galaxy-commits February 2013

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commit/galaxy-central: inithello: Enhance twill automated repository installation framework to get a list of repositories from the tool shed API, install, run functional tests defined in the tools' XML, and report success or failure back to the tool shed.
by commits-noreply＠bitbucket.org 27 Feb '13

27 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9d87d7c61912/ changeset: 9d87d7c61912 user: inithello date: 2013-02-27 20:28:12 summary: Enhance twill automated repository installation framework to get a list of repositories from the tool shed API, install, run functional tests defined in the tools' XML, and report success or failure back to the tool shed. affected #: 3 files diff -r fabb0ae1edabf77f9aceb018fa5a988ce05500f9 -r 9d87d7c6191284aaf48ade4462256131c0345c8d test/install_and_test_tool_shed_repositories/base/twilltestcase.py --- a/test/install_and_test_tool_shed_repositories/base/twilltestcase.py +++ b/test/install_and_test_tool_shed_repositories/base/twilltestcase.py @@ -55,7 +55,7 @@ name = repository_info_dict[ 'name' ] owner = repository_info_dict[ 'owner' ] changeset_revision = repository_info_dict[ 'changeset_revision' ] - encoded_repository_id = repository_info_dict[ 'encoded_repository_id' ] + encoded_repository_id = repository_info_dict[ 'repository_id' ] tool_shed_url = repository_info_dict[ 'tool_shed_url' ] preview_params = urllib.urlencode( dict( repository_id=encoded_repository_id, changeset_revision=changeset_revision ) ) self.visit_url( '%s/repository/preview_tools_in_changeset?%s' % ( tool_shed_url, preview_params ) ) diff -r fabb0ae1edabf77f9aceb018fa5a988ce05500f9 -r 9d87d7c6191284aaf48ade4462256131c0345c8d 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 @@ -3,7 +3,7 @@ from install_and_test_tool_shed_repositories.base.twilltestcase import InstallTestRepository log = logging.getLogger(__name__) -class TestInstallRepositories( InstallTestRepository ): +class InstallTestRepositories( InstallTestRepository ): """Abstract test case that installs and uninstalls a predefined list of repositories.""" def do_installation( self, repository_info_dict ): self.logout() @@ -35,11 +35,11 @@ G = globals() # Eliminate all previous tests from G. for key, val in G.items(): - if key.startswith( 'TestInstallRepository_' ) or key.startswith( 'TestUninstallRepository_' ): + if key.startswith( 'TestInstallRepository_' ) or key.startswith( 'TestUninstallRepository_' ) or key.startswith( 'TestForTool_' ): del G[ key ] # Create a new subclass with a method named install_repository_XXX that installs the repository specified by the provided dict. name = "TestInstallRepository_" + repository_dict[ 'name' ] - baseclasses = ( TestInstallRepositories, ) + baseclasses = ( InstallTestRepositories, ) namespace = dict() def make_install_method( repository_dict ): def test_install_repository( self ): @@ -61,11 +61,11 @@ G = globals() # Eliminate all previous tests from G. for key, val in G.items(): - if key.startswith( 'TestInstallRepository_' ) or key.startswith( 'TestUninstallRepository_' ): + if key.startswith( 'TestInstallRepository_' ) or key.startswith( 'TestUninstallRepository_' ) or key.startswith( 'TestForTool_' ): del G[ key ] # Create a new subclass with a method named install_repository_XXX that installs the repository specified by the provided dict. name = "TestUninstallRepository_" + repository_dict[ 'name' ] - baseclasses = ( TestInstallRepositories, ) + baseclasses = ( InstallTestRepositories, ) namespace = dict() def make_uninstall_method( repository_dict ): def test_install_repository( self ): diff -r fabb0ae1edabf77f9aceb018fa5a988ce05500f9 -r 9d87d7c6191284aaf48ade4462256131c0345c8d 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 @@ -4,7 +4,7 @@ # order to run functional tests on repository tools after installation. The install_and_test_tool_shed_repositories.sh # will execute this script with the appropriate parameters. -import os, sys, shutil, tempfile, re, string +import os, sys, shutil, tempfile, re, string, urllib # Assume we are run from the galaxy root directory, add lib to the python path cwd = os.getcwd() @@ -19,7 +19,7 @@ default_galaxy_locales = 'en' default_galaxy_test_file_dir = "test-data" os.environ[ 'GALAXY_INSTALL_TEST_TMP_DIR' ] = galaxy_test_tmp_dir -new_path = [ os.path.join( cwd, "lib" ), os.path.join( cwd, 'test' ) ] +new_path = [ os.path.join( cwd, "lib" ), os.path.join( cwd, 'test' ), os.path.join( cwd, 'scripts', 'api' ) ] new_path.extend( sys.path ) sys.path = new_path @@ -48,6 +48,7 @@ from galaxy.app import UniverseApplication from galaxy.web import buildapp from galaxy.util import parse_xml +from galaxy.util.json import from_json_string, to_json_string import nose.core import nose.config @@ -56,6 +57,8 @@ from base.util import parse_tool_panel_config +from common import update + log = logging.getLogger( 'install_and_test_repositories' ) default_galaxy_test_port_min = 10000 @@ -95,7 +98,10 @@ ''' # Define a default location to find the list of repositories to check. -galaxy_repository_list = os.environ.get( 'GALAXY_INSTALL_TEST_REPOSITORY_FILE', 'repository_list.json' ) +galaxy_repository_list = os.environ.get( 'GALAXY_INSTALL_TEST_REPOSITORY_LIST_LOCATIOM', 'repository_list.json' ) +galaxy_tool_shed_url = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHED_URL', 'http://toolshed.local:10001' ) +tool_shed_api_key = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY', None ) +assert tool_shed_api_key is not None, 'Unable to proceed without API key.' if 'GALAXY_INSTALL_TEST_SECRET' not in os.environ: galaxy_encode_secret = 'changethisinproductiontoo' @@ -103,7 +109,28 @@ else: galaxy_encode_secret = os.environ[ 'GALAXY_INSTALL_TEST_SECRET' ] -def get_repositories_to_install( format='json' ): +def get_api_url( base, parts=[], params=None, key=None ): + if 'api' in parts and parts.index( 'api' ) != 0: + parts.pop( parts.index( 'api' ) ) + parts.insert( 0, 'api' ) + elif 'api' not in parts: + parts.insert( 0, 'api' ) + url = '%s/%s' % ( base, '/'.join( parts ) ) + if key: + url += '?%s' % urllib.urlencode( dict( key=key ) ) + else: + url += '?%s' % urllib.urlencode( dict( key=tool_shed_api_key ) ) + if params: + url += '&%s' % params + return url + +def get_repository_info_from_api( url, repository_info_dict ): + parts = [ 'api', 'repositories', repository_info_dict[ 'repository_id' ] ] + api_url = get_api_url( base=url, parts=parts ) + extended_dict = json_from_url( api_url ) + return extended_dict + +def get_repositories_to_install( location, source='file', format='json' ): ''' Get a list of repository info dicts to install. This method expects a json list of dicts with the following structure: [ @@ -118,11 +145,34 @@ ] NOTE: If the tool shed URL specified in any dict is not present in the tool_sheds_conf.xml, the installation will fail. ''' + if source == 'file': + listing = file( location, 'r' ).read() + elif source == 'url': + assert tool_shed_api_key is not None, 'Cannot proceed without tool shed API key.' + params = urllib.urlencode( dict( downloadable='true' ) ) + api_url = get_api_url( base=location, parts=[ 'repository_revisions' ], params=params ) + if format == 'json': + return json_from_url( api_url ) + else: + raise AssertionError( 'Do not know how to handle source type %s.' % source ) if format == 'json': - return simplejson.loads( file( galaxy_repository_list, 'r' ).read() ) + return from_json_string( listing ) else: raise AssertonError( 'Unknown format %s.' % format ) +def json_from_url( url ): + url_handle = urllib.urlopen( url ) + url_contents = url_handle.read() + return from_json_string( url_contents ) + +def register_test_failure( url, metadata_id, test_errors ): + params = dict( tools_functionally_correct='false', do_not_test='true', tool_test_errors=test_errors ) + return update( tool_shed_api_key, '%s/api/%s' % ( galaxy_tool_shed_url, '/'.join( [ 'repository_revisions', metadata_id ] ) ), params ) + +def register_test_success( url, metadata_id ): + params = dict( tools_functionally_correct='true', do_not_test='false' ) + return update( tool_shed_api_key, '%s/api/%s' % ( galaxy_tool_shed_url, '/'.join( [ 'repository_revisions', metadata_id ] ) ), params ) + def run_tests( test_config ): loader = nose.loader.TestLoader( config=test_config ) plug_loader = test_config.plugins.prepareTestLoader( loader ) @@ -162,6 +212,7 @@ galaxy_migrated_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_MIGRATED_TOOL_CONF', os.path.join( galaxy_test_tmp_dir, 'test_migrated_tool_conf.xml' ) ) galaxy_tool_sheds_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF', os.path.join( galaxy_test_tmp_dir, 'test_tool_sheds_conf.xml' ) ) galaxy_shed_tools_dict = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_DICT_FILE', os.path.join( galaxy_test_tmp_dir, 'shed_tool_dict' ) ) + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( dict() ) ) if 'GALAXY_INSTALL_TEST_TOOL_DATA_PATH' in os.environ: tool_data_path = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DATA_PATH' ) else: @@ -302,8 +353,13 @@ log.info( "Tests will be run against %s:%s" % ( galaxy_test_host, galaxy_test_port ) ) success = False try: + repository_status = [] # Iterate through a list of repository info dicts. - for repository_dict in get_repositories_to_install(): + for repository_dict in get_repositories_to_install( galaxy_tool_shed_url, source='url' ): + metadata_revision_id = repository_dict[ 'id' ] + repository_dict[ 'tool_shed_url' ] = galaxy_tool_shed_url + repository_info = get_repository_info_from_api( galaxy_tool_shed_url, repository_dict ) + repository_dict = dict( repository_info.items() + repository_dict.items() ) # Generate the method that will install this repository into the running Galaxy instance. test_install_repositories.generate_install_method( repository_dict ) os.environ[ 'GALAXY_INSTALL_TEST_HOST' ] = galaxy_test_host @@ -319,9 +375,12 @@ if success: log.debug( 'Installation of %s succeeded, running any defined functional tests.' % repository_dict[ 'name' ] ) # Parse the tool panel config to get the test-data path for this repository. - shed_tools_dict = parse_tool_panel_config( galaxy_shed_tool_conf_file, {} ) + if not os.path.exists( galaxy_shed_tools_dict ): + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( dict() ) ) + shed_tools_dict = parse_tool_panel_config( galaxy_shed_tool_conf_file, from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) + log.debug( shed_tools_dict ) # Write this to a file, so the functional test framework can find it. - file( galaxy_shed_tools_dict, 'w' ).write( simplejson.dumps( shed_tools_dict ) ) + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) # Set up the environment so that test.functional.test_toolbox can find the Galaxy server we configured in this framework. os.environ[ 'GALAXY_TOOL_SHED_TEST_FILE' ] = galaxy_shed_tools_dict os.environ[ 'GALAXY_TEST_HOST' ] = galaxy_test_host @@ -337,10 +396,52 @@ # Run the configured tests. result = run_tests( test_config ) success = result.wasSuccessful() + repository_dict[ 'functional_tests_passed' ] = success if success: + register_test_success( galaxy_tool_shed_url, metadata_revision_id ) log.debug( 'Repository %s installed and passed functional tests.' % repository_dict[ 'name' ] ) else: + # If the functional tests fail, log the output and submit it to the tool shed whence the repository was installed. + repository_dict[ 'tool_test_errors' ] = [] + for failure in result.failures: + label = str( failure[0] ) + log_output = failure[1].replace( '\\n', '\n' ) + log_output = re.sub( r'control \d+:.+', r'', log_output ) + log_output = re.sub( r'\n+', r'\n', log_output ) + appending_to = 'output' + tmp_output = {} + output = {} + for line in log_output.split( '\n' ): + if line.startswith( 'Traceback' ): + appending_to = 'traceback' + elif 'request returned None from get_history' in line: + continue + elif '>> begin captured logging <<' in line: + appending_to = 'logging' + continue + elif '>> begin captured stdout <<' in line: + appending_to = 'stdout' + continue + elif '>> begin captured stderr <<' in line: + appending_to = 'stderr' + continue + if appending_to not in tmp_output: + tmp_output[ appending_to ] = [] + tmp_output[ appending_to ].append( line ) + for output_type in tmp_output: + output[ output_type ] = '\n'.join( tmp_output[ output_type ] ) + repository_dict[ 'tool_test_errors' ].append( dict( test=label, output=output ) ) + register_test_failure( galaxy_tool_shed_url, metadata_revision_id, repository_dict[ 'tool_test_errors' ] ) log.debug( 'Repository %s installed, but did not pass functional tests.' % repository_dict[ 'name' ] ) + repository_status.append( repository_dict ) + # Delete the completed tool functional tests from the test_toolbox.__dict__, otherwise nose will find them and try to re-run the + # tests after uninstalling the repository. + tests_to_delete = [] + for key in test_toolbox.__dict__: + if key.startswith( 'TestForTool_' ): + tests_to_delete.append( key ) + for key in tests_to_delete: + del test_toolbox.__dict__[ key ] # Generate an uninstall method for this repository, so that the next repository has a clean environment for testing. test_install_repositories.generate_uninstall_method( repository_dict ) # Set up nose to run the generated uninstall method as a functional test. 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: Remove some unneeded data from the repository metadata API collection view.
by commits-noreply＠bitbucket.org 27 Feb '13

27 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fabb0ae1edab/ changeset: fabb0ae1edab user: inithello date: 2013-02-27 20:23:07 summary: Remove some unneeded data from the repository metadata API collection view. affected #: 1 file diff -r b9c7813848e989d1a228a53745bb57f958b05467 -r fabb0ae1edabf77f9aceb018fa5a988ce05500f9 lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py +++ b/lib/galaxy/webapps/community/model/__init__.py @@ -191,8 +191,7 @@ fp.close() class RepositoryMetadata( object, APIItem ): - api_collection_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable', 'tools_functionally_correct', - 'do_not_test', 'time_last_tested', 'tool_test_errors' ) + api_collection_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable' ) api_element_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable', 'tools_functionally_correct', 'do_not_test', 'time_last_tested', 'tool_test_errors' ) def __init__( self, id=None, repository_id=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False, downloadable=False, 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: Attempt to resolve issue with tool shed registry when running buildbot functional tests.
by commits-noreply＠bitbucket.org 27 Feb '13

27 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b9c7813848e9/ changeset: b9c7813848e9 user: inithello date: 2013-02-27 20:12:07 summary: Attempt to resolve issue with tool shed registry when running buildbot functional tests. affected #: 1 file diff -r 8bad40b5b8ab0aee26c09ef8d59ca15227e1fec3 -r b9c7813848e989d1a228a53745bb57f958b05467 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -314,6 +314,7 @@ log.info( "Functional tests will be run against %s:%s" % ( galaxy_test_host, galaxy_test_port ) ) success = False try: + tool_configs = app.config.tool_configs # What requires these? Handy for (eg) functional tests to save outputs? if galaxy_test_save: os.environ[ 'GALAXY_TEST_SAVE' ] = galaxy_test_save @@ -337,7 +338,6 @@ # Eliminate the migrated_tool_panel_config from the app's tool_configs, append the list of installed_tool_panel_configs, # and reload the app's toolbox. relative_migrated_tool_panel_config = os.path.join( app.config.root, migrated_tool_panel_config ) - tool_configs = app.config.tool_configs if relative_migrated_tool_panel_config in tool_configs: tool_configs.remove( relative_migrated_tool_panel_config ) for installed_tool_panel_config in installed_tool_panel_configs: 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: Clean up remaining references to galaxy.util.shed_util_common.
by commits-noreply＠bitbucket.org 27 Feb '13

27 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8bad40b5b8ab/ changeset: 8bad40b5b8ab user: inithello date: 2013-02-27 17:16:10 summary: Clean up remaining references to galaxy.util.shed_util_common. affected #: 2 files diff -r b985587c33926d8d38fa4456b51eecbc68953bb9 -r 8bad40b5b8ab0aee26c09ef8d59ca15227e1fec3 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -920,7 +920,7 @@ def tool_shed_repository( self ): # If this tool is included in an installed tool shed repository, return it. if self.tool_shed: - return galaxy.util.shed_util_common.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( self.app, + return tool_shed.util.shed_util_common.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( self.app, self.tool_shed, self.repository_name, self.repository_owner, diff -r b985587c33926d8d38fa4456b51eecbc68953bb9 -r 8bad40b5b8ab0aee26c09ef8d59ca15227e1fec3 lib/tool_shed/galaxy_install/__init__.py --- a/lib/tool_shed/galaxy_install/__init__.py +++ b/lib/tool_shed/galaxy_install/__init__.py @@ -28,7 +28,7 @@ ElementInclude.include( root ) tool_path = root.get( 'tool_path', None ) if tool_path: - tool_shed = galaxy.util.shed_util_common.clean_tool_shed_url( tool_shed_repository.tool_shed ) + tool_shed = tool_shed.util.shed_util_common.clean_tool_shed_url( tool_shed_repository.tool_shed ) relative_path = os.path.join( tool_path, tool_shed, 'repos', 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: Rename community template path to tool_shed.
