools.py --- a/scripts/manage_tools.py +++ b/scripts/manage_tools.py @@ -7,7 +7,9 @@ from galaxy import eggs import pkg_resources +pkg_resources.require( "SQLAlchemy" ) pkg_resources.require( "decorator" ) +pkg_resources.require( "Tempita " ) pkg_resources.require( "sqlalchemy-migrate" ) from migrate.versioning.shell import main Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Require decorator egg wherever we have sqlalchemy-migrate. Should be able to resolve dependencies and do this automatically
by commits-noreply＠bitbucket.org 03 May '13

03 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5aec1f220d4f/ Changeset: 5aec1f220d4f User: dannon Date: 2013-05-03 18:31:20 Summary: Require decorator egg wherever we have sqlalchemy-migrate. Should be able to resolve dependencies and do this automatically Affected #: 4 files diff -r b908c9fa3c46f1b625a6d32d991392380c79685a -r 5aec1f220d4f1bccc9ac3f2b014d2727e0f0f907 lib/galaxy/webapps/tool_shed/model/migrate/check.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/check.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/check.py @@ -3,6 +3,7 @@ from galaxy import eggs import pkg_resources +pkg_resources.require( "decorator" ) pkg_resources.require( "sqlalchemy-migrate" ) pkg_resources.require( "Tempita" ) diff -r b908c9fa3c46f1b625a6d32d991392380c79685a -r 5aec1f220d4f1bccc9ac3f2b014d2727e0f0f907 lib/tool_shed/galaxy_install/migrate/check.py --- a/lib/tool_shed/galaxy_install/migrate/check.py +++ b/lib/tool_shed/galaxy_install/migrate/check.py @@ -1,6 +1,7 @@ import sys, os, logging, subprocess from galaxy import eggs import pkg_resources +pkg_resources.require( "decorator" ) pkg_resources.require( "sqlalchemy-migrate" ) from migrate.versioning import repository, schema diff -r b908c9fa3c46f1b625a6d32d991392380c79685a -r 5aec1f220d4f1bccc9ac3f2b014d2727e0f0f907 scripts/db_shell.py --- a/scripts/db_shell.py +++ b/scripts/db_shell.py @@ -19,6 +19,7 @@ from galaxy import eggs import pkg_resources +pkg_resources.require( "decorator" ) pkg_resources.require( "sqlalchemy-migrate" ) pkg_resources.require( "SQLAlchemy" ) diff -r b908c9fa3c46f1b625a6d32d991392380c79685a -r 5aec1f220d4f1bccc9ac3f2b014d2727e0f0f907 scripts/manage_tools.py --- a/scripts/manage_tools.py +++ b/scripts/manage_tools.py @@ -7,6 +7,7 @@ from galaxy import eggs import pkg_resources +pkg_resources.require( "decorator" ) pkg_resources.require( "sqlalchemy-migrate" ) from migrate.versioning.shell import main Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Require decorator egg in migrate/check to prevent sqlalchemy-migrate from dying in certain environments
by commits-noreply＠bitbucket.org 03 May '13

03 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b908c9fa3c46/ Changeset: b908c9fa3c46 User: dannon Date: 2013-05-03 18:26:40 Summary: Require decorator egg in migrate/check to prevent sqlalchemy-migrate from dying in certain environments Affected #: 1 file diff -r 4d4d8dd42491a81869642f1cfcb2f552e4af5a40 -r b908c9fa3c46f1b625a6d32d991392380c79685a lib/galaxy/model/migrate/check.py --- a/lib/galaxy/model/migrate/check.py +++ b/lib/galaxy/model/migrate/check.py @@ -4,6 +4,7 @@ from galaxy import eggs eggs.require( "SQLAlchemy" ) +eggs.require( "decorator" ) #Required by sqlalchemy-migrate eggs.require( "Tempita " ) #Required by sqlalchemy-migrate eggs.require( "sqlalchemy-migrate" ) 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: Column cleanup in the repositories grid in the tool shed.
