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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 14 Nov '13

14 Nov '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e54372d60f11/ Changeset: e54372d60f11 Branch: stable User: jgoecks Date: 2013-11-14 17:00:19 Summary: Trackster: only allow datasets with proper dbkey to be added to visualization. This is a regression because summary data format [bigwig] requires a proper dbkey. Affected #: 1 file diff -r 88a08db3c73393ef4f64b0c2f50262d5aa03967b -r e54372d60f111f4be26868ba416649697b551a13 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -86,15 +86,19 @@ class DbKeyColumn( grids.GridColumn ): """ Column for filtering by and displaying dataset dbkey. """ def filter( self, trans, user, query, dbkey ): - """ Filter by dbkey; datasets without a dbkey are returned as well. """ - # use raw SQL b/c metadata is a BLOB + """ Filter by dbkey. """ + # Use raw SQL b/c metadata is a BLOB. dbkey_user, dbkey = decode_dbkey( dbkey ) dbkey = dbkey.replace("'", "\\'") - return query.filter( or_( \ - or_( "metadata like '%%\"dbkey\": [\"%s\"]%%'" % dbkey, "metadata like '%%\"dbkey\": \"%s\"%%'" % dbkey ), \ - or_( "metadata like '%%\"dbkey\": [\"?\"]%%'", "metadata like '%%\"dbkey\": \"?\"%%'" ) \ - ) - ) + return query.filter( or_( "metadata like '%%\"dbkey\": [\"%s\"]%%'" % dbkey, "metadata like '%%\"dbkey\": \"%s\"%%'" % dbkey ) ) + + #Use this query when datasets with matching dbkey *or* no dbkey can be added to the visualization. + #return query.filter( or_( \ + # or_( "metadata like '%%\"dbkey\": [\"%s\"]%%'" % dbkey, "metadata like '%%\"dbkey\": \"%s\"%%'" % dbkey ), \ + # or_( "metadata like '%%\"dbkey\": [\"?\"]%%'", "metadata like '%%\"dbkey\": \"?\"%%'" ) \ + # ) + # ) + class HistoryColumn( grids.GridColumn ): """ Column for filtering by history id. """ https://bitbucket.org/galaxy/galaxy-central/commits/516df888b97a/ Changeset: 516df888b97a User: jgoecks Date: 2013-11-14 17:00:58 Summary: Merge stable with default branch. Affected #: 1 file diff -r 7553213e0646fd4337ceacc78820990c6ce0c710 -r 516df888b97a164b7ff2d8235f5d4ea6462e185d lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -86,15 +86,19 @@ class DbKeyColumn( grids.GridColumn ): """ Column for filtering by and displaying dataset dbkey. """ def filter( self, trans, user, query, dbkey ): - """ Filter by dbkey; datasets without a dbkey are returned as well. """ - # use raw SQL b/c metadata is a BLOB + """ Filter by dbkey. """ + # Use raw SQL b/c metadata is a BLOB. dbkey_user, dbkey = decode_dbkey( dbkey ) dbkey = dbkey.replace("'", "\\'") - return query.filter( or_( \ - or_( "metadata like '%%\"dbkey\": [\"%s\"]%%'" % dbkey, "metadata like '%%\"dbkey\": \"%s\"%%'" % dbkey ), \ - or_( "metadata like '%%\"dbkey\": [\"?\"]%%'", "metadata like '%%\"dbkey\": \"?\"%%'" ) \ - ) - ) + return query.filter( or_( "metadata like '%%\"dbkey\": [\"%s\"]%%'" % dbkey, "metadata like '%%\"dbkey\": \"%s\"%%'" % dbkey ) ) + + #Use this query when datasets with matching dbkey *or* no dbkey can be added to the visualization. + #return query.filter( or_( \ + # or_( "metadata like '%%\"dbkey\": [\"%s\"]%%'" % dbkey, "metadata like '%%\"dbkey\": \"%s\"%%'" % dbkey ), \ + # or_( "metadata like '%%\"dbkey\": [\"?\"]%%'", "metadata like '%%\"dbkey\": \"?\"%%'" ) \ + # ) + # ) + class HistoryColumn( grids.GridColumn ): """ Column for filtering by history 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: guerler: UI: Fix async submit of grids
by commits-noreply＠bitbucket.org 14 Nov '13

14 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7553213e0646/ Changeset: 7553213e0646 User: guerler Date: 2013-11-14 08:31:07 Summary: UI: Fix async submit of grids Affected #: 1 file diff -r 1c4bb73d630a21bf2057bdbb8b604eb0dab4ea0e -r 7553213e0646fd4337ceacc78820990c6ce0c710 static/scripts/galaxy.grids.js --- a/static/scripts/galaxy.grids.js +++ b/static/scripts/galaxy.grids.js @@ -133,27 +133,8 @@ // Code to handle grid operations: filtering, sorting, paging, and operations. // -// Init operation buttons. -function init_operation_buttons() { - // Initialize operation buttons. - $('input[name=operation]:submit').each(function() { - $(this).click( function() { - var operation_name = $(this).val(); - // For some reason, $('input[name=id]:checked').val() does not return all ids for checked boxes. - // The code below performs this function. - var item_ids = []; - $('input[name=id]:checked').each(function() { - item_ids.push( $(this).val() ); - }); - do_operation(operation_name, item_ids); - }); - }); -} - // Initialize grid controls function init_grid_controls() { - init_operation_buttons(); - // Initialize submit image elements. $('.submit-image').each( function() { // On mousedown, add class to simulate click. @@ -498,7 +479,6 @@ // Init grid. init_grid_elements(); - init_operation_buttons(); make_popup_menus(); // Hide loading overlay. @@ -558,11 +538,13 @@ if(!confirm(confirmation_text)) return false; - // set up hidden field to parse the command/operation to controller - $('#operation').val(selected_button.value); - - // submit form - selected_button.form.submit(); + // add ids + var operation_name = selected_button.value; + var item_ids = []; + $('input[name=id]:checked').each(function() { + item_ids.push( $(this).val() ); + }); + do_operation(operation_name, item_ids); // return return 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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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 14 Nov '13

14 Nov '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/88a08db3c733/ Changeset: 88a08db3c733 Branch: stable User: jgoecks Date: 2013-11-14 00:41:23 Summary: Implement a hack to avoid infinite recursion in custom builds. Affected #: 1 file diff -r 9bde6f2b9c59a29a35b85b7fe3c2e3bef3ae6a2e -r 88a08db3c73393ef4f64b0c2f50262d5aa03967b lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -206,12 +206,19 @@ db_datasets[ "chromInfo" ] = db_dataset incoming[ "chromInfo" ] = db_dataset.file_name else: - # For custom builds, chrom info resides in converted dataset; for built-in builds, chrom info resides in tool-data/shared. + # -- Get chrom_info from either a custom or built-in build. -- + chrom_info = None if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ): # Custom build. custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ] - if 'fasta' in custom_build_dict: + # HACK: the attempt to get chrom_info below will trigger the + # fasta-to-len converter if the dataset is not available or, + # which will in turn create a recursive loop when + # running the fasta-to-len tool. So, use a hack in the second + # condition below to avoid getting chrom_info when running the + # fasta-to-len converter. + if 'fasta' in custom_build_dict and tool.id != 'CONVERTER_fasta_to_len': build_fasta_dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'fasta' ] ) chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name https://bitbucket.org/galaxy/galaxy-central/commits/1c4bb73d630a/ Changeset: 1c4bb73d630a User: jgoecks Date: 2013-11-14 00:42:54 Summary: Merge stable branch to default. Affected #: 0 files 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: Implement a hack to avoid infinite recursion in custom builds.
by commits-noreply＠bitbucket.org 14 Nov '13

14 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/39256e03655f/ Changeset: 39256e03655f User: jgoecks Date: 2013-11-14 00:41:23 Summary: Implement a hack to avoid infinite recursion in custom builds. Affected #: 1 file diff -r a9d90d2d13e121ffda929baa6ffab6ee43e8892f -r 39256e03655f35b03b940d2b91fc2436106f4e88 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -206,12 +206,19 @@ db_datasets[ "chromInfo" ] = db_dataset incoming[ "chromInfo" ] = db_dataset.file_name else: - # For custom builds, chrom info resides in converted dataset; for built-in builds, chrom info resides in tool-data/shared. + # -- Get chrom_info from either a custom or built-in build. -- + chrom_info = None if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ): # Custom build. custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ] - if 'fasta' in custom_build_dict: + # HACK: the attempt to get chrom_info below will trigger the + # fasta-to-len converter if the dataset is not available or, + # which will in turn create a recursive loop when + # running the fasta-to-len tool. So, use a hack in the second + # condition below to avoid getting chrom_info when running the + # fasta-to-len converter. + if 'fasta' in custom_build_dict and tool.id != 'CONVERTER_fasta_to_len': build_fasta_dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'fasta' ] ) chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name 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: jmchilton: LWR: Expand user properties (__user_name__, __user_email__, __user_id__) in job params before creating client.
by commits-noreply＠bitbucket.org 13 Nov '13

13 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a9d90d2d13e1/ Changeset: a9d90d2d13e1 User: jmchilton Date: 2013-11-13 23:37:11 Summary: LWR: Expand user properties (__user_name__, __user_email__, __user_id__) in job params before creating client. This was final piece of puzzle for running jobs as real user through LWR. Now on just needs to add <param id="submit_user">$__user_name__</param> to LWR destination in job_conf.xml on Galaxy side to pass this information to the LWR. More complicated on the LWR side obviously, need to configure DRMAA, set job manager to be 'queued_external_drmaa', and setup sudo rules. Will add some details to LWR documentation shortly. Affected #: 1 file diff -r 521b4ff9060b72f1f8c9f5977f8c4fa2b0bd7877 -r a9d90d2d13e121ffda929baa6ffab6ee43e8892f lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -108,7 +108,10 @@ job_id = job_wrapper.job_id if hasattr(job_wrapper, 'task_id'): job_id = "%s_%s" % (job_id, job_wrapper.task_id) - return self.get_client( job_wrapper.job_destination.params, job_id ) + params = job_wrapper.job_destination.params.copy() + for key, value in params.iteritems(): + params[key] = model.User.expand_user_properties( job_wrapper.get_job().user, value ) + return self.get_client( params, job_id ) def get_client_from_state(self, job_state): job_destination_params = job_state.job_destination.params 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: Improved temporary directory management in the Tool Shed.
by commits-noreply＠bitbucket.org 13 Nov '13