by commits-noreply＠bitbucket.org 26 Feb '13

26 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b985587c3392/ changeset: b985587c3392 user: greg date: 2013-02-26 23:12:52 summary: Rename community template path to tool_shed. affected #: 101 files diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -36,7 +36,7 @@ message=message, status=status ) else: - return trans.fill_template( '/webapps/community/admin/index.mako', + return trans.fill_template( '/webapps/tool_shed/admin/index.mako', message=message, status=status ) @web.expose @@ -49,7 +49,7 @@ message=message, status=status ) else: - return trans.fill_template( '/webapps/community/admin/center.mako', + return trans.fill_template( '/webapps/tool_shed/admin/center.mako', message=message, status=status ) @web.expose diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -454,7 +454,7 @@ """ Column that displays community ratings for an item. """ def get_value( self, trans, grid, item ): ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, item, webapp_model=trans.model ) - return trans.fill_template( "community_rating.mako", + return trans.fill_template( "tool_shed_rating.mako", ave_item_rating=ave_item_rating, num_ratings=num_ratings, item_id=trans.security.encode_id( item.id ) ) diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -403,7 +403,7 @@ # Grid definition title = "Repository Metadata" model_class = model.RepositoryMetadata - template='/webapps/community/repository/grid.mako' + template='/webapps/tool_shed/repository/grid.mako' default_sort_key = "name" columns = [ IdColumn( "Id", @@ -567,7 +567,7 @@ action='manage_categories', message=message, status=status ) ) - return trans.fill_template( '/webapps/community/category/create_category.mako', + return trans.fill_template( '/webapps/tool_shed/category/create_category.mako', name=name, description=description, message=message, @@ -667,7 +667,7 @@ action='manage_categories', message=message, status=status ) ) - return trans.fill_template( '/webapps/community/category/edit_category.mako', + return trans.fill_template( '/webapps/tool_shed/category/edit_category.mako', category=category, message=message, status=status ) @@ -677,7 +677,7 @@ if 'f-free-text-search' in kwd: # Trick to enable searching repository name, description from the CategoryGrid. # What we've done is rendered the search box for the RepositoryGrid on the grid.mako - # template for the CategoryGrid. See ~/templates/webapps/community/category/grid.mako. + # template for the CategoryGrid. See ~/templates/webapps/tool_shed/category/grid.mako. # Since we are searching repositories and not categories, redirect to browse_repositories(). return trans.response.send_redirect( web.url_for( controller='admin', action='browse_repositories', @@ -714,7 +714,7 @@ if 'regenerate_statistics_button' in kwd: trans.app.shed_counter.generate_statistics() message = "Successfully regenerated statistics" - return trans.fill_template( '/webapps/community/admin/statistics.mako', + return trans.fill_template( '/webapps/tool_shed/admin/statistics.mako', message=message, status=status ) @web.expose @@ -726,7 +726,7 @@ message = util.restore_text( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) repositories_select_field = suc.build_repository_ids_select_field( trans ) - return trans.fill_template( '/webapps/community/admin/reset_metadata_on_selected_repositories.mako', + return trans.fill_template( '/webapps/tool_shed/admin/reset_metadata_on_selected_repositories.mako', repositories_select_field=repositories_select_field, message=message, status=status ) diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -46,7 +46,7 @@ return 0 title = "Categories" model_class = model.Category - template='/webapps/community/category/grid.mako' + template='/webapps/tool_shed/category/grid.mako' default_sort_key = "name" columns = [ NameColumn( "Name", @@ -82,7 +82,7 @@ return 0 title = "Categories of valid repositories" model_class = model.Category - template='/webapps/community/category/valid_grid.mako' + template='/webapps/tool_shed/category/valid_grid.mako' default_sort_key = "name" columns = [ CategoryGrid.NameColumn( "Name", @@ -172,7 +172,7 @@ # Grid definition title = "Repositories" model_class = model.Repository - template='/webapps/community/repository/grid.mako' + template='/webapps/tool_shed/repository/grid.mako' default_sort_key = "name" columns = [ NameColumn( "Name", @@ -503,7 +503,7 @@ # Grid definition title = "Matching repositories" model_class = model.RepositoryMetadata - template='/webapps/community/repository/grid.mako' + template='/webapps/tool_shed/repository/grid.mako' default_sort_key = "Repository.name" columns = [ NameColumn( "Repository name", @@ -571,7 +571,7 @@ # The request came from the tool shed. if 'f-free-text-search' in kwd: # Trick to enable searching repository name, description from the CategoryGrid. What we've done is rendered the search box for the - # RepositoryGrid on the grid.mako template for the CategoryGrid. See ~/templates/webapps/community/category/grid.mako. Since we + # RepositoryGrid on the grid.mako template for the CategoryGrid. See ~/templates/webapps/tool_shed/category/grid.mako. Since we # are searching repositories and not categories, redirect to browse_repositories(). if 'id' in kwd and 'f-free-text-search' in kwd and kwd[ 'id' ] == kwd[ 'f-free-text-search' ]: # The value of 'id' has been set to the search string, which is a repository name. We'll try to get the desired encoded repository @@ -629,7 +629,7 @@ repository.name, repository.user.username, downloadable_revision.changeset_revision ) - return trans.fill_template( '/webapps/community/repository/browse_invalid_tools.mako', + return trans.fill_template( '/webapps/tool_shed/repository/browse_invalid_tools.mako', cntrller=cntrller, invalid_tools_dict=invalid_tools_dict, message=message, @@ -747,7 +747,7 @@ suc.update_repository( repo ) is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) - return trans.fill_template( '/webapps/community/repository/browse_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository/browse_repository.mako', repository=repository, metadata=metadata, commit_message=commit_message, @@ -937,7 +937,7 @@ repository = suc.get_repository_in_tool_shed( trans, id ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) if trans.user and trans.user.email: - return trans.fill_template( "/webapps/community/repository/contact_owner.mako", + return trans.fill_template( "/webapps/tool_shed/repository/contact_owner.mako", repository=repository, metadata=metadata, message=message, @@ -1032,7 +1032,7 @@ action='view_repository', message=message, id=trans.security.encode_id( repository.id ) ) ) - return trans.fill_template( '/webapps/community/repository/create_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository/create_repository.mako', name=name, description=description, long_description=long_description, @@ -1073,7 +1073,7 @@ is_malicious = suc.changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, repository_id, changeset_revision ) try: - return trans.fill_template( "/webapps/community/repository/tool_form.mako", + return trans.fill_template( "/webapps/tool_shed/repository/tool_form.mako", repository=repository, metadata=metadata, changeset_revision=changeset_revision, @@ -1197,7 +1197,7 @@ message = "No search performed - each field must contain the same number of comma-separated items." status = "error" exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) - return trans.fill_template( '/webapps/community/repository/find_tools.mako', + return trans.fill_template( '/webapps/tool_shed/repository/find_tools.mako', tool_id=self.__stringify( tool_ids ), tool_name=self.__stringify( tool_names ), tool_version=self.__stringify( tool_versions ), @@ -1286,7 +1286,7 @@ exact_matches_checked = False workflow_names = [] exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) - return trans.fill_template( '/webapps/community/repository/find_workflows.mako', + return trans.fill_template( '/webapps/tool_shed/repository/find_workflows.mako', workflow_name=self.__stringify( workflow_names ), exact_matches_check_box=exact_matches_check_box, message=message, @@ -1690,7 +1690,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - return trans.fill_template( '/webapps/community/repository/help.mako', message=message, status=status, **kwd ) + return trans.fill_template( '/webapps/tool_shed/repository/help.mako', message=message, status=status, **kwd ) def __in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ): found = False if tool_id and not tool_name and not tool_version: @@ -1762,7 +1762,7 @@ user_id = params.get( 'user_id', None ) repository_id = params.get( 'repository_id', None ) changeset_revision = params.get( 'changeset_revision', None ) - return trans.fill_template( '/webapps/community/index.mako', + return trans.fill_template( '/webapps/tool_shed/index.mako', repository_metadata=repository_metadata, has_reviewed_repositories=has_reviewed_repositories, has_deprecated_repositories=has_deprecated_repositories, @@ -1813,7 +1813,7 @@ elif error_message: message = error_message try: - return trans.fill_template( "/webapps/community/repository/tool_form.mako", + return trans.fill_template( "/webapps/tool_shed/repository/tool_form.mako", repository=repository, changeset_revision=changeset_revision, tool=tool, @@ -1872,7 +1872,7 @@ .order_by( trans.model.Repository.table.c.name ): if user.email in repository.email_alerts: email_alert_repositories.append( repository ) - return trans.fill_template( "/webapps/community/user/manage_email_alerts.mako", + return trans.fill_template( "/webapps/tool_shed/user/manage_email_alerts.mako", new_repo_alert_check_box=new_repo_alert_check_box, email_alert_repositories=email_alert_repositories, message=message, @@ -2056,7 +2056,7 @@ review_id = None can_browse_repository_reviews = suc.can_browse_repository_reviews( trans, repository ) containers_dict = suc.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) - return trans.fill_template( '/webapps/community/repository/manage_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository/manage_repository.mako', repo_name=repo_name, description=description, long_description=long_description, @@ -2163,7 +2163,7 @@ add_id_to_name=False, downloadable=False ) containers_dict = suc.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) - return trans.fill_template( '/webapps/community/repository/preview_tools_in_changeset.mako', + return trans.fill_template( '/webapps/tool_shed/repository/preview_tools_in_changeset.mako', repository=repository, containers_dict=containers_dict, repository_metadata_id=repository_metadata_id, @@ -2230,7 +2230,7 @@ rra = self.get_user_item_rating( trans.sa_session, trans.user, repository, webapp_model=trans.model ) is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) - return trans.fill_template( '/webapps/community/repository/rate_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository/rate_repository.mako', repository=repository, metadata=metadata, avg_rating=avg_rating, @@ -2242,7 +2242,7 @@ status=status ) @web.expose def reset_all_metadata( self, trans, id, **kwd ): - # This method is called only from the ~/templates/webapps/community/repository/manage_repository.mako template. + # This method is called only from the ~/templates/webapps/tool_shed/repository/manage_repository.mako template. # It resets all metadata on the complete changelog for a single repository in the tool shed. invalid_file_tups, metadata_dict = suc.reset_all_metadata_on_repository_in_tool_shed( trans, id, **kwd ) if invalid_file_tups: @@ -2405,7 +2405,7 @@ message = "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>." status = "error" is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) - return trans.fill_template( '/webapps/community/repository/browse_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository/browse_repository.mako', repo=repo, repository=repository, commit_message=commit_message, @@ -2672,7 +2672,7 @@ changesets.insert( 0, change_dict ) is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) - return trans.fill_template( '/webapps/community/repository/view_changelog.mako', + return trans.fill_template( '/webapps/tool_shed/repository/view_changelog.mako', repository=repository, metadata=metadata, changesets=changesets, @@ -2703,7 +2703,7 @@ diffs.append( suc.to_safe_string( diff, to_html=True ) ) is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, id, ctx_str ) - return trans.fill_template( '/webapps/community/repository/view_changeset.mako', + return trans.fill_template( '/webapps/tool_shed/repository/view_changeset.mako', repository=repository, metadata=metadata, ctx=ctx, @@ -2810,7 +2810,7 @@ review_id = None containers_dict = suc.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) can_browse_repository_reviews = suc.can_browse_repository_reviews( trans, repository ) - return trans.fill_template( '/webapps/community/repository/view_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository/view_repository.mako', repo=repo, repository=repository, repository_metadata_id=repository_metadata_id, @@ -2893,7 +2893,7 @@ review_id = trans.security.encode_id( review.id ) else: review_id = None - return trans.fill_template( "/webapps/community/repository/view_tool_metadata.mako", + return trans.fill_template( "/webapps/tool_shed/repository/view_tool_metadata.mako", repository=repository, metadata=metadata, tool=tool, @@ -2919,7 +2919,7 @@ repository = suc.get_repository_in_tool_shed( trans, trans.security.encode_id( repository_metadata.repository_id ) ) changeset_revision = repository_metadata.changeset_revision metadata = repository_metadata.metadata - return trans.fill_template( "/webapps/community/repository/view_workflow.mako", + return trans.fill_template( "/webapps/tool_shed/repository/view_workflow.mako", repository=repository, changeset_revision=changeset_revision, repository_metadata_id=repository_metadata_id, diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/webapps/community/controllers/repository_review.py --- a/lib/galaxy/webapps/community/controllers/repository_review.py +++ b/lib/galaxy/webapps/community/controllers/repository_review.py @@ -27,7 +27,7 @@ return component.description title = "Repository review components" model_class = model.Component - template='/webapps/community/repository_review/grid.mako' + template='/webapps/tool_shed/repository_review/grid.mako' default_sort_key = "name" columns = [ NameColumn( "Name", @@ -89,7 +89,7 @@ return rval title = "All reviewed repositories" model_class = model.Repository - template='/webapps/community/repository_review/grid.mako' + template='/webapps/tool_shed/repository_review/grid.mako' default_sort_key = "Repository.name" columns = [ RepositoryGrid.NameColumn( "Repository name", @@ -196,7 +196,7 @@ return '' title = "Reviews by user" model_class = model.RepositoryReview - template='/webapps/community/repository_review/grid.mako' + template='/webapps/tool_shed/repository_review/grid.mako' default_sort_key = 'repository_id' columns = [ RepositoryNameColumn( "Repository Name", @@ -316,7 +316,7 @@ repository = review.repository repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) - return trans.fill_template( '/webapps/community/repository_review/browse_review.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/browse_review.mako', repository=repository, changeset_revision_label=changeset_revision_label, review=review, @@ -361,7 +361,7 @@ action='manage_components', message=message, status=status ) ) - return trans.fill_template( '/webapps/community/repository_review/create_component.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/create_component.mako', name=name, description=description, message=message, @@ -456,7 +456,7 @@ action='manage_components', message=message, status=status ) ) - return trans.fill_template( '/webapps/community/repository_review/edit_component.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/edit_component.mako', component=component, message=message, status=status ) @@ -576,7 +576,7 @@ selected_value=selected_value, for_component=False ) rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) - return trans.fill_template( '/webapps/community/repository_review/edit_review.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/edit_review.mako', repository=repository, review=review, changeset_revision_label=changeset_revision_label, @@ -688,7 +688,7 @@ installable=installable, can_add_review=can_add_review ) reviews_dict[ changeset_revision ] = revision_dict - return trans.fill_template( '/webapps/community/repository_review/reviews_of_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/reviews_of_repository.mako', repository=repository, reviews_dict=reviews_dict, mine=mine, @@ -709,7 +709,7 @@ installable = changeset_revision in [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ] rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) reviews = suc.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) - return trans.fill_template( '/webapps/community/repository_review/reviews_of_changeset_revision.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako', repository=repository, changeset_revision=changeset_revision, changeset_revision_label=changeset_revision_label, @@ -773,7 +773,7 @@ repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) previous_reviews_dict = suc.get_previous_repository_reviews( trans, repository, changeset_revision ) rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) - return trans.fill_template( '/webapps/community/repository_review/select_previous_review.