December 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: carlfeberhard: api/history_contents: temporarily disabling get_display_types
by Bitbucket 17 Dec '12

17 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a3ecba6f3e0c/ changeset: a3ecba6f3e0c user: carlfeberhard date: 2012-12-17 16:50:34 summary: api/history_contents: temporarily disabling get_display_types affected #: 1 file diff -r 4033d81b3311e105f79377cfe64df5861851f5d1 -r a3ecba6f3e0c1ecc719a42b6bccfa0b32746ba27 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -196,7 +196,7 @@ hda_dict[ 'meta_files' ] = meta_files hda_dict[ 'display_apps' ] = get_display_apps( trans, hda ) - hda_dict[ 'display_types' ] = get_display_types( trans, hda ) + #hda_dict[ 'display_types' ] = get_display_types( trans, hda ) hda_dict[ 'visualizations' ] = hda.get_visualizations() hda_dict[ 'peek' ] = to_unicode( hda.display_peek() ) 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: Missed an import.
by Bitbucket 14 Dec '12

14 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4033d81b3311/ changeset: 4033d81b3311 user: greg date: 2012-12-14 22:37:42 summary: Missed an import. affected #: 1 file diff -r f14ca41c8cf34779d0b89979320488ebe04eb943 -r 4033d81b3311e105f79377cfe64df5861851f5d1 lib/galaxy/tool_shed/tool_dependencies/install_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/install_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/install_util.py @@ -1,7 +1,7 @@ import sys, os, subprocess, tempfile import common_util import fabric_util -from galaxy.tool_shed.encoding_util import tool_shed_encode +from galaxy.tool_shed.encoding_util import encoding_sep, tool_shed_encode, tool_shed_decode from galaxy.model.orm import and_ from galaxy import eggs 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: More tool shed functional test enhancements.
by Bitbucket 14 Dec '12

14 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f14ca41c8cf3/ changeset: f14ca41c8cf3 user: inithello date: 2012-12-14 22:20:22 summary: More tool shed functional test enhancements. affected #: 13 files diff -r 33d4ab5cc642f2bdc5ad8670abf4400063bb8415 -r f14ca41c8cf34779d0b89979320488ebe04eb943 lib/galaxy/visualization/genomes.py --- a/lib/galaxy/visualization/genomes.py +++ b/lib/galaxy/visualization/genomes.py @@ -1,9 +1,11 @@ -import os, re, sys, glob +import os, re, sys, glob, logging from bx.seq.twobit import TwoBitFile from galaxy.util.json import from_json_string from galaxy import model from galaxy.util.bunch import Bunch +log = logging.getLogger( __name__ ) + # FIXME: copied from tracks.py # Message strings returned to browser messages = Bunch( @@ -166,13 +168,18 @@ self.genomes[ key ] = Genome( key, len_file=f ) # Add genome data (twobit files) to genomes. - for line in open( os.path.join( app.config.tool_data_path, "twobit.loc" ) ): - if line.startswith("#"): continue - val = line.split() - if len( val ) == 2: - key, path = val - if key in self.genomes: - self.genomes[ key ].twobit_file = path + # FIXME: If a galaxy instance does not have ~/tool-data/twobit.loc file, the following error is thrown: + # IOError: [Errno 2] No such file or directory: '~/tool-data/twobit.loc' + try: + for line in open( os.path.join( app.config.tool_data_path, "twobit.loc" ) ): + if line.startswith("#"): continue + val = line.split() + if len( val ) == 2: + key, path = val + if key in self.genomes: + self.genomes[ key ].twobit_file = path + except IOError, e: + log.exception( str( e ) ) def get_build( self, dbkey ): """ Returns build for the given key. """ diff -r 33d4ab5cc642f2bdc5ad8670abf4400063bb8415 -r f14ca41c8cf34779d0b89979320488ebe04eb943 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -1,6 +1,7 @@ import galaxy.webapps.community.util.hgweb_config import galaxy.model as galaxy_model -import common, string, os, re, test_db_util +import common, string, os, re, test_db_util, simplejson +import galaxy.util as util from base.twilltestcase import tc, from_json_string, TwillTestCase, security, urllib from galaxy.tool_shed.encoding_util import tool_shed_encode @@ -23,8 +24,10 @@ self.galaxy_host = os.environ.get( 'GALAXY_TEST_HOST' ) self.galaxy_port = os.environ.get( 'GALAXY_TEST_PORT' ) self.galaxy_url = "http://%s:%s" % ( self.galaxy_host, self.galaxy_port ) + self.shed_tool_data_table_conf = os.environ.get( 'TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF' ) self.file_dir = os.environ.get( 'TOOL_SHED_TEST_FILE_DIR', None ) self.tool_shed_test_file = None + self.tool_data_path = os.environ.get( 'GALAXY_TEST_TOOL_DATA_PATH' ) self.shed_tools_dict = {} self.home() def browse_category( self, category, strings_displayed=[], strings_not_displayed=[] ): @@ -439,9 +442,14 @@ repo = hg.repository( ui.ui(), self.get_repo_path( repository ) ) tip_ctx = repo.changectx( repo.changelog.tip() ) return tip_ctx.rev() < 0 + def reset_installed_repository_metadata( self, repository ): + url = '/admin_toolshed/reset_repository_metadata?id=%s' % self.security.encode_id( repository.id ) + self.visit_galaxy_url( url ) + self.check_for_strings( [ 'Metadata has been reset' ] ) def reset_repository_metadata( self, repository ): url = '/repository/reset_all_metadata?id=%s' % self.security.encode_id( repository.id ) self.visit_url( url ) + self.check_for_strings( [ 'All repository metadata has been reset.' ] ) def revoke_write_access( self, repository, username ): url = '/repository/manage_repository?user_access_button=Remove&id=%s&remove_auth=%s' % \ ( self.security.encode_id( repository.id ), username ) @@ -466,6 +474,10 @@ def tip_has_metadata( self, repository ): tip = self.get_repository_tip( repository ) return test_db_util.get_repository_metadata_by_repository_id_changeset_revision( repository.id, tip ) + def update_installed_repository( self, installed_repository, strings_displayed=[], strings_not_displayed=[] ): + url = '/admin_toolshed/check_for_updates?id=%s' % self.security.encode_id( installed_repository.id ) + self.visit_galaxy_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) def upload_file( self, repository, filename, @@ -482,6 +494,27 @@ tc.formfile( "1", "file_data", self.get_filename( filename, filepath ) ) tc.submit( "upload_button" ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def verify_installed_repository_metadata_unchanged( self, name, owner ): + installed_repository = test_db_util.get_installed_repository_by_name_owner( name, owner ) + differs = False + metadata = installed_repository.metadata + self.reset_installed_repository_metadata( installed_repository ) + new_metadata = installed_repository.metadata + # This test assumes that the different metadata components will always appear in the same order. If this is ever not + # the case, this test must be updated. + for metadata_key in [ 'datatypes', 'tools', 'tool_dependencies', 'repository_dependencies', 'workflows' ]: + if ( metadata_key in metadata and metadata_key not in new_metadata ) or \ + ( metadata_key not in metadata and metadata_key in new_metadata ): + differs = True + break + elif metadata_key not in metadata and metadata_key not in new_metadata: + continue + else: + if metadata[ metadata_key ] != new_metadata[ metadata_key ]: + differs = True + break + if differs: + raise AssertionError( 'Metadata for installed repository %s differs after metadata reset.' % name ) def verify_installed_repository_on_browse_page( self, installed_repository, strings_displayed=[], strings_not_displayed=[] ): url = '/admin_toolshed/browse_repositories' self.visit_galaxy_url( url ) @@ -491,6 +524,17 @@ installed_repository.tool_shed, installed_repository.installed_changeset_revision ] ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def verify_installed_repository_data_table_entries( self, data_tables=[] ): + data_table = util.parse_xml( self.shed_tool_data_table_conf ) + found = False + for table_elem in data_table.findall( 'table' ): + for data_table in data_tables: + if 'name' in table_elem.attrib and table_elem.attrib[ 'name' ] == data_table: + file_elem = table_elem.find( 'file' ) + assert os.path.exists( file_elem.attrib[ 'path' ] ), 'Tool data table file %s not found.' % file_elem.path + found = True + break + assert found, 'No entry for %s in %s.' % ( data_table, self.shed_tool_data_table_conf ) def verify_tool_metadata_for_installed_repository( self, installed_repository, strings_displayed=[], strings_not_displayed=[] ): repository_id = self.security.encode_id( installed_repository.id ) for tool in installed_repository.metadata[ 'tools' ]: @@ -499,6 +543,11 @@ url = '/admin_toolshed/view_tool_metadata?repository_id=%s&tool_id=%s' % ( repository_id, urllib.quote_plus( tool[ 'id' ] ) ) self.visit_galaxy_url( url ) self.check_for_strings( strings, strings_not_displayed ) + def verify_unchanged_repository_metadata( self, repository ): + self.check_repository_changelog( repository ) + html = self.last_page() + self.reset_repository_metadata( repository ) + self.check_repository_changelog( repository, strings_displayed=[ html ] ) def visit_galaxy_url( self, url ): url = '%s%s' % ( self.galaxy_url, url ) self.visit_url( url ) diff -r 33d4ab5cc642f2bdc5ad8670abf4400063bb8415 -r f14ca41c8cf34779d0b89979320488ebe04eb943 test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -155,3 +155,7 @@ tip_changeset = self.get_repository_tip( repository ) search_fields = dict( tool_id='Filter1', tool_name='filter', tool_version='2.2.0' ) self.search_for_valid_tools( search_fields=search_fields, strings_displayed=[ tip_changeset ], strings_not_displayed=[] ) + def test_0085_verify_repository_metadata( self ): + '''Verify that resetting the metadata does not change it.''' + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + self.verify_unchanged_repository_metadata( repository ) diff -r 33d4ab5cc642f2bdc5ad8670abf4400063bb8415 -r f14ca41c8cf34779d0b89979320488ebe04eb943 test/tool_shed/functional/test_0020_basic_repository_dependencies.py --- a/test/tool_shed/functional/test_0020_basic_repository_dependencies.py +++ b/test/tool_shed/functional/test_0020_basic_repository_dependencies.py @@ -68,3 +68,9 @@ changeset_revision = self.get_repository_tip( datatypes_repository ) strings_displayed = [ datatypes_repository_name, common.test_user_1_name, changeset_revision, 'Repository dependencies' ] self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + def test_0040_verify_repository_metadata( self ): + '''Verify that resetting the metadata does not change it.''' + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + self.verify_unchanged_repository_metadata( emboss_repository ) + self.verify_unchanged_repository_metadata( datatypes_repository ) diff -r 33d4ab5cc642f2bdc5ad8670abf4400063bb8415 -r f14ca41c8cf34779d0b89979320488ebe04eb943 test/tool_shed/functional/test_0030_repository_dependency_revisions.py --- a/test/tool_shed/functional/test_0030_repository_dependency_revisions.py +++ b/test/tool_shed/functional/test_0030_repository_dependency_revisions.py @@ -131,3 +131,11 @@ self.display_manage_repository_page( repository, changeset_revision=changeset_revision, strings_displayed=[ str( metadata ) for metadata in repository_dependency_metadata ] ) + def test_0040_verify_repository_metadata( self ): + '''Verify that resetting the metadata does not change it.''' + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + emboss_5_repository = test_db_util.get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name ) + emboss_6_repository = test_db_util.get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name ) + datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + for repository in [ emboss_repository, emboss_5_repository, emboss_6_repository, datatypes_repository ]: + self.verify_unchanged_repository_metadata( repository ) diff -r 33d4ab5cc642f2bdc5ad8670abf4400063bb8415 -r f14ca41c8cf34779d0b89979320488ebe04eb943 test/tool_shed/functional/test_0040_repository_circular_dependencies.py --- a/test/tool_shed/functional/test_0040_repository_circular_dependencies.py +++ b/test/tool_shed/functional/test_0040_repository_circular_dependencies.py @@ -97,3 +97,9 @@ # In this case, the displayed dependency will specify the tip revision, but this will not always be the case. self.check_repository_dependency( filtering_repository, freebayes_repository, self.get_repository_tip( freebayes_repository ) ) self.check_repository_dependency( freebayes_repository, filtering_repository, self.get_repository_tip( filtering_repository ) ) + def test_0035_verify_repository_metadata( self ): + '''Verify that resetting the metadata does not change it.''' + freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + for repository in [ freebayes_repository, filtering_repository ]: + self.verify_unchanged_repository_metadata( repository ) diff -r 33d4ab5cc642f2bdc5ad8670abf4400063bb8415 -r f14ca41c8cf34779d0b89979320488ebe04eb943 test/tool_shed/functional/test_0050_circular_n_levels.py --- a/test/tool_shed/functional/test_0050_circular_n_levels.py +++ b/test/tool_shed/functional/test_0050_circular_n_levels.py @@ -147,3 +147,11 @@ for changeset_revision in self.get_repository_metadata_revisions( emboss_repository ): self.check_repository_dependency( freebayes_repository, emboss_repository, changeset_revision ) self.display_manage_repository_page( freebayes_repository, strings_displayed=[ 'Freebayes depends on the filtering repository.' ] ) + def test_0035_verify_repository_metadata( self ): + '''Verify that resetting the metadata does not change it.''' + emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) + emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + for repository in [ emboss_datatypes_repository, emboss_repository, freebayes_repository, filtering_repository ]: + self.verify_unchanged_repository_metadata( repository ) diff -r 33d4ab5cc642f2bdc5ad8670abf4400063bb8415 -r f14ca41c8cf34779d0b89979320488ebe04eb943 test/tool_shed/functional/test_0060_workflows.py --- a/test/tool_shed/functional/test_0060_workflows.py +++ b/test/tool_shed/functional/test_0060_workflows.py @@ -54,3 +54,7 @@ commit_message="Uploaded filtering 2.2.0", remove_repo_files_not_in_tar='No' ) self.load_workflow_image( repository, workflow_name, strings_not_displayed=[ '#EBBCB2' ] ) + def test_0025_verify_repository_metadata( self ): + '''Verify that resetting the metadata does not change it.''' + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + self.verify_unchanged_repository_metadata( repository ) diff -r 33d4ab5cc642f2bdc5ad8670abf4400063bb8415 -r f14ca41c8cf34779d0b89979320488ebe04eb943 test/tool_shed/functional/test_1000_install_basic_repository.py --- a/test/tool_shed/functional/test_1000_install_basic_repository.py +++ b/test/tool_shed/functional/test_1000_install_basic_repository.py @@ -28,4 +28,7 @@ self.verify_installed_repository_on_browse_page( installed_repository ) self.display_installed_repository_manage_page( installed_repository, strings_displayed=[ 'Installed tool shed repository', 'Tools', 'Filter1' ] ) - self.verify_tool_metadata_for_installed_repository( installed_repository ) \ No newline at end of file + self.verify_tool_metadata_for_installed_repository( installed_repository ) + def test_0025_verify_installed_repository_metadata( self ): + '''Verify that resetting the metadata on an installed repository does not change the metadata.''' + self.verify_installed_repository_metadata_unchanged( 'filtering_0000', common.test_user_1_name ) diff -r 33d4ab5cc642f2bdc5ad8670abf4400063bb8415 -r f14ca41c8cf34779d0b89979320488ebe04eb943 test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py @@ -25,3 +25,10 @@ strings_displayed=[ 'Installed tool shed repository', 'Tools', 'FreeBayes' ] ) self.check_installed_repository_tool_dependencies( installed_repository, dependencies_installed=False ) self.verify_tool_metadata_for_installed_repository( installed_repository ) + def test_0020_verify_installed_repository_metadata( self ): + '''Verify that resetting the metadata on an installed repository does not change the metadata.''' + self.verify_installed_repository_metadata_unchanged( 'freebayes_0010', common.test_user_1_name ) + def test_0025_verify_sample_files( self ): + '''Verify that the installed repository populated shed_tool_data_table.xml and the sample files.''' + self.verify_installed_repository_data_table_entries( data_tables=[ 'sam_fa_indexes' ] ) + diff -r 33d4ab5cc642f2bdc5ad8670abf4400063bb8415 -r f14ca41c8cf34779d0b89979320488ebe04eb943 test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py --- a/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py +++ b/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py @@ -25,3 +25,6 @@ strings_displayed=[ 'Installed tool shed repository', 'Tools', 'antigenic' ] ) self.check_installed_repository_tool_dependencies( installed_repository, dependencies_installed=False ) self.verify_tool_metadata_for_installed_repository( installed_repository ) + def test_0020_verify_installed_repository_metadata( self ): + '''Verify that resetting the metadata on an installed repository does not change the metadata.''' + self.verify_installed_repository_metadata_unchanged( 'emboss_0020', common.test_user_1_name ) diff -r 33d4ab5cc642f2bdc5ad8670abf4400063bb8415 -r f14ca41c8cf34779d0b89979320488ebe04eb943 test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py --- a/test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py +++ b/test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py @@ -27,3 +27,7 @@ strings_displayed=[ 'Installed tool shed repository', 'Tools', 'antigenic' ] ) self.check_installed_repository_tool_dependencies( installed_repository, dependencies_installed=False ) self.verify_tool_metadata_for_installed_repository( installed_repository ) + self.update_installed_repository( installed_repository, strings_displayed=[ "there are no updates available" ] ) + def test_0025_verify_installed_repository_metadata( self ): + '''Verify that resetting the metadata on an installed repository does not change the metadata.''' + self.verify_installed_repository_metadata_unchanged( 'emboss_0030', common.test_user_1_name ) diff -r 33d4ab5cc642f2bdc5ad8670abf4400063bb8415 -r f14ca41c8cf34779d0b89979320488ebe04eb943 test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -68,6 +68,14 @@ </toolbox> ''' +tool_conf_xml = '''<?xml version="1.0"?