13 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/521b4ff9060b/ Changeset: 521b4ff9060b User: greg Date: 2013-11-13 22:17:33 Summary: Improved temporary directory management in the Tool Shed. Affected #: 6 files diff -r c70a6f517aa96506b3245db857025f567aac0511 -r 521b4ff9060b72f1f8c9f5977f8c4fa2b0bd7877 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1093,7 +1093,8 @@ str( repository.name ), changeset_revision, file_type, - export_repository_dependencies ) + export_repository_dependencies, + api=False ) repositories_archive_filename = os.path.basename( repositories_archive.name ) if error_message: message = error_message @@ -1104,6 +1105,8 @@ opened_archive = open( repositories_archive.name ) # Make sure the file is removed from disk after the contents have been downloaded. os.unlink( repositories_archive.name ) + repositories_archive_path, file_name = os.path.split( repositories_archive ) + suc.remove_dir( repositories_archive_path ) return opened_archive repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) metadata = repository_metadata.metadata @@ -3091,6 +3094,7 @@ work_dir ) if message: status = 'error' + suc.remove_dir( work_dir ) break if guid: tool_lineage = self.get_versions_of_tool( trans, repository, repository_metadata, guid ) diff -r c70a6f517aa96506b3245db857025f567aac0511 -r 521b4ff9060b72f1f8c9f5977f8c4fa2b0bd7877 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -248,6 +248,8 @@ status = 'error' # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. tool_util.reset_tool_data_tables( trans.app ) + if uploaded_directory: + suc.remove_dir( uploaded_directory ) trans.response.send_redirect( web.url_for( controller='repository', action='browse_repository', id=repository_id, @@ -255,6 +257,8 @@ message=message, status=status ) ) else: + if uploaded_directory: + suc.remove_dir( uploaded_directory ) status = 'error' # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. tool_util.reset_tool_data_tables( trans.app ) diff -r c70a6f517aa96506b3245db857025f567aac0511 -r 521b4ff9060b72f1f8c9f5977f8c4fa2b0bd7877 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -464,10 +464,7 @@ if display_path: # Load proprietary datatype display applications self.app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict ) - try: - shutil.rmtree( work_dir ) - except: - pass + suc.remove_dir( work_dir ) def install_repository( self, repository_elem, tool_shed_repository, install_dependencies, is_repository_dependency=False ): """Install a single repository, loading contained tools into the tool panel.""" diff -r c70a6f517aa96506b3245db857025f567aac0511 -r 521b4ff9060b72f1f8c9f5977f8c4fa2b0bd7877 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -575,10 +575,7 @@ tool_shed_repository=tool_shed_repository, tool_dependencies_config=tool_dependencies_config, tool_dependencies=tool_shed_repository.tool_dependencies ) - try: - shutil.rmtree( work_dir ) - except: - pass + suc.remove_dir( work_dir ) suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.INSTALLED ) else: # An error occurred while cloning the repository, so reset everything necessary to enable another attempt. @@ -817,10 +814,7 @@ for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status in [ trans.model.ToolDependency.installation_status.ERROR ]: repair_dict = add_repair_dict_entry( repository.name, installed_tool_dependency.error_message ) - try: - shutil.rmtree( work_dir ) - except: - pass + suc.remove_dir( work_dir ) suc.update_tool_shed_repository_status( trans.app, repository, trans.model.ToolShedRepository.installation_status.INSTALLED ) return repair_dict diff -r c70a6f517aa96506b3245db857025f567aac0511 -r 521b4ff9060b72f1f8c9f5977f8c4fa2b0bd7877 lib/tool_shed/util/export_util.py --- a/lib/tool_shed/util/export_util.py +++ b/lib/tool_shed/util/export_util.py @@ -103,7 +103,7 @@ attributes, sub_elements = get_repository_attributes_and_sub_elements( ordered_repository, archive_name ) elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=sub_elements ) exported_repository_registry.exported_repository_elems.append( elem ) - shutil.rmtree( work_dir ) + suc.remove_dir( work_dir ) # Keep information about the export in a file name export_info.xml in the archive. sub_elements = generate_export_elem( tool_shed_url, repository, changeset_revision, export_repository_dependencies, api ) export_elem = xml_util.create_element( 'export_info', attributes=None, sub_elements=sub_elements ) diff -r c70a6f517aa96506b3245db857025f567aac0511 -r 521b4ff9060b72f1f8c9f5977f8c4fa2b0bd7877 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -747,6 +747,7 @@ # Reset the value of the app's tool_data_path and tool_data_table_config_path to their respective original values. app.config.tool_data_path = original_tool_data_path app.config.tool_data_table_config_path = original_tool_data_table_config_path + suc.remove_dir( work_dir ) return metadata_dict, invalid_file_tups def generate_package_dependency_metadata( app, elem, valid_tool_dependencies_dict, invalid_tool_dependencies_dict ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: Dave Bouvier: When running the install and test framework, explicitly uninstall any tool dependency that is not in the state Installed.
by commits-noreply＠bitbucket.org 13 Nov '13

13 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c70a6f517aa9/ Changeset: c70a6f517aa9 User: Dave Bouvier Date: 2013-11-13 20:46:25 Summary: When running the install and test framework, explicitly uninstall any tool dependency that is not in the state Installed. Affected #: 2 files diff -r e6b3faf87f026f03412ff7b1b133fa0872c8be45 -r c70a6f517aa96506b3245db857025f567aac0511 test/install_and_test_tool_shed_repositories/base/test_db_util.py --- a/test/install_and_test_tool_shed_repositories/base/test_db_util.py +++ b/test/install_and_test_tool_shed_repositories/base/test_db_util.py @@ -36,12 +36,17 @@ return role raise AssertionError( "Private role not found for user '%s'" % user.email ) -def get_tool_dependencies_for_installed_repository( repository_id, status=None ): +def get_tool_dependencies_for_installed_repository( repository_id, status=None, exclude_status=None ): if status is not None: return sa_session.query( model.ToolDependency ) \ .filter( and_( model.ToolDependency.table.c.tool_shed_repository_id == repository_id, model.ToolDependency.table.c.status == status ) ) \ .all() + elif exclude_status is not None: + return sa_session.query( model.ToolDependency ) \ + .filter( and_( model.ToolDependency.table.c.tool_shed_repository_id == repository_id, + model.ToolDependency.table.c.status != exclude_status ) ) \ + .all() else: return sa_session.query( model.ToolDependency ) \ .filter( model.ToolDependency.table.c.tool_shed_repository_id == repository_id ) \ diff -r e6b3faf87f026f03412ff7b1b133fa0872c8be45 -r c70a6f517aa96506b3245db857025f567aac0511 test/install_and_test_tool_shed_repositories/base/twilltestcase.py --- a/test/install_and_test_tool_shed_repositories/base/twilltestcase.py +++ b/test/install_and_test_tool_shed_repositories/base/twilltestcase.py @@ -150,10 +150,10 @@ else: strings_displayed.append( 'has been uninstalled' ) self.check_for_strings( strings_displayed, strings_not_displayed=[] ) - # Get all tool dependencies that are in an error state and uninstall them explicitly, so that the next installation attempt + # Get all tool dependencies that are not in an installed state and uninstall them explicitly, so that the next installation attempt # may succeed. - error_state = model.ToolDependency.installation_status.ERROR - tool_dependencies = test_db_util.get_tool_dependencies_for_installed_repository( installed_repository.id, status=error_state ) + installed_state = model.ToolDependency.installation_status.INSTALLED + tool_dependencies = test_db_util.get_tool_dependencies_for_installed_repository( installed_repository.id, exclude_status=installed_state ) if len( tool_dependencies ) > 0: encoded_tool_dependency_ids = [ self.security.encode_id( tool_dependency.id ) for tool_dependency in tool_dependencies ] self.uninstall_tool_dependencies( self.security.encode_id( installed_repository.id ), encoded_tool_dependency_ids ) 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: 2 new changesets
by commits-noreply＠bitbucket.org 13 Nov '13

13 Nov '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9bde6f2b9c59/ Changeset: 9bde6f2b9c59 Branch: stable User: Dave Bouvier Date: 2013-11-13 20:16:29 Summary: Fix for downloading jar files in tool dependencies. Affected #: 1 file diff -r 8b60ec04bea623eeb7ba3b370302cf4e123119d7 -r 9bde6f2b9c59a29a35b85b7fe3c2e3bef3ae6a2e lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -430,7 +430,7 @@ if dst: dst.close() if extract: - if istar( file_path ) or iszip( file_path ): + if istar( file_path ) or ( iszip( file_path ) and not isjar( file_path ) ): archive = CompressedFile( file_path ) extraction_path = archive.extract( install_dir ) else: https://bitbucket.org/galaxy/galaxy-central/commits/e6b3faf87f02/ Changeset: e6b3faf87f02 User: Dave Bouvier Date: 2013-11-13 20:18:36 Summary: Merge in fix from stable. Affected #: 1 file diff -r 846962cad9648e2a76ba4bd2d6f85079ec78056c -r e6b3faf87f026f03412ff7b1b133fa0872c8be45 lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -430,7 +430,7 @@ if dst: dst.close() if extract: - if istar( file_path ) or iszip( file_path ): + if istar( file_path ) or ( iszip( file_path ) and not isjar( file_path ) ): archive = CompressedFile( file_path ) extraction_path = archive.extract( install_dir ) else: 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: Dave Bouvier: More fixes for recent changes to the datatypes registry.
by commits-noreply＠bitbucket.org 13 Nov '13