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/select_previous_review.mako', repository=repository, changeset_revision=changeset_revision, changeset_revision_label=changeset_revision_label, diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -204,7 +204,7 @@ # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. suc.reset_tool_data_tables( trans.app ) selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] - return trans.fill_template( '/webapps/community/repository/upload.mako', + return trans.fill_template( '/webapps/tool_shed/repository/upload.mako', repository=repository, url=url, commit_message=commit_message, diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/webapps/galaxy/controllers/admin.py --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -733,7 +733,7 @@ status = util.restore_text( kwd.get( 'status', 'done' ) ) migration_stages_dict = odict() migration_modules = [] - migration_scripts_dir = os.path.abspath( os.path.join( trans.app.config.root, 'lib', 'galaxy', 'tool_shed', 'migrate', 'versions' ) ) + migration_scripts_dir = os.path.abspath( os.path.join( trans.app.config.root, 'lib', 'tool_shed', 'galaxy_install', 'migrate', 'versions' ) ) migration_scripts_dir_contents = os.listdir( migration_scripts_dir ) for item in migration_scripts_dir_contents: if os.path.isfile( os.path.join( migration_scripts_dir, item ) ) and item.endswith( '.py' ): diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -735,7 +735,7 @@ message=message, status=status ) else: - return trans.fill_template( '/webapps/community/user/manage_info.mako', + return trans.fill_template( '/webapps/tool_shed/user/manage_info.mako', cntrller=cntrller, user=user, email=email, diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/common.mako --- a/templates/admin/tool_shed_repository/common.mako +++ b/templates/admin/tool_shed_repository/common.mako @@ -1,4 +1,4 @@ -<%namespace file="/webapps/community/repository/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /><%def name="browse_files(title_text, directory_path)"><script type="text/javascript"> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/manage_repository.mako --- a/templates/admin/tool_shed_repository/manage_repository.mako +++ b/templates/admin/tool_shed_repository/manage_repository.mako @@ -1,6 +1,6 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/community/repository/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /><%namespace file="/admin/tool_shed_repository/common.mako" import="*" /><%def name="stylesheets()"> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/reselect_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /><%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" /><%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" /> -<%namespace file="/webapps/community/repository/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /><%def name="stylesheets()"> ${parent.stylesheets()} diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako --- a/templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako +++ b/templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako @@ -1,6 +1,6 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/community/common/common.mako" import="common_misc_javascripts" /> +<%namespace file="/webapps/tool_shed/common/common.mako" import="common_misc_javascripts" /><%def name="javascripts()"> ${parent.javascripts()} diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako --- a/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako +++ b/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /><%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" /><%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" /> -<%namespace file="/webapps/community/repository/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /><%def name="stylesheets()"> ${parent.stylesheets()} diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/select_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /><%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" /><%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" /> -<%namespace file="/webapps/community/repository/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /><%def name="stylesheets()"> ${parent.stylesheets()} diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/view_workflow.mako --- a/templates/admin/tool_shed_repository/view_workflow.mako +++ b/templates/admin/tool_shed_repository/view_workflow.mako @@ -1,7 +1,7 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/community/common/common.mako" import="*" /> -<%namespace file="/webapps/community/repository/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/common/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /><% from galaxy.web.framework.helpers import time_ago @@ -11,7 +11,7 @@ <%! def inherit(context): if context.get('use_panels'): - return '/webapps/community/base_panels.mako' + return '/webapps/tool_shed/base_panels.mako' else: return '/base.mako' %> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/community_rating.mako --- a/templates/community_rating.mako +++ /dev/null @@ -1,33 +0,0 @@ -<% - label = "ratings" - if num_ratings == 1: - label = "rating" -%> -<div> - <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="1" - %if ave_item_rating > 0 and ave_item_rating <= 1.5: - checked="checked" - %endif - - /> - <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="2" - %if ave_item_rating > 1.5 and ave_item_rating <= 2.5: - checked="checked" - %endif - /> - <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="3" - %if ave_item_rating > 2.5 and ave_item_rating <= 3.5: - checked="checked" - %endif - /> - <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="4" - %if ave_item_rating > 3.5 and ave_item_rating <= 4.5: - checked="checked" - %endif - /> - <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="5" - %if ave_item_rating > 4.5: - checked="checked" - %endif - /> -</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/tool_shed_rating.mako --- /dev/null +++ b/templates/tool_shed_rating.mako @@ -0,0 +1,33 @@ +<% + label = "ratings" + if num_ratings == 1: + label = "rating" +%> +<div> + <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="1" + %if ave_item_rating > 0 and ave_item_rating <= 1.5: + checked="checked" + %endif + + /> + <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="2" + %if ave_item_rating > 1.5 and ave_item_rating <= 2.5: + checked="checked" + %endif + /> + <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="3" + %if ave_item_rating > 2.5 and ave_item_rating <= 3.5: + checked="checked" + %endif + /> + <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="4" + %if ave_item_rating > 3.5 and ave_item_rating <= 4.5: + checked="checked" + %endif + /> + <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="5" + %if ave_item_rating > 4.5: + checked="checked" + %endif + /> +</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/user/dbkeys.mako --- a/templates/user/dbkeys.mako +++ b/templates/user/dbkeys.mako @@ -1,7 +1,7 @@ <%! def inherit(context): if context.get('use_panels'): - return '/base_panels.mako' + return '/webapps/galaxy/base_panels.mako' else: return '/base.mako' %> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/user/login.mako --- a/templates/user/login.mako +++ b/templates/user/login.mako @@ -1,7 +1,7 @@ <%! def inherit(context): if context.get('use_panels'): - return '/base_panels.mako' + return '/webapps/galaxy/base_panels.mako' else: return '/base.mako' %> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/user/logout.mako --- a/templates/user/logout.mako +++ b/templates/user/logout.mako @@ -1,4 +1,4 @@ -<%inherit file="/base_panels.mako"/> +<%inherit file="/webapps/galaxy/base_panels.mako"/><%namespace file="/message.mako" import="render_msg" /> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/user/openid_associate.mako --- a/templates/user/openid_associate.mako +++ b/templates/user/openid_associate.mako @@ -1,7 +1,7 @@ <%! def inherit(context): if context.get('use_panels'): - return '/base_panels.mako' + return '/webapps/galaxy/base_panels.mako' else: return '/base.mako' %> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/admin/center.mako --- a/templates/webapps/community/admin/center.mako +++ /dev/null @@ -1,50 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - - -<%def name="title()">Galaxy Administration</%def> - -%if message: - ${render_msg( message, status )} -%endif - -<h2>Administration</h2> - -<p>The menu on the left provides the following features</p> -<ul> - <li> - <strong>Categories</strong> - <p/> - <ul> - <li> - <strong>Manage categories</strong> - </li> - <p/> - </ul> - </li> - <li> - <strong>Security</strong> - <p/> - <ul> - <li> - <strong>Manage users</strong> - provides a view of the registered users and all groups and non-private roles associated - with each user. - </li> - <p/> - <li> - <strong>Manage groups</strong> - provides a view of all groups along with the members of the group and the roles associated with - each group (both private and non-private roles). The group names include a link to a page that allows you to manage the users and - roles that are associated with the group. - </li> - <p/> - <li> - <strong>Manage roles</strong> - provides a view of all non-private roles along with the role type, and the users and groups that - are associated with the role. The role names include a link to a page that allows you to manage the users and groups that are associated - with the role. The page also includes a view of the data library datasets that are associated with the role and the permissions applied - to each dataset. - </li> - </ul> - </li> - <p/> -</ul> -<br/> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako +++ /dev/null @@ -1,139 +0,0 @@ -<%inherit file="/webapps/community/base_panels.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="stylesheets()"> - ## Include "base.css" for styling tool menu and forms (details) - ${h.css( "base", "autocomplete_tagging", "tool_menu" )} - - ## But make sure styles for the layout take precedence - ${parent.stylesheets()} - - <style type="text/css"> - body { margin: 0; padding: 0; overflow: hidden; } - #left { - background: #C1C9E5 url(${h.url_for('/static/style/menu_bg.png')}) top repeat-x; - } - </style> -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} -</%def> - -<%def name="init()"> - <% - self.has_left_panel=True - self.has_right_panel=False - self.active_view="tools" - %> - %if trans.app.config.require_login and not trans.user: - <script type="text/javascript"> - if ( window != top ) { - top.location.href = location.href; - } - </script> - %endif -</%def> - -<%def name="left_panel()"> - <% can_review_repositories = trans.app.security_agent.user_can_review_repositories( trans.user ) %> - <div class="unified-panel-header" unselectable="on"> - <div class='unified-panel-header-inner'>Administration</div> - </div> - <div class="page-container" style="padding: 10px;"> - <div class="toolMenu"> - <div class="toolSectionList"> - <div class="toolSectionTitle"> - Repositories - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories' )}">Browse by category</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repositories' )}">Browse all repositories</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories_in_tool_shed' )}">Reset selected metadata</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repository_metadata' )}">Browse metadata</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='admin' )}">Browse invalid tools</a> - </div> - </div> - </div> - %if can_review_repositories: - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Reviewing Repositories - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - %if trans.user.repository_reviews: - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_reviewed_by_me' )}">Repositories reviewed by me</a> - </div> - %endif - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_with_reviews' )}">All reviewed repositories</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_without_reviews' )}">Repositories with no reviews</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_components' )}">Manage review components</a> - </div> - </div> - </div> - %endif - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Categories - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='manage_categories' )}">Manage categories</a> - </div> - </div> - </div> - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Security - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='users' )}">Manage users</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='groups' )}">Manage groups</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='roles' )}">Manage roles</a> - </div> - </div> - </div> - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Statistics - </div> - <div class="toolSectionBody"> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='regenerate_statistics' )}">View shed statistics</a> - </div> - </div> - </div> - </div> - </div> -</%def> - -<%def name="center_panel()"> - <% - center_url = h.url_for(controller='admin', action='center' ) - %> - <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe> -</%def> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/admin/reset_metadata_on_selected_repositories.mako --- a/templates/webapps/community/admin/reset_metadata_on_selected_repositories.mako +++ /dev/null @@ -1,40 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/community/common/common.mako" import="common_misc_javascripts" /> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${common_misc_javascripts()} -</%def> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="warningmessage"> - Resetting metadata may take a while because this process clones each change set in each selected repository's change log to a temporary location on disk. - Wait until this page redirects after clicking the <b>Reset metadata on selected repositories</b> button, as doing anything else will not be helpful. Watch - the tool shed paster log to pass the time if necessary. -</div> - -<div class="toolForm"> - <div class="toolFormTitle">Reset all metadata on each selected repository</div> - <form name="reset_metadata_on_selected_repositories" id="reset_metadata_on_selected_repositories" action="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories_in_tool_shed' )}" method="post" > - <div class="form-row"> - Check each repository for which you want to reset metadata. Repository names are followed by owners in parentheses. - </div> - <div style="clear: both"></div> - <div class="form-row"> - <input type="checkbox" id="checkAll" name="select_all_repositories_checkbox" value="true" onclick="checkAllFields('repository_ids');"/><input type="hidden" name="select_all_repositories_checkbox" value="true"/><b>Select/unselect all repositories</b> - </div> - <div style="clear: both"></div> - <div class="form-row"> - ${repositories_select_field.get_html()} - </div> - <div style="clear: both"></div> - <div class="form-row"> - <input type="submit" name="reset_metadata_on_selected_repositories_button" value="Reset metadata on selected repositories"/> - </div> - </form> - </div> -</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/admin/statistics.mako --- a/templates/webapps/community/admin/statistics.mako +++ /dev/null @@ -1,56 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Tool shed statistics generated on ${trans.app.shed_counter.generation_time}</div> - <form name="regenerate_statistics" id="regenerate_statistics" action="${h.url_for( controller='admin', action='regenerate_statistics' )}" method="post" > - <div class="form-row"> - <table class="grid"> - <tr> - <th>Item</th> - <th>Count</th> - </tr> - <tr> - <td>Total repositories</td> - <td>${trans.app.shed_counter.repositories | h}</td> - </tr> - ##<tr> - ## <td>Empty repositories</td> - ## <td>${trans.app.shed_counter.new_repositories | h}</td> - ##</tr> - <tr> - <td>Deleted repositories</td> - <td>${trans.app.shed_counter.deleted_repositories | h}</td> - </tr> - <tr> - <td>Valid tools</td> - <td>${trans.app.shed_counter.valid_tools | h}</td> - </tr> - <tr> - <td>Invalid tools</td> - <td>${trans.app.shed_counter.invalid_tools | h}</td> - </tr> - <tr> - <td>Workflows</td> - <td>${trans.app.shed_counter.workflows | h}</td> - </tr> - <tr> - <td>Proprietary datatypes</td> - <td>${trans.app.shed_counter.proprietary_datatypes | h}</td> - </tr> - <tr> - <td>Total clones</td> - <td>${trans.app.shed_counter.total_clones | h}</td> - </tr> - </table> - </div> - <div class="form-row"> - <input type="submit" name="regenerate_statistics_button" value="Regenerate statistics"/> - </div> - </form> - </div> -</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/base_panels.mako --- a/templates/webapps/community/base_panels.mako +++ /dev/null @@ -1,133 +0,0 @@ -<%inherit file="/base/base_panels.mako"/> - -## Default title -<%def name="title()">Galaxy Tool Shed</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} -</%def> - -## Masthead -<%def name="masthead()"> - - ## Tab area, fills entire width - <div style="position: relative; right: -50%; float: left;"> - <div style="display: block; position: relative; right: 50%;"> - - <ul class="nav" border="0" cellspacing="0"> - - <%def name="tab( id, display, href, target='_parent', visible=True, extra_class='', menu_options=None )"> - <% - cls = "" - a_cls = "" - extra = "" - if extra_class: - cls += " " + extra_class - if self.active_view == id: - cls += " active" - if menu_options: - cls += " dropdown" - a_cls += " dropdown-toggle" - extra = "<b class='caret'></b>" - style = "" - if not visible: - style = "display: none;" - %> - <li class="${cls}" style="${style}"> - %if href: - <a class="${a_cls}" data-toggle="dropdown" target="${target}" href="${href}">${display}${extra}</a> - %else: - <a class="${a_cls}" data-toggle="dropdown">${display}${extra}</a> - %endif - %if menu_options: - <ul class="dropdown-menu"> - %for menu_item in menu_options: - %if not menu_item: - <li class="divider"></li> - %else: - <li> - %if len ( menu_item ) == 1: - ${menu_item[0]} - %elif len ( menu_item ) == 2: - <% name, link = menu_item %> - <a href="${link}">${name | h}</a> - %else: - <% name, link, target = menu_item %> - <a target="${target}" href="${link}">${name | h}</a> - %endif - </li> - %endif - %endfor - </ul> - %endif - </li> - </%def> - - ## Repositories tab. - ${tab( "repositories", "Repositories", h.url_for( controller='/repository', action='index' ) )} - - ## Admin tab. - ${tab( "admin", "Admin", h.url_for( controller='/admin', action='index' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )} - - ## Help tab. - <% - menu_options = [] - qa_url = app.config.get( "qa_url", None ) - if qa_url: - menu_options = [ [_('Galaxy Q&A'), qa_url, "_blank" ] ] - menu_options.extend( [ - [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], - [_('Tool shed wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/Tool%20Shed" ), "_blank" ], - [_('Galaxy wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], - [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], - [_('How to Cite Galaxy'), app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ] - ] ) - tab( "help", _("Help"), None, menu_options=menu_options ) - %> - - ## User tabs. - <% - # Menu for user who is not logged in. - menu_options = [ [ _("Login"), h.url_for( controller='/user', action='login' ), "galaxy_main" ] ] - if app.config.allow_user_creation: - menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user' ), "galaxy_main" ] ) - extra_class = "loggedout-only" - visible = ( trans.user == None ) - tab( "user", _("User"), None, visible=visible, menu_options=menu_options ) - # Menu for user who is logged in. - if trans.user: - email = trans.user.email - else: - email = "" - menu_options = [ [ '<a>Logged in as <span id="user-email">%s</span></a>' % email ] ] - if app.config.use_remote_user: - if app.config.remote_user_logout_href: - menu_options.append( [ _('Logout'), app.config.remote_user_logout_href, "_top" ] ) - else: - menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user' ), "galaxy_main" ] ) - menu_options.append( [ _('API Keys'), h.url_for( controller='/user', action='api_keys', cntrller='user' ), "galaxy_main" ] ) - logout_url = h.url_for( controller='/user', action='logout' ) - menu_options.append( [ 'Logout', logout_url, "_top" ] ) - menu_options.append( None ) - if app.config.use_remote_user: - menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user' ), "galaxy_main" ] ) - - extra_class = "loggedin-only" - visible = ( trans.user != None ) - tab( "user", "User", None, visible=visible, menu_options=menu_options ) - %> - </ul> - </div> - </div> - - ## Logo, layered over tabs to be clickable - <div class="title"> - <a href="${h.url_for( app.config.get( 'logo_url', '/' ) )}"> - <img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}"> - Galaxy Tool Shed - %if app.config.brand: - <span>/ ${app.config.brand}</span> - %endif - </a> - </div> -</%def> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/category/create_category.mako --- a/templates/webapps/community/category/create_category.mako +++ /dev/null @@ -1,34 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - $(function(){ - $("input:text:first").focus(); - }) - </script> -</%def> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Create Category</div> - <div class="toolFormBody"> - <form name="create_category_form" id="create_category_form" action="${h.url_for(controller='admin', action='create_category' )}" method="post" > - <div class="form-row"> - <label>Name:</label> - <input name="name" type="textfield" value="${name | h}" size=40"/> - </div> - <div class="form-row"> - <label>Description:</label> - <input