by commits-noreply＠bitbucket.org 03 May '13

03 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4d4d8dd42491/ Changeset: 4d4d8dd42491 User: greg Date: 2013-05-03 17:26:12 Summary: Column cleanup in the repositories grid in the tool shed. Affected #: 2 files diff -r 4a1a2b6b4e8a14db4a7689ef09b8a2db965ddc8f -r 4d4d8dd42491a81869642f1cfcb2f552e4af5a40 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 @@ -95,7 +95,9 @@ kwd[ 'id' ] = trans.security.encode_id( repository.id ) except: pass - return self.browse_repositories( trans, **kwd ) + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + **kwd ) ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() if operation in [ "repositories_by_category", "repositories_by_user" ]: diff -r 4a1a2b6b4e8a14db4a7689ef09b8a2db965ddc8f -r 4d4d8dd42491a81869642f1cfcb2f552e4af5a40 lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -211,11 +211,7 @@ key="description", attach_popup=False ), MetadataRevisionColumn( "Metadata Revisions" ), - TipRevisionColumn( "Tip Revision" ), - CategoryColumn( "Category", - model_class=model.Category, - key="Category.name", - attach_popup=False ), + ToolsFunctionallyCorrectColumn( "Tools Verified" ), UserColumn( "Owner", model_class=model.User, link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fixes for rendering the Repository Actions menu in the tool shed.
by commits-noreply＠bitbucket.org 03 May '13

03 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4a1a2b6b4e8a/ Changeset: 4a1a2b6b4e8a User: greg Date: 2013-05-03 17:10:45 Summary: Fixes for rendering the Repository Actions menu in the tool shed. Affected #: 2 files diff -r 15329256872bf03a3831bc5e3a970cbe8611a3fe -r 4a1a2b6b4e8a14db4a7689ef09b8a2db965ddc8f templates/webapps/tool_shed/common/repository_actions_menu.mako --- a/templates/webapps/tool_shed/common/repository_actions_menu.mako +++ b/templates/webapps/tool_shed/common/repository_actions_menu.mako @@ -5,19 +5,55 @@ from tool_shed.util.review_util import can_browse_repository_reviews, changeset_revision_reviewed_by_user, get_review_by_repository_id_changeset_revision_user_id from tool_shed.util.shed_util_common import changeset_is_malicious - has_metadata = repository.metadata_revisions - has_readme = metadata and 'readme' in metadata + if repository.metadata_revisions: + has_metadata = True + else: + has_metadata = False + is_admin = trans.user_is_admin() - is_deprecated = repository.deprecated - is_new = repository.is_new( trans.app ) - is_malicious = changeset_is_malicious( trans, trans.security.encode_id( repository.id ), repository.tip( trans.app ) ) + + if repository.deprecated: + is_deprecated = True + else: + is_deprecated = False + + if repository.is_new( trans.app ): + is_new = True + else: + is_new = False + + if changeset_is_malicious( trans, trans.security.encode_id( repository.id ), repository.tip( trans.app ) ): + is_malicious = True + else: + is_malicious = False can_browse_contents = not is_new - can_browse_reviews = can_browse_repository_reviews( trans, repository ) - can_contact_owner = trans.user and trans.user != repository.user - can_deprecate = not is_new and trans.user and ( is_admin or repository.user == trans.user ) and not is_deprecated - can_push = not is_deprecated and trans.app.security_agent.can_push( trans.app, trans.user, repository ) - can_download = not is_deprecated and not is_new and ( not is_malicious or can_push ) + + if can_browse_repository_reviews( trans, repository ): + can_browse_reviews = True + else: + can_browse_reviews = False + + if trans.user and trans.user != repository.user: + can_contact_owner = True + else: + can_contact_owner = False + + if not is_new and trans.user and ( is_admin or repository.user == trans.user ) and not is_deprecated: + can_deprecate = True + else: + can_deprecate = False + + if not is_deprecated and trans.app.security_agent.can_push( trans.app, trans.user, repository ): + can_push = True + else: + can_push = False + + if not is_deprecated and not is_new and ( not is_malicious or can_push ): + can_download = True + else: + can_download = False + if not is_deprecated: if repo and len( repo ) > 0: can_reset_all_metadata = True @@ -25,16 +61,30 @@ can_reset_all_metadata = False else: can_reset_all_metadata = False - can_upload = can_push and not is_deprecated - can_rate = not is_new and not is_deprecated and trans.user and repository.user != trans.user - if changeset_revision: - can_review_repository = has_metadata and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user ) - reviewed_by_user = changeset_revision_reviewed_by_user( trans, trans.user, repository, changeset_revision ) + + if can_push and not is_deprecated: + can_upload = True + else: + can_upload = False + + if not is_new and not is_deprecated and trans.user and repository.user != trans.user: + can_rate = True + else: + can_rate = False + + if changeset_revision is not None: + if has_metadata and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user ): + can_review_repository = True + else: + can_review_repository = False + if changeset_revision_reviewed_by_user( trans, trans.user, repository, changeset_revision ): + reviewed_by_user = True + else: + reviewed_by_user = False else: can_review_repository = False reviewed_by_user = False - # Determine if the current changeset revision has been reviewed by the current user. if reviewed_by_user: review = get_review_by_repository_id_changeset_revision_user_id( trans=trans, repository_id=trans.security.encode_id( repository.id ), @@ -44,17 +94,29 @@ else: review_id = None - can_set_metadata = not is_new and not is_deprecated - if changeset_revision: + if not is_new and not is_deprecated: + can_set_metadata = True + else: + can_set_metadata = False + + if changeset_revision is not None: if changeset_revision == repository.tip( trans.app ): changeset_revision_is_repository_tip = True else: changeset_revision_is_repository_tip = False else: changeset_revision_is_repository_tip = False - can_set_malicious = metadata and can_set_metadata and is_admin and changeset_revision_is_repository_tip - can_undeprecate = trans.user and ( is_admin or repository.user == trans.user ) and is_deprecated - can_manage = is_admin or repository.user == trans.user + + if trans.user and ( is_admin or repository.user == trans.user ) and is_deprecated: + can_undeprecate = True + else: + can_undeprecate = False + + if is_admin or repository.user == trans.user: + can_manage = True + else: + can_manage = False + can_view_change_log = not is_new if can_push: @@ -69,6 +131,9 @@ %if can_upload: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif + %if can_undeprecate: + <a class="action-button" href="${h.url_for( controller='repository', action='deprecate', id=trans.security.encode_id( repository.id ), mark_deprecated=False )}">Mark repository as not deprecated</a> + %endif %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> diff -r 15329256872bf03a3831bc5e3a970cbe8611a3fe -r 4a1a2b6b4e8a14db4a7689ef09b8a2db965ddc8f templates/webapps/tool_shed/repository/manage_repository.mako --- a/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/templates/webapps/tool_shed/repository/manage_repository.mako @@ -6,19 +6,56 @@ <% from galaxy.web.framework.helpers import time_ago + from tool_shed.util.shed_util_common import changeset_is_malicious - has_metadata = repository.metadata_revisions - has_readme = metadata and 'readme' in metadata + if repository.metadata_revisions: + has_metadata = True + else: + has_metadata = False + is_admin = trans.user_is_admin() is_new = repository.is_new( trans.app ) - is_deprecated = repository.deprecated - can_push = not is_deprecated and trans.app.security_agent.can_push( trans.app, trans.user, repository ) - can_download = not is_deprecated and not is_new and ( not is_malicious or can_push ) - can_review_repository = has_metadata and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user ) - can_set_metadata = not is_new and not is_deprecated - changeset_revision_is_repository_tip = changeset_revision == repository.tip( trans.app ) - can_set_malicious = metadata and can_set_metadata and is_admin and changeset_revision_is_repository_tip + if repository.deprecated: + is_deprecated = True + else: + is_deprecated = False + + if changeset_is_malicious( trans, trans.security.encode_id( repository.id ), repository.tip( trans.app ) ): + is_malicious = True + else: + is_malicious = False + + if not is_deprecated and trans.app.security_agent.can_push( trans.app, trans.user, repository ): + can_push = True + else: + can_push = False + + if not is_deprecated and not is_new and ( not is_malicious or can_push ): + can_download = True + else: + can_download = False + + if has_metadata and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user ): + can_review_repository = True + else: + can_review_repository = False + + if not is_new and not is_deprecated: + can_set_metadata = True + else: + can_set_metadata = False + + if changeset_revision == repository.tip( trans.app ): + changeset_revision_is_repository_tip = True + else: + changeset_revision_is_repository_tip = False + + if metadata and can_set_metadata and is_admin and changeset_revision_is_repository_tip: + can_set_malicious = True + else: + can_set_malicious = False + can_view_change_log = not is_new if changeset_revision_is_repository_tip: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: only query feature tracks for feature locations.
