galaxy-commits March 2013

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commit/galaxy-central: inithello: Fix issue where the check script was unsetting the galaxy environment information.
by commits-noreply＠bitbucket.org 12 Mar '13

12 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6ea891cafbbb/ changeset: 6ea891cafbbb user: inithello date: 2013-03-12 14:36:56 summary: Fix issue where the check script was unsetting the galaxy environment information. affected #: 1 file diff -r b89a535240e5cb5fc123264b6294f86a577d02d9 -r 6ea891cafbbb7f9435887ca86b0823e1b8709882 lib/tool_shed/scripts/check_repositories_for_functional_tests.py --- a/lib/tool_shed/scripts/check_repositories_for_functional_tests.py +++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py @@ -172,10 +172,6 @@ # a user can't install. # Initialize the repository_status dict with the test environment, but leave the test_errors empty. repository_status = {} - repository_status[ 'test_environment' ] = get_test_environment() - repository_status[ 'test_environment' ][ 'tool_shed_database_version' ] = get_database_version( app ) - repository_status[ 'test_environment' ][ 'tool_shed_mercurial_version' ] = __version__.version - repository_status[ 'test_environment' ][ 'tool_shed_revision' ] = get_repository_current_revision( os.getcwd() ) repository_status[ 'invalid_tests' ] = [] metadata_records_to_check = app.sa_session.query( app.model.RepositoryMetadata ) \ .filter( and_( app.model.RepositoryMetadata.table.c.downloadable == True, @@ -186,6 +182,13 @@ for metadata_record in metadata_records_to_check: if metadata_record.tool_test_errors: repository_status = metadata_record.tool_test_errors + if 'test_environment' in repository_status: + repository_status[ 'test_environment' ] = get_test_environment( repository_status[ 'test_environment' ] ) + else: + repository_status[ 'test_environment' ] = get_test_environment() + repository_status[ 'test_environment' ][ 'tool_shed_database_version' ] = get_database_version( app ) + repository_status[ 'test_environment' ][ 'tool_shed_mercurial_version' ] = __version__.version + repository_status[ 'test_environment' ][ 'tool_shed_revision' ] = get_repository_current_revision( os.getcwd() ) name = metadata_record.repository.name owner = metadata_record.repository.user.username changeset_revision = str( metadata_record.changeset_revision ) 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: Include tool shed environment information when displaying functional test results in the tool shed.
by commits-noreply＠bitbucket.org 12 Mar '13

12 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b89a535240e5/ changeset: b89a535240e5 user: greg date: 2013-03-12 14:06:52 summary: Include tool shed environment information when displaying functional test results in the tool shed. affected #: 1 file diff -r be95601bd33fde791b42dff3e7446d0ccdcf7fd1 -r b89a535240e5cb5fc123264b6294f86a577d02d9 templates/webapps/tool_shed/repository/display_tool_functional_test_results.mako --- a/templates/webapps/tool_shed/repository/display_tool_functional_test_results.mako +++ b/templates/webapps/tool_shed/repository/display_tool_functional_test_results.mako @@ -136,25 +136,30 @@ </div><div class="form-row"><table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"><td><b>Test environment</td></tr> + <tr bgcolor="#D8D8D8" width="100%"><td><b>Tool Shed environment</td></tr></table></div><div class="form-row"> - <label>Architecture:</label> - ${test_environment_dict.get( 'architecture', 'unknown' ) | h} + <label>Tool shed version:</label> + ${test_environment_dict.get( 'tool_shed_revision', 'unknown' ) | h} <div style="clear: both"></div></div><div class="form-row"> - <label>Python version:</label> - ${test_environment_dict.get( 'python_version', 'unknown' ) | h} + <label>Tool shed database version:</label> + ${test_environment_dict.get( 'tool_shed_database_version', 'unknown' ) | h} <div style="clear: both"></div></div><div class="form-row"> - <label>Operating system:</label> - ${test_environment_dict.get( 'system', 'unknown' ) | h} + <label>Mercurial version:</label> + ${test_environment_dict.get( 'tool_shed_mercurial_version', 'unknown' ) | h} <div style="clear: both"></div></div><div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"><td><b>Galaxy environment</td></tr> + </table> + </div> + <div class="form-row"><label>Galaxy version:</label> ${test_environment_dict.get( 'galaxy_revision', 'unknown' ) | h} <div style="clear: both"></div> @@ -164,6 +169,21 @@ ${test_environment_dict.get( 'galaxy_database_version', 'unknown' ) | h} <div style="clear: both"></div></div> + <div class="form-row"> + <label>Architecture:</label> + ${test_environment_dict.get( 'architecture', 'unknown' ) | h} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Operating system:</label> + ${test_environment_dict.get( 'system', 'unknown' ) | h} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Python version:</label> + ${test_environment_dict.get( 'python_version', 'unknown' ) | h} + <div style="clear: both"></div> + </div> %if test_errors: <div class="form-row"><table width="100%"> 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: Fix for installing and testing repositories where all functional tests fail.
by commits-noreply＠bitbucket.org 11 Mar '13

11 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5d9328262021/ changeset: 5d9328262021 user: inithello date: 2013-03-11 19:21:32 summary: Fix for installing and testing repositories where all functional tests fail. affected #: 1 file diff -r c07417582dd369a02625d3b3d170718fd69bdd12 -r 5d9328262021b414c9005f79b0c97605acdd4c94 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 @@ -155,9 +155,11 @@ self.passed[ test_identifier ].append( fixed_test_id ) def getTestStatus( self, test_identifier ): - tests_passed = self.passed[ test_identifier ] - del self.passed[ test_identifier ] - return tests_passed + if test_identifier in self.passed: + tests_passed = self.passed[ test_identifier ] + del self.passed[ test_identifier ] + return tests_passed + return [] def execute_uninstall_method( repository_dict ): # Delete any configured tool functional tests from the test_toolbox.__dict__, otherwise nose will find them 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: Improve structure of invalid tools dict. Clarify summary and detailed log output. Add check for required environment variables.