name="description" type="textfield" value="${description | h}" size=40"/> - </div> - <div class="form-row"> - <input type="submit" name="create_category_button" value="Save"/> - </div> - </form> - </div> -</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/category/edit_category.mako --- a/templates/webapps/community/category/edit_category.mako +++ /dev/null @@ -1,43 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Change category name and description</div> - <div class="toolFormBody"> - <form name="edit_category" action="${h.url_for( controller='admin', action='edit_category' )}" method="post" > - <div class="form-row"> - <label>Name:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${category.name | h}" size="40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Description:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input name="description" type="textfield" value="${category.description | h}" size=40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="hidden" name="rename" value="submitted"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="hidden" name="id" value="${trans.security.encode_id( category.id )}"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="edit_category_button" value="Save"/> - </div> - </form> - </div> -</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/category/grid.mako --- a/templates/webapps/community/category/grid.mako +++ /dev/null @@ -1,64 +0,0 @@ -<%namespace file="/display_common.mako" import="render_message" /> -<%namespace file="/grid_base.mako" import="*" /> -<%namespace file="/grid_common.mako" import="*" /> -<%inherit file="/grid_base.mako" /> - -## Render grid header. -## TODO: This is very similar to this directory's valid_grid.mako, so see if we can re-use this code in a better way. -<%def name="render_grid_header( grid, repo_grid, render_title=True)"> - <div class="grid-header"> - %if render_title: - ${grid_title()} - %endif - %if grid.global_actions: - <ul class="manage-table-actions"> - %if len( grid.global_actions ) < 4: - %for action in grid.global_actions: - <li><a class="action-button" href="${h.url_for( **action.url_args )}">${action.label | h}</a></li> - %endfor - %else: - <li><a class="action-button" id="action-8675309-popup" class="menubutton">Actions</a></li> - <div popupmenu="action-8675309-popup"> - %for action in grid.global_actions: - <a class="action-button" href="${h.url_for( **action.url_args )}">${action.label | h}</a> - %endfor - </div> - %endif - </ul> - %endif - ${render_grid_filters( repo_grid, render_advanced_search=False )} - </div> -</%def> - -<%def name="make_grid( grid, repo_grid )"> - <div class="loading-elt-overlay"></div> - <table> - <tr> - <td width="75%">${self.render_grid_header( grid, repo_grid )}</td> - <td></td> - <td></td> - </tr> - <tr> - <td width="100%" id="grid-message" valign="top">${render_message( message, status )}</td> - <td></td> - <td></td> - </tr> - </table> - ${render_grid_table( grid, show_item_checkboxes )} -</%def> - -<%def name="grid_body( grid )"> - <% - from galaxy.webapps.community.controllers.repository import RepositoryGrid - repo_grid = RepositoryGrid() - %> - ${self.make_grid( grid, repo_grid )} -</%def> - -<%def name="center_panel()"> - <div style="overflow: auto; height: 100%"> - <div class="page-container" style="padding: 10px;"> - ${self.grid_body( grid )} - </div> - </div> -</%def> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/category/valid_grid.mako --- a/templates/webapps/community/category/valid_grid.mako +++ /dev/null @@ -1,63 +0,0 @@ -<%namespace file="/display_common.mako" import="render_message" /> -<%namespace file="/grid_base.mako" import="*" /> -<%namespace file="/grid_common.mako" import="*" /> -<%inherit file="/grid_base.mako" /> - -## Render grid header. -<%def name="render_grid_header( grid, repo_grid, render_title=True)"> - <div class="grid-header"> - %if render_title: - ${grid_title()} - %endif - %if grid.global_actions: - <ul class="manage-table-actions"> - %if len( grid.global_actions ) < 4: - %for action in grid.global_actions: - <li><a class="action-button" href="${h.url_for( **action.url_args )}">${action.label | h}</a></li> - %endfor - %else: - <li><a class="action-button" id="action-8675309-popup" class="menubutton">Actions</a></li> - <div popupmenu="action-8675309-popup"> - %for action in grid.global_actions: - <a class="action-button" href="${h.url_for( **action.url_args )}">${action.label | h}</a> - %endfor - </div> - %endif - </ul> - %endif - ${render_grid_filters( repo_grid, render_advanced_search=False )} - </div> -</%def> - -<%def name="make_grid( grid, repo_grid )"> - <div class="loading-elt-overlay"></div> - <table> - <tr> - <td width="75%">${self.render_grid_header( grid, repo_grid )}</td> - <td></td> - <td></td> - </tr> - <tr> - <td width="100%" id="grid-message" valign="top">${render_message( message, status )}</td> - <td></td> - <td></td> - </tr> - </table> - ${render_grid_table( grid, show_item_checkboxes )} -</%def> - -<%def name="grid_body( grid )"> - <% - from galaxy.webapps.community.controllers.repository import ValidRepositoryGrid - repo_grid = ValidRepositoryGrid() - %> - ${self.make_grid( grid, repo_grid )} -</%def> - -<%def name="center_panel()"> - <div style="overflow: auto; height: 100%"> - <div class="page-container" style="padding: 10px;"> - ${self.grid_body( grid )} - </div> - </div> -</%def> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/common/common.mako --- a/templates/webapps/community/common/common.mako +++ /dev/null @@ -1,84 +0,0 @@ -<%def name="common_misc_javascripts()"> - <script type="text/javascript"> - function checkAllFields( name ) - { - var chkAll = document.getElementById( 'checkAll' ); - var checks = document.getElementsByTagName( 'input' ); - var boxLength = checks.length; - var allChecked = false; - var totalChecked = 0; - if ( chkAll.checked == true ) - { - for ( i=0; i < boxLength; i++ ) - { - if ( checks[i].name.indexOf( name ) != -1 ) - { - checks[i].checked = true; - } - } - } - else - { - for ( i=0; i < boxLength; i++ ) - { - if ( checks[i].name.indexOf( name ) != -1 ) - { - checks[i].checked = false - } - } - } - } - </script> -</%def> - -<%def name="render_star_rating( name, rating, disabled=False )"> - <% - if disabled: - disabled_str = ' disabled="disabled"' - else: - disabled_str = '' - html = '' - for index in range( 1, 6 ): - html += '<input name="%s" type="radio" class="star" value="%s" %s' % ( str( name ), str( index ), disabled_str ) - if rating > ( index - 0.5 ) and rating < ( index + 0.5 ): - html += ' checked="checked"' - html += '/>' - %> - ${html} -</%def> - -<%def name="render_long_description( description_text )"> - <style type="text/css"> - #description_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style> - <div class="form-row"> - <label>Detailed description:</label> - <table id="description_table"> - <tr><td>${description_text}</td></tr> - </table> - <div style="clear: both"></div> - </div> -</%def> - -<%def name="render_review_comment( comment_text )"> - <style type="text/css"> - #reviews_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style> - <table id="reviews_table"> - <tr><td>${comment_text}</td></tr> - </table> -</%def> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako +++ /dev/null @@ -1,165 +0,0 @@ -<%inherit file="/webapps/community/base_panels.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ## Include "base.css" for styling tool menu and forms (details) - ${h.css( "base", "autocomplete_tagging", "tool_menu" )} - - ## But make sure styles for the layout take precedence - ${parent.stylesheets()} - - <style type="text/css"> - body { margin: 0; padding: 0; overflow: hidden; } - #left { - background: #C1C9E5 url(${h.url_for('/static/style/menu_bg.png')}) top repeat-x; - } - </style> -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} -</%def> - -<%def name="init()"> - <% - self.has_left_panel=True - self.has_right_panel=False - self.active_view="tools" - %> - %if trans.app.config.require_login and not trans.user: - <script type="text/javascript"> - if ( window != top ) { - top.location.href = location.href; - } - </script> - %endif -</%def> - -<%def name="left_panel()"> - <% can_review_repositories = trans.app.security_agent.user_can_review_repositories( trans.user ) %> - <div class="unified-panel-header" unselectable="on"> - <div class='unified-panel-header-inner'>${trans.app.shed_counter.valid_tools | h} valid tools on ${trans.app.shed_counter.generation_time | h}</div> - </div> - <div class="page-container" style="padding: 10px;"> - <div class="toolMenu"> - <div class="toolSectionList"> - %if user_id or repository_id: - ## The route in was a sharable url, and may have included a changeset_revision, although we don't check for it. - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - All Repositories - </div> - <div class="toolTitle"> - <a href="${h.url_for( controller='repository', action='index' )}">Browse by category</a> - </div> - %else: - %if repository_metadata: - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Search - </div> - <div class="toolSectionBody"> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a> - </div> - </div> - %endif - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - All Repositories - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories' )}">Browse by category</a> - </div> - %if trans.user: - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - My Repositories and Tools - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='repositories_i_own' )}">Repositories I own</a> - </div> - %if has_reviewed_repositories: - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='reviewed_repositories_i_own' )}">Reviewed repositories I own</a> - </div> - %endif - %if has_deprecated_repositories: - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='deprecated_repositories_i_own' )}">Deprecated repositories I own</a> - </div> - %endif - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='my_writable_repositories' )}">My writable repositories</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='repository' )}">My invalid tools</a> - </div> - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Available Actions - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='create_repository' )}">Create new repository</a> - </div> - %if can_review_repositories: - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Reviewing Repositories - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - %if trans.user.repository_reviews: - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_reviewed_by_me' )}">Repositories reviewed by me</a> - </div> - %endif - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_with_reviews' )}">All reviewed repositories</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_without_reviews' )}">Repositories with no reviews</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_components' )}">Manage review components</a> - </div> - </div> - </div> - %endif - %else: - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Available Actions - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='/user', action='login' )}">Login to create a repository</a> - </div> - %endif - %endif - </div> - </div> - </div> -</%def> - -<%def name="center_panel()"> - <% - if trans.app.config.require_login and not trans.user: - center_url = h.url_for( controller='user', action='login', message=message, status=status ) - elif repository_id and changeset_revision: - # Route in was a sharable url: /view/{owner}/{name}/{changeset_revision}. - center_url = h.url_for( controller='repository', action='view_repository', id=repository_id, changeset_revision=changeset_revision, message=message, status=status ) - elif repository_id: - # Route in was a sharable url: /view/{owner}/{name}. - center_url = h.url_for( controller='repository', action='view_repository', id=repository_id, message=message, status=status ) - elif user_id: - # Route in was a sharable url: /view/{owner}. - center_url = h.url_for( controller='repository', action='browse_repositories', operation="repositories_by_user", user_id=user_id, message=message, status=status ) - else: - center_url = h.url_for( controller='repository', action='browse_categories', message=message, status=status ) - %> - <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe> -</%def> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/message.mako --- a/templates/webapps/community/message.mako +++ /dev/null @@ -1,1 +0,0 @@ -<%inherit file="../../message.mako"/> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/repository/browse_invalid_tools.mako --- a/templates/webapps/community/repository/browse_invalid_tools.mako +++ /dev/null @@ -1,44 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - %if invalid_tools_dict: - <div class="toolFormTitle">Invalid tools<i> - click the tool config file name to see why the tool is invalid</i></div> - <div class="form-row"> - <table class="grid"> - <tr> - <th>Tool config</th> - <th>Repository name</th> - <th>Repository owner</th> - <th>Changeset revision</th> - </tr> - %for invalid_tool_config, repository_tup in invalid_tools_dict.items(): - <% repository_id, repository_name, repository_owner, changeset_revision = repository_tup %> - <tr> - <td> - <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository_id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision )}"> - ${invalid_tool_config} - </a> - </td> - <td>${repository_name | h}</td> - <td>${repository_owner | h}</td> - <td>${changeset_revision | h}</td> - </tr> - %endfor - </table> - </div> - </div> - %else: - <div class="form-row"> - %if cntrller == 'admin' and trans.user_is_admin(): - No repositories in this tool shed contain invalid tools. - %else: - None of your repositories contain invalid tools. - %endif - </div> - %endif -</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/repository/browse_repository.mako --- a/templates/webapps/community/repository/browse_repository.mako +++ /dev/null @@ -1,156 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/community/common/common.mako" import="*" /> -<%namespace file="/webapps/community/repository/common.mako" import="*" /> - -<% - from galaxy.web.framework.helpers import time_ago - is_admin = trans.user_is_admin() - is_new = repository.is_new( trans.app ) - can_contact_owner = trans.user and trans.user != repository.user - can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository ) - can_upload = can_push and ( not repository.deprecated ) - can_download = not is_new and ( not is_malicious or can_push ) - can_browse_contents = not is_new - can_rate = trans.user and repository.user != trans.user - can_manage = is_admin or repository.user == trans.user - can_view_change_log = not is_new - has_readme = metadata and 'readme' in metadata -%> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/community/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "jquery.rating", "dynatree_skin/ui.dynatree" )} - <style type="text/css"> - ul.fileBrowser, - ul.toolFile { - margin-left: 0; - padding-left: 0; - list-style: none; - } - ul.fileBrowser { - margin-left: 20px; - } - .fileBrowser li, - .toolFile li { - padding-left: 20px; - background-repeat: no-repeat; - background-position: 0; - min-height: 20px; - } - .toolFile li { - background-image: url( ${h.url_for( '/static/images/silk/page_white_compressed.png' )} ); - } - .fileBrowser li { - background-image: url( ${h.url_for( '/static/images/silk/page_white.png' )} ); - } - </style> -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js( "libs/jquery/jquery.rating", "libs/jquery/jquery-ui", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )} - ${common_javascripts(repository)} -</%def> - -<br/><br/> -<ul class="manage-table-actions"> - %if is_new: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> - %else: - <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> - <div popupmenu="repository-${repository.id}-popup"> - %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">Manage repository</a> - %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a> - %endif - %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> - %endif - %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> - %endif - %if can_rate: - <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> - %endif - %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='zip' )}">Download as a zip file</a> - %endif - </div> - %endif -</ul> - -%if message: - ${render_msg( message, status )} -%endif - -%if can_browse_contents: - <div class="toolForm"> - <div class="toolFormTitle">Browse ${repository.name | h} revision ${repository.tip( trans.app ) | h} (repository tip)</div> - %if can_download: - <div class="form-row"> - <label>Clone this repository:</label> - ${render_clone_str( repository )} - </div> - %endif - %if can_push: - <form name="select_files_to_delete" id="select_files_to_delete" action="${h.url_for( controller='repository', action='select_files_to_delete', id=trans.security.encode_id( repository.id ))}" method="post" > - <div class="form-row" > - <label>Contents:</label> - <div id="tree" > - Loading... - </div> - <div class="toolParamHelp" style="clear: both;"> - Click on a file to display it's contents below. You may delete files from the repository by clicking the check box next to each file and clicking the <b>Delete selected files</b> button. - </div> - <input id="selected_files_to_delete" name="selected_files_to_delete" type="hidden" value=""/> - </div> - <div class="form-row"> - <label>Message:</label> - <div class="form-row-input"> - %if commit_message: - <textarea name="commit_message" rows="3" cols="35">${commit_message | h}</textarea> - %else: - <textarea name="commit_message" rows="3" cols="35"></textarea> - %endif - </div> - <div class="toolParamHelp" style="clear: both;"> - This is the commit message for the mercurial change set that will be created if you delete selected files. - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="select_files_to_delete_button" value="Delete selected files"/> - </div> - <div class="form-row"> - <div id="file_contents" class="toolParamHelp" style="clear: both;background-color:#FAFAFA;"></div> - </div> - </form> - %else: - <div class="toolFormBody"> - <div class="form-row" > - <label>Contents:</label> - <div id="tree" > - Loading... - </div> - </div> - <div class="form-row"> - <div id="file_contents" class="toolParamHelp" style="clear: both;background-color:#FAFAFA;"></div> - </div> - </div> - %endif - </div> - <p/> -%endif 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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commit/galaxy-central: inithello: Added name attribute to MigrateToolsApplication to generate a correct metadata dict for migrated tools.
by commits-noreply＠bitbucket.org 26 Feb '13

26 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ddfdfd2fce3e/ changeset: ddfdfd2fce3e user: inithello date: 2013-02-26 22:59:17 summary: Added name attribute to MigrateToolsApplication to generate a correct metadata dict for migrated tools. affected #: 1 file diff -r b9a7f2ae70a830e7ad5ef2a4c7e24f43d4575fa1 -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 lib/tool_shed/galaxy_install/migrate/common.py --- a/lib/tool_shed/galaxy_install/migrate/common.py +++ b/lib/tool_shed/galaxy_install/migrate/common.py @@ -14,6 +14,7 @@ def __init__( self, tools_migration_config ): install_dependencies = 'install_dependencies' in sys.argv galaxy_config_file = 'universe_wsgi.ini' + self.name = 'galaxy' if '-c' in sys.argv: pos = sys.argv.index( '-c' ) sys.argv.pop( pos ) 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: jgoecks: Add missing import.