13 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/846962cad964/ Changeset: 846962cad964 User: Dave Bouvier Date: 2013-11-13 20:11:54 Summary: More fixes for recent changes to the datatypes registry. Affected #: 1 file diff -r 25a48c98802a8552fc6fac4a5c719a6c1839173a -r 846962cad9648e2a76ba4bd2d6f85079ec78056c lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -85,6 +85,13 @@ return imported_module if root_dir and config: + # If handling_proprietary_datatypes is determined as True below, we'll have an elem that looks something like this: + # <datatype display_in_upload="true" + # extension="blastxml" + # mimetype="application/xml" + # proprietary_datatype_module="blast" + # proprietary_path="[cloned repository path]" + # type="galaxy.datatypes.blast:BlastXml" /> handling_proprietary_datatypes = False # Parse datatypes_conf.xml tree = galaxy.util.parse_xml( config ) @@ -117,9 +124,13 @@ type_extension = elem.get( 'type_extension', None ) mimetype = elem.get( 'mimetype', None ) display_in_upload = galaxy.util.string_as_bool( elem.get( 'display_in_upload', False ) ) + # If make_subclass is True, it does not necessarily imply that we are subclassing a datatype that is contained + # in the distribution. make_subclass = galaxy.util.string_as_bool( elem.get( 'subclass', False ) ) # Proprietary datatypes included in installed tool shed repositories will include two special attributes # (proprietary_path and proprietary_datatype_module) if they depend on proprietary datatypes classes. + # The value of proprietary_path is the path to the cloned location of the tool shed repository's contained + # datatypes_conf.xml file. proprietary_path = elem.get( 'proprietary_path', None ) proprietary_datatype_module = elem.get( 'proprietary_datatype_module', None ) if proprietary_path is not None or proprietary_datatype_module is not None and not handling_proprietary_datatypes: @@ -182,21 +193,22 @@ except Exception, e: full_path = os.path.join( proprietary_path, proprietary_datatype_module ) self.log.debug( "Exception importing proprietary code file %s: %s" % ( str( full_path ), str( e ) ) ) - ok = False finally: lock.release() - if ok: - if datatype_class is None: - try: - # The datatype class name must be contained in one of the datatype modules in the Galaxy distribution. - fields = datatype_module.split( '.' ) - module = __import__( fields.pop( 0 ) ) - for mod in fields: - module = getattr( module, mod ) - datatype_class = getattr( module, datatype_class_name ) - except Exception, e: - self.log.exception( 'Error importing datatype module %s: %s' % ( str( datatype_module ), str( e ) ) ) - ok = False + # Either the above exception was thrown because the proprietary_datatype_module is not derived from a class + # in the repository, or we are loading Galaxy's datatypes. In either case we'll look in the registry. + if datatype_class is None: + try: + # The datatype class name must be contained in one of the datatype modules in the Galaxy distribution. + fields = datatype_module.split( '.' ) + module = __import__( fields.pop( 0 ) ) + for mod in fields: + module = getattr( module, mod ) + datatype_class = getattr( module, datatype_class_name ) + self.log.debug( 'Retrieved datatype module %s from the datatype registry.' % str( datatype_module ) ) + except Exception, e: + self.log.exception( 'Error importing datatype module %s: %s' % ( str( datatype_module ), str( e ) ) ) + ok = False elif type_extension is not None: try: datatype_class = self.datatypes_by_extension[ type_extension ].__class__ 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: Fixes for recent changes to the datatypes registry.
by commits-noreply＠bitbucket.org 13 Nov '13

