[galaxy-commits] commit/galaxy-central: 2 new changesets

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b5f22685678d/ changeset: b5f22685678d user: inithello date: 2013-03-05 16:23:21 summary: Script to check repositories and determine whether functional tests are defined for all tools, and set the do_not_test flag accordingly. Cleaned up the install and test framework and functional test common methods. affected #: 3 files diff -r d1f875d0f213c0ba5d858b34ac76d314803a6efb -r b5f22685678d6938467ef17c336e154f88698289 lib/tool_shed/scripts/check_repositories_for_functional_tests.py --- /dev/null +++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py @@ -0,0 +1,274 @@ +#!/usr/bin/env python + +import os, sys, logging, tempfile + +new_path = [ os.path.join( os.getcwd(), "lib" ), os.path.join( os.getcwd(), "test" ) ] +new_path.extend( sys.path[1:] ) +sys.path = new_path + +log = logging.getLogger() +log.setLevel( 10 ) +log.addHandler( logging.StreamHandler( sys.stdout ) ) + +from galaxy import eggs +import pkg_resources +pkg_resources.require( "SQLAlchemy >= 0.4" ) +pkg_resources.require( 'mercurial' ) +from mercurial import hg, ui, commands + +import time, ConfigParser, shutil +from datetime import datetime, timedelta +from time import strftime +from optparse import OptionParser + +import galaxy.webapps.tool_shed.config as tool_shed_config +import galaxy.webapps.tool_shed.model.mapping +import sqlalchemy as sa +from galaxy.model.orm import and_, not_, distinct +from galaxy.util.json import from_json_string, to_json_string +from galaxy.web import url_for +from tool_shed.util.shed_util_common import clone_repository, get_configured_ui + +from base.util import get_test_environment + +assert sys.version_info[:2] >= ( 2, 4 ) + +def main(): + '''Script that checks repositories to see if the tools contained within them have functional tests defined.''' + parser = OptionParser() + parser.add_option( "-i", "--info_only", action="store_true", dest="info_only", help="info about the requested action", default=False ) + parser.add_option( "-v", "--verbose", action="store_true", dest="verbose", help="verbose mode, print the name, owner, and changeset revision of each repository", default=False ) + ( options, args ) = parser.parse_args() + ini_file = args[0] + config_parser = ConfigParser.ConfigParser( {'here':os.getcwd()} ) + config_parser.read( ini_file ) + config_dict = {} + for key, value in config_parser.items( "app:main" ): + config_dict[key] = value + config = tool_shed_config.Configuration( **config_dict ) + + now = strftime( "%Y-%m-%d %H:%M:%S" ) + print "#############################################################################" + print "# %s - Checking repositories for tools with functional tests." % now + app = FlagRepositoriesApplication( config ) + + if options.info_only: + print "# Displaying info only ( --info_only )" + if options.verbose: + print "# Displaying extra information ( --verbose )" + + check_and_flag_repositories( app, info_only=options.info_only, verbose=options.verbose ) + +def check_and_flag_repositories( app, info_only=False, verbose=False ): + ''' + This method will iterate through all records in the repository_metadata table, checking each one for tool metadata, + then checking the tool metadata for tests. + Each tool's metadata should look something like: + { + "add_to_tool_panel": true, + "description": "", + "guid": "toolshed.url:9009/repos/owner/name/tool_id/1.2.3", + "id": "tool_wrapper", + "name": "Map with Tool Wrapper", + "requirements": [], + "tests": [ + { + "inputs": [ [ "parameter", "value" ], [ "other_parameter", "other_value" ], ], + "name": "Test-1", + "outputs": [ + [ + "output_field_name", + "output_file_name.bed" + ] + ], + "required_files": [ '1.bed', '2.bed', '3.bed' ] + } + ], + "tool_config": "database/community_files/000/repo_1/tool_wrapper.xml", + "tool_type": "default", + "version": "1.2.3", + "version_string_cmd": null + } + + If the "tests" attribute is missing or empty, this script will mark the metadata record (which is specific to a changeset revision of a repository) + not to be tested. If each "tools" attribute has at least one valid "tests" entry, this script will do nothing, and leave it available for the install + and test repositories script to process. If the tested changeset revision does not have a test-data directory, this script will also mark the revision + not to be tested. + + If any error is encountered, the script will update the repository_metadata.tool_test_errors attribute with the following structure: + { + "test_environment": + { + "python_version": "2.7.2", + "architecture": "x86_64", + "system": "Darwin 12.2.0" + }, + "test_errors": + [ + { + "test_id": "Something that will easily identify what the problem is", + "stdout": "The output of the test, or a more detailed description of what was tested and why it failed." + }, + ] + } + ''' + start = time.time() + repository_ids_to_check = [] + tool_count = 0 + has_tests = 0 + no_tests = 0 + no_tools = 0 + # Get the list of metadata records to check for functional tests and test data. Limit this to records that have not been flagged do_not_test + # or tools_functionally_correct. Also filter out changeset revisions that are not downloadable, because it's redundant to test a revision that + # a user can't install. + metadata_records_to_check = app.sa_session.query( app.model.RepositoryMetadata ) \ + .filter( and_( app.model.RepositoryMetadata.table.c.downloadable == True, + app.model.RepositoryMetadata.table.c.do_not_test == False, + app.model.RepositoryMetadata.table.c.tools_functionally_correct == False ) ) \ + .all() + for metadata_record in metadata_records_to_check: + name = metadata_record.repository.name + owner = metadata_record.repository.user.username + changeset_revision = str( metadata_record.changeset_revision ) + repository_status = {} + # If this changeset revision has no tools, we don't need to do anything here, the install and test script has a filter for returning + # only repositories that contain tools. + if 'tools' not in metadata_record.metadata: + no_tools += 1 + continue + else: + # Initialize the repository_status dict with the test environment, but leave the test_errors empty. + repository_status[ 'test_environment' ] = get_test_environment() + repository_status[ 'test_errors' ] = [] + # Loop through all the tools in this metadata record, checking each one for defined functional tests. + for tool_metadata in metadata_record.metadata[ 'tools' ]: + tool_count += 1 + tool_id = tool_metadata[ 'id' ] + if verbose: + print '# Checking for functional tests in changeset revision %s of %s, tool ID %s.' % \ + ( changeset_revision, name, tool_id ) + # If there are no tests, this tool should not be tested, since the tool functional tests only report failure if the test itself fails, + # not if it's missing or undefined. Filtering out those repositories at this step will reduce the number of "false negatives" the + # automated functional test framework produces. + if 'tests' not in tool_metadata or not tool_metadata[ 'tests' ]: + if verbose: + print '# No functional tests defined for %s.' % tool_id + if 'test_errors' not in repository_status: + repository_status[ 'test_errors' ] = [] + test_id = 'Functional tests for %s' % tool_id + # The repository_metadata.tool_test_errors attribute should always have the following structure: + # { + # "environment": + # { + # "python_version": "2.7.2", + # "architecture": "x86_64", + # "system": "Darwin 12.2.0" + # }, + # "test_errors": + # [ + # { + # "test_id": "Something that will easily identify what the problem is", + # "stdout": "The output of the test, or a more detailed description of what was tested and why it failed." + # }, + # ] + # } + # Optionally, "stderr" and "traceback" may be included in a test_errors dict, if they are relevant. + test_errors = dict( test_id=test_id, + stdout='No functional tests defined in changeset revision %s of repository %s owned by %s.' % \ + ( changeset_revision, name, owner ) ) + repository_status[ 'test_errors' ].append( test_errors ) + no_tests += 1 + else: + has_tests += 1 + if verbose: + if not repository_status[ 'test_errors' ]: + print '# All tools have functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + else: + print '# Some tools missing functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + has_test_data = False + # Clone the repository up to the changeset revision we're checking. + repo_dir = metadata_record.repository.repo_path( app ) + repo = hg.repository( get_configured_ui(), repo_dir ) + work_dir = tempfile.mkdtemp() + cloned_ok, error_message = clone_repository( repo_dir, work_dir, changeset_revision ) + if cloned_ok: + # Iterate through all the directories in the cloned changeset revision and determine whether there's a + # directory named test-data. If this directory is not present, update the metadata record for the changeset + # revision we're checking. + for root, dirs, files in os.walk( work_dir ): + if '.hg' in dirs: + dirs.remove( '.hg' ) + if 'test-data' in dirs: + has_test_data = True + break + # Remove the cloned path. + if os.path.exists( work_dir ): + shutil.rmtree( work_dir ) + if not has_test_data: + if verbose: + print '# Test data missing in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + repository_status[ 'test_environment' ] = get_test_environment() + test_id = 'Find functional test data for %s' % metadata_record.repository.name + # The repository_metadata.tool_test_errors attribute should always have the following structure: + # { + # "test_environment": + # { + # "python_version": "2.7.2", + # "architecture": "x86_64", + # "system": "Darwin 12.2.0" + # }, + # "test_errors": + # [ + # { + # "test_id": "Something that will easily identify what the problem is", + # "stdout": "The output of the test, or a more detailed description of what was tested and why it failed." + # }, + # ] + # } + # Optionally, "stderr" and "traceback" may be included in a test_errors dict, if they are relevant. + test_errors = dict( test_id=test_id, + stdout='No test data found for changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) ) + repository_status[ 'test_errors' ].append( test_errors ) + else: + if verbose: + print '# Test data found in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + if not info_only: + if repository_status[ 'test_errors' ]: + metadata_record.do_not_test = True + metadata_record.tools_functionally_correct = False + metadata_record.tool_test_errors = to_json_string( repository_status ) + metadata_record.time_last_tested = datetime.utcnow() + app.sa_session.add( metadata_record ) + app.sa_session.flush() + stop = time.time() + print '# Checked %d tools in %d changeset revisions.' % ( tool_count, len( metadata_records_to_check ) ) + print '# Found %d changeset revisions without tools.' % no_tools + print '# Found %d tools without functional tests.' % no_tests + print '# Found %d tools with functional tests.' % has_tests + if info_only: + print '# Database not updated, info_only set.' + print "# Elapsed time: ", stop - start + print "#############################################################################" + +class FlagRepositoriesApplication( object ): + """Encapsulates the state of a Universe application""" + def __init__( self, config ): + if config.database_connection is False: + config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % config.database + # Setup the database engine and ORM + self.model = galaxy.webapps.tool_shed.model.mapping.init( config.file_path, config.database_connection, engine_options={}, create_tables=False ) + self.hgweb_config_manager = self.model.hgweb_config_manager + self.hgweb_config_manager.hgweb_config_dir = config.hgweb_config_dir + print "# Using configured hgweb.config file: ", self.hgweb_config_manager.hgweb_config + @property + def sa_session( self ): + """ + Returns a SQLAlchemy session -- currently just gets the current + session from the threadlocal session context, but this is provided + to allow migration toward a more SQLAlchemy 0.4 style of use. + """ + return self.model.context.current + def shutdown( self ): + pass + +if __name__ == "__main__": main() diff -r d1f875d0f213c0ba5d858b34ac76d314803a6efb -r b5f22685678d6938467ef17c336e154f88698289 test/base/util.py --- a/test/base/util.py +++ b/test/base/util.py @@ -1,4 +1,4 @@ -import os, sys, logging +import os, sys, logging, platform log = logging.getLogger(__name__) @@ -36,6 +36,14 @@ return None, repository_name, changeset_revision return last_galaxy_test_file_dir, last_tested_repository_name, last_tested_changeset_revision +def get_test_environment(): + rval = {} + rval[ 'python_version' ] = platform.python_version() + rval[ 'architecture' ] = platform.machine() + os, hostname, os_version, uname, arch, processor = platform.uname() + rval[ 'system' ] = '%s %s' % ( os, os_version ) + return rval + def parse_tool_panel_config( config, shed_tools_dict ): """ Parse a shed-related tool panel config to generate the shed_tools_dict. This only happens when testing tools installed from the tool shed. diff -r d1f875d0f213c0ba5d858b34ac76d314803a6efb -r b5f22685678d6938467ef17c336e154f88698289 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 @@ -180,7 +180,7 @@ do_not_test='false', downloadable='true', malicious='false', - must_include_tools='true' ) ) + includes_tools='true' ) ) api_url = get_api_url( base=location, parts=[ 'repository_revisions' ], params=params ) if format == 'json': return json_from_url( api_url ) @@ -394,7 +394,7 @@ log.info( "The embedded Galaxy application is running on %s:%s" % ( galaxy_test_host, galaxy_test_port ) ) log.info( "Repositories will be installed from the tool shed at %s" % galaxy_tool_shed_url ) success = False - repository_status = {} + repository_status = dict() try: # Iterate through a list of repository info dicts. log.info( "Retrieving repositories to install from the URL:\n%s\n" % str( galaxy_tool_shed_url ) ) https://bitbucket.org/galaxy/galaxy-central/commits/dbe53e2c1eab/ changeset: dbe53e2c1eab user: inithello date: 2013-03-05 16:23:55 summary: Removed the must_include_tools filter from the repository revisions API controller, since repository_metadata now has a flag includes_tools. affected #: 1 file diff -r b5f22685678d6938467ef17c336e154f88698289 -r dbe53e2c1eab2b377880e87c4d2bd770dc470b80 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -47,27 +47,20 @@ do_not_test = kwd.get( 'do_not_test', None ) if do_not_test is not None: clause_list.append( trans.model.RepositoryMetadata.table.c.do_not_test == util.string_as_bool( do_not_test ) ) - # Filter by must_include_tools if received. - must_include_tools = kwd.get( 'must_include_tools', False ) + # Filter by includes_tools if received. + includes_tools = kwd.get( 'includes_tools', None ) + if includes_tools is not None: + clause_list.append( trans.model.RepositoryMetadata.table.c.includes_tools == util.string_as_bool( includes_tools ) ) try: query = trans.sa_session.query( trans.app.model.RepositoryMetadata ) \ .filter( and_( *clause_list ) ) \ .order_by( trans.app.model.RepositoryMetadata.table.c.repository_id ) \ .all() for repository_metadata in query: - if must_include_tools: - metadata = repository_metadata.metadata - if 'tools' in metadata: - ok_to_return = True - else: - ok_to_return = False - else: - ok_to_return = True - if ok_to_return: - item = repository_metadata.get_api_value( view='collection', - value_mapper=default_value_mapper( trans, repository_metadata ) ) - item[ 'url' ] = web.url_for( 'repository_revision', id=trans.security.encode_id( repository_metadata.id ) ) - rval.append( item ) + item = repository_metadata.get_api_value( view='collection', + value_mapper=default_value_mapper( trans, repository_metadata ) ) + item[ 'url' ] = web.url_for( 'repository_revision', id=trans.security.encode_id( repository_metadata.id ) ) + rval.append( item ) except Exception, e: rval = "Error in the Tool Shed repository_revisions API in index: " + str( e ) log.error( rval + ": %s" % str( e ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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