> +<toolbox> + <section name="Get Data" id="getext"> + <tool file="data_source/upload.xml"/> + </section> +</toolbox> +''' + tool_data_table_conf_xml_template = '''<?xml version="1.0"?><tables></tables> @@ -113,8 +121,14 @@ shed_db_path = os.path.join( tempdir, 'database' ) shed_tool_data_table_conf_file = os.environ.get( 'TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF', os.path.join( tool_shed_test_tmp_dir, 'shed_tool_data_table_conf.xml' ) ) galaxy_tool_data_table_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_DATA_TABLE_CONF', os.path.join( tool_shed_test_tmp_dir, 'tool_data_table_conf.xml' ) ) - galaxy_shed_tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_tool_conf.xml' ) ) + galaxy_tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_tool_conf.xml' ) ) + galaxy_shed_tool_conf_file = os.environ.get( 'GALAXY_TEST_SHED_TOOL_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_shed_tool_conf.xml' ) ) galaxy_tool_sheds_conf_file = os.environ.get( 'GALAXY_TEST_SHED_TOOLS_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_sheds_conf.xml' ) ) + if 'GALAXY_TEST_TOOL_DATA_PATH' in os.environ: + tool_data_path = os.environ.get( 'GALAXY_TEST_TOOL_DATA_PATH' ) + else: + tool_data_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) + os.environ[ 'GALAXY_TEST_TOOL_DATA_PATH' ] = tool_data_path if 'GALAXY_TEST_DBPATH' in os.environ: galaxy_db_path = os.environ[ 'GALAXY_TEST_DBPATH' ] else: @@ -153,7 +167,7 @@ file( galaxy_tool_data_table_conf_file, 'w' ).write( tool_data_table_conf_xml_template ) # Generate the shed_tool_data_table_conf.xml file. file( shed_tool_data_table_conf_file, 'w' ).write( tool_data_table_conf_xml_template ) - + os.environ[ 'TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF' ] = shed_tool_data_table_conf_file # ---- Build Tool Shed Application -------------------------------------------------- toolshedapp = None global_conf = { '__file__' : 'community_wsgi.ini.sample' } @@ -231,6 +245,8 @@ # ---- Optionally start up a Galaxy instance ------------------------------------------------------ if 'TOOL_SHED_TEST_OMIT_GALAXY' not in os.environ: + # Generate the tool_conf.xml file. + file( galaxy_tool_conf_file, 'w' ).write( tool_conf_xml ) # Generate the shed_tool_conf.xml file. tool_sheds_conf_template_parser = string.Template( tool_sheds_conf_xml_template ) tool_sheds_conf_xml = tool_sheds_conf_template_parser.safe_substitute( shed_url=tool_shed_test_host, shed_port=tool_shed_test_port ) @@ -251,10 +267,11 @@ database_engine_option_pool_size = '10', file_path = galaxy_file_path, tool_path = tool_path, + tool_data_path = tool_data_path, tool_dependency_dir=galaxy_tool_dependency_dir, shed_tool_path=galaxy_shed_tool_path, update_integrated_tool_panel = False, - tool_config_file = galaxy_shed_tool_conf_file, + tool_config_file = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ], tool_sheds_config_file = galaxy_tool_sheds_conf_file, datatype_converters_config_file = "datatype_converters_conf.xml.sample", tool_parse_help = False, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: history panel: do not render body html until hda is expanded
by Bitbucket 14 Dec '12

14 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/33d4ab5cc642/ changeset: 33d4ab5cc642 user: carlfeberhard date: 2012-12-14 21:41:51 summary: history panel: do not render body html until hda is expanded affected #: 1 file diff -r f45730d9e8904783f5f8a29cf2a2a0c93e5a2047 -r 33d4ab5cc642f2bdc5ad8670abf4400063bb8415 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -77,6 +77,7 @@ itemWrapper.append( this._render_warnings() ); itemWrapper.append( this._render_titleBar() ); + this.body = $( this._render_body() ); itemWrapper.append( this.body ); @@ -321,18 +322,31 @@ }, // ......................................................................... state body renderers - /** Render the (expanded) body of an HDA, dispatching to other functions based on the HDA state + /** Render the enclosing div of the hda body and, if expanded, the html in the body * @returns {jQuery} rendered DOM */ //TODO: only render these on expansion (or already expanded) _render_body : function(){ - //this.log( this + '_render_body' ); - var body = $( '<div/>' ) .attr( 'id', 'info-' + this.model.get( 'id' ) ) .addClass( 'historyItemBody' ) - .attr( 'style', 'display: block' ); + .attr( 'style', 'display: none' ); + if( this.expanded ){ + // only render the body html if it's being shown + this._render_body_html( body ); + body.show(); + } + return body; + }, + + /** Render the (expanded) body of an HDA, dispatching to other functions based on the HDA state + * @param {jQuery} body the body element to append the html to + */ + //TODO: only render these on expansion (or already expanded) + _render_body_html : function( body ){ + //this.log( this + '_render_body' ); + body.html( '' ); //TODO: not a fan of this dispatch switch( this.model.get( 'state' ) ){ case HistoryDatasetAssociation.STATES.NEW : @@ -375,13 +389,6 @@ body.append( $( '<div>Error: unknown dataset state "' + this.model.get( 'state' ) + '".</div>' ) ); } body.append( '<div style="clear: both"></div>' ); - - if( this.expanded ){ - body.show(); - } else { - body.hide(); - } - return body; }, /** Render inaccessible, not-owned by curr user. @@ -514,17 +521,17 @@ * @fires body-collapsed when a body has been collapsed */ toggleBodyVisibility : function( event, expanded ){ - var hdaView = this, - $body = this.$el.find( '.historyItemBody' ); - expanded = ( expanded === undefined )?( !$body.is( ':visible' ) ):( expanded ); + var hdaView = this; + this.expanded = ( expanded === undefined )?( !this.body.is( ':visible' ) ):( expanded ); //this.log( 'toggleBodyVisibility, expanded:', expanded, '$body:', $body ); - if( expanded ){ - $body.slideDown( 'fast', function(){ + if( this.expanded ){ + hdaView._render_body_html( hdaView.body ); + this.body.slideDown( 'fast', function(){ hdaView.trigger( 'body-expanded', hdaView.model.get( 'id' ) ); }); } else { - $body.slideUp( 'fast', function(){ + this.body.slideUp( 'fast', function(){ hdaView.trigger( 'body-collapsed', hdaView.model.get( 'id' ) ); }); } 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: carlfeberhard: Make hda name text selectable