13 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/25a48c98802a/ Changeset: 25a48c98802a User: greg Date: 2013-11-13 17:50:27 Summary: Fixes for recent changes to the datatypes registry. Affected #: 1 file diff -r 17ee3fa154b35f856a79be1691c5ed60832618c6 -r 25a48c98802a8552fc6fac4a5c719a6c1839173a lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -72,16 +72,18 @@ def load_datatypes( self, root_dir=None, config=None, deactivate=False, override=True ): """ - Parse a datatypes XML file located at root_dir/config. If deactivate is True, an installed tool shed - repository that includes proprietary datatypes is being deactivated, so appropriate loaded datatypes - will be removed from the registry. The value of override will be False when a tool shed repository is - being installed. Since installation is occurring after the datatypes registry has been initialized, its - contents cannot be overridden by new introduced conflicting data types. + Parse a datatypes XML file located at root_dir/config (if processing the Galaxy distributed config) or contained within + an installed Tool Shed repository. If deactivate is True, an installed Tool Shed repository that includes custom datatypes + is being deactivated or uninstalled, so appropriate loaded datatypes will be removed from the registry. The value of + override will be False when a Tool Shed repository is being installed. Since installation is occurring after the datatypes + registry has been initialized at server startup, it's contents cannot be overridden by newly introduced conflicting data types. """ + def __import_module( full_path, datatype_module, datatype_class_name ): open_file_obj, file_name, description = imp.find_module( datatype_module, [ full_path ] ) imported_module = imp.load_module( datatype_class_name, open_file_obj, file_name, description ) return imported_module + if root_dir and config: handling_proprietary_datatypes = False # Parse datatypes_conf.xml @@ -105,9 +107,11 @@ # Proprietary datatype's <registration> tag may have special attributes, proprietary_converter_path and proprietary_display_path. proprietary_converter_path = registration.get( 'proprietary_converter_path', None ) proprietary_display_path = registration.get( 'proprietary_display_path', None ) - if proprietary_converter_path or proprietary_display_path and not handling_proprietary_datatypes: + if proprietary_converter_path is not None or proprietary_display_path is not None and not handling_proprietary_datatypes: handling_proprietary_datatypes = True for elem in registration.findall( 'datatype' ): + # Keep a status of the process steps to enable stopping the process of handling the datatype if necessary. + ok = True extension = elem.get( 'extension', None ) dtype = elem.get( 'type', None ) type_extension = elem.get( 'type_extension', None ) @@ -118,11 +122,11 @@ # (proprietary_path and proprietary_datatype_module) if they depend on proprietary datatypes classes. proprietary_path = elem.get( 'proprietary_path', None ) proprietary_datatype_module = elem.get( 'proprietary_datatype_module', None ) - if proprietary_path or proprietary_datatype_module and not handling_proprietary_datatypes: + if proprietary_path is not None or proprietary_datatype_module is not None and not handling_proprietary_datatypes: handling_proprietary_datatypes = True if deactivate: - # We are deactivating an installed tool shed repository, so eliminate the - # datatype elem from the in-memory list of datatype elems. + # We are deactivating or uninstalling an installed tool shed repository, so eliminate the datatype + # elem from the in-memory list of datatype elems. for in_memory_elem in self.datatype_elems: in_memory_extension = in_memory_elem.get( 'extension', None ) if in_memory_extension == extension: @@ -131,30 +135,33 @@ in_memory_mimetype = elem.get( 'mimetype', None ) in_memory_display_in_upload = galaxy.util.string_as_bool( elem.get( 'display_in_upload', False ) ) in_memory_make_subclass = galaxy.util.string_as_bool( elem.get( 'subclass', False ) ) - if in_memory_dtype == dtype and in_memory_type_extension == type_extension and in_memory_mimetype == mimetype \ - and in_memory_display_in_upload == display_in_upload and in_memory_make_subclass == make_subclass: + if in_memory_dtype == dtype and \ + in_memory_type_extension == type_extension and \ + in_memory_mimetype == mimetype and \ + in_memory_display_in_upload == display_in_upload and \ + in_memory_make_subclass == make_subclass: self.datatype_elems.remove( in_memory_elem ) - if extension and extension in self.datatypes_by_extension: - # We are deactivating an installed tool shed repository, so eliminate the datatype from the registry. - # TODO: Handle deactivating datatype converters, etc before removing from self.datatypes_by_extension. - self.log.debug( "Removing datatype with extension '%s' from the registry." % extension ) + if extension is not None and extension in self.datatypes_by_extension: + # We are deactivating or uninstalling an installed tool shed repository, so eliminate the datatype + # from the registry. TODO: Handle deactivating datatype converters, etc before removing from + # self.datatypes_by_extension. del self.datatypes_by_extension[ extension ] if extension in self.upload_file_formats: self.upload_file_formats.remove( extension ) - can_process_datatype = False + self.log.debug( "Removed datatype with extension '%s' from the registry." % extension ) else: - # We are loading new datatypes. Keep an in-memory list of datatype elems to enable persistence. - if extension not in self.datatypes_by_extension: - self.datatype_elems.append( elem ) - can_process_datatype = ( extension and ( dtype or type_extension ) ) and \ - ( extension not in self.datatypes_by_extension or override ) + # We are loading new datatype, so we'll make sure it is correctly defined before proceeding. + can_process_datatype = False + if extension is not None: + if dtype is not None or type_extension is not None: + if override or extension not in self.datatypes_by_extension: + can_process_datatype = True if can_process_datatype: - ok = True - if dtype: + if dtype is not None: try: fields = dtype.split( ':' ) - datatype_module = fields[0] - datatype_class_name = fields[1] + datatype_module = fields[ 0 ] + datatype_class_name = fields[ 1 ] except Exception, e: self.log.exception( 'Error parsing datatype definition for dtype %s: %s' % ( str( dtype ), str( e ) ) ) ok = False @@ -175,115 +182,141 @@ except Exception, e: full_path = os.path.join( proprietary_path, proprietary_datatype_module ) self.log.debug( "Exception importing proprietary code file %s: %s" % ( str( full_path ), str( e ) ) ) + ok = False finally: lock.release() - if datatype_class is None: - try: - # The datatype class name must be contained in one of the datatype modules in the Galaxy distribution. - fields = datatype_module.split( '.' ) - module = __import__( fields.pop(0) ) - for mod in fields: - module = getattr( module, mod ) - datatype_class = getattr( module, datatype_class_name ) - except Exception, e: - self.log.exception( 'Error importing datatype module %s: %s' % ( str( datatype_module ), str( e ) ) ) - elif type_extension: - datatype_class = self.datatypes_by_extension[ type_extension ].__class__ - if not deactivate: - # A new tool shed repository that contains proprietary datatypes is being installed, and since installation - # is occurring after the datatypes registry has been initialized, its contents cannot be overridden by new - # introduced conflicting data types. - if make_subclass: - datatype_class = type( datatype_class_name, ( datatype_class, ), {} ) - if extension in self.datatypes_by_extension: - self.log.warning( "Overriding conflicting datatype with extension '%s', using datatype from %s." % ( extension, config ) ) - self.datatypes_by_extension[ extension ] = datatype_class() - if mimetype is None: - # Use default mime type as per datatype spec - mimetype = self.datatypes_by_extension[ extension ].get_mime() - self.mimetypes_by_extension[ extension ] = mimetype - if datatype_class.track_type: - self.available_tracks.append( extension ) - if display_in_upload and extension not in self.upload_file_formats: - self.upload_file_formats.append( extension ) - # Max file size cut off for setting optional metadata - self.datatypes_by_extension[ extension ].max_optional_metadata_filesize = elem.get( 'max_optional_metadata_filesize', None ) - for converter in elem.findall( 'converter' ): - # Build the list of datatype converters which will later be loaded into the calling app's toolbox. - converter_config = converter.get( 'file', None ) - target_datatype = converter.get( 'target_datatype', None ) - depends_on = converter.get( 'depends_on', None ) - if depends_on and target_datatype: - if extension not in self.converter_deps: - self.converter_deps[extension] = {} - self.converter_deps[extension][target_datatype] = depends_on.split(',') - if converter_config and target_datatype: - #if imported_modules: - if proprietary_converter_path: - self.proprietary_converters.append( ( converter_config, extension, target_datatype ) ) + if ok: + if datatype_class is None: + try: + # The datatype class name must be contained in one of the datatype modules in the Galaxy distribution. + fields = datatype_module.split( '.' ) + module = __import__( fields.pop( 0 ) ) + for mod in fields: + module = getattr( module, mod ) + datatype_class = getattr( module, datatype_class_name ) + except Exception, e: + self.log.exception( 'Error importing datatype module %s: %s' % ( str( datatype_module ), str( e ) ) ) + ok = False + elif type_extension is not None: + try: + datatype_class = self.datatypes_by_extension[ type_extension ].__class__ + except Exception, e: + self.log.exception( 'Error determining datatype_class for type_extension %s: %s' % ( str( type_extension ), str( e ) ) ) + ok = False + if ok: + if not deactivate: + # A new tool shed repository that contains custom datatypes is being installed, and since installation is + # occurring after the datatypes registry has been initialized at server startup, its contents cannot be + # overridden by new introduced conflicting data types unless the value of override is True. + if extension in self.datatypes_by_extension: + # Because of the way that the value of can_process_datatype was set above, we know that the value of + # override is True. + self.log.warning( "Overriding conflicting datatype with extension '%s', using datatype from %s." % \ + ( str( extension ), str( config ) ) ) + if make_subclass: + datatype_class = type( datatype_class_name, ( datatype_class, ), {} ) + self.datatypes_by_extension[ extension ] = datatype_class() + if mimetype is None: + # Use default mimetype per datatype specification. + mimetype = self.datatypes_by_extension[ extension ].get_mime() + self.mimetypes_by_extension[ extension ] = mimetype + if datatype_class.track_type: + self.available_tracks.append( extension ) + if display_in_upload and extension not in self.upload_file_formats: + self.upload_file_formats.append( extension ) + # Max file size cut off for setting optional metadata. + self.datatypes_by_extension[ extension ].max_optional_metadata_filesize = elem.get( 'max_optional_metadata_filesize', None ) + for converter in elem.findall( 'converter' ): + # Build the list of datatype converters which will later be loaded into the calling app's toolbox. + converter_config = converter.get( 'file', None ) + target_datatype = converter.get( 'target_datatype', None ) + depends_on = converter.get( 'depends_on', None ) + if depends_on is not None and target_datatype is not None: + if extension not in self.converter_deps: + self.converter_deps[ extension ] = {} + self.converter_deps[ extension ][ target_datatype ] = depends_on.split( ',' ) + if converter_config and target_datatype: + if proprietary_converter_path: + self.proprietary_converters.append( ( converter_config, extension, target_datatype ) ) + else: + self.converters.append( ( converter_config, extension, target_datatype ) ) + # Add composite files. + for composite_file in elem.findall( 'composite_file' ): + name = composite_file.get( 'name', None ) + if name is None: + self.log.warning( "You must provide a name for your composite_file (%s)." % composite_file ) + optional = composite_file.get( 'optional', False ) + mimetype = composite_file.get( 'mimetype', None ) + self.datatypes_by_extension[ extension ].add_composite_file( name, optional=optional, mimetype=mimetype ) + for display_app in elem.findall( 'display' ): + if proprietary_display_path: + if elem not in self.proprietary_display_app_containers: + self.proprietary_display_app_containers.append( elem ) else: - self.converters.append( ( converter_config, extension, target_datatype ) ) - for composite_file in elem.findall( 'composite_file' ): - # add composite files - name = composite_file.get( 'name', None ) - if name is None: - self.log.warning( "You must provide a name for your composite_file (%s)." % composite_file ) - optional = composite_file.get( 'optional', False ) - mimetype = composite_file.get( 'mimetype', None ) - self.datatypes_by_extension[extension].add_composite_file( name, optional=optional, mimetype=mimetype ) - for display_app in elem.findall( 'display' ): - #if imported_modules: - if proprietary_display_path: - if elem not in self.proprietary_display_app_containers: - self.proprietary_display_app_containers.append( elem ) - else: - if elem not in self.display_app_containers: - self.display_app_containers.append( elem ) - elif ( extension and ( dtype or type_extension ) ) and ( extension in self.datatypes_by_extension and not override ): - self.log.warning( "Ignoring conflicting datatype with extension '%s' from %s." % ( extension, config ) ) - # Load datatype sniffers from the config + if elem not in self.display_app_containers: + self.display_app_containers.append( elem ) + # Processing the new datatype elem is now complete, so make sure the element defining it is retained by appending + # the new datatype to the in-memory list of datatype elems to enable persistence. + self.datatype_elems.append( elem ) + else: + if extension is not None: + if dtype is not None or type_extension is not None: + if extension in self.datatypes_by_extension: + if not override: + # Do not load the datatype since it conflicts with an existing datatype which we are not supposed + # to override. + self.log.warning( "Ignoring conflicting datatype with extension '%s' from %s." % ( extension, config ) ) + # Load datatype sniffers from the config - we'll do this even if one or more datatypes were not properly processed in the config + # since sniffers are not tightly coupled with datatypes. self.load_datatype_sniffers( root, deactivate=deactivate, handling_proprietary_datatypes=handling_proprietary_datatypes, override=override ) self.upload_file_formats.sort() - # Persist the xml form of the registry into a temporary file so that it - # can be loaded from the command line by tools and set_metadata processing. + # Persist the xml form of the registry into a temporary file so that it can be loaded from the command line by tools and + # set_metadata processing. self.to_xml_file() self.set_default_values() def append_to_sniff_order(): # Just in case any supported data types are not included in the config's sniff_order section. for ext in self.datatypes_by_extension: - datatype = self.datatypes_by_extension[ext] + datatype = self.datatypes_by_extension[ ext ] included = False for atype in self.sniff_order: - if isinstance(atype, datatype.__class__): + if isinstance( atype, datatype.__class__ ): included = True break if not included: - self.sniff_order.append(datatype) + self.sniff_order.append( datatype ) append_to_sniff_order() def load_datatype_sniffers( self, root, deactivate=False, handling_proprietary_datatypes=False, override=False ): - # Load datatype sniffers from the received XML config + """ + Process the sniffers element from a parsed a datatypes XML file located at root_dir/config (if processing the Galaxy + distributed config) or contained within an installed Tool Shed repository. If deactivate is True, an installed Tool + Shed repository that includes custom sniffers is being deactivated or uninstalled, so appropriate loaded sniffers will + be removed from the registry. The value of override will be False when a Tool Shed repository is being installed. + Since installation is occurring after the datatypes registry has been initialized at server startup, it's contents + cannot be overridden by newly introduced conflicting sniffers. + """ sniffer_elem_classes = [ e.attrib[ 'type' ] for e in self.sniffer_elems ] sniffers = root.find( 'sniffers' ) if sniffers: for elem in sniffers.findall( 'sniffer' ): + # Keep a status of the process steps to enable stopping the process of handling the sniffer if necessary. + ok = True dtype = elem.get( 'type', None ) - ok = True - if dtype: + if dtype is not None: try: fields = dtype.split( ":" ) - datatype_module = fields[0] - datatype_class_name = fields[1] + datatype_module = fields[ 0 ] + datatype_class_name = fields[ 1 ] module = None except Exception, e: self.log.exception( 'Error determining datatype class or module for dtype %s: %s' % ( str( dtype ), str( e ) ) ) ok = False if ok: - #if imported_modules: if handling_proprietary_datatypes: # See if one of the imported modules contains the datatype class name. for imported_module in self.imported_modules: @@ -307,23 +340,21 @@ ok = False if ok: if deactivate: + # We are deactivating or uninstalling an installed Tool Shed repository, so eliminate the appropriate sniffers. sniffer_class = elem.get( 'type', None ) if sniffer_class is not None: for index, s_e_c in enumerate( sniffer_elem_classes ): if sniffer_class == s_e_c: del self.sniffer_elems[ index ] - self.log.debug( "Deactivated sniffer for datatype '%s'" % dtype ) + self.log.debug( "Removed sniffer element for datatype '%s'" % str( dtype ) ) break - for sniffer_class in self.sniff_order: - if sniffer_class.__class__ == aclass.__class__: - self.sniff_order.remove( sniffer_class ) - self.log.debug( "Removed sniffer class for datatype '%s' from sniff order" % dtype ) - break + for sniffer_class in self.sniff_order: + if sniffer_class.__class__ == aclass.__class__: + self.sniff_order.remove( sniffer_class ) + self.log.debug( "Removed sniffer class for datatype '%s' from sniff order" % str( dtype ) ) + break else: - # Keep an in-memory list of sniffer elems to enable persistence. - if elem not in self.sniffer_elems: - self.sniffer_elems.append( elem ) - # See if we have a conflicting sniffer already loaded. + # We are loading new sniffer, so see if we have a conflicting sniffer already loaded. conflict = False for conflict_loc, sniffer_class in enumerate( self.sniff_order ): if sniffer_class.__class__ == aclass.__class__: @@ -331,7 +362,7 @@ conflict = True if override: del self.sniff_order[ conflict_loc ] - self.log.debug( "Replaced conflicting sniffer for datatype '%s'" % dtype ) + self.log.debug( "Removed conflicting sniffer for datatype '%s'" % dtype ) break if conflict: if override: @@ -340,6 +371,11 @@ else: self.sniff_order.append( aclass ) self.log.debug( "Loaded sniffer for datatype '%s'" % dtype ) + # Processing the new sniffer elem is now complete, so make sure the element defining it is loaded if necessary. + sniffer_class = elem.get( 'type', None ) + if sniffer_class is not None: + if sniffer_class not in sniffer_elem_classes: + self.sniffer_elems.append( elem ) def get_datatype_class_by_name( self, name ): """ @@ -370,28 +406,28 @@ # #return datatype - def get_available_tracks(self): + def get_available_tracks( self ): return self.available_tracks - def get_mimetype_by_extension(self, ext, default = 'application/octet-stream' ): + def get_mimetype_by_extension( self, ext, default='application/octet-stream' ): """Returns a mimetype based on an extension""" try: - mimetype = self.mimetypes_by_extension[ext] + mimetype = self.mimetypes_by_extension[ ext ] except KeyError: #datatype was never declared mimetype = default - self.log.warning('unknown mimetype in data factory %s' % ext) + self.log.warning( 'unknown mimetype in data factory %s' % str( ext ) ) return mimetype - def get_datatype_by_extension(self, ext ): + def get_datatype_by_extension( self, ext ): """Returns a datatype based on an extension""" try: - builder = self.datatypes_by_extension[ext] + builder = self.datatypes_by_extension[ ext ] except KeyError: builder = data.Text() return builder - def change_datatype(self, data, ext): + def change_datatype( self, data, ext ): data.extension = ext # call init_meta and copy metadata from itself. The datatype # being converted *to* will handle any metadata copying and @@ -401,11 +437,11 @@ data.init_meta( copy_from=data ) return data - def old_change_datatype(self, data, ext): + def old_change_datatype( self, data, ext ): """Creates and returns a new datatype based on an existing data and an extension""" - newdata = factory(ext)(id=data.id) + newdata = factory( ext )( id=data.id ) for key, value in data.__dict__.items(): - setattr(newdata, key, value) + setattr( newdata, key, value ) newdata.ext = ext return newdata @@ -422,9 +458,9 @@ # Load converters defined by local datatypes_conf.xml. converters = self.converters for elem in converters: - tool_config = elem[0] - source_datatype = elem[1] - target_datatype = elem[2] + tool_config = elem[ 0 ] + source_datatype = elem[ 1 ] + target_datatype = elem[ 2 ] if installed_repository_dict: converter_path = installed_repository_dict[ 'converter_path' ] else: @@ -636,11 +672,11 @@ } # super supertype fix for input steps in workflows. if 'data' not in self.datatypes_by_extension: - self.datatypes_by_extension['data'] = data.Data() - self.mimetypes_by_extension['data'] = 'application/octet-stream' + self.datatypes_by_extension[ 'data' ] = data.Data() + self.mimetypes_by_extension[ 'data' ] = 'application/octet-stream' # Default values - the order in which we attempt to determine data types is critical # because some formats are much more flexibly defined than others. - if len(self.sniff_order) < 1: + if len( self.sniff_order ) < 1: self.sniff_order = [ binary.Bam(), binary.Sff(), @@ -666,27 +702,27 @@ tabular.Eland() ] - def get_converters_by_datatype(self, ext): + def get_converters_by_datatype( self, ext ): """Returns available converters by source type""" converters = odict() - source_datatype = type(self.get_datatype_by_extension(ext)) + source_datatype = type( self.get_datatype_by_extension( ext ) ) for ext2, dict in self.datatype_converters.items(): - converter_datatype = type(self.get_datatype_by_extension(ext2)) - if issubclass(source_datatype, converter_datatype): - converters.update(dict) + converter_datatype = type( self.get_datatype_by_extension( ext2 ) ) + if issubclass( source_datatype, converter_datatype ): + converters.update( dict ) #Ensure ext-level converters are present if ext in self.datatype_converters.keys(): - converters.update(self.datatype_converters[ext]) + converters.update( self.datatype_converters[ ext ] ) return converters - def get_converter_by_target_type(self, source_ext, target_ext): + def get_converter_by_target_type( self, source_ext, target_ext ): """Returns a converter based on source and target datatypes""" - converters = self.get_converters_by_datatype(source_ext) + converters = self.get_converters_by_datatype( source_ext ) if target_ext in converters.keys(): - return converters[target_ext] + return converters[ target_ext ] return None - def find_conversion_destination_for_dataset_by_extensions( self, dataset, accepted_formats, converter_safe = True ): + def find_conversion_destination_for_dataset_by_extensions( self, dataset, accepted_formats, converter_safe=True ): """Returns ( target_ext, existing converted dataset )""" for convert_ext in self.get_converters_by_datatype( dataset.ext ): if self.get_datatype_by_extension( convert_ext ).matches_any( accepted_formats ): @@ -728,8 +764,7 @@ def to_xml_file( self ): if self.xml_filename is not None: - # If persisted previously, attempt to remove - # the temporary file in which we were written. + # If persisted previously, attempt to remove the temporary file in which we were written. try: os.unlink( self.xml_filename ) except: 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: 2 new changesets
by commits-noreply＠bitbucket.org 13 Nov '13

