1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/41e739778945/ Changeset: 41e739778945 User: greg Date: 2013-12-03 21:16:14 Summary: Fixes for filtering repository revision to be tested by the Tool Shed's install and test framework, and a new Tool Shed API script to enable analyzing the the Tool Shed's install and test framework. Affected #: 3 files

diff -r 5830078f639cd0b145ca3975f9c621c3d3b69cf1 -r 41e739778945ac5f564785b59b2a90051676d4f2 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 @@ -65,7 +65,7 @@ trans.response.status = 500 return message

- @web.expose_api + @web.expose_api_anonymous def index( self, trans, **kwd ): """ GET /api/repository_revisions @@ -107,9 +107,10 @@ skip_tool_test = kwd.get( 'skip_tool_test', None ) if skip_tool_test is not None: skip_tool_test = util.string_as_bool( skip_tool_test ) - if skip_tool_test: skipped_metadata_ids_subquery = select( [ trans.app.model.SkipToolTest.table.c.repository_metadata_id ] ) - if skipped_metadata_ids_subquery: + if skip_tool_test: + clause_list.append( trans.model.RepositoryMetadata.id.in_( skipped_metadata_ids_subquery ) ) + else: clause_list.append( not_( trans.model.RepositoryMetadata.id.in_( skipped_metadata_ids_subquery ) ) ) # Generate and execute the query. try: @@ -131,7 +132,7 @@ trans.response.status = 500 return message

- @web.expose_api + @web.expose_api_anonymous def show( self, trans, id, **kwd ): """ GET /api/repository_revisions/{encoded_repository_metadata_id}

diff -r 5830078f639cd0b145ca3975f9c621c3d3b69cf1 -r 41e739778945ac5f564785b59b2a90051676d4f2 lib/tool_shed/scripts/api/get_filtered_repository_revisions.py --- /dev/null +++ b/lib/tool_shed/scripts/api/get_filtered_repository_revisions.py @@ -0,0 +1,150 @@ +#!/usr/bin/env python +""" +Get a list of dictionaries, each of which defines a repository revision, that is filtered by a combination of one or more +of the following. + +- do_not_test : true / false +- downloadable : true / false +- includes_tools : true / false +- malicious : true / false +- missing_test_components : true / false +- skip_tool_test : true / false +- test_install_error : true / false +- tools_functionally_correct : true / false + +Results can also be restricted to the latest downloadable revision of each repository. + +This script is useful for analyzing the Tool Shed's install and test framework. + +Here is a working example of how to use this script. +./get_filtered_repository_revisions.py --url http://testtoolshed.g2.bx.psu.edu +""" + +import argparse +import os +import sys +import urllib + +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import get +from galaxy.util.json import from_json_string +import tool_shed.util.shed_util_common as suc + +def get_api_url( base, parts=[], params=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 = suc.url_join( base, *parts ) + if params: + url += '?%s' % params + return url + +def get_latest_downloadable_changeset_revision( url, name, owner ): + error_message = '' + parts = [ 'api', 'repositories', 'get_ordered_installable_revisions' ] + params = urllib.urlencode( dict( name=name, owner=owner ) ) + api_url = get_api_url( base=url, parts=parts, params=params ) + changeset_revisions, error_message = json_from_url( api_url ) + if error_message: + return None, error_message + if changeset_revisions: + return changeset_revisions[ -1 ], error_message + else: + return suc.INITIAL_CHANGELOG_HASH, error_message + +def get_repository_dict( url, repository_dict ): + error_message = '' + parts = [ 'api', 'repositories', repository_dict[ 'repository_id' ] ] + api_url = get_api_url( base=url, parts=parts ) + extended_dict, error_message = json_from_url( api_url ) + if error_message: + return None, error_message + name = str( extended_dict[ 'name' ] ) + owner = str( extended_dict[ 'owner' ] ) + latest_changeset_revision, error_message = get_latest_downloadable_changeset_revision( url, name, owner ) + if error_message: + print error_message + extended_dict[ 'latest_revision' ] = str( latest_changeset_revision ) + return extended_dict, error_message + +def json_from_url( url ): + error_message = '' + url_handle = urllib.urlopen( url ) + url_contents = url_handle.read() + try: + parsed_json = from_json_string( url_contents ) + except Exception, e: + error_message = str( url_contents ) + return None, error_message + return parsed_json, error_message + +def string_as_bool( string ): + if str( string ).lower() in [ 'true' ]: + return True + else: + return False + +def main( options ): + base_tool_shed_url = options.tool_shed_url.rstrip( '/' ) + latest_revision_only = string_as_bool( options.latest_revision_only ) + do_not_test = str( options.do_not_test ) + downloadable = str( options.downloadable ) + includes_tools = str( options.includes_tools ) + malicious = str( options.malicious ) + missing_test_components = str( options.missing_test_components ) + skip_tool_test = str( options.skip_tool_test ) + test_install_error = str( options.test_install_error ) + tools_functionally_correct = str( options.tools_functionally_correct ) + parts=[ 'repository_revisions' ] + params = urllib.urlencode( dict( do_not_test=do_not_test, + downloadable=downloadable, + includes_tools=includes_tools, + malicious=malicious, + missing_test_components=missing_test_components, + skip_tool_test=skip_tool_test, + test_install_error=test_install_error, + tools_functionally_correct=tools_functionally_correct ) ) + api_url = get_api_url( base=base_tool_shed_url, parts=parts, params=params ) + baseline_repository_dicts, error_message = json_from_url( api_url ) + if error_message: + print error_message + repository_dicts = [] + for baseline_repository_dict in baseline_repository_dicts: + # 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_dict, error_message = get_repository_dict( base_tool_shed_url, baseline_repository_dict ) + if error_message: + print 'Error getting additional details from the API: ', error_message + repository_dicts.append( baseline_repository_dict ) + else: + # Don't test empty repositories. + changeset_revision = baseline_repository_dict[ 'changeset_revision' ] + if changeset_revision != suc.INITIAL_CHANGELOG_HASH: + # Merge the dictionary returned from /api/repository_revisions with the detailed repository_dict and + # append it to the list of repository_dicts to install and test. + if latest_revision_only: + latest_revision = repository_dict[ 'latest_revision' ] + if changeset_revision == latest_revision: + repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) + else: + repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) + print '\n\n', repository_dicts + print '\nThe url:\n\n', api_url, '\n\nreturned ', len( repository_dicts ), ' repository dictionaries...' + +if __name__ == '__main__': + parser = argparse.ArgumentParser( description='Get a filtered list of repository dictionaries.' ) + parser.add_argument( "-u", "--url", dest="tool_shed_url", required=True, help="Tool Shed URL" ) + parser.add_argument( "-l", "--latest_revision_only", dest="latest_revision_only", default=True, + help="Restrict results to latest downloadable revision only" ) + parser.add_argument( "-n", "--do_not_test", help="do_not_test", default=False ) + parser.add_argument( "-d", "--downloadable", help="downloadable", default=True ) + parser.add_argument( "-i", "--includes_tools", help="includes_tools", default=True ) + parser.add_argument( "-m", "--malicious", help="malicious", default=False ) + parser.add_argument( "-c", "--missing_test_components", help="missing_test_components", default=False ) + parser.add_argument( "-s", "--skip_tool_test", help="skip_tool_test", default=False ) + parser.add_argument( "-e", "--test_install_error", help="test_install_error", default=False ) + parser.add_argument( "-t", "--tools_functionally_correct", help="tools_functionally_correct", default=True ) + options = parser.parse_args() + main( options )