by Bitbucket 14 Dec '12

14 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f45730d9e890/ changeset: f45730d9e890 user: carlfeberhard date: 2012-12-14 20:53:41 summary: Make hda name text selectable affected #: 1 file diff -r 4b4ea995233684e49259a8126257a2d226b8a026 -r f45730d9e8904783f5f8a29cf2a2a0c93e5a2047 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -537,9 +537,6 @@ .historyItemTitle { text-decoration: underline; cursor: pointer; - -webkit-user-select: none; - -moz-user-select: none; - -khtml-user-select: none; } .historyItemTitle:hover { text-decoration: underline; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Remove deprecated parameters from Tophat2 wrapper.
by Bitbucket 14 Dec '12

14 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4b4ea9952336/ changeset: 4b4ea9952336 user: jgoecks date: 2012-12-14 19:10:39 summary: Remove deprecated parameters from Tophat2 wrapper. affected #: 2 files diff -r 52ecc79edd361051da70e81d63cb670a3a265dc7 -r 4b4ea995233684e49259a8126257a2d226b8a026 tools/ngs_rna/tophat2_wrapper.py --- a/tools/ngs_rna/tophat2_wrapper.py +++ b/tools/ngs_rna/tophat2_wrapper.py @@ -20,8 +20,6 @@ where each end is 50bp, you should set -r to be 200. There is no default, \ and this parameter is required for paired end runs.') parser.add_option( '', '--mate-std-dev', dest='mate_std_dev', help='Standard deviation of distribution on inner distances between male pairs.' ) - parser.add_option( '-n', '--transcriptome-mismatches', dest='transcriptome_mismatches' ) - parser.add_option( '', '--genome-read-mismatches', dest='genome_read_mismatches' ) parser.add_option( '', '--read-mismatches', dest='read_mismatches' ) parser.add_option( '', '--bowtie-n', action="store_true", dest='bowtie_n' ) parser.add_option( '', '--report-discordant-pair-alignments', action="store_true", dest='report_discordant_pairs' ) @@ -171,10 +169,6 @@ # need to warn user of this fact #sys.stdout.write( "Max insertion length and max deletion length options don't work in Tophat v1.2.0\n" ) - if options.transcriptome_mismatches: - opts += ' --transcriptome-mismatches %i' % int( options.transcriptome_mismatches ) - if options.genome_read_mismatches: - opts += ' --genome-read-mismatches %i' % int( options.genome_read_mismatches ) if options.read_mismatches: opts += ' --read-mismatches %i' % int( options.read_mismatches ) if options.bowtie_n: diff -r 52ecc79edd361051da70e81d63cb670a3a265dc7 -r 4b4ea995233684e49259a8126257a2d226b8a026 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -45,8 +45,6 @@ ## Set params. --settings=$params.settingsType #if $params.settingsType == "full": - -n $params.transcriptome_mismatches - --genome-read-mismatches $params.genome_read_mismatches --read-mismatches $params.read_mismatches #if str($params.bowtie_n) == "Yes": --bowtie-n @@ -167,8 +165,6 @@ <option value="fr-firststrand">FR First Strand</option><option value="fr-secondstrand">FR Second Strand</option></param> - <param name="transcriptome_mismatches" type="integer" value="2" label="Transcriptome mismatches" help="Maximum number of mismatches allowed when reads are aligned to the transcriptome. When Bowtie2 is used, this number is also used to decide whether or not to further re-align some of the transcriptome-mapped reads to the genome. If the alignment score of the best alignment among multiple candidates for a read is lower than 'bowtie2-min-score', which is internally defined as (max_penalty - 1) * max_mismatches, then the reads will be kept for re-alignment through the rest of the pipeline. You can specify max_penalty via '--b2-mp' option." /> - <param name="genome_read_mismatches" type="integer" value="2" label="Genome read mismatches" help="When whole reads are first mapped on the genome, this many mismatches in each read alignment are allowed. The default is 2. This number is also used to decide whether to further re-align some of the reads (by splitting them into segments) with a similar scoring threshold scheme as described for the --transcriptome-mismatches option above." /><param name="read_mismatches" type="integer" value="2" label="Final read mismatches" help="Final read alignments having more than these many mismatches are discarded." /><param name="bowtie_n" type="select" label="Use bowtie -n mode"><option selected="true" value="No">No</option> @@ -425,8 +421,6 @@ <param name="ownFile" value="tophat_in1.fasta"/><param name="settingsType" value="full"/><param name="library_type" value="FR Unstranded"/> - <param name="transcriptome_mismatches" value="2"/> - <param name="genome_read_mismatches" value="2"/><param name="read_mismatches" value="2"/><param name="bowtie_n" value="No"/><param name="anchor_length" value="8"/> @@ -478,8 +472,6 @@ <param name="mate_inner_distance" value="20"/><param name="settingsType" value="full"/><param name="library_type" value="FR Unstranded"/> - <param name="transcriptome_mismatches" value="3"/> - <param name="genome_read_mismatches" value="4"/><param name="read_mismatches" value="5"/><param name="bowtie_n" value="Yes"/><param name="mate_std_dev" value="20"/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Allow spaces in Cuffdiff group names.