by commits-noreply＠bitbucket.org 11 Mar '13

11 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c07417582dd3/ changeset: c07417582dd3 user: inithello date: 2013-03-11 18:49:12 summary: Improve structure of invalid tools dict. Clarify summary and detailed log output. Add check for required environment variables. affected #: 3 files diff -r a2f58a2b87876f8db9a8703782633b84f4dc13ef -r c07417582dd369a02625d3b3d170718fd69bdd12 install_and_test_tool_shed_repositories.sh --- a/install_and_test_tool_shed_repositories.sh +++ b/install_and_test_tool_shed_repositories.sh @@ -2,5 +2,42 @@ # A good place to look for nose info: http://somethingaboutorange.com/mrl/projects/nose/ -python test/install_and_test_tool_shed_repositories/functional_tests.py $* -v --with-nosehtml --html-report-file ./test/install_and_test_tool_shed_repositories/run_functional_tests.html test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py test/functional/test_toolbox.py +# The test/install_and_test_tool_shed_repositories/functional_tests.py can not be executed directly, because it must have certain functional test definitions +# in sys.argv. Running it through this shell script is the best way to ensure that it has the required definitions. +# This script requires the following environment variables: +# GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY - must be set to the API key for the tool shed that is being checked. +# GALAXY_INSTALL_TEST_TOOL_SHED_URL - must be set to a URL that the tool shed is listening on. +# If the tool shed url is not specified in tool_sheds_conf.xml, GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF must be set to a tool sheds configuration file +# that does specify that url, otherwise repository installation will fail. + +if [ -z $GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY ] ; then + echo "This script requires the GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY environment variable to be set and non-empty." + exit 1 +fi + +if [ -z $GALAXY_INSTALL_TEST_TOOL_SHED_URL ] ; then + echo "This script requires the GALAXY_INSTALL_TEST_TOOL_SHED_URL environment variable to be set and non-empty." + exit 1 +fi + +if [ -z "$GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF" ] ; then + if grep --quiet $GALAXY_INSTALL_TEST_TOOL_SHED_URL tool_sheds_conf.xml; then + echo "Tool sheds configuration tool_sheds_conf.xml ok, proceeding." + else + echo "ERROR: Tool sheds configuration tool_sheds_conf.xml does not have an entry for $GALAXY_INSTALL_TEST_TOOL_SHED_URL." + exit 1 + fi +else + if grep --quiet $GALAXY_INSTALL_TEST_TOOL_SHED_URL $GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF; then + echo "Tool sheds configuration $GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF ok, proceeding." + else + echo "ERROR: Tool sheds configuration $GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF does not have an entry for $GALAXY_INSTALL_TEST_TOOL_SHED_URL" + exit 1 + fi +fi + +python test/install_and_test_tool_shed_repositories/functional_tests.py $* -v --with-nosehtml --html-report-file \ + test/install_and_test_tool_shed_repositories/run_functional_tests.html \ + test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ + test/functional/test_toolbox.py diff -r a2f58a2b87876f8db9a8703782633b84f4dc13ef -r c07417582dd369a02625d3b3d170718fd69bdd12 lib/tool_shed/scripts/check_repositories_for_functional_tests.py --- a/lib/tool_shed/scripts/check_repositories_for_functional_tests.py +++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py @@ -55,7 +55,11 @@ type="int", help="Control the amount of detail in the log output. --verbosity=1 is " "the same as -v") ( options, args ) = parser.parse_args() - ini_file = args[0] + 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 = {} @@ -161,6 +165,8 @@ has_tests = 0 no_tests = 0 no_tools = 0 + valid_revisions = 0 + invalid_revisions = 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. @@ -173,6 +179,7 @@ repository_status[ 'invalid_tests' ] = [] 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.includes_tools == True, app.model.RepositoryMetadata.table.c.do_not_test == False, app.model.RepositoryMetadata.table.c.tools_functionally_correct == False ) ) \ .all() @@ -185,87 +192,14 @@ repository_status[ 'invalid_tests' ] = [] if metadata_record.repository.id not in checked_repository_ids: checked_repository_ids.append( metadata_record.repository.id ) - if verbosity >= 1: - print '# Checking for functional tests in changeset revision %s of %s, owned by %s.' % \ - ( changeset_revision, name, owner ) + if verbosity >= 1: + print '# -------------------------------------------------------------------------------------------' + print '# Now checking revision %s of %s, owned by %s.' % ( changeset_revision, name, owner ) # 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: - # 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' ] - tool_version = tool_metadata[ 'version' ] - tool_guid = tool_metadata[ 'guid' ] - if verbosity >= 2: - print "# Checking tool ID '%s' in changeset revision %s of %s." % \ - ( tool_id, changeset_revision, name ) - # 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 verbosity >= 2: - print '# No functional tests defined for %s.' % tool_id - # The repository_metadata.tool_test_errors attribute should always have the following structure: - # { - # "test_environment": - # { - # "galaxy_revision": "9001:abcd1234", - # "galaxy_database_version": "114", - # "tool_shed_revision": "9001:abcd1234", - # "tool_shed_mercurial_version": "2.3.1", - # "tool_shed_database_version": "17", - # "python_version": "2.7.2", - # "architecture": "x86_64", - # "system": "Darwin 12.2.0" - # }, - # "test_errors": - # [ - # { - # "test_id": "The test ID, generated by twill", - # "tool_id": "The tool ID that was tested", - # "tool_version": "The tool version that was tested", - # "stderr": "The output of the test, or a more detailed description of what was tested and what the outcome was." - # "traceback": "The captured traceback." - # }, - # ] - # "passed_tests": - # [ - # { - # "test_id": "The test ID, generated by twill", - # "tool_id": "The tool ID that was tested", - # "tool_version": "The tool version that was tested", - # "stderr": "The output of the test, or a more detailed description of what was tested and what the outcome was." - # }, - # ] - # "invalid_tests": - # [ - # { - # "tool_id": "The tool ID that does not have functional tests defined.", - # "tool_version": "The version of the tool." - # "tool_guid": "The guid of the tool." - # "reason_test_is_invalid": "A short explanation of what is invalid. - # }, - # ] - # } - # Optionally, "traceback" may be included in a test_errors dict, if it is relevant. No script should overwrite anything other - # than the list relevant to what it is testing. - test_errors = dict( tool_id=tool_id, tool_version=tool_version, tool_guid=tool_guid ) - repository_status[ 'invalid_tests' ].append( test_errors ) - no_tests += 1 - else: - if verbosity >= 2: - print "# Tool ID '%s' in changeset revision %s of %s has one or more valid functional tests defined." % \ - ( tool_id, changeset_revision, name ) - has_tests += 1 - if verbosity >= 1: - if not repository_status[ 'invalid_tests' ]: - 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 ) @@ -285,9 +219,47 @@ # Remove the cloned repository path. if os.path.exists( work_dir ): shutil.rmtree( work_dir ) - if not has_test_data: - if verbosity >= 1: + if verbosity >= 1: + if not has_test_data: print '# Test data missing in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + else: + print '# Test data found in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + print '# Checking for functional tests in changeset revision %s of %s, owned by %s.' % \ + ( changeset_revision, name, owner ) + # 