by commits-noreply＠bitbucket.org 03 May '13

03 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/15329256872b/ Changeset: 15329256872b User: jgoecks Date: 2013-05-03 16:52:11 Summary: Trackster: only query feature tracks for feature locations. Affected #: 1 file diff -r cf2db2f91c7f4ca284daea800aa9596c27ff809b -r 15329256872bf03a3831bc5e3a970cbe8611a3fe static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -438,6 +438,7 @@ this.obj_type = obj_dict.obj_type; this.drawables = []; }; + extend(DrawableCollection.prototype, Drawable.prototype, { /** * Unpack and add drawables to the collection. @@ -560,6 +561,26 @@ */ get_drawables: function() { return this.drawables; + }, + + /** + * Returns all <track_type> tracks in collection. + */ + get_tracks: function(track_type) { + // Initialize queue with copy of drawables array. + var queue = this.drawables.slice(0), + tracks = [], + drawable; + while (queue.length !== 0) { + drawable = queue.shift(); + if (drawable instanceof track_type) { + tracks.push(drawable); + } + else if (drawable.drawables) { + queue = queue.concat(drawable.drawables); + } + } + return tracks; } }); @@ -967,8 +988,8 @@ source: function(request, response) { // Using current text, query each track and create list of all matching features. var all_features = [], - feature_search_deferreds = $.map(view.get_drawables(), function(drawable) { - return drawable.data_manager.search_features(request.term).success(function(dataset_features) { + feature_search_deferreds = $.map(view.get_tracks(FeatureTrack), function(t) { + return t.data_manager.search_features(request.term).success(function(dataset_features) { all_features = all_features.concat(dataset_features); }); }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Do not allow deleted datasets to be displayed.
by commits-noreply＠bitbucket.org 03 May '13

03 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cf2db2f91c7f/ Changeset: cf2db2f91c7f User: dan Date: 2013-05-03 16:38:16 Summary: Do not allow deleted datasets to be displayed. Affected #: 1 file diff -r af7b3b73130b9288112fd06d2cecbcfe649703c5 -r cf2db2f91c7f4ca284daea800aa9596c27ff809b lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -290,6 +290,8 @@ raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( hda_id ) ) if not self._can_access_dataset( trans, data ): return trans.show_error_message( "You are not allowed to access this dataset" ) + if data.deleted: + return trans.show_error_message( "The dataset you are attempting to view has been deleted." ) if data.state == trans.model.Dataset.states.UPLOAD: return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to view it." ) return data 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: 4 new changesets
by commits-noreply＠bitbucket.org 03 May '13

03 May '13

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/259865426c21/ Changeset: 259865426c21 Branch: stable User: dannon Date: 2013-04-17 03:38:38 Summary: Disable select2 for Input Dataset steps on the run workflow page. Affected #: 1 file diff -r 47ddf167c9f11c903a438c0979e101fe7535f061 -r 259865426c21fbfcfdcf4f8279487fee86ad1736 templates/webapps/galaxy/workflow/run.mako --- a/templates/webapps/galaxy/workflow/run.mako +++ b/templates/webapps/galaxy/workflow/run.mako @@ -40,12 +40,12 @@ select.val($('option:last', select).val()); } select.closest('.form-row').children('label').children('span.mode-icon').hide(); - select.removeAttr('multiple').refresh_select2().removeAttr('size'); + select.removeAttr('multiple').removeAttr('size'); placeholder = 'type to filter'; } else { $('.multiinput', select.closest('.form-row')).removeClass('disabled'); select.closest('.form-row').children('label').children('span.mode-icon').show(); - select.attr('multiple', 'multiple').refresh_select2().attr('size', 8); + select.attr('multiple', 'multiple').attr('size', 8); placeholder = 'type to filter, [enter] to select all'; } $('input.multiinput-filter', select.parent()).attr( @@ -79,7 +79,10 @@ $("#new_history_cbx").click(function(){ $("#new_history_input").toggle(this.checked); }); - $('span.multiinput_wrap select[name*="|input"]').removeAttr('multiple').refresh_select2().each(function(i, s) { + // The destroy on the following line is temporary and