13 Nov '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/82d876e06000/ Changeset: 82d876e06000 User: Dave Bouvier Date: 2013-11-13 16:46:38 Summary: Restore files that were deleted due to a tool migration, but are still used in test/functiona/test_get_data.py. Affected #: 2 files diff -r 95b5323cef58cab0cc76f9b392fe2c9c83254030 -r 82d876e06000b1d52ec65661da2b2245dd4e76ca test-data/1.bam Binary file test-data/1.bam has changed diff -r 95b5323cef58cab0cc76f9b392fe2c9c83254030 -r 82d876e06000b1d52ec65661da2b2245dd4e76ca test-data/3unsorted.bam Binary file test-data/3unsorted.bam has changed https://bitbucket.org/galaxy/galaxy-central/commits/17ee3fa154b3/ Changeset: 17ee3fa154b3 User: Dave Bouvier Date: 2013-11-13 17:23:54 Summary: Fix error in test_get_data.py's url paste upload test. Affected #: 1 file diff -r 82d876e06000b1d52ec65661da2b2245dd4e76ca -r 17ee3fa154b35f856a79be1691c5ed60832618c6 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -224,9 +224,9 @@ """Pasted data in the upload utility""" self.visit_page( "tool_runner/index?tool_id=upload1" ) try: - tc.fv( "1", "file_type", ftype ) - tc.fv( "1", "dbkey", dbkey ) - tc.fv( "1", "url_paste", url_paste ) + self.refresh_form( "file_type", ftype ) #Refresh, to support composite files + tc.fv( "tool_form", "dbkey", dbkey ) + tc.fv( "tool_form", "url_paste", url_paste ) tc.submit( "runtool_btn" ) self.home() except Exception, e: 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: allow break/wrap of title on non-whitespace
by commits-noreply＠bitbucket.org 13 Nov '13

13 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/95b5323cef58/ Changeset: 95b5323cef58 User: carlfeberhard Date: 2013-11-13 16:38:47 Summary: History panel: allow break/wrap of title on non-whitespace Affected #: 2 files diff -r d61de8f362929483c2a6a6cb8e7b7be77fa5cfa4 -r 95b5323cef58cab0cc76f9b392fe2c9c83254030 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1540,7 +1540,7 @@ .dataset [class$=messagesmall]{margin:6px 10px 2px 8px;font-size:90%} .dataset .help-text{font-weight:normal;font-style:italic;font-size:90%;color:#555} .dataset .dataset-title-bar{cursor:pointer;padding:6px 10px 6px 8px} -.dataset .dataset-title-bar .dataset-title{display:inline;font-weight:bold;text-decoration:underline;word-break:normal;line-height:16px} +.dataset .dataset-title-bar .dataset-title{display:inline;font-weight:bold;text-decoration:underline;word-wrap:break-word;word-break:break-all;line-height:16px} .dataset .dataset-primary-actions{float:right;margin:6px 10px 0}.dataset .dataset-primary-actions .icon-btn{margin-left:2px} .dataset .dataset-body{display:none;background-color:rgba(255,255,255,0.30000000000000004);padding:6px 10px 6px 8px}.dataset .dataset-body [class$=messagesmall]{margin:0px 0px 8px 0px} .dataset .dataset-body label{margin:0px;padding:0px;font-weight:normal} diff -r d61de8f362929483c2a6a6cb8e7b7be77fa5cfa4 -r 95b5323cef58cab0cc76f9b392fe2c9c83254030 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -257,7 +257,8 @@ display: inline; font-weight: bold; text-decoration: underline; - word-break: normal; + word-wrap: break-word; + word-break: break-all; line-height: 16px; } } 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: Dave Bouvier: Clean up commit 11300:04663654f82d.
by commits-noreply＠bitbucket.org 12 Nov '13

12 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d61de8f36292/ Changeset: d61de8f36292 User: Dave Bouvier Date: 2013-11-12 22:08:56 Summary: Clean up commit 11300:04663654f82d. Affected #: 2 files diff -r 9f04c4d80165d1f5261caf736aa11dbd86e36de3 -r d61de8f362929483c2a6a6cb8e7b7be77fa5cfa4 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -108,7 +108,6 @@ if proprietary_converter_path or proprietary_display_path and not handling_proprietary_datatypes: handling_proprietary_datatypes = True for elem in registration.findall( 'datatype' ): - self.log.debug( elem.attrib ) extension = elem.get( 'extension', None ) dtype = elem.get( 'type', None ) type_extension = elem.get( 'type_extension', None ) @@ -161,7 +160,6 @@ ok = False if ok: datatype_class = None - self.log.debug( [ proprietary_path, proprietary_datatype_module, datatype_class_name ] ) if proprietary_path and proprietary_datatype_module and datatype_class_name: # We need to change the value of sys.path, so do it in a way that is thread-safe. lock = threading.Lock() @@ -183,7 +181,6 @@ try: # The datatype class name must be contained in one of the datatype modules in the Galaxy distribution. fields = datatype_module.split( '.' ) - self.log.debug( fields ) module = __import__( fields.pop(0) ) for mod in fields: module = getattr( module, mod ) @@ -196,7 +193,6 @@ # A new tool shed repository that contains proprietary datatypes is being installed, and since installation # is occurring after the datatypes registry has been initialized, its contents cannot be overridden by new # introduced conflicting data types. - self.log.warning( "Ignoring conflicting datatype with extension '%s' from %s." % ( extension, config ) ) if make_subclass: datatype_class = type( datatype_class_name, ( datatype_class, ), {} ) if extension in self.datatypes_by_extension: @@ -243,6 +239,8 @@ else: if elem not in self.display_app_containers: self.display_app_containers.append( elem ) + elif ( extension and ( dtype or type_extension ) ) and ( extension in self.datatypes_by_extension and not override ): + self.log.warning( "Ignoring conflicting datatype with extension '%s' from %s." % ( extension, config ) ) # Load datatype sniffers from the config self.load_datatype_sniffers( root, deactivate=deactivate, diff -r 9f04c4d80165d1f5261caf736aa11dbd86e36de3 -r d61de8f362929483c2a6a6cb8e7b7be77fa5cfa4 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -54,7 +54,7 @@ common_install_util.activate_repository( trans, repository ) except Exception, e: error_message = "Error activating repository %s: %s" % ( repository.name, str( e ) ) - log.debug( error_message ) + log.exception( error_message ) message = '%s.<br/>You may be able to resolve this by uninstalling and then reinstalling the repository. Click <a href="%s">here</a> to uninstall the repository.' \ % ( error_message, web.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) ) ) status = 'error' 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: Dave Bouvier: Fix display of status images for installed tool shed repositories when using a proxy prefix.
by commits-noreply＠bitbucket.org 12 Nov '13