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' ] + tool_version = tool_metadata[ 'version' ] + tool_guid = tool_metadata[ 'guid' ] + if verbosity >= 2: + print "# Checking tool ID '%s' in changeset revision %s of %s." % \ + ( tool_id, changeset_revision, name ) + # 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. + tool_has_tests = True + if 'tests' not in tool_metadata or not tool_metadata[ 'tests' ]: + tool_has_tests = False + if verbosity >= 2: + print '# No functional tests defined for %s.' % tool_id + no_tests += 1 + else: + tool_has_tests = True + if verbosity >= 2: + print "# Tool ID '%s' in changeset revision %s of %s has one or more valid functional tests defined." % \ + ( tool_id, changeset_revision, name ) + has_tests += 1 + failure_reason = '' + problem_found = False + if not has_test_data: + failure_reason += 'Repository does not have a test-data directory. ' + problem_found = True + if not tool_has_tests: + failure_reason += 'Functional test definitions missing for %s. ' % tool_id + problem_found = True + test_errors = dict( tool_id=tool_id, tool_version=tool_version, tool_guid=tool_guid, + reason_test_is_invalid=failure_reason ) # The repository_metadata.tool_test_errors attribute should always have the following structure: # { # "test_environment": @@ -323,21 +295,28 @@ # "invalid_tests": # [ # { - # "tool_id": "The tool ID that does not have functional tests defined.", + # "tool_id": "The ID of the tool that does not have valid tests.", # "tool_version": "The version of the tool." # "tool_guid": "The guid of the tool." - # "reason_test_is_invalid": "A short explanation of what is invalid. + # "reason_test_is_invalid": "A short explanation of what is invalid." # }, # ] # } + # # Optionally, "traceback" may be included in a test_errors dict, if it is relevant. No script should overwrite anything other # than the list relevant to what it is testing. - test_errors = dict( tool_id=None, tool_version=None, tool_guid=None, - reason_test_is_invalid="Repository %s is missing a test-data directory." % name ) - repository_status[ 'invalid_tests' ].append( test_errors ) + # Only append this error dict if it hasn't already been added. + if problem_found: + if test_errors not in repository_status[ 'invalid_tests' ]: + repository_status[ 'invalid_tests' ].append( test_errors ) + if not repository_status[ 'invalid_tests' ]: + valid_revisions += 1 + if verbosity >= 1: + print '# All tools have functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) else: + invalid_revisions += 1 if verbosity >= 1: - print '# Test data found in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + print '# Some tools missing functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) if not info_only: # If repository_status[ 'test_errors' ] is empty, no issues were found, and we can just update time_last_tested with the platform # on which this script was run. @@ -356,8 +335,10 @@ app.sa_session.add( metadata_record ) app.sa_session.flush() stop = time.time() + print '# -------------------------------------------------------------------------------------------' print '# Checked %d repositories with %d tools in %d changeset revisions.' % ( len( checked_repository_ids ), tool_count, len( metadata_records_to_check ) ) - print '# Skipped %d changeset revisions without tools.' % no_tools + print '# %d revisions found with functional tests and test data for all tools.' % valid_revisions + print '# %d revisions found with one or more tools missing functional tests and/or test data.' % invalid_revisions print '# Found %d tools without functional tests.' % no_tests print '# Found %d tools with functional tests.' % has_tests if info_only: diff -r a2f58a2b87876f8db9a8703782633b84f4dc13ef -r c07417582dd369a02625d3b3d170718fd69bdd12 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 @@ -104,11 +104,20 @@ </tables> ''' -# Define a default location to find the list of repositories to check. -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://localhost:9009' ) +# The tool shed url and api key must be set for this script to work correctly. Additionally, if the tool shed url does not +# point to one of the defaults, the GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF needs to point to a tool sheds configuration file +# that contains a definition for that tool shed. + +galaxy_tool_shed_url = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHED_URL', None ) 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 tool_shed_api_key is None: + print "This script requires the GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY environment variable to be set and non-empty." + exit( 1 ) + +if galaxy_tool_shed_url is None: + print "This script requires the GALAXY_INSTALL_TEST_TOOL_SHED_URL environment variable to be set and non-empty." + exit( 1 ) if 'GALAXY_INSTALL_TEST_SECRET' not in os.environ: galaxy_encode_secret = 'changethisinproductiontoo' @@ -462,8 +471,7 @@ # Get a list of repositories to test from the tool shed specified in the GALAXY_INSTALL_TEST_TOOL_SHED_URL environment variable. log.info( "Retrieving repositories to install from the URL:\n%s\n" % str( galaxy_tool_shed_url ) ) repositories_to_install = get_repositories_to_install( galaxy_tool_shed_url, source='url' ) - log.info( "Retrieved %d repositories to install..." % len( repositories_to_install ) ) - repositories_tested = len( repositories_to_install ) + log.info( "Retrieved %d repositories from the API." % len( repositories_to_install ) ) for repository_to_install_dict in repositories_to_install: # We need to get some details from the tool shed API, such as repository name and owner, to pass on to the # module that will generate the install methods. @@ -473,13 +481,15 @@ # and therefore do not need to be checked. If they are undeleted, this script will then test them the next time it runs. if repository_info_dict[ 'deleted' ]: log.info( "Skipping revision %s of repository id %s (%s/%s) since the repository is deleted..." % \ - ( repository_info_dict[ 'changeset_revision' ], - repository_info_dict[ 'repository_id' ], + ( repository_to_install_dict[ 'changeset_revision' ], + repository_to_install_dict[ 'repository_id' ], repository_info_dict[ 'owner' ], repository_info_dict[ 'name' ] ) ) continue # Now merge the dict returned from /api/repository_revisions with the detailed dict we just retrieved. detailed_repository_list.append( dict( repository_info_dict.items() + repository_to_install_dict.items() ) ) + repositories_tested = len( detailed_repository_list ) + log.info( 'After removing deleted repositories from the list, %d remain to be tested.' % repositories_tested ) if '-list_repositories' in sys.argv: log.info( "The API returned the following repositories, not counting deleted:" ) for repository_info_dict in detailed_repository_list: @@ -741,15 +751,15 @@ print "# Repository revisions tested: %d" % repositories_tested if repositories_tested > 0: if repositories_passed: - print "# " + print '# ----------------------------------------------------------------------------------' print "# Repositories passed:" show_summary_output( repositories_passed ) if repositories_failed: - print "# " + print '# ----------------------------------------------------------------------------------' print "# Repositories failed:" show_summary_output( repositories_failed ) if repositories_failed_install: - print "# " + print '# ----------------------------------------------------------------------------------' print "# Repositories not installed correctly:" show_summary_output( repositories_failed_install ) print "####################################################################################" 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: Do not display unnecessary invalid test tesults when displaying functional test results in the tool shed.