by Bitbucket 14 Dec '12

14 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/52ecc79edd36/ changeset: 52ecc79edd36 user: jgoecks date: 2012-12-14 18:47:44 summary: Allow spaces in Cuffdiff group names. affected #: 2 files diff -r 3a71d40d7b9922e13c1e2d9d50d4ed6b85408137 -r 52ecc79edd361051da70e81d63cb670a3a265dc7 tools/ngs_rna/cuffdiff_wrapper.py --- a/tools/ngs_rna/cuffdiff_wrapper.py +++ b/tools/ngs_rna/cuffdiff_wrapper.py @@ -172,7 +172,7 @@ if options.groups: cmd += " --labels " for label in options.labels: - cmd += label + "," + cmd += '"%s",' % label cmd = cmd[:-1] cmd += " " + options.inputA + " " diff -r 3a71d40d7b9922e13c1e2d9d50d4ed6b85408137 -r 52ecc79edd361051da70e81d63cb670a3a265dc7 tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -59,7 +59,7 @@ ## Replicates. --labels #for $group in $group_analysis.groups - ${group.group} + "${group.group}" #end for --files #for $group in $group_analysis.groups Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: History importing/exporting: (a) create BAIs when importing BAM datasets and (b) bug fixes and code cleanup.
by Bitbucket 14 Dec '12

14 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3a71d40d7b99/ changeset: 3a71d40d7b99 user: jgoecks date: 2012-12-14 17:48:27 summary: History importing/exporting: (a) create BAIs when importing BAM datasets and (b) bug fixes and code cleanup. affected #: 4 files diff -r 4929a37823b5454178bf811b6b65f2216c7ac4c3 -r 3a71d40d7b9922e13c1e2d9d50d4ed6b85408137 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -686,7 +686,7 @@ if self.app.config.set_metadata_externally: self.external_output_metadata.cleanup_external_metadata( self.sa_session ) galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper( self.job_id ).cleanup_after_job( self.sa_session ) - galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper( self.job_id ).cleanup_after_job( self.sa_session ) + galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper( self.app, self.job_id ).cleanup_after_job() galaxy.tools.genome_index.GenomeIndexToolWrapper( self.job_id ).postprocessing( self.sa_session, self.app ) self.app.object_store.delete(self.get_job(), base_dir='job_work', entire_dir=True, dir_only=True, extra_dir=str(self.job_id)) except: diff -r 4929a37823b5454178bf811b6b65f2216c7ac4c3 -r 3a71d40d7b9922e13c1e2d9d50d4ed6b85408137 lib/galaxy/tools/actions/history_imp_exp.py --- a/lib/galaxy/tools/actions/history_imp_exp.py +++ b/lib/galaxy/tools/actions/history_imp_exp.py @@ -34,8 +34,7 @@ archive_dir = os.path.abspath( tempfile.mkdtemp() ) jiha = trans.app.model.JobImportHistoryArchive( job=job, archive_dir=archive_dir ) trans.sa_session.add( jiha ) - job_wrapper = JobImportHistoryArchiveWrapper( job ) - + # # Add parameters to job_parameter table. # diff -r 4929a37823b5454178bf811b6b65f2216c7ac4c3 -r 3a71d40d7b9922e13c1e2d9d50d4ed6b85408137 lib/galaxy/tools/actions/metadata.py --- a/lib/galaxy/tools/actions/metadata.py +++ b/lib/galaxy/tools/actions/metadata.py @@ -13,17 +13,14 @@ """ Execute using a web transaction. """ - user_id = None - if trans.user: - user_id = trans.user.id job, odict = self.execute_via_app( tool, trans.app, trans.get_galaxy_session().id, - trans.history.id, user_id, incoming, set_output_hid, + trans.history.id, trans.user, incoming, set_output_hid, overwrite, history, job_params ) # FIXME: can remove this when logging in execute_via_app method. trans.log_event( "Added set external metadata job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) return job, odict - def execute_via_app( self, tool, app, session_id, history_id, user_id = None, + def execute_via_app( self, tool, app, session_id, history_id, user=None, incoming = {}, set_output_hid = False, overwrite = True, history=None, job_params=None ): """ @@ -50,8 +47,8 @@ job.session_id = session_id job.history_id = history_id job.tool_id = tool.id - if user_id: - job.user_id = user_id + if user: + job.user_id = user.id if job_params: job.params = to_json_string( job_params ) start_job_state = job.state #should be job.states.NEW diff -r 4929a37823b5454178bf811b6b65f2216c7ac4c3 -r 3a71d40d7b9922e13c1e2d9d50d4ed6b85408137 lib/galaxy/tools/imp_exp/__init__.py --- a/lib/galaxy/tools/imp_exp/__init__.py +++ b/lib/galaxy/tools/imp_exp/__init__.py @@ -3,7 +3,7 @@ from galaxy.tools.parameters.basic import UnvalidatedValue from galaxy.web.framework.helpers import to_unicode from galaxy.model.item_attrs import UsesAnnotations -from galaxy.util.json import * +from galaxy.util.json import from_json_string, to_json_string from galaxy.web.base.controller import UsesHistoryMixin log = logging.getLogger(__name__) @@ -47,10 +47,12 @@ Class provides support for performing jobs that import a history from an archive. """ - def __init__( self, job_id ): + def __init__( self, app, job_id ): + self.app = app self.job_id = job_id + self.sa_session = self.app.model.context - def cleanup_after_job( self, db_session ): + def cleanup_after_job( self ): """ Set history, datasets, and jobs' attributes and clean up archive directory. """ # @@ -88,7 +90,7 @@ # Import history. # - jiha = db_session.query( model.JobImportHistoryArchive ).filter_by( job_id=self.job_id ).first() + jiha = self.sa_session.query( model.JobImportHistoryArchive ).filter_by( job_id=self.job_id ).first() if jiha: try: archive_dir = jiha.archive_dir @@ -107,13 +109,13 @@ new_history.importing = True new_history.hid_counter = history_attrs['hid_counter'] new_history.genome_build = history_attrs['genome_build'] - db_session.add( new_history ) + self.sa_session.add( new_history ) jiha.history = new_history - db_session.flush() + self.sa_session.flush() # Add annotation, tags. if user: - self.add_item_annotation( db_session, user, new_history, history_attrs[ 'annotation' ] ) + self.add_item_annotation( self.sa_session, user, new_history, history_attrs[ 'annotation' ] ) """ TODO: figure out to how add tags to item. for tag, value in history_attrs[ 'tags' ].items(): @@ -153,16 +155,16 @@ metadata = metadata, history = new_history, create_dataset = True, - sa_session = db_session ) + sa_session = self.sa_session ) hda.state = hda.states.OK - db_session.add( hda ) - db_session.flush() + self.sa_session.add( hda ) + self.sa_session.flush() new_history.add_dataset( hda, genome_build = None ) hda.hid = dataset_attrs['hid'] # Overwrite default hid set when HDA added to history. # TODO: Is there a way to recover permissions? Is this needed? #permissions = trans.app.security_agent.history_get_default_permissions( new_history ) #trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) - db_session.flush() + self.sa_session.flush() # Do security check and move/copy dataset data. temp_dataset_file_name = \ @@ -177,13 +179,25 @@ # Set tags, annotations. if user: - self.add_item_annotation( db_session, user, hda, dataset_attrs[ 'annotation' ] ) + self.add_item_annotation( self.sa_session, user, hda, dataset_attrs[ 'annotation' ] ) # TODO: Set tags. """ for tag, value in dataset_attrs[ 'tags' ].items(): trans.app.tag_handler.apply_item_tags( trans, trans.user, hda, get_tag_str( tag, value ) ) - db_session.flush() + self.sa_session.flush() """ + + # Although metadata is set above, need to set metadata to recover BAI for BAMs. + if hda.extension == 'bam': + if self.app.config.set_metadata_externally: + self.app.datatypes_registry.set_external_metadata_tool.tool_action.execute_via_app( + self.app.datatypes_registry.set_external_metadata_tool, self.app, jiha.job.session_id, + new_history.id, jiha.job.user, incoming={ 'input1': hda }, overwrite=False + ) + else: + message = 'Attributes updated' + hda.set_meta() + hda.datatype.after_setting_metadata( hda ) # # Create jobs. @@ -198,7 +212,7 @@ """ Hook to 'decode' an HDA; method uses history and HID to get the HDA represented by the encoded object. This only works because HDAs are created above. """ if obj_dct.get( '__HistoryDatasetAssociation__', False ): - return db_session.query( model.HistoryDatasetAssociation ) \ + return self.sa_session.query( model.HistoryDatasetAssociation ) \ .filter_by( history=new_history, hid=obj_dct['hid'] ).first() return obj_dct jobs_attrs = from_json_string( jobs_attr_str, object_hook=as_hda ) @@ -214,8 +228,8 @@ imported_job.tool_version = job_attrs[ 'tool_version' ] imported_job.set_state( job_attrs[ 'state' ] ) imported_job.imported = True - db_session.add( imported_job ) - db_session.flush() + self.sa_session.add( imported_job ) + self.sa_session.flush() class HistoryDatasetAssociationIDEncoder( simplejson.JSONEncoder ): """ Custom JSONEncoder for a HistoryDatasetAssociation that encodes an HDA as its ID. """ @@ -235,7 +249,7 @@ # Transform parameter values when necessary. if isinstance( value, model.HistoryDatasetAssociation ): # HDA input: use hid to find input. - input_hda = db_session.query( model.HistoryDatasetAssociation ) \ + input_hda = self.sa_session.query( model.HistoryDatasetAssociation ) \ .filter_by( history=new_history, hid=value.hid ).first() value = input_hda.id #print "added parameter %s-->%s to job %i" % ( name, value, imported_job.id ) @@ -246,22 +260,23 @@ # Connect jobs to output datasets. for output_hid in job_attrs[ 'output_datasets' ]: #print "%s job has output dataset %i" % (imported_job.id, output_hid) - output_hda = db_session.query( model.HistoryDatasetAssociation ) \ + output_hda = self.sa_session.query( model.HistoryDatasetAssociation ) \ .filter_by( history=new_history, hid=output_hid ).first() if output_hda: imported_job.add_output_dataset( output_hda.name, output_hda ) - # Done importing. - new_history.importing = False + self.sa_session.flush() - db_session.flush() + # Done importing. + new_history.importing = False + self.sa_session.flush() # Cleanup. if os.path.exists( archive_dir ): shutil.rmtree( archive_dir ) except Exception, e: jiha.job.stderr += "Error cleaning up history import job: %s" % e - db_session.flush() + self.sa_session.flush() class JobExportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations ): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: api/histories, show: remove get_api_value for each dataset in get_dataset_state_summaries
by Bitbucket 14 Dec '12

14 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4929a37823b5/ changeset: 4929a37823b5 user: carlfeberhard date: 2012-12-14 17:05:43 summary: api/histories, show: remove get_api_value for each dataset in get_dataset_state_summaries affected #: 1 file diff -r 742aac57ec941aa89ac7ca07548bf531127bc31b -r 4929a37823b5454178bf811b6b65f2216c7ac4c3 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -75,14 +75,10 @@ # cycle through datasets saving each ds' state for dataset in datasets: - dataset_dict = dataset.get_api_value( view='element' ) - item_state = dataset_dict[ 'state' ] - - if not dataset_dict['deleted']: + item_state = dataset.state + if not dataset.deleted: state_counts[ item_state ] = state_counts[ item_state ] + 1 - - state_ids[ item_state ].append( trans.security.encode_id( dataset_dict[ 'id' ] ) ) - + state_ids[ item_state ].append( trans.security.encode_id( dataset.id ) ) return ( state_counts, state_ids ) # try to load the history, by most_recently_used or the given id 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: Don't munge the Galaxy root's tool_data_table_conf.sml file or the shed_tool_data_table_conf.xml file when running tool shed functional tests.