12 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9f04c4d80165/ Changeset: 9f04c4d80165 User: Dave Bouvier Date: 2013-11-12 21:36:13 Summary: Fix display of status images for installed tool shed repositories when using a proxy prefix. Affected #: 1 file diff -r 43231941e9705c69b2b6942c27b551ea6c12734c -r 9f04c4d80165d1f5261caf736aa11dbd86e36de3 lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py --- a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py +++ b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py @@ -2,6 +2,7 @@ from galaxy import model, util from galaxy.web.framework.helpers import iff, grids +from galaxy.web import url_for from galaxy.model.orm import or_ import tool_shed.util.shed_util_common as suc from tool_shed.util import tool_dependency_util @@ -13,42 +14,42 @@ deprecated_tip_str = 'class="icon-button" title="This repository is deprecated in the Tool Shed"' else: deprecated_tip_str = '' - return '<img src="/static/images/icon_error_sml.gif" %s/>' % deprecated_tip_str + return '<img src="%s/images/icon_error_sml.gif" %s/>' % ( url_for( '/static' ), deprecated_tip_str ) def generate_includes_workflows_img_str( include_mouse_over=False ): if include_mouse_over: deprecated_tip_str = 'class="icon-button" title="This repository contains exported workflows"' else: deprecated_tip_str = '' - return '<img src="/static/images/fugue/gear.png" %s/>' % deprecated_tip_str + return '<img src="%s/images/fugue/gear.png" %s/>' % ( url_for( '/static' ), deprecated_tip_str ) def generate_latest_revision_img_str( include_mouse_over=False ): if include_mouse_over: latest_revision_tip_str = 'class="icon-button" title="This is the latest installable revision of this repository"' else: latest_revision_tip_str = '' - return '<img src="/static/june_2007_style/blue/ok_small.png" %s/>' % latest_revision_tip_str + return '<img src="%s/june_2007_style/blue/ok_small.png" %s/>' % ( url_for( '/static' ), latest_revision_tip_str ) def generate_revision_updates_img_str( include_mouse_over=False ): if include_mouse_over: revision_updates_tip_str = 'class="icon-button" title="Updates are available in the Tool Shed for this revision"' else: revision_updates_tip_str = '' - return '<img src="/static/images/icon_warning_sml.gif" %s/>' % revision_updates_tip_str + return '<img src="%s/images/icon_warning_sml.gif" %s/>' % ( url_for( '/static' ), revision_updates_tip_str ) def generate_revision_upgrades_img_str( include_mouse_over=False ): if include_mouse_over: revision_upgrades_tip_str = 'class="icon-button" title="A newer installable revision is available for this repository"' else: revision_upgrades_tip_str = '' - return '<img src="/static/images/up.gif" %s/>' % revision_upgrades_tip_str + return '<img src="%s/images/up.gif" %s/>' % ( url_for( '/static' ), revision_upgrades_tip_str ) def generate_unknown_img_str( include_mouse_over=False ): if include_mouse_over: unknown_tip_str = 'class="icon-button" title="Unable to get information from the Tool Shed"' else: unknown_tip_str = '' - return '<img src="/static/june_2007_style/blue/question-octagon-frame.png" %s/>' % unknown_tip_str + return '<img src="%s/june_2007_style/blue/question-octagon-frame.png" %s/>' % ( url_for( '/static' ), unknown_tip_str ) class InstalledRepositoryGrid( grids.Grid ): 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: 3 new changesets
by commits-noreply＠bitbucket.org 12 Nov '13