by commits-noreply＠bitbucket.org 11 Mar '13

11 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a2f58a2b8787/ changeset: a2f58a2b8787 user: greg date: 2013-03-11 15:49:12 summary: Do not display unnecessary invalid test tesults when displaying functional test results in the tool shed. affected #: 1 file diff -r 15fe17fcdeb7d7a86f605bc93600242c843d897d -r a2f58a2b87876f8db9a8703782633b84f4dc13ef templates/webapps/tool_shed/repository/display_tool_functional_test_results.mako --- a/templates/webapps/tool_shed/repository/display_tool_functional_test_results.mako +++ b/templates/webapps/tool_shed/repository/display_tool_functional_test_results.mako @@ -253,7 +253,7 @@ guid = test_results_dict.get( 'tool_guid', None ) tool_id = test_results_dict.get( 'tool_id', None ) tool_version = test_results_dict.get( 'tool_version', None ) - reason_test_is_invalid = test_results_dict.get( 'reason_test_is_invalid', 'unknown' ) + reason_test_is_invalid = test_results_dict.get( 'reason_test_is_invalid', None ) if reason_test_is_invalid: reason_test_is_invalid = to_safe_string( reason_test_is_invalid, to_html=True ) %> @@ -262,10 +262,12 @@ <td colspan="2" bgcolor="#FFFFCC">Tool id: <b>${tool_id}</b> version: <b>${tool_version}</b></td></tr> %endif - <tr> - <td><b>Reason test is invalid</b></td> - <td>${reason_test_is_invalid}</td> - </tr> + %if reason_test_is_invalid: + <tr> + <td><b>Reason test is invalid</b></td> + <td>${reason_test_is_invalid}</td> + </tr> + %endif %endfor </table></div> 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: Enhancesments for displaying functional tests run against installed tool shed repositories that contain tools.
by commits-noreply＠bitbucket.org 11 Mar '13

11 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/15fe17fcdeb7/ changeset: 15fe17fcdeb7 user: greg date: 2013-03-11 15:38:15 summary: Enhancesments for displaying functional tests run against installed tool shed repositories that contain tools. affected #: 1 file diff -r 0a6b63eca3ff6a72cd874bf36f73a2b5905aff65 -r 15fe17fcdeb7d7a86f605bc93600242c843d897d templates/webapps/tool_shed/repository/display_tool_functional_test_results.mako --- a/templates/webapps/tool_shed/repository/display_tool_functional_test_results.mako +++ b/templates/webapps/tool_shed/repository/display_tool_functional_test_results.mako @@ -28,11 +28,15 @@ # about the test environment even if all tests passed and the repository_metadata.tools_functionally_correct column is set to True. tool_test_errors = repository_metadata.tool_test_errors test_environment_dict = tool_test_errors.get( 'test_environment', None ) + invalid_tests = tool_test_errors.get( 'invalid_tests', [] ) test_errors = tool_test_errors.get( 'test_errors', [] ) + tests_passed = tool_test_errors.get( 'tests_passed', [] ) else: tool_test_errors = None test_environment_dict = {} + invalid_tests = [] test_errors = [] + tests_passed = [] if can_push: browse_label = 'Browse or delete repository tip files' @@ -121,7 +125,7 @@ <b>Repository name:</b><br/> ${repository.name} %endif -%if tool_test_errors: +%if invalid_tests or tool_test_errors or tests_passed: <p/><div class="toolForm"><div class="toolFormTitle">Tool functional test results</div> @@ -151,61 +155,48 @@ <div style="clear: both"></div></div><div class="form-row"> - <table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"><td><b>Test results</td></tr> - </table> + <label>Galaxy version:</label> + ${test_environment_dict.get( 'galaxy_revision', 'unknown' ) | h} + <div style="clear: both"></div></div><div class="form-row"> - <table class="grid"> - %for test_results_dict in test_errors: - <% - test_id = test_results_dict.get( 'test_id', 'unknown' ) - if test_id != 'unknown': - # The test_id looks something like: - # test_tool_000003 (functional.test_toolbox.TestForTool_localhost:9009/repos/test/bwa_mappers/bwa_color_wrapper/1.0.2) - # Highlight the tool id and version. - test_id_items = test_id.split( '/' ) - tool_id = test_id_items[ -2 ] - tool_id = '<b>%s</b>' % tool_id - test_id_items[ -2 ] = tool_id - tool_version = test_id_items[ -1 ] - tool_version = '<b>%s</b>' % ( tool_version.rstrip( ')' ) ) - tool_version = '%s)' % tool_version - test_id_items[ -1 ] = tool_version - test_id = '/'.join( test_id_items ) - test_id_items = test_id.split( ' ' ) - test_num = test_id_items[ 0 ] - test_num = '<b>%s</b>' % test_num - test_id_items[ 0 ] = test_num - test_id = ' '.join( test_id_items ) - - test_status = '<font color="green">Test passed</font>' - stdout = test_results_dict.get( 'stdout', '' ) - if stdout: - stdout = to_safe_string( stdout, to_html=True ) + <label>Galaxy database version:</label> + ${test_environment_dict.get( 'galaxy_database_version', 'unknown' ) | h} + <div style="clear: both"></div> + </div> + %if test_errors: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"><td><b>Tests that failed</td></tr> + </table> + </div> + <div class="form-row"> + <table class="grid"> + %for test_results_dict in test_errors: + <% + test_id = test_results_dict.get( 'test_id', 'unknown' ) + tool_id = test_results_dict.get( 'tool_id', 'unknown' ) + tool_version = test_results_dict.get( 'tool_version', 'unknown' ) + test_status = '<font color="red">Test failed</font>' + stderr = test_results_dict.get( 'stderr', '' ) if stderr: stderr = to_safe_string( stderr, to_html=True ) - test_status = '<font color="red">Test failed</font>' traceback = test_results_dict.get( 'traceback', '' ) if traceback: traceback = to_safe_string( traceback, to_html=True ) - test_status = '<font color="red">Test failed</font>' - %> - <tr> - <td bgcolor="#FFFFCC"><b>Test id</b></td> - <td bgcolor="#FFFFCC">${test_id}</td> - </tr> - <tr> - <td><b>Status</b></td> - <td>${test_status}</td> - </tr> - %if repository_metadata.tools_functionally_correct: + %><tr> - <td><b>Stdout</b></td> - <td>${stdout}</td> + <td colspan="2" bgcolor="#FFFFCC">Tool id: <b>${tool_id}</b> version: <b>${tool_version}</b></td></tr> - %else: + <tr> + <td><b>Test id</b></td> + <td>${test_id}</td> + </tr> + <tr> + <td><b>Status</b></td> + <td>${test_status}</td> + </tr><tr><td><b>Stderr</b></td><td>${stderr}</td> @@ -214,11 +205,71 @@ <td><b>Traceback</b></td><td>${traceback}</td></tr> - %endif - %endfor - </table> - <div style="clear: both"></div> - </div> + %endfor + </table> + <div style="clear: both"></div> + </div> + %endif + %if tests_passed: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"><td><b>Tests that passed successfully</td></tr> + </table> + </div> + <div class="form-row"> + <table class="grid"> + %for test_results_dict in tests_passed: + <% + test_id = test_results_dict.get( 'test_id', 'unknown' ) + tool_id = test_results_dict.get( 'tool_id', 'unknown' ) + tool_version = test_results_dict.get( 'tool_version', 'unknown' ) + test_status = '<font color="green">Test passed</font>' + %> + <tr> + <td colspan="2" bgcolor="#FFFFCC">Tool id: <b>${tool_id}</b> version: <b>${tool_version}</b></td> + </tr> + <tr> + <td><b>Test id</b></td> + <td>${test_id}</td> + </tr> + <tr> + <td><b>Status</b></td> + <td>${test_status}</td> + </tr> + %endfor + </table> + </div> + %endif + %if invalid_tests: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"><td><b>Invalid tests</td></tr> + </table> + </div> + <div class="form-row"> + <table class="grid"> + %for test_results_dict in invalid_tests: + <% + guid = test_results_dict.get( 'tool_guid', None ) + tool_id = test_results_dict.get( 'tool_id', None ) + tool_version = test_results_dict.get( 'tool_version', None ) + reason_test_is_invalid = test_results_dict.get( 'reason_test_is_invalid', 'unknown' ) + if reason_test_is_invalid: + reason_test_is_invalid = to_safe_string( reason_test_is_invalid, to_html=True ) + %> + %if tool_id or tool_version: + <tr> + <td colspan="2" bgcolor="#FFFFCC">Tool id: <b>${tool_id}</b> version: <b>${tool_version}</b></td> + </tr> + %endif + <tr> + <td><b>Reason test is invalid</b></td> + <td>${reason_test_is_invalid}</td> + </tr> + %endfor + </table> + </div> + %endif </div></div> %endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Refactor summary output. Improve handling of empty tool_test_errors dict. Refactor repository information retrieval.
by commits-noreply＠bitbucket.org 10 Mar '13

10 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0a6b63eca3ff/ changeset: 0a6b63eca3ff user: inithello date: 2013-03-11 05:47:47 summary: Refactor summary output. Improve handling of empty tool_test_errors dict. Refactor repository information retrieval. affected #: 2 files diff -r 2b4d6af45a04ddb49c2c87a0ead3874503d35832 -r 0a6b63eca3ff6a72cd874bf36f73a2b5905aff65 install_and_test_tool_shed_repositories.sh --- a/install_and_test_tool_shed_repositories.sh +++ b/install_and_test_tool_shed_repositories.sh @@ -1,7 +1,6 @@ #!/bin/sh # A good place to look for nose info: http://somethingaboutorange.com/mrl/projects/nose/ -#rm -f ./test/tool_shed/run_functional_tests.log -python test/install_and_test_tool_shed_repositories/functional_tests.py -v --with-nosehtml --html-report-file ./test/install_and_test_tool_shed_repositories/run_functional_tests.html test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py test/functional/test_toolbox.py +python test/install_and_test_tool_shed_repositories/functional_tests.py $* -v --with-nosehtml --html-report-file ./test/install_and_test_tool_shed_repositories/run_functional_tests.html test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py test/functional/test_toolbox.py diff -r 2b4d6af45a04ddb49c2c87a0ead3874503d35832 -r 0a6b63eca3ff6a72cd874bf36f73a2b5905aff65 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 @@ -242,6 +242,8 @@ api_path = metadata_dict[ 'url' ].split( '/' ) api_url = get_api_url( base=tool_shed_url, parts=api_path ) repository_metadata = json_from_url( api_url ) + if repository_metadata[ 'tool_test_errors' ] is None: + return {} return repository_metadata[ 'tool_test_errors' ] def json_from_url( url ): @@ -276,16 +278,22 @@ result = test_runner.run( tests ) return result, test_config.plugins._plugins +def show_summary_output( repository_info_dicts ): + repositories_by_owner = dict() + for repository in repository_info_dicts: + if repository[ 'owner' ] not in repositories_by_owner: + repositories_by_owner[ repository[ 'owner' ] ] = [] + repositories_by_owner[ repository[ 'owner' ] ].append( repository ) + for owner in repositories_by_owner: + print "# " + for repository in repositories_by_owner[ owner ]: + print "# %s owned by %s, changeset revision %s" % ( repository[ 'name' ], repository[ 'owner' ], repository[ 'changeset_revision' ] ) + def main(): # ---- Configuration ------------------------------------------------------ galaxy_test_host = os.environ.get( 'GALAXY_INSTALL_TEST_HOST', default_galaxy_test_host ) galaxy_test_port = os.environ.get( 'GALAXY_INSTALL_TEST_PORT', str( default_galaxy_test_port_max ) ) - # Initialize some variables for the summary that will be printed to stdout. - repositories_tested = 0 - repositories_passed = [] - repositories_failed = [] - tool_path = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_PATH', 'tools' ) if 'HTTP_ACCEPT_LANGUAGE' not in os.environ: os.environ[ 'HTTP_ACCEPT_LANGUAGE' ] = default_galaxy_locales @@ -444,38 +452,19 @@ 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 + # Initialize some variables for the summary that will be printed to stdout. + repositories_tested = 0 + repositories_passed = [] + repositories_failed = [] + repositories_failed_install = [] try: - # Iterate through a list of repository info dicts. + detailed_repository_list = [] + # Get a list of repositories to test from the tool shed specified in the GALAXY_INSTALL_TEST_TOOL_SHED_URL environment variable. log.info( "Retrieving repositories to install from the URL:\n%s\n" % str( galaxy_tool_shed_url ) ) repositories_to_install = get_repositories_to_install( galaxy_tool_shed_url, source='url' ) log.info( "Retrieved %d repositories to install..." % len( repositories_to_install ) ) repositories_tested = len( repositories_to_install ) - # This loop will iterate through the list of repositories returned by the above method, skipping any that are marked - # as deleted. For each repository, it will generate a test method that will use Twill to install that repository into the - # embedded Galaxy application that was started up, selecting to install repository and tool