by commits-noreply＠bitbucket.org 26 Feb '13

26 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b9a7f2ae70a8/ changeset: b9a7f2ae70a8 user: jgoecks date: 2013-02-26 22:42:11 summary: Add missing import. affected #: 1 file diff -r 5d71d6193bbaf758ae901de19a601bce6c34aeca -r b9a7f2ae70a830e7ad5ef2a4c7e24f43d4575fa1 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -6,6 +6,7 @@ from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesVisualizationMixin from galaxy.web.framework.helpers import time_ago, grids from galaxy import util +from galaxy.datatypes.interval import Bed from galaxy.util.json import from_json_string from galaxy.util.sanitize_html import sanitize_html from galaxy.visualization.genomes import decode_dbkey 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: Force absolute imprts in Galaxy's app.
by commits-noreply＠bitbucket.org 26 Feb '13

26 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5d71d6193bba/ changeset: 5d71d6193bba user: greg date: 2013-02-26 22:33:57 summary: Force absolute imprts in Galaxy's app. affected #: 1 file diff -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e -r 5d71d6193bbaf758ae901de19a601bce6c34aeca lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -1,3 +1,4 @@ +from __future__ import absolute_import import sys, os, atexit from galaxy import config, jobs, util, tools, web @@ -151,10 +152,10 @@ self.memdump = memdump.Memdump() # Transfer manager client if self.config.get_bool( 'enable_beta_job_managers', False ): - from jobs import transfer_manager + from galaxy.jobs import transfer_manager self.transfer_manager = transfer_manager.TransferManager( self ) # Start the job manager - from jobs import manager + from galaxy.jobs import manager self.job_manager = manager.JobManager( self ) # FIXME: These are exposed directly for backward compatibility self.job_queue = self.job_manager.job_queue 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: Move ~/lib/galaxy/tool_shed to ~/lib/tool_shed, and move the ~/lib/galaxy/util/shed_util componets to ~/lib/tool_shed/util.
by commits-noreply＠bitbucket.org 26 Feb '13

26 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6f0050c4e06e/ changeset: 6f0050c4e06e user: greg date: 2013-02-26 21:52:51 summary: Move ~/lib/galaxy/tool_shed to ~/lib/tool_shed, and move the ~/lib/galaxy/util/shed_util componets to ~/lib/tool_shed/util. affected #: 77 files diff -r e9e09d1ab51752db592eee71032ec5fc33f6ee57 -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -3,8 +3,8 @@ from galaxy import config, jobs, util, tools, web import galaxy.tools.search import galaxy.tools.data -import galaxy.tool_shed -import galaxy.tool_shed.tool_shed_registry +import tool_shed.galaxy_install +import tool_shed.tool_shed_registry from galaxy.web import security import galaxy.model import galaxy.datatypes.registry @@ -41,7 +41,7 @@ db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database # Set up the tool sheds registry if os.path.isfile( self.config.tool_sheds_config ): - self.tool_shed_registry = galaxy.tool_shed.tool_shed_registry.Registry( self.config.root, self.config.tool_sheds_config ) + self.tool_shed_registry = tool_shed.tool_shed_registry.Registry( self.config.root, self.config.tool_sheds_config ) else: self.tool_shed_registry = None log.debug( 'self.config.tool_sheds_config: %s, self.tool_shed_registry: %s', @@ -51,7 +51,7 @@ from galaxy.model.migrate.check import create_or_verify_database create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self ) # Alert the Galaxy admin to tools that have been moved from the distribution to the tool shed. - from galaxy.tool_shed.migrate.check import verify_tools + from tool_shed.galaxy_install.migrate.check import verify_tools verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) # Object store manager self.object_store = build_object_store_from_config(self.config) @@ -64,7 +64,7 @@ object_store = self.object_store, trace_logger=self.trace_logger ) # Manage installed tool shed repositories. - self.installed_repository_manager = galaxy.tool_shed.InstalledRepositoryManager( self ) + self.installed_repository_manager = tool_shed.galaxy_install.InstalledRepositoryManager( self ) # Create an empty datatypes registry. self.datatypes_registry = galaxy.datatypes.registry.Registry() # Load proprietary datatypes defined in datatypes_conf.xml files in all installed tool shed repositories. We @@ -105,7 +105,7 @@ self.data_managers = DataManagers( self ) # If enabled, poll respective tool sheds to see if updates are available for any installed tool shed repositories. if self.config.get_bool( 'enable_tool_shed_check', False ): - from tool_shed import update_manager + from tool_shed.galaxy_install import update_manager self.update_manager = update_manager.UpdateManager( self ) # Load proprietary datatype converters and display applications. self.installed_repository_manager.load_proprietary_converters_and_display_applications() diff -r e9e09d1ab51752db592eee71032ec5fc33f6ee57 -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3031,6 +3031,10 @@ pass class ToolShedRepository( object ): + api_collection_visible_keys = ( 'id', 'name', 'tool_shed', 'owner', 'installed_changeset_revision', 'changeset_revision', 'ctx_rev', 'includes_datatypes', + 'update_available', 'deleted', 'uninstalled', 'dist_to_shed', 'status', 'error_message' ) + api_element_visible_keys = ( 'id', 'name', 'tool_shed', 'owner', 'installed_changeset_revision', 'changeset_revision', 'ctx_rev', 'includes_datatypes', + 'update_available', 'deleted', 'uninstalled', 'dist_to_shed', 'status', 'error_message' ) installation_status = Bunch( NEW='New', CLONING='Cloning', SETTING_TOOL_VERSIONS='Setting tool versions', @@ -3066,6 +3070,10 @@ self.dist_to_shed = dist_to_shed self.status = status self.error_message = error_message + def as_dict( self, trans ): + tsr_dict = self.get_api_value( view='element' ) + tsr_dict[ 'id' ] = trans.security.encode_id( self.id ) + return tsr_dict def repo_files_directory( self, app ): repo_path = self.repo_path( app ) if repo_path: @@ -3153,6 +3161,22 @@ if self.shed_config_filename == shed_tool_conf_dict[ 'config_filename' ]: return shed_tool_conf_dict return default + def get_api_value( self, view='collection', value_mapper=None ): + if value_mapper is None: + value_mapper = {} + rval = {} + try: + visible_keys = self.__getattribute__( 'api_' + view + '_visible_keys' ) + except AttributeError: + raise Exception( 'Unknown API view: %s' % view ) + for key in visible_keys: + try: + rval[ key ] = self.__getattribute__( key ) + if key in value_mapper: + rval[ key ] = value_mapper.get( key )( rval[ key ] ) + except AttributeError: + rval[ key ] = None + return rval @property def can_install( self ): return self.status == self.installation_status.NEW diff -r e9e09d1ab51752db592eee71032ec5fc33f6ee57 -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py @@ -0,0 +1,44 @@ +""" +Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +def upgrade(): + print __doc__ + + metadata.reflect() + # Create the table. + try: + cmd = "UPDATE migrate_tools set repository_path='lib/galaxy/tool_shed/migrate';" + db_session.execute( cmd ) + except Exception, e: + log.debug( "Updating migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + try: + cmd = "UPDATE migrate_tools set repository_path='lib/galaxy/tool_shed/migrate';" + db_session.execute( cmd ) + except Exception, e: + log.debug( "Updating migrate_tools.repository_path column to point to the old location lib/galaxy/tool_shed/migrate failed: %s" % str( e ) ) diff -r e9e09d1ab51752db592eee71032ec5fc33f6ee57 -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e lib/galaxy/tool_shed/__init__.py --- a/lib/galaxy/tool_shed/__init__.py +++ /dev/null @@ -1,57 +0,0 @@ -""" -Classes encapsulating the management of repositories installed from Galaxy tool sheds. -""" -import os -import galaxy.util.shed_util -import galaxy.util.shed_util_common -from galaxy.model.orm import and_ - -from galaxy import eggs -import pkg_resources - -pkg_resources.require( 'elementtree' ) -from elementtree import ElementTree, ElementInclude - -class InstalledRepositoryManager( object ): - def __init__( self, app ): - self.app = app - self.model = self.app.model - self.sa_session = self.model.context.current - self.tool_configs = self.app.config.tool_configs - if self.app.config.migrated_tools_config not in self.tool_configs: - self.tool_configs.append( self.app.config.migrated_tools_config ) - self.installed_repository_dicts = [] - def get_repository_install_dir( self, tool_shed_repository ): - for tool_config in self.tool_configs: - tree = ElementTree.parse( tool_config ) - root = tree.getroot() - ElementInclude.include( root ) - tool_path = root.get( 'tool_path', None ) - if tool_path: - tool_shed = galaxy.util.shed_util_common.clean_tool_shed_url( tool_shed_repository.tool_shed ) - relative_path = os.path.join( tool_path, - tool_shed, - 'repos', - tool_shed_repository.owner, - tool_shed_repository.name, - tool_shed_repository.installed_changeset_revision ) - if os.path.exists( relative_path ): - return relative_path - return None - def load_proprietary_datatypes( self ): - for tool_shed_repository in self.sa_session.query( self.model.ToolShedRepository ) \ - .filter( and_( self.model.ToolShedRepository.table.c.includes_datatypes==True, - self.model.ToolShedRepository.table.c.deleted==False ) ) \ - .order_by( self.model.ToolShedRepository.table.c.id ): - relative_install_dir = self.get_repository_install_dir( tool_shed_repository ) - if relative_install_dir: - installed_repository_dict = galaxy.util.shed_util.load_installed_datatypes( self.app, tool_shed_repository, relative_install_dir ) - if installed_repository_dict: - self.installed_repository_dicts.append( installed_repository_dict ) - def load_proprietary_converters_and_display_applications( self, deactivate=False ): - for installed_repository_dict in self.installed_repository_dicts: - if installed_repository_dict[ 'converter_path' ]: - galaxy.util.shed_util.load_installed_datatype_converters( self.app, installed_repository_dict, deactivate=deactivate ) - if installed_repository_dict[ 'display_path' ]: - galaxy.util.shed_util.load_installed_display_applications( self.app, installed_repository_dict, deactivate=deactivate ) - diff -r e9e09d1ab51752db592eee71032ec5fc33f6ee57 -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e lib/galaxy/tool_shed/common_util.py --- a/lib/galaxy/tool_shed/common_util.py +++ /dev/null @@ -1,93 +0,0 @@ -import os, urllib2 -from galaxy import util -from galaxy.util.odict import odict -from galaxy.tool_shed import encoding_util - -REPOSITORY_OWNER = 'devteam' - -def check_for_missing_tools( app, tool_panel_configs, latest_tool_migration_script_number ): - # Get the 000x_tools.xml file associated with the current migrate_tools version number. - tools_xml_file_path = os.path.abspath( os.path.join( 'scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number ) ) - # Parse the XML and load the file attributes for later checking against the proprietary tool_panel_config. - migrated_tool_configs_dict = odict() - tree = util.parse_xml( tools_xml_file_path ) - root = tree.getroot() - tool_shed = root.get( 'name' ) - tool_shed_url = get_tool_shed_url_from_tools_xml_file_path( app, tool_shed ) - # The default behavior is that the tool shed is down. - tool_shed_accessible = False - if tool_shed_url: - for elem in root: - if elem.tag == 'repository': - tool_dependencies = [] - tool_dependencies_dict = {} - repository_name = elem.get( 'name' ) - changeset_revision = elem.get( 'changeset_revision' ) - url = '%s/repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s&from_install_manager=True' % \ - ( tool_shed_url, repository_name, REPOSITORY_OWNER, changeset_revision ) - try: - response = urllib2.urlopen( url ) - text = response.read() - response.close() - tool_shed_accessible = True - except Exception, e: - # Tool shed may be unavailable - we have to set tool_shed_accessible since we're looping. - tool_shed_accessible = False - print "The URL\n%s\nraised the exception:\n%s\n" % ( url, str( e ) ) - if tool_shed_accessible: - if text: - tool_dependencies_dict = encoding_util.tool_shed_decode( text ) - for dependency_key, requirements_dict in tool_dependencies_dict.items(): - tool_dependency_name = requirements_dict[ 'name' ] - tool_dependency_version = requirements_dict[ 'version' ] - tool_dependency_type = requirements_dict[ 'type' ] - tool_dependency_readme = requirements_dict.get( 'readme', '' ) - tool_dependencies.append( ( tool_dependency_name, tool_dependency_version, tool_dependency_type, tool_dependency_readme ) ) - for tool_elem in elem.findall( 'tool' ): - migrated_tool_configs_dict[ tool_elem.get( 'file' ) ] = tool_dependencies - if tool_shed_accessible: - # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names. - missing_tool_configs_dict = odict() - for tool_panel_config in tool_panel_configs: - tree = util.parse_xml( tool_panel_config ) - root = tree.getroot() - for elem in root: - if elem.tag == 'tool': - missing_tool_configs_dict = check_tool_tag_set( elem, migrated_tool_configs_dict, missing_tool_configs_dict ) - elif elem.tag == 'section': - for section_elem in elem: - if section_elem.tag == 'tool': - missing_tool_configs_dict = check_tool_tag_set( section_elem, migrated_tool_configs_dict, missing_tool_configs_dict ) - else: - exception_msg = '\n\nThe entry for the main Galaxy tool shed at %s is missing from the %s file. ' % ( tool_shed, app.config.tool_sheds_config ) - exception_msg += 'The entry for this tool shed must always be available in this file, so re-add it before attempting to start your Galaxy server.\n' - raise Exception( exception_msg ) - return tool_shed_accessible, missing_tool_configs_dict -def check_tool_tag_set( elem, migrated_tool_configs_dict, missing_tool_configs_dict ): - file_path = elem.get( 'file', None ) - if file_path: - path, name = os.path.split( file_path ) - if name in migrated_tool_configs_dict: - tool_dependencies = migrated_tool_configs_dict[ name ] - missing_tool_configs_dict[ name ] = tool_dependencies - return missing_tool_configs_dict -def get_non_shed_tool_panel_configs( app ): - # Get the non-shed related tool panel configs - there can be more than one, and the default is tool_conf.xml. - config_filenames = [] - for config_filename in app.config.tool_configs: - # Any config file that includes a tool_path attribute in the root tag set like the following is shed-related. - # <toolbox tool_path="../shed_tools"> - tree = util.parse_xml( config_filename ) - root = tree.getroot() - tool_path = root.get( 'tool_path', None ) - if tool_path is None: - config_filenames.append( config_filename ) - return config_filenames -def get_tool_shed_url_from_tools_xml_file_path( app, tool_shed ): - search_str = '://%s' % tool_shed - for shed_name, shed_url in app.tool_shed_registry.tool_sheds.items(): - if shed_url.find( search_str ) >= 0: - if shed_url.endswith( '/' ): - shed_url = shed_url.rstrip( '/' ) - return shed_url - return None diff -r e9e09d1ab51752db592eee71032ec5fc33f6ee57 -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e lib/galaxy/tool_shed/encoding_util.py --- a/lib/galaxy/tool_shed/encoding_util.py +++ /dev/null @@ -1,44 +0,0 @@ -import binascii, logging -from galaxy.util.hash_util import hmac_new -from galaxy.util.json import json_fix - -from galaxy import eggs -import pkg_resources - -pkg_resources.require( "simplejson" ) -import simplejson - -log = logging.getLogger( __name__ ) - -encoding_sep = '__esep__' -encoding_sep2 = '__esepii__' - -def tool_shed_decode( value ): - # Extract and verify hash - a, b = value.split( ":" ) - value = binascii.unhexlify( b ) - test = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) - assert a == test - # Restore from string - values = None - try: - values = simplejson.loads( value ) - except Exception, e: - log.debug( "Decoding json value from tool shed for value '%s' threw exception: %s" % ( str( value ), str( e ) ) ) - if values is not None: - try: - return json_fix( values ) - except Exception, e: - log.debug( "Fixing decoded json values '%s' from tool shed threw exception: %s" % ( str( values ), str( e ) ) ) - fixed_values = values - if values is None: - values = value - return values -def tool_shed_encode( val ): - if isinstance( val, dict ): - value = simplejson.dumps( val ) - else: - value = val - a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) - b = binascii.hexlify( value ) - return "%s:%s" % ( a, b ) \ No newline at end of file diff -r e9e09d1ab51752db592eee71032ec5fc33f6ee57 -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ /dev/null @@ -1,372 +0,0 @@ -""" -Manage automatic installation of tools configured in the xxx.xml files in ~/scripts/migrate_tools (e.g., 0002_tools.xml). -All of the tools were at some point included in the Galaxy distribution, but are now hosted in the main Galaxy tool shed. -""" -import os, urllib2, tempfile -from galaxy import util -from galaxy.tools import ToolSection -from galaxy.util.json import from_json_string, to_json_string -import galaxy.util.shed_util as shed_util -import galaxy.util.shed_util_common as suc -from galaxy.util.odict import odict -from galaxy.tool_shed import common_util - -class InstallManager( object ): - def __init__( self, app, latest_migration_script_number, tool_shed_install_config, migrated_tools_config, install_dependencies ): - """ - Check tool settings in tool_shed_install_config and install all repositories that are not already installed. The tool - panel configuration file is the received migrated_tools_config, which is the reserved file named migrated_tools_conf.xml. - """ - self.app = app - self.toolbox = self.app.toolbox - self.migrated_tools_config = migrated_tools_config - # If install_dependencies is True but tool_dependency_dir is not set, do not attempt to install