12 Nov '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/04663654f82d/ Changeset: 04663654f82d User: Dave Bouvier Date: 2013-11-12 20:57:26 Summary: Clean up the load_datatypes method in the datatypes registry. Make the code pep8 compliant. Only load sniffers if they have not already been loaded. Do not load sniffers for datatypes that are being deactivated. Refactor loading of datatype sniffers into its own method. Improve exception handling when loading datatypes. Affected #: 1 file diff -r 41037d908be82d9790170cbd632924586f45735d -r 04663654f82d1f9401749503e321ecda5ce16275 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -1,16 +1,38 @@ """ Provides mapping between extensions and datatypes, mime-types, etc. """ -import os, sys, tempfile, threading, logging, imp -import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex, graph +import os +import sys +import tempfile +import threading +import logging +import imp +import data +import tabular +import interval +import images +import sequence +import qualityscore +import genetics +import xml +import coverage +import tracks +import chrominfo +import binary +import assembly +import ngsindex +import graph import galaxy.util from galaxy.util.odict import odict from display_applications.application import DisplayApplication + class ConfigurationError( Exception ): pass + class Registry( object ): + def __init__( self ): self.log = logging.getLogger(__name__) self.log.addHandler( logging.NullHandler() ) @@ -47,6 +69,7 @@ self.datatype_elems = [] self.sniffer_elems = [] self.xml_filename = None + def load_datatypes( self, root_dir=None, config=None, deactivate=False, override=True ): """ Parse a datatypes XML file located at root_dir/config. If deactivate is True, an installed tool shed @@ -85,38 +108,34 @@ if proprietary_converter_path or proprietary_display_path and not handling_proprietary_datatypes: handling_proprietary_datatypes = True for elem in registration.findall( 'datatype' ): - try: - extension = elem.get( 'extension', None ) - dtype = elem.get( 'type', None ) - type_extension = elem.get( 'type_extension', None ) - mimetype = elem.get( 'mimetype', None ) - display_in_upload = galaxy.util.string_as_bool( elem.get( 'display_in_upload', False ) ) - make_subclass = galaxy.util.string_as_bool( elem.get( 'subclass', False ) ) - # Proprietary datatypes included in installed tool shed repositories will include two special attributes - # (proprietary_path and proprietary_datatype_module) if they depend on proprietary datatypes classes. - proprietary_path = elem.get( 'proprietary_path', None ) - proprietary_datatype_module = elem.get( 'proprietary_datatype_module', None ) - if proprietary_path or proprietary_datatype_module and not handling_proprietary_datatypes: - handling_proprietary_datatypes = True - if deactivate: - # We are deactivating an installed tool shed repository, so eliminate the - # datatype elem from the in-memory list of datatype elems. - for in_memory_elem in self.datatype_elems: - in_memory_extension = in_memory_elem.get( 'extension', None ) - if in_memory_extension == extension: - in_memory_dtype = elem.get( 'type', None ) - in_memory_type_extension = elem.get( 'type_extension', None ) - in_memory_mimetype = elem.get( 'mimetype', None ) - in_memory_display_in_upload = galaxy.util.string_as_bool( elem.get( 'display_in_upload', False ) ) - in_memory_make_subclass = galaxy.util.string_as_bool( elem.get( 'subclass', False ) ) - if in_memory_dtype == dtype and in_memory_type_extension == type_extension and in_memory_mimetype == mimetype \ - and in_memory_display_in_upload == display_in_upload and in_memory_make_subclass == make_subclass: - self.datatype_elems.remove( in_memory_elem ) - else: - # Keep an in-memory list of datatype elems to enable persistence. - if extension not in self.datatypes_by_extension: - self.datatype_elems.append( elem ) - if extension and extension in self.datatypes_by_extension and deactivate: + self.log.debug( elem.attrib ) + extension = elem.get( 'extension', None ) + dtype = elem.get( 'type', None ) + type_extension = elem.get( 'type_extension', None ) + mimetype = elem.get( 'mimetype', None ) + display_in_upload = galaxy.util.string_as_bool( elem.get( 'display_in_upload', False ) ) + make_subclass = galaxy.util.string_as_bool( elem.get( 'subclass', False ) ) + # Proprietary datatypes included in installed tool shed repositories will include two special attributes + # (proprietary_path and proprietary_datatype_module) if they depend on proprietary datatypes classes. + proprietary_path = elem.get( 'proprietary_path', None ) + proprietary_datatype_module = elem.get( 'proprietary_datatype_module', None ) + if proprietary_path or proprietary_datatype_module and not handling_proprietary_datatypes: + handling_proprietary_datatypes = True + if deactivate: + # We are deactivating an installed tool shed repository, so eliminate the + # datatype elem from the in-memory list of datatype elems. + for in_memory_elem in self.datatype_elems: + in_memory_extension = in_memory_elem.get( 'extension', None ) + if in_memory_extension == extension: + in_memory_dtype = elem.get( 'type', None ) + in_memory_type_extension = elem.get( 'type_extension', None ) + in_memory_mimetype = elem.get( 'mimetype', None ) + in_memory_display_in_upload = galaxy.util.string_as_bool( elem.get( 'display_in_upload', False ) ) + in_memory_make_subclass = galaxy.util.string_as_bool( elem.get( 'subclass', False ) ) + if in_memory_dtype == dtype and in_memory_type_extension == type_extension and in_memory_mimetype == mimetype \ + and in_memory_display_in_upload == display_in_upload and in_memory_make_subclass == make_subclass: + self.datatype_elems.remove( in_memory_elem ) + if extension and extension in self.datatypes_by_extension: # We are deactivating an installed tool shed repository, so eliminate the datatype from the registry. # TODO: Handle deactivating datatype converters, etc before removing from self.datatypes_by_extension. self.log.debug( "Removing datatype with extension '%s' from the registry." % extension ) @@ -124,156 +143,432 @@ if extension in self.upload_file_formats: self.upload_file_formats.remove( extension ) can_process_datatype = False - else: - can_process_datatype = ( extension and ( dtype or type_extension ) ) and ( extension not in self.datatypes_by_extension or override ) + else: + # We are loading new datatypes. Keep an in-memory list of datatype elems to enable persistence. + if extension not in self.datatypes_by_extension: + self.datatype_elems.append( elem ) + can_process_datatype = ( extension and ( dtype or type_extension ) ) and \ + ( extension not in self.datatypes_by_extension or override ) if can_process_datatype: + ok = True if dtype: - fields = dtype.split( ':' ) - datatype_module = fields[0] - datatype_class_name = fields[1] - datatype_class = None - if proprietary_path and proprietary_datatype_module and datatype_class_name: - # We need to change the value of sys.path, so do it in a way that is thread-safe. - lock = threading.Lock() - lock.acquire( True ) - try: - imported_module = __import_module( proprietary_path, proprietary_datatype_module, datatype_class_name ) - if imported_module not in self.imported_modules: - self.imported_modules.append( imported_module ) - if hasattr( imported_module, datatype_class_name ): - datatype_class = getattr( imported_module, datatype_class_name ) - except Exception, e: - full_path = os.path.join( proprietary_path, proprietary_datatype_module ) - self.log.debug( "Exception importing proprietary code file %s: %s" % ( str( full_path ), str( e ) ) ) - finally: - lock.release() - if datatype_class is None: - # The datatype class name must be contained in one of the datatype modules in the Galaxy distribution. - fields = datatype_module.split( '.' ) - module = __import__( fields.pop(0) ) - for mod in fields: - module = getattr( module, mod ) - datatype_class = getattr( module, datatype_class_name ) + try: + fields = dtype.split( ':' ) + datatype_module = fields[0] + datatype_class_name = fields[1] + except Exception, e: + self.log.exception( 'Error parsing datatype definition for dtype %s: %s' % ( str( dtype ), str( e ) ) ) + ok = False + if ok: + datatype_class = None + self.log.debug( [ proprietary_path, proprietary_datatype_module, datatype_class_name ] ) + if proprietary_path and proprietary_datatype_module and datatype_class_name: + # We need to change the value of sys.path, so do it in a way that is thread-safe. + lock = threading.Lock() + lock.acquire( True ) + try: + imported_module = __import_module( proprietary_path, + proprietary_datatype_module, + datatype_class_name ) + if imported_module not in self.imported_modules: + self.imported_modules.append( imported_module ) + if hasattr( imported_module, datatype_class_name ): + datatype_class = getattr( imported_module, datatype_class_name ) + except Exception, e: + full_path = os.path.join( proprietary_path, proprietary_datatype_module ) + self.log.debug( "Exception importing proprietary code file %s: %s" % ( str( full_path ), str( e ) ) ) + finally: + lock.release() + if datatype_class is None: + try: + # The datatype class name must be contained in one of the datatype modules in the Galaxy distribution. + fields = datatype_module.split( '.' ) + self.log.debug( fields ) + module = __import__( fields.pop(0) ) + for mod in fields: + module = getattr( module, mod ) + datatype_class = getattr( module, datatype_class_name ) + except Exception, e: + self.log.exception( 'Error importing datatype module %s: %s' % ( str( datatype_module ), str( e ) ) ) elif type_extension: - datatype_class = self.datatypes_by_extension[type_extension].__class__ - if make_subclass: - datatype_class = type( datatype_class_name, (datatype_class,), {} ) - if extension in self.datatypes_by_extension: - self.log.warning( "Overriding conflicting datatype with extension '%s', using datatype from %s." % ( extension, config ) ) - self.datatypes_by_extension[ extension ] = datatype_class() - if mimetype is None: - # Use default mime type as per datatype spec - mimetype = self.datatypes_by_extension[ extension ].get_mime() - self.mimetypes_by_extension[ extension ] = mimetype - if datatype_class.track_type: - self.available_tracks.append( extension ) - if display_in_upload and extension not in self.upload_file_formats: - self.upload_file_formats.append( extension ) - # Max file size cut off for setting optional metadata - self.datatypes_by_extension[ extension ].max_optional_metadata_filesize = elem.get( 'max_optional_metadata_filesize', None ) - for converter in elem.findall( 'converter' ): - # Build the list of datatype converters which will later be loaded into the calling app's toolbox. - converter_config = converter.get( 'file', None ) - target_datatype = converter.get( 'target_datatype', None ) - depends_on = converter.get( 'depends_on', None ) - if depends_on and target_datatype: - if extension not in self.converter_deps: - self.converter_deps[extension] = {} - self.converter_deps[extension][target_datatype] = depends_on.split(',') - if converter_config and target_datatype: + datatype_class = self.datatypes_by_extension[ type_extension ].__class__ + if not deactivate: + # A new tool shed repository that contains proprietary datatypes is being installed, and since installation + # is occurring after the datatypes registry has been initialized, its contents cannot be overridden by new + # introduced conflicting data types. + self.log.warning( "Ignoring conflicting datatype with extension '%s' from %s." % ( extension, config ) ) + if make_subclass: + datatype_class = type( datatype_class_name, ( datatype_class, ), {} ) + if extension in self.datatypes_by_extension: + self.log.warning( "Overriding conflicting datatype with extension '%s', using datatype from %s." % ( extension, config ) ) + self.datatypes_by_extension[ extension ] = datatype_class() + if mimetype is None: + # Use default mime type as per datatype spec + mimetype = self.datatypes_by_extension[ extension ].get_mime() + self.mimetypes_by_extension[ extension ] = mimetype + if datatype_class.track_type: + self.available_tracks.append( extension ) + if display_in_upload and extension not in self.upload_file_formats: + self.upload_file_formats.append( extension ) + # Max file size cut off for setting optional metadata + self.datatypes_by_extension[ extension ].max_optional_metadata_filesize = elem.get( 'max_optional_metadata_filesize', None ) + for converter in elem.findall( 'converter' ): + # Build the list of datatype converters which will later be loaded into the calling app's toolbox. + converter_config = converter.get( 'file', None ) + target_datatype = converter.get( 'target_datatype', None ) + depends_on = converter.get( 'depends_on', None ) + if depends_on and target_datatype: + if extension not in self.converter_deps: + self.converter_deps[extension] = {} + self.converter_deps[extension][target_datatype] = depends_on.split(',') + if converter_config and target_datatype: + #if imported_modules: + if proprietary_converter_path: + self.proprietary_converters.append( ( converter_config, extension, target_datatype ) ) + else: + self.converters.append( ( converter_config, extension, target_datatype ) ) + for composite_file in elem.findall( 'composite_file' ): + # add composite files + name = composite_file.get( 'name', None ) + if name is None: + self.log.warning( "You must provide a name for your composite_file (%s)." % composite_file ) + optional = composite_file.get( 'optional', False ) + mimetype = composite_file.get( 'mimetype', None ) + self.datatypes_by_extension[extension].add_composite_file( name, optional=optional, mimetype=mimetype ) + for display_app in elem.findall( 'display' ): #if imported_modules: - if proprietary_converter_path: - self.proprietary_converters.append( ( converter_config, extension, target_datatype ) ) + if proprietary_display_path: + if elem not in self.proprietary_display_app_containers: + self.proprietary_display_app_containers.append( elem ) else: - self.converters.append( ( converter_config, extension, target_datatype ) ) - for composite_file in elem.findall( 'composite_file' ): - # add composite files - name = composite_file.get( 'name', None ) - if name is None: - self.log.warning( "You must provide a name for your composite_file (%s)." % composite_file ) - optional = composite_file.get( 'optional', False ) - mimetype = composite_file.get( 'mimetype', None ) - self.datatypes_by_extension[extension].add_composite_file( name, optional=optional, mimetype=mimetype ) - for display_app in elem.findall( 'display' ): - #if imported_modules: - if proprietary_display_path: - if elem not in self.proprietary_display_app_containers: - self.proprietary_display_app_containers.append( elem ) - else: - if elem not in self.display_app_containers: - self.display_app_containers.append( elem ) - elif not deactivate: - # A new tool shed repository that contains proprietary datatypes is being installed, and since installation - # is occurring after the datatypes registry has been initialized, its contents cannot be overridden by new - # introduced conflicting data types. - self.log.warning( "Ignoring conflicting datatype with extension '%s' from %s." % ( extension, config ) ) - except Exception, e: - if deactivate: - self.log.warning( "Error deactivating datatype with extension '%s': %s" % ( extension, str( e ) ) ) - else: - self.log.warning( "Error loading datatype with extension '%s': %s" % ( extension, str( e ) ) ) + if elem not in self.display_app_containers: + self.display_app_containers.append( elem ) # Load datatype sniffers from the config - sniffers = root.find( 'sniffers' ) - if sniffers: - for elem in sniffers.findall( 'sniffer' ): - # Keep an in-memory list of sniffer elems to enable persistence. - if elem not in self.sniffer_elems: - self.sniffer_elems.append( elem ) - dtype = elem.get( 'type', None ) - if dtype: - try: - fields = dtype.split( ":" ) - datatype_module = fields[0] - datatype_class_name = fields[1] - module = None - #if imported_modules: - if handling_proprietary_datatypes: - # See if one of the imported modules contains the datatype class name. - for imported_module in self.imported_modules: - if hasattr( imported_module, datatype_class_name ): - module = imported_module - break - if module is None: + self.load_datatype_sniffers( root, + deactivate=deactivate, + handling_proprietary_datatypes=handling_proprietary_datatypes, + override=override ) + self.upload_file_formats.sort() + # Persist the xml form of the registry into a temporary file so that it + # can be loaded from the command line by tools and set_metadata processing. + self.to_xml_file() + self.set_default_values() + + def append_to_sniff_order(): + # Just in case any supported data types are not included in the config's sniff_order section. + for ext in self.datatypes_by_extension: + datatype = self.datatypes_by_extension[ext] + included = False + for atype in self.sniff_order: + if isinstance(atype, datatype.