dependencies if they are - # defined. If the installation completes successfully, it will then generate a test case for each functional test - # defined for each tool in the repository, and execute the generated test cases. When this completes, it will record - # the result of the tests, and if any failed, the traceback and captured output of the tool that was run. - # After all tests have completed, the repository is uninstalled, so that the previous test cases don't interfere with - # the next repository's functional tests. for repository_to_install_dict in repositories_to_install: - """ - Each repository_to_install_dict looks something like: - { - "changeset_revision": "13fa22a258b5", - "downloadable": true, - "id": "529fd61ab1c6cc36", - "malicious": false, - "repository_id": "529fd61ab1c6cc36", - "url": "/api/repository_revisions/529fd61ab1c6cc36" - } - """ - repository_status = dict() - repository_id = repository_to_install_dict.get( 'repository_id', None ) - changeset_revision = repository_to_install_dict.get( 'changeset_revision', None ) - metadata_revision_id = repository_to_install_dict.get( 'id', None ) - # Add the URL for the tool shed we're installing from, so the automated installation methods go to the right place. - repository_to_install_dict[ 'tool_shed_url' ] = galaxy_tool_shed_url # We need to get some details from the tool shed API, such as repository name and owner, to pass on to the # module that will generate the install methods. repository_info_dict = get_repository_info_from_api( galaxy_tool_shed_url, repository_to_install_dict ) @@ -483,13 +472,31 @@ # and functionally correct tools that someone has previously installed. Deleted repositories have never been installed, # and therefore do not need to be checked. If they are undeleted, this script will then test them the next time it runs. if repository_info_dict[ 'deleted' ]: - log.info( "Skipping revision %s of repository id %s since the repository is deleted..." % ( str( changeset_revision ), str( repository_id ) ) ) + log.info( "Skipping revision %s of repository id %s (%s/%s) since the repository is deleted..." % \ + ( repository_info_dict[ 'changeset_revision' ], + repository_info_dict[ 'repository_id' ], + repository_info_dict[ 'owner' ], + repository_info_dict[ 'name' ] ) ) continue - log.info( "Installing and testing revision %s of repository id %s..." % ( str( changeset_revision ), str( repository_id ) ) ) - # Add repository details to the basic repository dict. - repository_dict = dict( repository_info_dict.items() + repository_to_install_dict.items() ) + # Now merge the dict returned from /api/repository_revisions with the detailed dict we just retrieved. + detailed_repository_list.append( dict( repository_info_dict.items() + repository_to_install_dict.items() ) ) + if '-list_repositories' in sys.argv: + log.info( "The API returned the following repositories, not counting deleted:" ) + for repository_info_dict in detailed_repository_list: + log.info( "%s owned by %s changeset revision %s" % ( repository_info_dict.get( 'name', None ), + repository_info_dict.get( 'owner', None ), + repository_info_dict.get( 'changeset_revision', None ) ) ) + # This loop will iterate through the list of repositories generated by the above code, having already filtered out any + # that were marked as deleted. For each repository, it will generate a test method that will use Twill to install that + # repository into the embedded Galaxy application that was started up, selecting to install repository and tool + # dependencies if they are defined. If the installation completes successfully, it will then generate a test case for + # each functional test defined for each tool in the repository, and execute the generated test cases. When this completes, + # it will record the result of the tests, and if any failed, the traceback and captured output of the tool that was run. + # After all tests have completed, the repository is uninstalled, so that the previous test cases don't interfere with + # the next repository's functional tests. + for repository_info_dict in detailed_repository_list: """ - After the addition of the repository details, each repository_dict should now contain something like: + Each repository_info_dict looks something like: { "changeset_revision": "13fa22a258b5", "contents_url": "/api/repositories/529fd61ab1c6cc36/contents", @@ -510,11 +517,19 @@ "user_id": "529fd61ab1c6cc36" } """ - name = repository_dict[ 'name' ] - owner = repository_dict[ 'owner' ] + repository_status = dict() + repository_id = repository_info_dict.get( 'repository_id', None ) + changeset_revision = repository_info_dict.get( 'changeset_revision', None ) + metadata_revision_id = repository_info_dict.get( 'id', None ) + # Add the URL for the tool shed we're installing from, so the automated installation methods go to the right place. + repository_info_dict[ 'tool_shed_url' ] = galaxy_tool_shed_url + log.info( "Installing and testing revision %s of repository id %s..." % ( str( changeset_revision ), str( repository_id ) ) ) + # Get the name and owner out of the repository info dict. + name = repository_info_dict[ 'name' ] + owner = repository_info_dict[ 'owner' ] # Use the repository information dict to generate an install method that will install the repository into the embedded # Galaxy application, with tool dependencies and repository dependencies, if any. - test_install_repositories.generate_install_method( repository_dict ) + test_install_repositories.generate_install_method( repository_info_dict ) os.environ[ 'GALAXY_INSTALL_TEST_HOST' ] = galaxy_test_host # Configure nose to run the install method as a test. test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) @@ -526,7 +541,7 @@ # If the installation succeeds, configure and run functional tests for this repository. This is equivalent to # sh run_functional_tests.sh -installed if success: - log.debug( 'Installation of %s succeeded, running all defined functional tests.' % repository_dict[ 'name' ] ) + log.debug( 'Installation of %s succeeded, running all defined functional tests.' % name ) # Generate the shed_tools_dict that specifies the location of test data