1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/d0fe08c597a4/ Changeset: d0fe08c597a4 User: greg Date: 2013-11-20 22:41:33 Summary: Add a script to check repositories of type tool dependency definition in the tool shed to prep for installation testing. Affected #: 3 files

diff -r f8bebd9e12f53fca874739df55a34b73be224c0b -r d0fe08c597a40b32a5d6c9a57b4be07f610fdfc7 lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py --- /dev/null +++ b/lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py @@ -0,0 +1,191 @@ +#!/usr/bin/env python + +from datetime import datetime +from optparse import OptionParser +from time import strftime + +import ConfigParser +import logging +import os +import shutil +import sys +import time +import 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 + +from galaxy import eggs +eggs.require( "SQLAlchemy >= 0.4" ) +eggs.require( 'mercurial' ) + +from mercurial import __version__ + +import galaxy.webapps.tool_shed.config as tool_shed_config +import galaxy.webapps.tool_shed.model.mapping + +from base.util import get_database_version +from base.util import get_repository_current_revision +from base.util import get_test_environment +from galaxy.model.orm import and_, not_, select +from galaxy.web import url_for +from tool_shed.repository_types.util import TOOL_DEPENDENCY_DEFINITION + +log = logging.getLogger() +log.setLevel( 10 ) +log.addHandler( logging.StreamHandler( sys.stdout ) ) + +assert sys.version_info[ :2 ] >= ( 2, 6 ) + +class RepositoriesApplication( 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 + +def main(): + '''Script that validates all repositories of type tool_dependency_definition.''' + 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( "-s", "--section", action="store", dest="section", default='server:main', + help=".ini file section from which to extract the host and port" ) + parser.add_option( "-v", "--verbose", action="count", dest="verbosity", default=1, help="Control the amount of detail in the log output." ) + parser.add_option( "--verbosity", action="store", dest="verbosity", metavar='VERBOSITY', type="int", + help="Control the amount of detail in the log output, --verbosity=1 is the same as -v" ) + ( options, args ) = parser.parse_args() + try: + ini_file = args[ 0 ] + except IndexError: + print "Usage: python %s <tool shed .ini file> [options]" % sys.argv[ 0 ] + exit( 127 ) + 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 ) + config_section = options.section + + now = strftime( "%Y-%m-%d %H:%M:%S" ) + print "#############################################################################" + print "# %s - Validating repositories of type %s on %s..." % ( TOOL_DEPENDENCY_DEFINITION, now ) + print "# This tool shed is configured to listen on %s:%s" % ( config_parser.get( config_section, 'host' ), config_parser.get( config_section, 'port' ) ) + + app = RepositoriesApplication( config ) + + if options.info_only: + print "# Displaying info only ( --info_only )" + if options.verbosity: + print "# Displaying extra information ( --verbosity = %d )" % options.verbosity + validate_repositories( app, info_only=options.info_only, verbosity=options.verbosity ) + +def validate_repositories( app, info_only=False, verbosity=1 ): + """ + Inspect records in the repository_metadata table that are associated with repositories of type TOOL_DEPENDENCY_DEFINITION + to ensure they are valid and set the repository_metadata.do_not_test column value to True if the metadata is invalid. + Each repository's metadata should look something like: + "{"tool_dependencies": + {"libpng/1.2.5": {"name": "libpng", + "readme": "README content", + "type": "package", + "version": "1.2.5"}}}" + or: + "{"repository_dependencies": + {"description": null, + "repository_dependencies": + [["http://localhost:9009", "package_libpng_1_2", "iuc", "5788512d4c0a", "True", "False"]]}, + "tool_dependencies": + {"libgd/2.1.0": + {"name": "libgd", "readme": "text"}, + "libpng/1.2.5": + {"name": "libpng", "type": "package", "version": "1.2.5"}}}" + """ + invalid_metadata = 0 + records_checked = 0 + skip_metadata_ids = [] + start = time.time() + valid_metadata = 0 + # Restrict testing to repositories of type TOOL_DEPENDENCY_DEFINITION + tool_dependency_defintion_repository_ids = [] + for repository in app.sa_session.query( app.model.Repository ) \ + .filter( and_( app.model.Repository.table.c.deleted == False, + app.model.Repository.table.c.type == TOOL_DEPENDENCY_DEFINITION ) ): + tool_dependency_defintion_repository_ids.append( repository.id ) + # Do not check metadata records that have an entry in the skip_tool_tests table, since they won't be tested anyway. + skip_metadata_ids = select( [ app.model.SkipToolTest.table.c.repository_metadata_id ] ) + # Get the list of metadata records to check, restricting it to records that have not been flagged do_not_test. + for repository_metadata in 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.repository_id.in_( tool_dependency_defintion_repository_ids ), + not_( app.model.RepositoryMetadata.table.c.id.in_( skip_metadata_ids ) ) ) ): + records_checked += 1 + # Create the repository_status dictionary, using the dictionary from the previous test run if available. + if repository_metadata.tool_test_results: + repository_status = repository_metadata.tool_test_results + else: + repository_status = {} + # Initialize the repository_status dictionary with the information about the current test environment. + last_test_environment = repository_status.get( 'test_environment', None ) + if last_test_environment is None: + test_environment = get_test_environment() + else: + test_environment = get_test_environment( last_test_environment ) + test_environment[ 'tool_shed_database_version' ] = get_database_version( app ) + test_environment[ 'tool_shed_mercurial_version' ] = __version__.version + test_environment[ 'tool_shed_revision' ] = get_repository_current_revision( os.getcwd() ) + repository_status[ 'test_environment' ] = test_environment + # Check the next repository revision. + changeset_revision = str( repository_metadata.changeset_revision ) + name = repository.name + owner = repository.user.username + metadata = repository_metadata.metadata + repository = repository_metadata.repository + if verbosity >= 1: + print '# -------------------------------------------------------------------------------------------' + print '# Checking revision %s of %s owned by %s.' % ( changeset_revision, name, owner ) + if metadata: + # Valid metadata will undoubtedly have a tool_dependencies entry or repository_dependencies entry. + repository_dependencies = metadata.get( 'repository_dependencies', None ) + tool_dependencies = metadata.get( 'tool_dependencies', None ) + if repository_dependencies or tool_dependencies: + print 'Revision %s of %s owned by %s has valid metadata.' % ( changeset_revision, name, owner ) + valid_metadata += 1 + else: + if verbosity >= 1: + print 'Revision %s of %s owned by %s has invalid metadata.' % ( changeset_revision, name, owner ) + invalid_metadata += 1 + if not info_only: + repository_metadata.tool_test_results = repository_status + repository_metadata.time_last_tested = datetime.utcnow() + app.sa_session.add( repository_metadata ) + app.sa_session.flush() + stop = time.time() + print '# -------------------------------------------------------------------------------------------' + print '# Checked %d repository revisions.' % records_checked + print '# %d revisions found with valid tool dependency definition metadata.' % valid_metadata + print '# %d revisions found with valid tool dependency definition metadata.' % invalid_metadata + if info_only: + print '# Database not updated with any information from this run.' + print "# Elapsed time: ", stop - start + print "#############################################################################" + +if __name__ == "__main__": main()