but print informative error message. - if install_dependencies and app.config.tool_dependency_dir is None: - message = 'You are attempting to install tool dependencies but do not have a value for "tool_dependency_dir" set in your universe_wsgi.ini ' - message += 'file. Set this location value to the path where you want tool dependencies installed and rerun the migration script.' - raise Exception( message ) - # Get the local non-shed related tool panel configs (there can be more than one, and the default name is tool_conf.xml). - self.proprietary_tool_confs = self.non_shed_tool_panel_configs - self.proprietary_tool_panel_elems = self.get_proprietary_tool_panel_elems( latest_migration_script_number ) - # Set the location where the repositories will be installed by retrieving the tool_path setting from migrated_tools_config. - tree = util.parse_xml( migrated_tools_config ) - root = tree.getroot() - self.tool_path = root.get( 'tool_path' ) - print "Repositories will be installed into configured tool_path location ", str( self.tool_path ) - # Parse tool_shed_install_config to check each of the tools. - self.tool_shed_install_config = tool_shed_install_config - tree = util.parse_xml( tool_shed_install_config ) - root = tree.getroot() - self.tool_shed = suc.clean_tool_shed_url( root.get( 'name' ) ) - self.repository_owner = common_util.REPOSITORY_OWNER - index, self.shed_config_dict = suc.get_shed_tool_conf_dict( app, self.migrated_tools_config ) - # Since tool migration scripts can be executed any number of times, we need to make sure the appropriate tools are defined in - # tool_conf.xml. If no tools associated with the migration stage are defined, no repositories will be installed on disk. - # The default behavior is that the tool shed is down. - tool_shed_accessible = False - tool_panel_configs = common_util.get_non_shed_tool_panel_configs( app ) - if tool_panel_configs: - # The missing_tool_configs_dict contents are something like: - # {'emboss_antigenic.xml': [('emboss', '5.0.0', 'package', '\nreadme blah blah blah\n')]} - tool_shed_accessible, missing_tool_configs_dict = common_util.check_for_missing_tools( app, tool_panel_configs, latest_migration_script_number ) - else: - # It doesn't matter if the tool shed is accessible since there are no migrated tools defined in the local Galaxy instance, but - # we have to set the value of tool_shed_accessible to True so that the value of migrate_tools.version can be correctly set in - # the database. - tool_shed_accessible = True - missing_tool_configs_dict = odict() - if tool_shed_accessible: - if len( self.proprietary_tool_confs ) == 1: - plural = '' - file_names = self.proprietary_tool_confs[ 0 ] - else: - plural = 's' - file_names = ', '.join( self.proprietary_tool_confs ) - if missing_tool_configs_dict: - for repository_elem in root: - self.install_repository( repository_elem, install_dependencies ) - else: - message = "\nNo tools associated with migration stage %s are defined in your " % str( latest_migration_script_number ) - message += "file%s named %s,\nso no repositories will be installed on disk.\n" % ( plural, file_names ) - print message - else: - message = "\nThe main Galaxy tool shed is not currently available, so skipped migration stage %s.\n" % str( latest_migration_script_number ) - message += "Try again later.\n" - print message - def get_guid( self, repository_clone_url, relative_install_dir, tool_config ): - if self.shed_config_dict.get( 'tool_path' ): - relative_install_dir = os.path.join( self.shed_config_dict['tool_path'], relative_install_dir ) - found = False - for root, dirs, files in os.walk( relative_install_dir ): - if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: - if '.hg' in dirs: - dirs.remove( '.hg' ) - for name in files: - if name == tool_config: - found = True - break - if found: - break - full_path = str( os.path.abspath( os.path.join( root, name ) ) ) - tool = self.toolbox.load_tool( full_path ) - return suc.generate_tool_guid( repository_clone_url, tool ) - def get_proprietary_tool_panel_elems( self, latest_tool_migration_script_number ): - # Parse each config in self.proprietary_tool_confs (the default is tool_conf.xml) and generate a list of Elements that are - # either ToolSection elements or Tool elements. These will be used to generate new entries in the migrated_tools_conf.xml - # file for the installed tools. - tools_xml_file_path = os.path.abspath( os.path.join( 'scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number ) ) - # Parse the XML and load the file attributes for later checking against the integrated elements from self.proprietary_tool_confs. - migrated_tool_configs = [] - tree = util.parse_xml( tools_xml_file_path ) - root = tree.getroot() - for elem in root: - if elem.tag == 'repository': - for tool_elem in elem: - migrated_tool_configs.append( tool_elem.get( 'file' ) ) - # Parse each file in self.proprietary_tool_confs and generate the integrated list of tool panel Elements that contain them. - tool_panel_elems = [] - for proprietary_tool_conf in self.proprietary_tool_confs: - tree = util.parse_xml( proprietary_tool_conf ) - root = tree.getroot() - for elem in root: - if elem.tag == 'tool': - # Tools outside of sections. - file_path = elem.get( 'file', None ) - if file_path: - name = suc.strip_path( file_path ) - if name in migrated_tool_configs: - if elem not in tool_panel_elems: - tool_panel_elems.append( elem ) - elif elem.tag == 'section': - # Tools contained in a section. - for section_elem in elem: - if section_elem.tag == 'tool': - file_path = section_elem.get( 'file', None ) - if file_path: - name = suc.strip_path( file_path ) - if name in migrated_tool_configs: - # Append the section, not the tool. - if elem not in tool_panel_elems: - tool_panel_elems.append( elem ) - return tool_panel_elems - def get_containing_tool_sections( self, tool_config ): - """ - If tool_config is defined somewhere in self.proprietary_tool_panel_elems, return True and a list of ToolSections in which the - tool is displayed. If the tool is displayed outside of any sections, None is appended to the list. - """ - tool_sections = [] - is_displayed = False - for proprietary_tool_panel_elem in self.proprietary_tool_panel_elems: - if proprietary_tool_panel_elem.tag == 'tool': - # The proprietary_tool_panel_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />. - proprietary_tool_config = proprietary_tool_panel_elem.get( 'file' ) - proprietary_name = suc.strip_path( proprietary_tool_config ) - if tool_config == proprietary_name: - # The tool is loaded outside of any sections. - tool_sections.append( None ) - if not is_displayed: - is_displayed = True - if proprietary_tool_panel_elem.tag == 'section': - # The proprietary_tool_panel_elem looks something like <section name="EMBOSS" id="EMBOSSLite">. - for section_elem in proprietary_tool_panel_elem: - if section_elem.tag == 'tool': - # The section_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />. - proprietary_tool_config = section_elem.get( 'file' ) - proprietary_name = suc.strip_path( proprietary_tool_config ) - if tool_config == proprietary_name: - # The tool is loaded inside of the section_elem. - tool_sections.append( ToolSection( proprietary_tool_panel_elem ) ) - if not is_displayed: - is_displayed = True - return is_displayed, tool_sections - def handle_repository_contents( self, tool_shed_repository, repository_clone_url, relative_install_dir, repository_elem, install_dependencies ): - """Generate the metadata for the installed tool shed repository, among other things.""" - tool_panel_dict_for_display = odict() - if self.tool_path: - repo_install_dir = os.path.join( self.tool_path, relative_install_dir ) - else: - repo_install_dir = relative_install_dir - for tool_elem in repository_elem: - # The tool_elem looks something like this: <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /> - tool_config = tool_elem.get( 'file' ) - guid = self.get_guid( repository_clone_url, relative_install_dir, tool_config ) - # See if tool_config is defined inside of a section in self.proprietary_tool_panel_elems. - is_displayed, tool_sections = self.get_containing_tool_sections( tool_config ) - if is_displayed: - tool_panel_dict_for_tool_config = shed_util.generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections ) - for k, v in tool_panel_dict_for_tool_config.items(): - tool_panel_dict_for_display[ k ] = v - else: - print 'The tool "%s" (%s) has not been enabled because it is not defined in a proprietary tool config (%s).' \ - % ( guid, tool_config, ", ".join( self.proprietary_tool_confs or [] ) ) - metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=self.app, - repository=tool_shed_repository, - changeset_revision=tool_shed_repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = self.shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=True ) - tool_shed_repository.metadata = metadata_dict - self.app.sa_session.add( tool_shed_repository ) - self.app.sa_session.flush() - if 'tool_dependencies' in metadata_dict: - # All tool_dependency objects must be created before the tools are processed even if no tool dependencies will be installed. - tool_dependencies = shed_util.create_tool_dependency_objects( self.app, tool_shed_repository, relative_install_dir, set_status=True ) - else: - tool_dependencies = None - if 'tools' in metadata_dict: - sample_files = metadata_dict.get( 'sample_files', [] ) - sample_files = [ str( s ) for s in sample_files ] - tool_index_sample_files = shed_util.get_tool_index_sample_files( sample_files ) - shed_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=self.tool_path ) - sample_files_copied = [ s for s in tool_index_sample_files ] - repository_tools_tups = suc.get_repository_tools_tups( self.app, metadata_dict ) - if repository_tools_tups: - # Handle missing data table entries for tool parameters that are dynamically generated select lists. - repository_tools_tups = shed_util.handle_missing_data_table_entry( self.app, relative_install_dir, self.tool_path, repository_tools_tups ) - # Handle missing index files for tool parameters that are dynamically generated select lists. - repository_tools_tups, sample_files_copied = shed_util.handle_missing_index_file( self.app, - self.tool_path, - sample_files, - repository_tools_tups, - sample_files_copied ) - # Copy remaining sample files included in the repository to the ~/tool-data directory of the local Galaxy instance. - shed_util.copy_sample_files( self.app, sample_files, tool_path=self.tool_path, sample_files_copied=sample_files_copied ) - if install_dependencies and tool_dependencies and 'tool_dependencies' in metadata_dict: - # Install tool dependencies. - shed_util.update_tool_shed_repository_status( self.app, - tool_shed_repository, - self.app.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) - # Get the tool_dependencies.xml file from disk. - tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', repo_install_dir ) - installed_tool_dependencies = shed_util.handle_tool_dependencies( app=self.app, - tool_shed_repository=tool_shed_repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=tool_dependencies ) - for installed_tool_dependency in installed_tool_dependencies: - if installed_tool_dependency.status == self.app.model.ToolDependency.installation_status.ERROR: - print '\nThe following error occurred from the InstallManager while installing tool dependency ', installed_tool_dependency.name, ':' - print installed_tool_dependency.error_message, '\n\n' - shed_util.add_to_tool_panel( self.app, - tool_shed_repository.name, - repository_clone_url, - tool_shed_repository.installed_changeset_revision, - repository_tools_tups, - self.repository_owner, - self.migrated_tools_config, - tool_panel_dict=tool_panel_dict_for_display, - new_install=True ) - if 'datatypes' in metadata_dict: - tool_shed_repository.status = self.app.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES - if not tool_shed_repository.includes_datatypes: - tool_shed_repository.includes_datatypes = True - self.app.sa_session.add( tool_shed_repository ) - self.app.sa_session.flush() - work_dir = tempfile.mkdtemp() - datatypes_config = suc.get_config_from_disk( 'datatypes_conf.xml', repo_install_dir ) - # Load proprietary data types required by tools. The value of override is not important here since the Galaxy server will be started - # after this installation completes. - converter_path, display_path = shed_util.alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, repo_install_dir, override=False ) #repo_install_dir was relative_install_dir - if converter_path or display_path: - # Create a dictionary of tool shed repository related information. - repository_dict = shed_util.create_repository_dict_for_proprietary_datatypes( tool_shed=self.tool_shed, - name=tool_shed_repository.name, - owner=self.repository_owner, - installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), - converter_path=converter_path, - display_path=display_path ) - if converter_path: - # Load proprietary datatype converters - self.app.datatypes_registry.load_datatype_converters( self.toolbox, installed_repository_dict=repository_dict ) - if display_path: - # Load proprietary datatype display applications - self.app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict ) - try: - shutil.rmtree( work_dir ) - except: - pass - def install_repository( self, repository_elem, install_dependencies ): - # Install a single repository, loading contained tools into the tool panel. - name = repository_elem.get( 'name' ) - description = repository_elem.get( 'description' ) - installed_changeset_revision = repository_elem.get( 'changeset_revision' ) - # Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision> - relative_clone_dir = os.path.join( self.tool_shed, 'repos', self.repository_owner, name, installed_changeset_revision ) - clone_dir = os.path.join( self.tool_path, relative_clone_dir ) - if self.__isinstalled( clone_dir ): - print "Skipping automatic install of repository '", name, "' because it has already been installed in location ", clone_dir - else: - tool_shed_url = self.__get_url_from_tool_shed( self.tool_shed ) - repository_clone_url = os.path.join( tool_shed_url, 'repos', self.repository_owner, name ) - relative_install_dir = os.path.join( relative_clone_dir, name ) - install_dir = os.path.join( clone_dir, name ) - ctx_rev = suc.get_ctx_rev( tool_shed_url, name, self.repository_owner, installed_changeset_revision ) - tool_shed_repository = suc.create_or_update_tool_shed_repository( app=self.app, - name=name, - description=description, - installed_changeset_revision=installed_changeset_revision, - ctx_rev=ctx_rev, - repository_clone_url=repository_clone_url, - metadata_dict={}, - status=self.app.model.ToolShedRepository.installation_status.NEW, - current_changeset_revision=None, - owner=self.repository_owner, - dist_to_shed=True ) - shed_util.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.CLONING ) - cloned_ok, error_message = suc.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev ) - if cloned_ok: - self.handle_repository_contents( tool_shed_repository=tool_shed_repository, - repository_clone_url=repository_clone_url, - relative_install_dir=relative_install_dir, - repository_elem=repository_elem, - install_dependencies=install_dependencies ) - self.app.sa_session.refresh( tool_shed_repository ) - metadata_dict = tool_shed_repository.metadata - if 'tools' in metadata_dict: - shed_util.update_tool_shed_repository_status( self.app, - tool_shed_repository, - self.app.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) - # Get the tool_versions from the tool shed for each tool in the installed change set. - url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \ - ( tool_shed_url, tool_shed_repository.name, self.repository_owner, installed_changeset_revision ) - response = urllib2.urlopen( url ) - text = response.read() - response.close() - if text: - tool_version_dicts = from_json_string( text ) - shed_util.handle_tool_versions( self.app, tool_version_dicts, tool_shed_repository ) - else: - # Set the tool versions since they seem to be missing for this repository in the tool shed. - # CRITICAL NOTE: These default settings may not properly handle all parent/child associations. - for tool_dict in metadata_dict[ 'tools' ]: - flush_needed = False - tool_id = tool_dict[ 'guid' ] - old_tool_id = tool_dict[ 'id' ] - tool_version = tool_dict[ 'version' ] - tool_version_using_old_id = shed_util.get_tool_version( self.app, old_tool_id ) - tool_version_using_guid = shed_util.get_tool_version( self.app, tool_id ) - if not tool_version_using_old_id: - tool_version_using_old_id = self.app.model.ToolVersion( tool_id=old_tool_id, - tool_shed_repository=tool_shed_repository ) - self.app.sa_session.add( tool_version_using_old_id ) - self.app.sa_session.flush() - if not tool_version_using_guid: - tool_version_using_guid = self.app.model.ToolVersion( tool_id=tool_id, - tool_shed_repository=tool_shed_repository ) - self.app.sa_session.add( tool_version_using_guid ) - self.app.sa_session.flush() - # Associate the two versions as parent / child. - tool_version_association = shed_util.get_tool_version_association( self.app, - tool_version_using_old_id, - tool_version_using_guid ) - if not tool_version_association: - tool_version_association = self.app.model.ToolVersionAssociation( tool_id=tool_version_using_guid.id, - parent_id=tool_version_using_old_id.id ) - self.app.sa_session.add( tool_version_association ) - self.app.sa_session.flush() - shed_util.