contained within this repository. If the repository # does not have a test-data directory, this will return has_test_data = False, and we will set the do_not_test flag to True, # and the tools_functionally_correct flag to False, as well as updating tool_test_errors. @@ -574,17 +589,18 @@ # }, # ] # } - repository_status = get_tool_test_errors_from_api( galaxy_tool_shed_url, repository_dict ) + repository_status = get_tool_test_errors_from_api( galaxy_tool_shed_url, repository_info_dict ) + if 'test_environment' not in repository_status: + repository_status[ 'test_environment' ] = {} test_environment = get_test_environment( repository_status[ 'test_environment' ] ) test_environment[ 'galaxy_database_version' ] = get_database_version( app ) test_environment[ 'galaxy_revision'] = get_repository_current_revision( os.getcwd() ) repository_status[ 'test_environment' ] = test_environment repository_status[ 'tests_passed' ] = [] repository_status[ 'test_errors' ] = [] + repository_status[ 'invalid_tests' ] = [] if not has_test_data: log.error( 'Test data is missing for this repository. Updating repository and skipping functional tests.' ) - repository_status[ 'test_environment' ] = get_test_environment() - test_id = 'Find functional test data for %s' % repository_dict[ 'name' ] # Record the lack of test data. test_errors = dict( tool_id=None, tool_version=None, tool_guid=None, reason_test_is_invalid="Repository %s is missing a test-data directory." % name ) @@ -593,7 +609,7 @@ register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, tests_passed=False ) # Run the cleanup method. This removes tool functional test methods from the test_toolbox module and uninstalls the # repository using Twill. - execute_uninstall_method( repository_dict ) + execute_uninstall_method( repository_info_dict ) # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. test_toolbox.toolbox = app.toolbox repositories_failed.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) @@ -618,9 +634,7 @@ # Run the configured tests. result, test_plugins = run_tests( test_config ) success = result.wasSuccessful() - # Record some information about the environment in which this test was run, in case a failure is specific to a certain processor - # architecture or operating system. - repository_dict[ 'test_environment' ] = test_environment + # Use the ReportResults nose plugin to get a list of tests that passed. for plugin in test_plugins: if hasattr( plugin, 'getTestStatus' ): test_identifier = '%s/%s' % ( owner, name ) @@ -637,10 +651,8 @@ # controller with the status of the test. This also sets the do_not_test and tools_functionally correct flags, and # updates the time_last_tested field to today's date. repositories_passed.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) - repository_status[ 'test_environment' ] = test_environment register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, tests_passed=True ) - log.debug( 'Revision %s of repository %s installed and passed functional tests.' % \ - ( repository_dict[ 'changeset_revision' ], repository_dict[ 'name' ] ) ) + log.debug( 'Revision %s of repository %s installed and passed functional tests.' % ( changeset_revision, name ) ) else: # If the functional tests fail, log the output and update the failed changeset revision's metadata record in the tool shed via the API. for failure in result.failures: @@ -686,14 +698,15 @@ repositories_failed.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, tests_passed=False ) log.debug( 'Revision %s of repository %s installed successfully, but did not pass functional tests.' % \ - ( repository_dict[ 'changeset_revision' ], repository_dict[ 'name' ] ) ) + ( changeset_revision, name ) ) # Run the cleanup method. This removes tool functional test methods from the test_toolbox module and uninstalls the # repository using Twill. - execute_uninstall_method( repository_dict ) + execute_uninstall_method( repository_info_dict ) # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. test_toolbox.toolbox = app.toolbox else: - log.debug( 'Repository %s failed to install correctly.' % repository_dict[ 'name' ] ) + repositories_failed_install.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) + log.debug( 'Repository %s failed to install correctly.' % name ) except: log.exception( "Failure running tests" ) @@ -728,29 +741,17 @@ print "# Repository revisions tested: %d" % repositories_tested if repositories_tested > 0: if repositories_passed: - passed_repositories_by_owner = dict() - for repository in repositories_passed: - if repository[ 'owner' ] not in passed_repositories_by_owner: - passed_repositories_by_owner[ repository[ 'owner' ] ] = [] - passed_repositories_by_owner[ repository[ 'owner' ] ].append( repository ) print "# " print "# Repositories passed:" - for owner in passed_repositories_by_owner: - print "# " - for repository in passed_repositories_by_owner[ owner ]: - print "# %s owned by %s, changeset revision %s" % ( repository[ 'name' ], repository[ 'owner' ], repository[ 'changeset_revision' ] ) + show_summary_output( repositories_passed ) if repositories_failed: - failed_repositories_by_owner = dict() - for repository in repositories_failed: - if repository[ 'owner' ] not in failed_repositories_by_owner: - failed_repositories_by_owner[ repository[ 'owner' ] ] = [] - failed_repositories_by_owner[ repository[ 'owner' ] ].append( repository ) print "# " print "# Repositories failed:" - for owner in failed_repositories_by_owner: - print "# " - for repository in failed_repositories_by_owner[ owner ]: - print "# %s owned by %s, changeset revision %s" % ( repository[ 'name' ], repository[ 'owner' ], repository[ 'changeset_revision' ] ) + show_summary_output( repositories_failed ) + if repositories_failed_install: + print "# " + print "# Repositories not installed correctly:" + show_summary_output( repositories_failed_install ) print "####################################################################################" if success: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Explicitly clear ReportResults.passed after each set of tests. Group test results by repository owner, and separate with a blank line.