diff -r f8bebd9e12f53fca874739df55a34b73be224c0b -r d0fe08c597a40b32a5d6c9a57b4be07f610fdfc7 templates/webapps/tool_shed/repository/manage_repository.mako --- a/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/templates/webapps/tool_shed/repository/manage_repository.mako @@ -203,7 +203,11 @@ %if includes_tools or repository.type == TOOL_DEPENDENCY_DEFINITION: <p/><div class="toolForm"> - <div class="toolFormTitle">Automated tool tests</div> + %if repository.type == TOOL_DEPENDENCY_DEFINITION: + <div class="toolFormTitle">Automated tool dependency test</div> + %else: + <div class="toolFormTitle">Automated tool tests</div> + %endif <div class="toolFormBody"><form name="skip_tool_tests" id="skip_tool_tests" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=repository_metadata.changeset_revision )}" method="post" ><div class="form-row">

diff -r f8bebd9e12f53fca874739df55a34b73be224c0b -r d0fe08c597a40b32a5d6c9a57b4be07f610fdfc7 test/base/util.py --- a/test/base/util.py +++ b/test/base/util.py @@ -1,6 +1,7 @@ -import os, sys, logging, platform - -log = logging.getLogger(__name__) +import logging +import os +import platform +import sys

cwd = os.getcwd() if cwd not in sys.path: @@ -16,23 +17,10 @@

eggs.require( 'mercurial' )

-from mercurial import hg, ui, commands +from mercurial import hg +from mercurial import ui

-def get_repository_current_revision( repo_path ): - ''' - This method uses the python mercurial API to get the current working directory's mercurial changeset hash. Note that if the author of mercurial - changes the API, this method will have to be updated or replaced. - ''' - # Initialize a mercurial repo object from the provided path. - repo = hg.repository( ui.ui(), repo_path ) - # Get the working directory's change context. - ctx = repo[ None ] - # Extract the changeset hash of the first parent of that change context (the most recent changeset to which the working directory was updated). - changectx = ctx.parents()[ 0 ] - # Also get the numeric revision, so we can return the customary id:hash changeset identifiers. - ctx_rev = changectx.rev() - hg_id = '%d:%s' % ( ctx_rev, str( changectx ) ) - return hg_id +log = logging.getLogger(__name__)

def get_database_version( app ): ''' @@ -74,7 +62,25 @@ return None, repository_name, changeset_revision return last_galaxy_test_file_dir, last_tested_repository_name, last_tested_changeset_revision

-def get_test_environment( current_environment={} ): +def get_repository_current_revision( repo_path ): + ''' + This method uses the python mercurial API to get the current working directory's mercurial changeset hash. Note that if the author of mercurial + changes the API, this method will have to be updated or replaced. + ''' + # Initialize a mercurial repo object from the provided path. + repo = hg.repository( ui.ui(), repo_path ) + # Get the working directory's change context. + ctx = repo[ None ] + # Extract the changeset hash of the first parent of that change context (the most recent changeset to which the working directory was updated). + changectx = ctx.parents()[ 0 ] + # Also get the numeric revision, so we can return the customary id:hash changeset identifiers. + ctx_rev = changectx.rev() + hg_id = '%d:%s' % ( ctx_rev, str( changectx ) ) + return hg_id + +def get_test_environment( current_environment=None ): + if current_environment is None: + current_environment = {} rval = current_environment rval[ 'python_version' ] = platform.python_version() rval[ 'architecture' ] = platform.machine() @@ -132,4 +138,3 @@ shed_tools_dict[ guid ] = galaxy_test_file_dir last_galaxy_test_file_dir = galaxy_test_file_dir return has_test_data, shed_tools_dict -

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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