by Bitbucket 14 Dec '12

14 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/742aac57ec94/ changeset: 742aac57ec94 user: greg date: 2012-12-14 16:59:53 summary: Don't munge the Galaxy root's tool_data_table_conf.sml file or the shed_tool_data_table_conf.xml file when running tool shed functional tests. affected #: 1 file diff -r a749bcb137928ede156899ca5ef4d2eef6e9f45c -r 742aac57ec941aa89ac7ca07548bf531127bc31b test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -68,6 +68,11 @@ </toolbox> ''' +tool_data_table_conf_xml_template = '''<?xml version="1.0"?> +<tables> +</tables> +''' + def run_tests( test_config ): loader = nose.loader.TestLoader( config=test_config ) plug_loader = test_config.plugins.prepareTestLoader( loader ) @@ -95,14 +100,8 @@ if not os.path.isabs( tool_shed_test_file_dir ): tool_shed_test_file_dir = tool_shed_test_file_dir ignore_files = () - if os.path.exists( 'tool_data_table_conf.test.xml' ): - tool_data_table_config_path = 'tool_data_table_conf.test.xml' - else: - tool_data_table_config_path = 'tool_data_table_conf.xml' - shed_tool_data_table_config = 'shed_tool_data_table_conf.xml' tool_dependency_dir = os.environ.get( 'TOOL_SHED_TOOL_DEPENDENCY_DIR', None ) use_distributed_object_store = os.environ.get( 'TOOL_SHED_USE_DISTRIBUTED_OBJECT_STORE', False ) - if not os.path.isdir( tool_shed_test_tmp_dir ): os.mkdir( tool_shed_test_tmp_dir ) tool_shed_test_proxy_port = None @@ -112,6 +111,8 @@ else: tempdir = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) shed_db_path = os.path.join( tempdir, 'database' ) + shed_tool_data_table_conf_file = os.environ.get( 'TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF', os.path.join( tool_shed_test_tmp_dir, 'shed_tool_data_table_conf.xml' ) ) + galaxy_tool_data_table_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_DATA_TABLE_CONF', os.path.join( tool_shed_test_tmp_dir, 'tool_data_table_conf.xml' ) ) galaxy_shed_tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_tool_conf.xml' ) ) galaxy_tool_sheds_conf_file = os.environ.get( 'GALAXY_TEST_SHED_TOOLS_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_sheds_conf.xml' ) ) if 'GALAXY_TEST_DBPATH' in os.environ: @@ -148,6 +149,11 @@ print "Directory location for hgweb.config:", hgweb_config_dir + # Generate the tool_data_table_conf.xml file. + file( galaxy_tool_data_table_conf_file, 'w' ).write( tool_data_table_conf_xml_template ) + # Generate the shed_tool_data_table_conf.xml file. + file( shed_tool_data_table_conf_file, 'w' ).write( tool_data_table_conf_xml_template ) + # ---- Build Tool Shed Application -------------------------------------------------- toolshedapp = None global_conf = { '__file__' : 'community_wsgi.ini.sample' } @@ -169,8 +175,8 @@ tool_path=tool_path, datatype_converters_config_file = 'datatype_converters_conf.xml.sample', tool_parse_help = False, - tool_data_table_config_path = tool_data_table_config_path, - shed_tool_data_table_config = shed_tool_data_table_config, + tool_data_table_config_path = galaxy_tool_data_table_conf_file, + shed_tool_data_table_config = shed_tool_data_table_conf_file, log_destination = "stdout", use_heartbeat = False, allow_user_creation = True, @@ -225,10 +231,11 @@ # ---- Optionally start up a Galaxy instance ------------------------------------------------------ if 'TOOL_SHED_TEST_OMIT_GALAXY' not in os.environ: - # Generate the shed_tool_conf.xml and tool_sheds_conf.xml files + # Generate the shed_tool_conf.xml file. tool_sheds_conf_template_parser = string.Template( tool_sheds_conf_xml_template ) tool_sheds_conf_xml = tool_sheds_conf_template_parser.safe_substitute( shed_url=tool_shed_test_host, shed_port=tool_shed_test_port ) file( galaxy_tool_sheds_conf_file, 'w' ).write( tool_sheds_conf_xml ) + # Generate the tool_sheds_conf.xml file. shed_tool_conf_template_parser = string.Template( shed_tool_conf_xml_template ) shed_tool_conf_xml = shed_tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_shed_tool_path ) file( galaxy_shed_tool_conf_file, 'w' ).write( shed_tool_conf_xml ) @@ -251,8 +258,8 @@ tool_sheds_config_file = galaxy_tool_sheds_conf_file, datatype_converters_config_file = "datatype_converters_conf.xml.sample", tool_parse_help = False, - tool_data_table_config_path = tool_data_table_config_path, - shed_tool_data_table_config = shed_tool_data_table_config, + tool_data_table_config_path = galaxy_tool_data_table_conf_file, + shed_tool_data_table_config = shed_tool_data_table_conf_file, log_destination = "stdout", use_heartbeat = False, allow_user_creation = True, 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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