by commits-noreply＠bitbucket.org 08 Mar '13

08 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2b4d6af45a04/ changeset: 2b4d6af45a04 user: inithello date: 2013-03-08 23:03:32 summary: Explicitly clear ReportResults.passed after each set of tests. Group test results by repository owner, and separate with a blank line. affected #: 1 file diff -r f25f3fee4da76fc0660ba27a1b26673d7592ddc1 -r 2b4d6af45a04ddb49c2c87a0ead3874503d35832 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 @@ -120,7 +120,7 @@ class ReportResults( Plugin ): '''Simple Nose plugin to record the IDs of all tests run, regardless of success.''' name = "reportresults" - passed = [] + passed = dict() def options( self, parser, env=os.environ ): super( ReportResults, self ).options( parser, env=env ) @@ -137,10 +137,18 @@ # Rearrange the test ID to match the format that is produced in test_results.failures test_id_parts = test_id.split( '.' ) fixed_test_id = '%s (%s)' % ( test_id_parts[ -1 ], '.'.join( test_id_parts[ :-1 ] ) ) - self.passed.append( fixed_test_id ) + test_parts = fixed_test_id.split( '/' ) + owner = test_parts[ -4 ] + name = test_parts[ -3 ] + test_identifier = '%s/%s' % ( owner, name ) + if test_identifier not in self.passed: + self.passed[ test_identifier ] = [] + self.passed[ test_identifier ].append( fixed_test_id ) - def getTestStatus( self ): - return self.passed + def getTestStatus( self, test_identifier ): + tests_passed = self.passed[ test_identifier ] + del self.passed[ test_identifier ] + return tests_passed def execute_uninstall_method( repository_dict ): # Delete any configured tool functional tests from the test_toolbox.__dict__, otherwise nose will find them @@ -615,7 +623,8 @@ repository_dict[ 'test_environment' ] = test_environment for plugin in test_plugins: if hasattr( plugin, 'getTestStatus' ): - tests_passed = plugin.getTestStatus() + test_identifier = '%s/%s' % ( owner, name ) + tests_passed = plugin.getTestStatus( test_identifier ) break repository_status[ 'tests_passed' ] = [] for test_id in tests_passed: @@ -670,7 +679,6 @@ if output_type in tmp_output: test_status[ output_type ] = '\n'.join( tmp_output[ output_type ] ) repository_status[ 'test_errors' ].append( test_status ) - log.debug( to_json_string( repository_status, indent=2, sort_keys=True ) ) # Call the register_test_result method, which executes a PUT request to the repository_revisions API controller with the outcome # of the tests, and updates tool_test_errors with the relevant log data. # This also sets the do_not_test and tools_functionally correct flags to the appropriate values, and updates the time_last_tested @@ -720,13 +728,29 @@ print "# Repository revisions tested: %d" % repositories_tested if repositories_tested > 0: if repositories_passed: + passed_repositories_by_owner = dict() + for repository in repositories_passed: + if repository[ 'owner' ] not in passed_repositories_by_owner: + passed_repositories_by_owner[ repository[ 'owner' ] ] = [] + passed_repositories_by_owner[ repository[ 'owner' ] ].append( repository ) + print "# " print "# Repositories passed:" - for repository in repositories_passed: - print "# %s owned by %s, changeset revision %s" % ( repository[ 'name' ], repository[ 'owner' ], repository[ 'changeset_revision' ] ) + for owner in passed_repositories_by_owner: + print "# " + for repository in passed_repositories_by_owner[ owner ]: + print "# %s owned by %s, changeset revision %s" % ( repository[ 'name' ], repository[ 'owner' ], repository[ 'changeset_revision' ] ) if repositories_failed: + failed_repositories_by_owner = dict() + for repository in repositories_failed: + if repository[ 'owner' ] not in failed_repositories_by_owner: + failed_repositories_by_owner[ repository[ 'owner' ] ] = [] + failed_repositories_by_owner[ repository[ 'owner' ] ].append( repository ) + print "# " print "# Repositories failed:" - for repository in repositories_failed: - print "# %s owned by %s, changeset revision %s" % ( repository[ 'name' ], repository[ 'owner' ], repository[ 'changeset_revision' ] ) + for owner in failed_repositories_by_owner: + print "# " + for repository in failed_repositories_by_owner[ owner ]: + print "# %s owned by %s, changeset revision %s" % ( repository[ 'name' ], repository[ 'owner' ], repository[ 'changeset_revision' ] ) print "####################################################################################" if success: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Remove unused yet exposed 'stdoutX' method of the datasets controller.
by commits-noreply＠bitbucket.org 08 Mar '13

08 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f25f3fee4da7/ changeset: f25f3fee4da7 user: dannon date: 2013-03-08 22:01:25 summary: Remove unused yet exposed 'stdoutX' method of the datasets controller. affected #: 1 file diff -r 619995bcb99feda43d9a369a7aa563108a19f3c7 -r f25f3fee4da76fc0660ba27a1b26673d7592ddc1 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -180,16 +180,6 @@ if not hda or not self._can_access_dataset( trans, hda ): return trans.show_error_message( "Either this dataset does not exist or you do not have permission to access it." ) return trans.fill_template( "dataset/errors.mako", hda=hda ) - @web.expose - def stdoutX( self, trans, dataset_id=None, **kwargs ): - trans.response.set_content_type( 'text/plain' ) - try: - hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) - assert hda and self._can_access_dataset( trans, hda ) - job = hda.creating_job_associations[0].job - except: - return "Invalid dataset ID or you are not allowed to access this dataset" - return job.stdout @web.expose def stdout( self, trans, dataset_id=None, **kwargs ): 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: Enhance the script that checks repositories for functional tests, adding support for multiple web frontends.
by commits-noreply＠bitbucket.org 08 Mar '13

08 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/619995bcb99f/ changeset: 619995bcb99f user: inithello date: 2013-03-08 20:44:57 summary: Enhance the script that checks repositories for functional tests, adding support for multiple web frontends. affected #: 1 file diff -r c937f80188d8026f2074f8a897e2ff2972d8da6d -r 619995bcb99feda43d9a369a7aa563108a19f3c7 lib/tool_shed/scripts/check_repositories_for_functional_tests.py --- a/lib/tool_shed/scripts/check_repositories_for_functional_tests.py +++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py @@ -38,6 +38,12 @@ '''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( "-s", + "--section", + action="store", + dest="section", + default='server:main', + help="which .ini file section to extract the host and port from" ) parser.add_option( "-v", "--verbose", action="count", dest="verbosity", @@ -57,10 +63,11 @@ 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 - Checking repositories for tools with functional tests." % now - print "# This tool shed is configured to listen on %s:%s." % ( config_parser.get( 'server:main', 'host' ), config_parser.get( 'server:main', 'port' ) ) + print "# This tool shed is configured to listen on %s:%s." % ( config_parser.get( config_section, 'host' ), config_parser.get( config_section, 'port' ) ) app = FlagRepositoriesApplication( config ) if options.info_only: 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 March 2013