diff -r 5830078f639cd0b145ca3975f9c621c3d3b69cf1 -r 41e739778945ac5f564785b59b2a90051676d4f2 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 @@ -292,26 +292,22 @@ log_data.append( test_status ) return log_data

-def get_api_url( base, parts=[], params=None, key=None ): +def get_api_url( base, parts=[], params=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 = suc.url_join( base, *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 + url += '?%s' % params return url

def get_latest_downloadable_changeset_revision( url, name, owner ): error_message = '' - api_url_parts = [ 'api', 'repositories', 'get_ordered_installable_revisions' ] + parts = [ 'api', 'repositories', 'get_ordered_installable_revisions' ] params = urllib.urlencode( dict( name=name, owner=owner ) ) - api_url = get_api_url( url, api_url_parts, params ) + api_url = get_api_url( base=url, parts=parts, params=params ) changeset_revisions, error_message = json_from_url( api_url ) if error_message: return None, error_message @@ -333,7 +329,7 @@ def get_repository_dict( url, repository_dict ): error_message = '' parts = [ 'api', 'repositories', repository_dict[ 'repository_id' ] ] - api_url = get_api_url( base=url, parts=parts ) + api_url = get_api_url( base=url, parts=parts, params=None ) extended_dict, error_message = json_from_url( api_url ) if error_message: return None, error_message @@ -366,13 +362,14 @@ if latest_revision_only: log.debug( 'Testing is restricted to the latest downloadable revision in this test run.' ) repository_dicts = [] + parts = [ 'repository_revisions' ] params = urllib.urlencode( dict( do_not_test='false', downloadable='true', includes_tools='true', malicious='false', missing_test_components='false', skip_tool_test='false' ) ) - api_url = get_api_url( base=tool_shed_url, parts=[ 'repository_revisions' ], params=params ) + api_url = get_api_url( base=tool_shed_url, parts=parts, params=params ) baseline_repository_dicts, error_message = json_from_url( api_url ) if error_message: return None, error_message @@ -457,8 +454,8 @@ column via the Tool Shed API. """ error_message = '' - api_path = [ 'api', 'repository_revisions', encoded_repository_metadata_id ] - api_url = get_api_url( base=tool_shed_url, parts=api_path ) + parts = [ 'api', 'repository_revisions', encoded_repository_metadata_id ] + api_url = get_api_url( base=tool_shed_url, parts=parts, params=None ) repository_metadata, error_message = json_from_url( api_url ) if error_message: return None, error_message

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

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