prevents + // select2 use on Input Dataset Steps, but allows elsewhere. We + // need a new widget to better handle pairwise matching. + $('span.multiinput_wrap select[name*="|input"]').removeAttr('multiple').select2("destroy").each(function(i, s) { var select = $(s); var new_width = Math.max(200, select.width()) + 20; // Find the label for this element. https://bitbucket.org/galaxy/galaxy-central/commits/b22d70ad9404/ Changeset: b22d70ad9404 Branch: stable User: dannon Date: 2013-04-17 03:47:17 Summary: Update multiselect tooltip, now functional. Was still using tipsy's 'original-title' attribute. Affected #: 1 file diff -r 259865426c21fbfcfdcf4f8279487fee86ad1736 -r b22d70ad94044a8cadf32e49385f414e60459e9d templates/webapps/galaxy/workflow/run.mako --- a/templates/webapps/galaxy/workflow/run.mako +++ b/templates/webapps/galaxy/workflow/run.mako @@ -91,7 +91,7 @@ if ($(this).hasClass('disabled')) return; toggle_multiinput(select); select.focus(); - }).attr('original-title', + }).attr('title', 'Enable/disable selection of multiple input ' + 'files. Each selected file will have an ' + 'instance of the workflow.').tooltip({placement: 'bottom'}) https://bitbucket.org/galaxy/galaxy-central/commits/fe1be67c576a/ Changeset: fe1be67c576a Branch: stable User: dannon Date: 2013-04-17 04:27:07 Summary: Add tooltips for (un)linking icon on run workflow page. Affected #: 1 file diff -r b22d70ad94044a8cadf32e49385f414e60459e9d -r fe1be67c576af3bc6890912b63863694b9eceb8c templates/webapps/galaxy/workflow/run.mako --- a/templates/webapps/galaxy/workflow/run.mako +++ b/templates/webapps/galaxy/workflow/run.mako @@ -141,13 +141,15 @@ $(function(){ $(".multi-mode").each(function(){ if($(this).val() == "matched") { - $(this).closest('.form-row').children('label').append($('<span class="icon-button link mode-icon"></span>') + $(this).closest('.form-row').children('label').append($('<span class="icon-button link mode-icon" title="This input is linked and will be run in matched order with other input datasets (ex: use this for matching forward and reverse reads)."></span>') .attr({id:$(this).attr("id")}) - .css("display", $(this).css("display"))); + .css("display", $(this).css("display")) + .tooltip({placement: 'bottom'})); } else { - $(this).closest('.form-row').children('label').append($('<span class="icon-button link-broken mode-icon"></span>') + $(this).closest('.form-row').children('label').append($('<span class="icon-button link-broken mode-icon" title="This input is not linked and each selection will be run against *all* other inputs."></span>') .attr({id:$(this).attr("id")}) - .css("display", $(this).css("display"))); + .css("display", $(this).css("display")) + .tooltip({placement: 'bottom'})); } }); $("span.mode-icon").click(function(){ https://bitbucket.org/galaxy/galaxy-central/commits/0899ad383fba/ Changeset: 0899ad383fba Branch: stable User: dannon Date: 2013-04-17 14:40:24 Summary: Fix more broken tooltips from the tipsy->bootstrap.tooltip() swap Affected #: 1 file diff -r fe1be67c576af3bc6890912b63863694b9eceb8c -r 0899ad383fba01c78077a3dfddb954bebaf6e72e templates/webapps/galaxy/workflow/editor.mako --- a/templates/webapps/galaxy/workflow/editor.mako +++ b/templates/webapps/galaxy/workflow/editor.mako @@ -1015,7 +1015,7 @@ ## Workflow name. <div id="workflow-name-area" class="form-row"><label>Name:</label> - <span id="workflow-name" class="tooltip editable-text" original-title="Click to rename workflow">${h.to_unicode( stored.name ) | h}</span> + <span id="workflow-name" class="tooltip editable-text" title="Click to rename workflow">${h.to_unicode( stored.name ) | h}</span></div> ## Workflow tags. <%namespace file="/tagging_common.mako" import="render_individual_tagging_element" /> @@ -1037,7 +1037,7 @@ ## Annotation elt. <div id="workflow-annotation-area" class="form-row"><label>Annotation / Notes:</label> - <div id="workflow-annotation" class="tooltip editable-text" original-title="Click to edit annotation"> + <div id="workflow-annotation" class="tooltip editable-text" title="Click to edit annotation"> %if annotation: ${h.to_unicode( annotation ) | h} %else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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galaxy-commits May 2013