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.INSTALLED ) - @property - def non_shed_tool_panel_configs( self ): - return common_util.get_non_shed_tool_panel_configs( self.app ) - def __get_url_from_tool_shed( self, tool_shed ): - # The value of tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is something like: - # http://toolshed.g2.bx.psu.edu/ - for shed_name, shed_url in self.app.tool_shed_registry.tool_sheds.items(): - if shed_url.find( tool_shed ) >= 0: - if shed_url.endswith( '/' ): - shed_url = shed_url.rstrip( '/' ) - return shed_url - # The tool shed from which the repository was originally installed must no longer be configured in tool_sheds_conf.xml. - return None - def __isinstalled( self, clone_dir ): - full_path = os.path.abspath( clone_dir ) - if os.path.exists( full_path ): - for root, dirs, files in os.walk( full_path ): - if '.hg' in dirs: - # Assume that the repository has been installed if we find a .hg directory. - return True - return False diff -r e9e09d1ab51752db592eee71032ec5fc33f6ee57 -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e lib/galaxy/tool_shed/migrate/check.py --- a/lib/galaxy/tool_shed/migrate/check.py +++ /dev/null @@ -1,171 +0,0 @@ -import sys, os, logging, subprocess -from galaxy import eggs -import pkg_resources -pkg_resources.require( "sqlalchemy-migrate" ) - -from migrate.versioning import repository, schema -from sqlalchemy import * -from galaxy.util.odict import odict -from galaxy.tool_shed import common_util - -log = logging.getLogger( __name__ ) - -# Path relative to galaxy -migrate_repository_directory = os.path.dirname( __file__ ).replace( os.getcwd() + os.path.sep, '', 1 ) -migrate_repository = repository.Repository( migrate_repository_directory ) -dialect_to_egg = { - "sqlite" : "pysqlite>=2", - "postgres" : "psycopg2", - "mysql" : "MySQL_python" -} - -def verify_tools( app, url, galaxy_config_file, engine_options={} ): - # Check the value in the migrate_tools.version database table column to verify that the number is in - # sync with the number of version scripts in ~/lib/galaxy/tools/migrate/versions. - dialect = ( url.split( ':', 1 ) )[0] - try: - egg = dialect_to_egg[ dialect ] - try: - pkg_resources.require( egg ) - log.debug( "%s egg successfully loaded for %s dialect" % ( egg, dialect ) ) - except: - # If the module is in the path elsewhere (i.e. non-egg), it'll still load. - log.warning( "%s egg not found, but an attempt will be made to use %s anyway" % ( egg, dialect ) ) - except KeyError: - # Let this go, it could possibly work with db's we don't support - log.error( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect ) - # Create engine and metadata - engine = create_engine( url, **engine_options ) - meta = MetaData( bind=engine ) - # The migrate_tools table was created in database version script 0092_add_migrate_tools_table.py. - version_table = Table( "migrate_tools", meta, autoload=True ) - # Verify that the code and the database are in sync. - db_schema = schema.ControlledSchema( engine, migrate_repository ) - latest_tool_migration_script_number = migrate_repository.versions.latest - if latest_tool_migration_script_number != db_schema.version: - # The default behavior is that the tool shed is down. - tool_shed_accessible = False - if app.new_installation: - # New installations will not be missing tools, so we don't need to worry about them. - missing_tool_configs_dict = odict() - else: - tool_panel_configs = common_util.get_non_shed_tool_panel_configs( app ) - if tool_panel_configs: - # The missing_tool_configs_dict contents are something like: - # {'emboss_antigenic.xml': [('emboss', '5.0.0', 'package', '\nreadme blah blah blah\n')]} - tool_shed_accessible, missing_tool_configs_dict = common_util.check_for_missing_tools( app, tool_panel_configs, latest_tool_migration_script_number ) - else: - # It doesn't matter if the tool shed is accessible since there are no migrated tools defined in the local Galaxy instance, but - # we have to set the value of tool_shed_accessible to True so that the value of migrate_tools.version can be correctly set in - # the database. - tool_shed_accessible = True - missing_tool_configs_dict = odict() - have_tool_dependencies = False - for k, v in missing_tool_configs_dict.items(): - if v: - have_tool_dependencies = True - break - config_arg = '' - if os.path.abspath( os.path.join( os.getcwd(), 'universe_wsgi.ini' ) ) != galaxy_config_file: - config_arg = ' -c %s' % galaxy_config_file.replace( os.path.abspath( os.getcwd() ), '.' ) - if not app.config.running_functional_tests: - if tool_shed_accessible: - # Automatically update the value of the migrate_tools.version database table column. - cmd = 'sh manage_tools.sh%s upgrade' % config_arg - proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT ) - return_code = proc.wait() - output = proc.stdout.read( 32768 ) - if return_code != 0: - raise Exception( "Error attempting to update the value of migrate_tools.version: %s" % output ) - elif missing_tool_configs_dict: - if len( tool_panel_configs ) == 1: - plural = '' - tool_panel_config_file_names = tool_panel_configs[ 0 ] - else: - plural = 's' - tool_panel_config_file_names = ', '.join( tool_panel_configs ) - msg = "\n>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" - msg += "\n\nThe list of files at the end of this message refers to tools that are configured to load into the tool panel for\n" - msg += "this Galaxy instance, but have been removed from the Galaxy distribution. These tools and their dependencies can be\n" - msg += "automatically installed from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.\n\n" - msg += "To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this,\n" - msg += "be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should\n" - msg += "be removed from your file%s named %s.\n\n" % ( plural, tool_panel_config_file_names ) - msg += "CRITICAL NOTE IF YOU PLAN TO INSTALL\n" - msg += "The location in which the tool repositories will be installed is the value of the 'tool_path' attribute in the <tool>\n" - msg += 'tag of the file named ./migrated_tool_conf.xml (i.e., <toolbox tool_path="../shed_tools">). The default location\n' - msg += "setting is '../shed_tools', which may be problematic for some cluster environments, so make sure to change it before\n" - msg += "you execute the installation process if appropriate. The configured location must be outside of the Galaxy installation\n" - msg += "directory or it must be in a sub-directory protected by a properly configured .hgignore file if the directory is within\n" - msg += "the Galaxy installation directory hierarchy. This is because tool shed repositories will be installed using mercurial's\n" - msg += "clone feature, which creates .hg directories and associated mercurial repository files. Not having .hgignore properly\n" - msg += "configured could result in undesired behavior when modifying or updating your local Galaxy instance or the tool shed\n" - msg += "repositories if they are in directories that pose conflicts. See mercurial's .hgignore documentation at the following\n" - msg += "URL for details.\n\nhttp://mercurial.selenic.com/wiki/.hgignore\n\n" - if have_tool_dependencies: - msg += "The following tool dependencies can also optionally be installed (see the option flag in the command below). If you\n" - msg += "choose to install them (recommended), they will be installed within the location specified by the 'tool_dependency_dir'\n" - msg += "setting in your main Galaxy configuration file (e.g., uninverse_wsgi.ini).\n" - processed_tool_dependencies = [] - for missing_tool_config, tool_dependencies in missing_tool_configs_dict.items(): - for tool_dependencies_tup in tool_dependencies: - if tool_dependencies_tup not in processed_tool_dependencies: - msg += "------------------------------------\n" - msg += "Tool Dependency\n" - msg += "------------------------------------\n" - msg += "Name: %s, Version: %s, Type: %s\n" % ( tool_dependencies_tup[ 0 ], - tool_dependencies_tup[ 1 ], - tool_dependencies_tup[ 2 ] ) - if tool_dependencies_tup[ 3 ]: - msg += "Requirements and installation information:\n" - msg += "%s\n" % tool_dependencies_tup[ 3 ] - else: - msg += "\n" - msg += "------------------------------------\n" - processed_tool_dependencies.append( tool_dependencies_tup ) - msg += "\n" - msg += "%s" % output.replace( 'done', '' ) - msg += "vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv\n" - msg += "sh ./scripts/migrate_tools/%04d_tools.sh\n" % latest_tool_migration_script_number - msg += "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n" - if have_tool_dependencies: - msg += "The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies'\n" - msg += "option to the above command like this:\n\n" - msg += "vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv\n" - msg += "sh ./scripts/migrate_tools/%04d_tools.sh install_dependencies\n" % latest_tool_migration_script_number - msg += "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n" - msg += "Tool dependencies can be installed after the repositories have been installed as well.\n\n" - msg += "After the installation process finishes, you can start your Galaxy server. As part of this installation process,\n" - msg += "entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these\n" - msg += "tools will continue to be loaded into your tool panel. Because of this, existing entries for these files should be\n" - msg += "removed from your file%s named %s, but only after the installation process finishes.\n\n" % ( plural, tool_panel_config_file_names ) - for missing_tool_config, tool_dependencies in missing_tool_configs_dict.items(): - msg += "%s\n" % missing_tool_config - msg += "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n" - raise Exception( msg ) - else: - log.debug( "The main Galaxy tool shed is not currently available, so skipped tool migration %s until next server startup" % db_schema.version ) - else: - log.info( "At migrate_tools version %d" % db_schema.version ) - -def migrate_to_current_version( engine, schema ): - # Changes to get to current version. - changeset = schema.changeset( None ) - for ver, change in changeset: - nextver = ver + changeset.step - log.info( 'Installing tools from version %s -> %s... ' % ( ver, nextver ) ) - old_stdout = sys.stdout - class FakeStdout( object ): - def __init__( self ): - self.buffer = [] - def write( self, s ): - self.buffer.append( s ) - def flush( self ): - pass - sys.stdout = FakeStdout() - try: - schema.runchange( ver, change, changeset.step ) - finally: - for message in "".join( sys.stdout.buffer ).split( "\n" ): - log.info( message ) - sys.stdout = old_stdout diff -r e9e09d1ab51752db592eee71032ec5fc33f6ee57 -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e lib/galaxy/tool_shed/migrate/common.py --- a/lib/galaxy/tool_shed/migrate/common.py +++ /dev/null @@ -1,81 +0,0 @@ -import sys, os, ConfigParser -import galaxy.config -import galaxy.datatypes.registry -from galaxy import tools -from galaxy.tools.data import * -import galaxy.model.mapping -import galaxy.tools.search -from galaxy.objectstore import build_object_store_from_config -from galaxy.tool_shed.common_util import * -import galaxy.tool_shed.tool_shed_registry -from galaxy.tool_shed import install_manager - -class MigrateToolsApplication( object ): - """Encapsulates the state of a basic Galaxy Universe application in order to initiate the Install Manager""" - def __init__( self, tools_migration_config ): - install_dependencies = 'install_dependencies' in sys.argv - galaxy_config_file = 'universe_wsgi.ini' - if '-c' in sys.argv: - pos = sys.argv.index( '-c' ) - sys.argv.pop( pos ) - galaxy_config_file = sys.argv.pop( pos ) - if not os.path.exists( galaxy_config_file ): - print "Galaxy config file does not exist (hint: use '-c config.ini' for non-standard locations): %s" % galaxy_config_file - sys.exit( 1 ) - config_parser = ConfigParser.ConfigParser( { 'here':os.getcwd() } ) - config_parser.read( galaxy_config_file ) - galaxy_config_dict = {} - for key, value in config_parser.items( "app:main" ): - galaxy_config_dict[ key ] = value - self.config = galaxy.config.Configuration( **galaxy_config_dict ) - if not self.config.database_connection: - self.config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database - self.config.update_integrated_tool_panel = True - self.object_store = build_object_store_from_config( self.config ) - # Setup the database engine and ORM - self.model = galaxy.model.mapping.init( self.config.file_path, - self.config.database_connection, - engine_options={}, - create_tables=False, - object_store=self.object_store ) - # Create an empty datatypes registry. - self.datatypes_registry = galaxy.datatypes.registry.Registry() - # Load the data types in the Galaxy distribution, which are defined in self.config.datatypes_config. - self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) - # Initialize tool data tables using the config defined by self.config.tool_data_table_config_path. - self.tool_data_tables = ToolDataTableManager( tool_data_path=self.config.tool_data_path, - config_filename=self.config.tool_data_table_config_path ) - # Load additional entries defined by self.config.shed_tool_data_table_config into tool data tables. - self.tool_data_tables.load_from_config_file( config_filename=self.config.shed_tool_data_table_config, - tool_data_path=self.tool_data_tables.tool_data_path, - from_shed_config=True ) - # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file. - tool_configs = self.config.tool_configs - if self.config.migrated_tools_config not in tool_configs: - tool_configs.append( self.config.migrated_tools_config ) - self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) - # Search support for tools - self.toolbox_search = galaxy.tools.search.ToolBoxSearch( self.toolbox ) - # Set up the tool sheds registry. - if os.path.isfile( self.config.tool_sheds_config ): - self.tool_shed_registry = galaxy.tool_shed.tool_shed_registry.Registry( self.config.root, self.config.tool_sheds_config ) - else: - self.tool_shed_registry = None - # Get the latest tool migration script number to send to the Install manager. - latest_migration_script_number = int( tools_migration_config.split( '_' )[ 0 ] ) - # The value of migrated_tools_config is migrated_tools_conf.xml, and is reserved for containing only those tools that have been - # eliminated from the distribution and moved to the tool shed. A side-effect of instantiating the InstallManager is the automatic - # installation of all appropriate tool shed repositories. - self.install_manager = install_manager.InstallManager( app=self, - latest_migration_script_number=latest_migration_script_number, - tool_shed_install_config=os.path.join( self.config.root, - 'scripts', - 'migrate_tools', - tools_migration_config ), - migrated_tools_config=self.config.migrated_tools_config, - install_dependencies=install_dependencies ) - @property - def sa_session( self ): - return self.model.context.current - def shutdown( self ): - self.object_store.shutdown() diff -r e9e09d1ab51752db592eee71032ec5fc33f6ee57 -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e lib/galaxy/tool_shed/migrate/migrate.cfg --- a/lib/galaxy/tool_shed/migrate/migrate.cfg +++ /dev/null @@ -1,20 +0,0 @@ -[db_settings] -# Used to identify which repository this database is versioned under. -# You can use the name of your project. -repository_id=GalaxyTools - -# The name of the database table used to track the schema version. -# This name shouldn't already be used by your project. -# If this is changed once a database is under version control, you'll need to -# change the table name in each database too. -version_table=migrate_tools - -# When committing a change script, Migrate will attempt to generate the -# sql for all supported databases; normally, if one of them fails - probably -# because you don't have that database installed - it is ignored and the -# commit continues, perhaps ending successfully. -# Databases in this list MUST compile successfully during a commit, or the -# entire commit will fail. List the databases your application will actually -# be using to ensure your updates to that database work properly. -# This must be a list; example: ['postgres','sqlite'] -required_dbs=[] \ No newline at end of file diff -r e9e09d1ab51752db592eee71032ec5fc33f6ee57 -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e lib/galaxy/tool_shed/migrate/versions/0001_tools.py --- a/lib/galaxy/tool_shed/migrate/versions/0001_tools.py +++ /dev/null @@ -1,9 +0,0 @@ -""" -Initialize the version column of the migrate_tools database table to 1. No tool migrations are handled in this version. -""" -import sys - -def upgrade(): - print __doc__ -def downgrade(): - pass diff -r e9e09d1ab51752db592eee71032ec5fc33f6ee57 -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e lib/galaxy/tool_shed/migrate/versions/0002_tools.py --- a/lib/galaxy/tool_shed/migrate/versions/0002_tools.py +++ /dev/null @@ -1,13 +0,0 @@ -""" -The Emboss 5.0.0 tools have been eliminated from the distribution and the Emboss datatypes have been removed from -datatypes_conf.xml.sample. You should remove the Emboss datatypes from your version of datatypes_conf.xml. The -repositories named emboss_5 and emboss_datatypes from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu -will be installed into your local Galaxy instance at the location discussed above by running the following command. -""" - -import sys - -def upgrade(): - print __doc__ -def downgrade(): - pass diff -r e9e09d1ab51752db592eee71032ec5fc33f6ee57 -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e lib/galaxy/tool_shed/migrate/versions/0003_tools.py --- a/lib/galaxy/tool_shed/migrate/versions/0003_tools.py +++ /dev/null @@ -1,12 +0,0 @@ -""" -The freebayes tool has been eliminated from the distribution . The repository named freebayes from the main -Galaxy tool shed at http://toolshed.g2.bx.psu.edu will be installed into your local Galaxy instance at the -location discussed above by running the following command. -""" - -import sys - -def upgrade(): - print __doc__ -def downgrade(): - pass diff -r e9e09d1ab51752db592eee71032ec5fc33f6ee57 -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e lib/galaxy/tool_shed/migrate/versions/0004_tools.py --- a/lib/galaxy/tool_shed/migrate/versions/0004_tools.py +++ /dev/null @@ -1,14 +0,0 @@ -""" -The NCBI BLAST+ tools have been eliminated from the distribution. The tools and -datatypes are now available in repositories named ncbi_blast_plus and -blast_datatypes, in the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu. -These repositories will be installed into your local Galaxy instance at the -location discussed above by running the following command. -""" - -import sys - -def upgrade(): - print __doc__ -def downgrade(): - pass diff -r e9e09d1ab51752db592eee71032ec5fc33f6ee57 -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e lib/galaxy/tool_shed/migrate/versions/0005_tools.py --- a/lib/galaxy/tool_shed/migrate/versions/0005_tools.py +++ /dev/null @@ -1,15 +0,0 @@ -""" -The tools "Map with BWA for Illumina" and "Map with BWA for SOLiD" have -been eliminated from the distribution. The tools are now available -in the repository named bwa_wrappers from the main Galaxy tool shed at -http://toolshed.g2.bx.psu.edu, and will be installed into your local -Galaxy instance at the location discussed above by running the following -command. -""" - -import sys - -def upgrade(): - print __doc__ -def downgrade(): - pass diff -r e9e09d1ab51752db592eee71032ec5fc33f6ee57 -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e lib/galaxy/tool_shed/migrate/versions/0006_tools.py --- a/lib/galaxy/tool_shed/migrate/versions/0006_tools.py +++ /dev/null @@ -1,20 +0,0 @@ -""" -The following tools have been eliminated from the distribution: -FASTQ to BAM, SAM to FASTQ, BAM Index Statistics, Estimate Library -Complexity, Insertion size metrics for PAIRED data, SAM/BAM Hybrid -Selection Metrics, bam/sam Cleaning, Add or Replace Groups, Replace -SAM/BAM Header, Paired Read Mate Fixer, Mark Duplicate reads, -SAM/BAM Alignment Summary Metrics, SAM/BAM GC Bias Metrics, and -Reorder SAM/BAM. The tools are now available in the repository -named picard from the main Galaxy tool shed at -http://toolshed.g2.bx.psu.edu, and will be installed into your -local Galaxy instance at the location discussed above by running -the following command. -""" - -import sys - -def upgrade(): - print __doc__ -def downgrade(): - pass diff -r e9e09d1ab51752db592eee71032ec5fc33f6ee57 -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e lib/galaxy/tool_shed/migrate/versions/0007_tools.py --- a/lib/galaxy/tool_shed/migrate/versions/0007_tools.py +++ /dev/null @@ -1,17 +0,0 @@ -""" -The following tools have been eliminated from the distribution: -Map with Bowtie for Illumina, Map with Bowtie for SOLiD, Lastz, -and Lastz paired reads. The tools are now available in the -repositories named bowtie_wrappers, bowtie_color_wrappers, lastz, -and lastz_paired_reads from the main Galaxy tool shed at -http://toolshed.g2.bx.psu.edu, and will be installed into your -local Galaxy instance at the location discussed above by running -the following command. -""" - -import sys - -def upgrade(): - print __doc__ -def downgrade(): - pass diff -r e9e09d1ab51752db592eee71032ec5fc33f6ee57 -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e lib/galaxy/tool_shed/tool_dependencies/common_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/common_util.py +++ /dev/null @@ -1,149 +0,0 @@ -import os, shutil, tarfile, urllib2, zipfile -from galaxy.datatypes import checkers - -def create_env_var_dict( elem, tool_dependency_install_dir=None, tool_shed_repository_install_dir=None ): - env_var_name = elem.get( 'name', 'PATH' ) - env_var_action = elem.get( 'action', 'prepend_to' ) - env_var_text = None - if elem.text and elem.text.find( 'REPOSITORY_INSTALL_DIR' ) >= 0: - if tool_shed_repository_install_dir and elem.text.find( '$REPOSITORY_INSTALL_DIR' ) != -1: - env_var_text = elem.text.replace( '$REPOSITORY_INSTALL_DIR', tool_shed_repository_install_dir ) - return dict( name=env_var_name, action=env_var_action, value=env_var_text ) - else: - env_var_text = elem.text.replace( '$REPOSITORY_INSTALL_DIR', tool_dependency_install_dir ) - return dict( name=env_var_name, action=env_var_action, value=env_var_text ) - if elem.text and elem.text.find( 'INSTALL_DIR' ) >= 0: - if tool_dependency_install_dir: - env_var_text = elem.text.replace( '$INSTALL_DIR', tool_dependency_install_dir ) - return dict( name=env_var_name, action=env_var_action, value=env_var_text ) - else: - env_var_text = elem.text.replace( '$INSTALL_DIR', tool_shed_repository_install_dir ) - return dict( name=env_var_name, action=env_var_action, value=env_var_text ) - if elem.text: - # Allow for environment variables that contain neither REPOSITORY_INSTALL_DIR nor INSTALL_DIR since there may be command line - # parameters that are tuned for a Galaxy instance. Allowing them to be set in one location rather than being hard coded into - # each tool config is the best approach. For example: - # <environment_variable name="GATK2_SITE_OPTIONS" action="set_to"> - # "--num_threads 4 --num_cpu_threads_per_data_thread 3 --phone_home STANDARD" - # </environment_variable> - return dict( name=env_var_name, action=env_var_action, value=elem.text) - return None -def create_or_update_env_shell_file( install_dir, env_var_dict ): - env_var_name = env_var_dict[ 'name' ] - env_var_action = env_var_dict[ 'action' ] - env_var_value = env_var_dict[ 'value' ] - if env_var_action == 'prepend_to': - changed_value = '%s:$%s' % ( env_var_value, env_var_name ) - elif env_var_action == 'set_to': - changed_value = '%s' % env_var_value - elif env_var_action == 'append_to': - changed_value = '$%s:%s' % ( env_var_name, env_var_value ) - env_shell_file_path = '%s/env.sh' % install_dir - if os.path.exists( env_shell_file_path ): - write_action = '>>' - else: - write_action = '>' - cmd = "echo '%s=%s; export %s' %s %s;chmod +x %s" % ( env_var_name, - changed_value, - env_var_name, - write_action, - env_shell_file_path, - env_shell_file_path ) - return cmd -def extract_tar( file_name, file_path ): - if isgzip( file_name ) or isbz2( file_name ): - # Open for reading with transparent compression. - tar = tarfile.open( file_name, 'r:*' ) - else: - tar = tarfile.open( file_name ) - tar.extractall( path=file_path ) - tar.close() -def extract_zip( archive_path, extraction_path ): - # TODO: change this method to use zipfile.Zipfile.extractall() when we stop supporting Python 2.5. - if not zipfile_ok( archive_path ): - return False - zip_archive = zipfile.ZipFile( archive_path, 'r' ) - for name in zip_archive.namelist(): - uncompressed_path = os.path.join( extraction_path, name ) - if uncompressed_path.endswith( '/' ): - if not os.path.isdir( uncompressed_path ): - os.makedirs( uncompressed_path ) - else: - file( uncompressed_path, 'wb' ).write( zip_archive.read( name ) ) - zip_archive.close() - return True -def isbz2( file_path ): - return checkers.is_bz2( file_path ) -def isgzip( file_path ): - return checkers.is_gzip( file_path ) -def istar( file_path ): - return tarfile.is_tarfile( file_path ) -def iszip( file_path ): - return checkers.check_zip( file_path ) -def make_directory( full_path ): - if not os.path.exists( full_path ): - os.makedirs( full_path ) -def move_directory_files( current_dir, source_dir, destination_dir ): - source_directory = os.path.abspath( os.path.join( current_dir, source_dir ) ) - destination_directory = os.path.join( destination_dir ) - if not os.path.isdir( destination_directory ): - os.makedirs( destination_directory ) - for file_name in os.listdir( source_directory ): - source_file = os.path.join( source_directory, file_name ) - destination_file = os.path.join( destination_directory, file_name ) - shutil.move( source_file, destination_file ) -def move_file( current_dir, source, destination_dir ): - source_file = os.path.abspath( os.path.join( current_dir, source ) ) - destination_directory = os.path.join( destination_dir ) - if not os.path.isdir( destination_directory ): - os.makedirs( destination_directory ) - shutil.move( source_file, destination_directory ) -def tar_extraction_directory( file_path, file_name ): - """Try to return the correct extraction directory.""" - file_name = file_name.strip() - extensions = [ '.tar.gz', '.tgz', '.tar.bz2', '.tar', '.zip' ] - for extension in extensions: - if file_name.find( extension ) > 0: - dir_name = file_name[ :-len( extension ) ] - if os.path.exists( os.path.abspath( os.path.join( file_path, dir_name ) ) ): - return dir_name - if os.path.exists( os.path.abspath( os.path.join( file_path, file_name ) ) ): - return os.path.abspath( file_path ) - raise ValueError( 'Could not find path to file %s' % os.path.abspath( os.path.join( file_path, file_name ) ) ) -def url_download( install_dir, downloaded_file_name, download_url ): - file_path = os.path.join( install_dir, downloaded_file_name ) - src = None - dst = None - try: - src = urllib2.urlopen( download_url ) - data = src.read() - dst = open( file_path,'wb' ) - dst.write( data ) - except: - if src: - src.close() - if dst: - dst.close() - return os.path.abspath( file_path ) -def zip_extraction_directory( file_path, file_name ): - """Try to return the correct extraction directory.""" - files = [ filename for filename in os.listdir( file_path ) if not filename.endswith( '.zip' ) ] - if len( files ) > 1: - return os.path.abspath( file_path ) - elif len( files ) == 1: - # If there is only on file it should be a directory. - if os.path.isdir( os.path.join( file_path, files[ 0 ] ) ): - return os.path.abspath( os.path.join( file_path, files[ 0 ] ) ) - raise ValueError( 'Could not find directory for the extracted file %s' % os.path.abspath( os.path.join( file_path, file_name ) ) ) -def zipfile_ok( path_to_archive ): - """ - This function is a bit pedantic and not functionally necessary. It checks whether there is no file pointing outside of the extraction, - because ZipFile.extractall() has some potential security holes. See python zipfile documentation for more details. - """ - basename = os.path.realpath( os.path.dirname( path_to_archive ) ) - zip_archive = zipfile.ZipFile( path_to_archive ) - for member in zip_archive.namelist(): - member_path = os.path.realpath( os.path.join( basename, member ) ) - if not member_path.startswith( basename ): - return False - return True diff -r e9e09d1ab51752db592eee71032ec5fc33f6ee57 -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e lib/galaxy/tool_shed/tool_dependencies/fabric_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py +++ /dev/null @@ -1,143 +0,0 @@ -# For Python 2.5 -from __future__ import with_statement - -import os, shutil, tempfile -from contextlib import contextmanager -import common_util - -from galaxy import eggs -import pkg_resources - -pkg_resources.require('ssh' ) -pkg_resources.require( 'Fabric' ) - -from fabric.api import env, lcd, local, settings - -INSTALLATION_LOG = 'INSTALLATION.log' - -def check_fabric_version(): - version = env.version - if int( version.split( "." )[ 0 ] ) < 1: - raise NotImplementedError( "Install Fabric version 1.0 or later." ) -def set_galaxy_environment( galaxy_user, tool_dependency_dir, host='localhost', shell='/bin/bash -l -c' ): - """General Galaxy environment configuration""" - env.user = galaxy_user - env.install_dir = tool_dependency_dir - env.host_string = host - env.shell = shell - env.use_sudo = False - env.safe_cmd = local - return env -@contextmanager -def make_tmp_dir(): - work_dir = tempfile.mkdtemp() - yield work_dir - if os.path.exists( work_dir ): - local( 'rm -rf %s' % work_dir ) -def handle_command( app, tool_dependency, install_dir, cmd ): - sa_session = app.model.context.current - output = local( cmd, capture=True ) - log_results( cmd, output, os.path.join( install_dir, INSTALLATION_LOG ) ) - if output.return_code: - tool_dependency.status = app.model.ToolDependency.installation_status.ERROR - tool_dependency.error_message = str( output.stderr ) - sa_session.add( tool_dependency ) - sa_session.flush() - return output.return_code -def install_and_build_package( app, tool_dependency, actions_dict ): - """Install a Galaxy tool dependency package either via a url or a mercurial or git clone command.""" - sa_session = app.model.context.current - install_dir = actions_dict[ 'install_dir' ] - package_name = actions_dict[ 'package_name' ] - actions = actions_dict.get( 'actions', None ) - filtered_actions = [] - if actions: - with make_tmp_dir() as work_dir: - with lcd( work_dir ): - # The first action in the list of actions will be the one that defines the installation process. There - # are currently only two supported processes; download_by_url and clone via a "shell_command" action type. - action_type, action_dict = actions[ 0 ] - if action_type == 'download_by_url': - # Eliminate the download_by_url action so remaining actions can be processed correctly. - filtered_actions = actions[ 1: ] - url = action_dict[ 'url' ] - if 'target_filename' in action_dict: - downloaded_filename = action_dict[ 'target_filename' ] - else: - downloaded_filename = os.path.split( url )[ -1 ] - downloaded_file_path = common_util.url_download( work_dir, downloaded_filename, url ) - if common_util.istar( downloaded_file_path ): - # <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1…</action> - common_util.extract_tar( downloaded_file_path, work_dir ) - dir = common_util.tar_extraction_directory( work_dir, downloaded_filename ) - elif common_util.iszip( downloaded_file_path ): - # <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-to…</action> - zip_archive_extracted = common_util.extract_zip( downloaded_file_path, work_dir ) - dir = common_util.zip_extraction_directory( work_dir, downloaded_filename ) - else: - dir = work_dir - elif action_type == 'shell_command': - # <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action> - # Eliminate the shell_command clone action so remaining actions can be processed correctly. - filtered_actions = actions[ 1: ] - return_code = handle_command( app, tool_dependency, install_dir, action_dict[ 'command' ] ) - if return_code: - return - dir = package_name - else: - # We're handling a complex repository dependency where we only have a set_environment tag set. - # <action type="set_environment"> - # <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - # </action> - filtered_actions = [ a for a in actions ] - dir = install_dir - if not os.path.exists( dir ): - os.makedirs( dir ) - # The package has been down-loaded, so we can now perform all of the actions defined for building it. - with lcd( dir ): - for action_tup in filtered_actions: - action_type, action_dict = action_tup - current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) - if action_type == 'make_directory': - common_util.make_directory( full_path=action_dict[ 'full_path' ] ) - elif action_type == 'move_directory_files': - common_util.move_directory_files( current_dir=current_dir, - source_dir=os.path.join( action_dict[ 'source_directory' ] ), - destination_dir=os.path.join( action_dict[ 'destination_directory' ] ) ) - elif action_type == 'move_file': - # TODO: Remove this hack that resets current_dir so that the pre-compiled bwa binary can be found. - # current_dir = '/Users/gvk/workspaces_2008/bwa/bwa-0.5.9' - common_util.move_file( current_dir=current_dir, - source=os.path.join( action_dict[ 'source' ] ), - destination_dir=os.path.join( action_dict[ 'destination' ] ) ) - elif action_type == 'set_environment': - # Currently the only action supported in this category is "environment_variable". - env_var_dicts = action_dict[ 'environment_variable' ] - for env_var_dict in env_var_dicts: - cmd = common_util.create_or_update_env_shell_file( install_dir, env_var_dict ) - return_code = handle_command( app, tool_dependency, install_dir, cmd ) - if return_code: - return - elif action_type == 'shell_command': - with settings( warn_only=True ): - return_code = handle_command( app, tool_dependency, install_dir, action_dict[ 'command' ] ) - if return_code: - return -def log_results( command, fabric_AttributeString, file_path ): - """ - Write attributes of fabric.operations._AttributeString (which is the output of executing command using fabric's local() method) - to a specified log file. - """ - if os.path.exists( file_path ): - logfile = open( file_path, 'ab' ) - else: - logfile = open( file_path, 'wb' ) - logfile.write( "\n#############################################\n" ) - logfile.write( '%s\nSTDOUT\n' % command ) - logfile.write( str( fabric_AttributeString.stdout ) ) - logfile.write( "\n#############################################\n" ) - logfile.write( "\n#############################################\n" ) - logfile.write( '%s\nSTDERR\n' % command ) - logfile.write( str( fabric_AttributeString.stderr ) ) - logfile.write( "\n#############################################\n" ) - logfile.close() 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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commit/galaxy-central: natefoo: Python 2.5 compatibility fix for lwr client updates.
by commits-noreply＠bitbucket.org 26 Feb '13

26 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e9e09d1ab517/ changeset: e9e09d1ab517 user: natefoo date: 2013-02-26 15:33:31 summary: Python 2.5 compatibility fix for lwr client updates. affected #: 1 file diff -r 993c232d34cda550a5605f87d7416467d4e2c33f -r e9e09d1ab51752db592eee71032ec5fc33f6ee57 lib/galaxy/jobs/runners/lwr_client/transport/standard.py --- a/lib/galaxy/jobs/runners/lwr_client/transport/standard.py +++ b/lib/galaxy/jobs/runners/lwr_client/transport/standard.py @@ -1,6 +1,7 @@ """ LWR HTTP Client layer based on Python Standard Library (urllib2) """ +from __future__ import with_statement import mmap import urllib2 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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galaxy-commits February 2013