__class__): + included = True + break + if not included: + self.sniff_order.append(datatype) + append_to_sniff_order() + + def load_datatype_sniffers( self, root, deactivate=False, handling_proprietary_datatypes=False, override=False ): + # Load datatype sniffers from the received XML config + sniffer_elem_classes = [ e.attrib[ 'type' ] for e in self.sniffer_elems ] + sniffers = root.find( 'sniffers' ) + if sniffers: + for elem in sniffers.findall( 'sniffer' ): + dtype = elem.get( 'type', None ) + ok = True + if dtype: + try: + fields = dtype.split( ":" ) + datatype_module = fields[0] + datatype_class_name = fields[1] + module = None + except Exception, e: + self.log.exception( 'Error determining datatype class or module for dtype %s: %s' % ( str( dtype ), str( e ) ) ) + ok = False + if ok: + #if imported_modules: + if handling_proprietary_datatypes: + # See if one of the imported modules contains the datatype class name. + for imported_module in self.imported_modules: + if hasattr( imported_module, datatype_class_name ): + module = imported_module + break + if module is None: + try: # The datatype class name must be contained in one of the datatype modules in the Galaxy distribution. module = __import__( datatype_module ) for comp in datatype_module.split( '.' )[ 1: ]: module = getattr( module, comp ) - aclass = getattr( module, datatype_class_name )() - if deactivate: - if elem in self.sniffer_elems: - self.sniffer_elems.remove( elem ) - for sniffer_class in self.sniff_order: - if sniffer_class.__class__ == aclass.__class__: - self.sniff_order.remove( sniffer_class ) - break - self.log.debug( "Deactivated sniffer for datatype '%s'" % dtype ) - else: - # See if we have a conflicting sniffer already loaded. - conflict = False - for conflict_loc, sniffer_class in enumerate( self.sniff_order ): - if sniffer_class.__class__ == aclass.__class__: - # We have a conflicting sniffer, so replace the one previously loaded. - conflict = True + except Exception, e: + self.log.exception( "Error importing datatype class for '%s': %s" % ( str( dtype ), str( e ) ) ) + ok = False + if ok: + try: + aclass = getattr( module, datatype_class_name )() + except Exception, e: + self.log.exception( 'Error calling method %s from class %s: %s' ( str( datatype_class_name ), str( module ), str( e ) ) ) + ok = False + if ok: + if deactivate: + sniffer_class = elem.get( 'type', None ) + if sniffer_class is not None: + for index, s_e_c in enumerate( sniffer_elem_classes ): + if sniffer_class == s_e_c: + del self.sniffer_elems[ index ] + self.log.debug( "Deactivated sniffer for datatype '%s'" % dtype ) + break + for sniffer_class in self.sniff_order: + if sniffer_class.__class__ == aclass.__class__: + self.sniff_order.remove( sniffer_class ) + self.log.debug( "Removed sniffer class for datatype '%s' from sniff order" % dtype ) + break + else: + # Keep an in-memory list of sniffer elems to enable persistence. + if elem not in self.sniffer_elems: + self.sniffer_elems.append( elem ) + # See if we have a conflicting sniffer already loaded. + conflict = False + for conflict_loc, sniffer_class in enumerate( self.sniff_order ): + if sniffer_class.__class__ == aclass.__class__: + # We have a conflicting sniffer, so replace the one previously loaded. + conflict = True + if override: + del self.sniff_order[ conflict_loc ] + self.log.debug( "Replaced conflicting sniffer for datatype '%s'" % dtype ) + break + if conflict: if override: - del self.sniff_order[ conflict_loc ] - self.log.debug( "Replaced conflicting sniffer for datatype '%s'" % dtype ) - break - if conflict: - if override: + self.sniff_order.append( aclass ) + self.log.debug( "Loaded sniffer for datatype '%s'" % dtype ) + else: self.sniff_order.append( aclass ) self.log.debug( "Loaded sniffer for datatype '%s'" % dtype ) - else: - self.sniff_order.append( aclass ) - self.log.debug( "Loaded sniffer for datatype '%s'" % dtype ) - except Exception, exc: + + def get_datatype_class_by_name( self, name ): + """ + Return the datatype class where the datatype's `type` attribute + (as defined in the datatype_conf.xml file) contains `name`. + """ + #TODO: too roundabout - would be better to generate this once as a map and store in this object + found_class = None + for ext, datatype_obj in self.datatypes_by_extension.items(): + datatype_obj_class = datatype_obj.__class__ + datatype_obj_class_str = str( datatype_obj_class ) + #print datatype_obj_class_str + if name in datatype_obj_class_str: + return datatype_obj_class + return None + # these seem to be connected to the dynamic classes being generated in this file, lines 157-158 + # they appear when a one of the three are used in inheritance with subclass="True" + #TODO: a possible solution is to def a fn in datatypes __init__ for creating the dynamic classes + + #remap = { + # 'galaxy.datatypes.registry.Tabular' : galaxy.datatypes.tabular.Tabular, + # 'galaxy.datatypes.registry.Text' : galaxy.datatypes.data.Text, + # 'galaxy.datatypes.registry.Binary' : galaxy.datatypes.binary.Binary + #} + #datatype_str = str( datatype ) + #if datatype_str in remap: + # datatype = remap[ datatype_str ] + # + #return datatype + + def get_available_tracks(self): + return self.available_tracks + + def get_mimetype_by_extension(self, ext, default = 'application/octet-stream' ): + """Returns a mimetype based on an extension""" + try: + mimetype = self.mimetypes_by_extension[ext] + except KeyError: + #datatype was never declared + mimetype = default + self.log.warning('unknown mimetype in data factory %s' % ext) + return mimetype + + def get_datatype_by_extension(self, ext ): + """Returns a datatype based on an extension""" + try: + builder = self.datatypes_by_extension[ext] + except KeyError: + builder = data.Text() + return builder + + def change_datatype(self, data, ext): + data.extension = ext + # call init_meta and copy metadata from itself. The datatype + # being converted *to* will handle any metadata copying and + # initialization. + if data.has_data(): + data.set_size() + data.init_meta( copy_from=data ) + return data + + def old_change_datatype(self, data, ext): + """Creates and returns a new datatype based on an existing data and an extension""" + newdata = factory(ext)(id=data.id) + for key, value in data.__dict__.items(): + setattr(newdata, key, value) + newdata.ext = ext + return newdata + + def load_datatype_converters( self, toolbox, installed_repository_dict=None, deactivate=False ): + """ + If deactivate is False, add datatype converters from self.converters or self.proprietary_converters + to the calling app's toolbox. If deactivate is True, eliminates relevant converters from the calling + app's toolbox. + """ + if installed_repository_dict: + # Load converters defined by datatypes_conf.xml included in installed tool shed repository. + converters = self.proprietary_converters + else: + # Load converters defined by local datatypes_conf.xml. + converters = self.converters + for elem in converters: + tool_config = elem[0] + source_datatype = elem[1] + target_datatype = elem[2] + if installed_repository_dict: + converter_path = installed_repository_dict[ 'converter_path' ] + else: + converter_path = self.converters_path + try: + config_path = os.path.join( converter_path, tool_config ) + converter = toolbox.load_tool( config_path ) + if installed_repository_dict: + # If the converter is included in an installed tool shed repository, set the tool + # shed related tool attributes. + converter.tool_shed = installed_repository_dict[ 'tool_shed' ] + converter.repository_name = installed_repository_dict[ 'repository_name' ] + converter.repository_owner = installed_repository_dict[ 'repository_owner' ] + converter.installed_changeset_revision = installed_repository_dict[ 'installed_changeset_revision' ] + converter.old_id = converter.id + # The converter should be included in the list of tools defined in tool_dicts. + tool_dicts = installed_repository_dict[ 'tool_dicts' ] + for tool_dict in tool_dicts: + if tool_dict[ 'id' ] == converter.id: + converter.guid = tool_dict[ 'guid' ] + converter.id = tool_dict[ 'guid' ] + break + if deactivate: + if converter.id in toolbox.tools_by_id: + del toolbox.tools_by_id[ converter.id ] + if source_datatype in self.datatype_converters: + if target_datatype in self.datatype_converters[ source_datatype ]: + del self.datatype_converters[ source_datatype ][ target_datatype ] + self.log.debug( "Deactivated converter: %s", converter.id ) + else: + toolbox.tools_by_id[ converter.id ] = converter + if source_datatype not in self.datatype_converters: + self.datatype_converters[ source_datatype ] = odict() + self.datatype_converters[ source_datatype ][ target_datatype ] = converter + self.log.debug( "Loaded converter: %s", converter.id ) + except Exception, e: + if deactivate: + self.log.exception( "Error deactivating converter from (%s): %s" % ( converter_path, str( e ) ) ) + else: + self.log.exception( "Error loading converter (%s): %s" % ( converter_path, str( e ) ) ) + + def load_display_applications( self, installed_repository_dict=None, deactivate=False ): + """ + If deactivate is False, add display applications from self.display_app_containers or + self.proprietary_display_app_containers to appropriate datatypes. If deactivate is + True, eliminates relevant display applications from appropriate datatypes. + """ + if installed_repository_dict: + # Load display applications defined by datatypes_conf.xml included in installed tool shed repository. + datatype_elems = self.proprietary_display_app_containers + else: + # Load display applications defined by local datatypes_conf.xml. + datatype_elems = self.display_app_containers + for elem in datatype_elems: + extension = elem.get( 'extension', None ) + for display_app in elem.findall( 'display' ): + display_file = display_app.get( 'file', None ) + if installed_repository_dict: + display_path = installed_repository_dict[ 'display_path' ] + display_file_head, display_file_tail = os.path.split( display_file ) + config_path = os.path.join( display_path, display_file_tail ) + else: + config_path = os.path.join( self.display_applications_path, display_file ) + try: + inherit = galaxy.util.string_as_bool( display_app.get( 'inherit', 'False' ) ) + display_app = DisplayApplication.from_file( config_path, self ) + if display_app: + if display_app.id in self.display_applications: if deactivate: - self.log.warning( "Error deactivating sniffer for datatype '%s': %s" % ( dtype, str( exc ) ) ) + del self.display_applications[ display_app.id ] else: - self.log.warning( "Error appending sniffer for datatype '%s' to sniff_order: %s" % ( dtype, str( exc ) ) ) - self.upload_file_formats.sort() - # Persist the xml form of the registry into a temporary file so that it - # can be loaded from the command line by tools and set_metadata processing. - self.to_xml_file() + # If we already loaded this display application, we'll use the first one loaded. + display_app = self.display_applications[ display_app.id ] + elif installed_repository_dict: + # If the display application is included in an installed tool shed repository, + # set the tool shed related tool attributes. + display_app.tool_shed = installed_repository_dict[ 'tool_shed' ] + display_app.repository_name = installed_repository_dict[ 'repository_name' ] + display_app.repository_owner = installed_repository_dict[ 'repository_owner' ] + display_app.installed_changeset_revision = installed_repository_dict[ 'installed_changeset_revision' ] + display_app.old_id = display_app.id + # The display application should be included in the list of tools defined in tool_dicts. + tool_dicts = installed_repository_dict[ 'tool_dicts' ] + for tool_dict in tool_dicts: + if tool_dict[ 'id' ] == display_app.id: + display_app.guid = tool_dict[ 'guid' ] + display_app.id = tool_dict[ 'guid' ] + break + if deactivate: + if display_app.id in self.display_applications: + del self.display_applications[ display_app.id ] + if extension in self.datatypes_by_extension: + if display_app.id in self.datatypes_by_extension[ extension ].display_applications: + del self.datatypes_by_extension[ extension ].display_applications[ display_app.id ] + if inherit and ( self.datatypes_by_extension[ extension ], display_app ) in self.inherit_display_application_by_class: + self.inherit_display_application_by_class.remove( ( self.datatypes_by_extension[ extension ], display_app ) ) + self.log.debug( "Deactivated display application '%s' for datatype '%s'." % ( display_app.id, extension ) ) + else: + self.display_applications[ display_app.id ] = display_app + self.datatypes_by_extension[ extension ].add_display_application( display_app ) + if inherit and ( self.datatypes_by_extension[ extension ], display_app ) not in self.inherit_display_application_by_class: + self.inherit_display_application_by_class.append( ( self.datatypes_by_extension[ extension ], display_app ) ) + self.log.debug( "Loaded display application '%s' for datatype '%s', inherit=%s." % ( display_app.id, extension, inherit ) ) + except Exception, e: + if deactivate: + self.log.exception( "Error deactivating display application (%s): %s" % ( config_path, str( e ) ) ) + else: + self.log.exception( "Error loading display application (%s): %s" % ( config_path, str( e ) ) ) + # Handle display_application subclass inheritance. + for extension, d_type1 in self.datatypes_by_extension.iteritems(): + for d_type2, display_app in self.inherit_display_application_by_class: + current_app = d_type1.get_display_application( display_app.id, None ) + if current_app is None and isinstance( d_type1, type( d_type2 ) ): + self.log.debug( "Adding inherited display application '%s' to datatype '%s'" % ( display_app.id, extension ) ) + d_type1.add_display_application( display_app ) + + def load_external_metadata_tool( self, toolbox ): + """Adds a tool which is used to set external metadata""" + # We need to be able to add a job to the queue to set metadata. The queue will currently only accept jobs with an associated + # tool. We'll create a special tool to be used for Auto-Detecting metadata; this is less than ideal, but effective + # Properly building a tool without relying on parsing an XML file is near impossible...so we'll create a temporary file + tool_xml_text = """ + <tool id="__SET_METADATA__" name="Set External Metadata" version="1.0.1" tool_type="set_metadata"> + <type class="SetMetadataTool" module="galaxy.tools"/> + <action module="galaxy.tools.actions.metadata" class="SetMetadataToolAction"/> + <command>$__SET_EXTERNAL_METADATA_COMMAND_LINE__</command> + <inputs> + <param format="data" name="input1" type="data" label="File to set metadata on."/> + <param name="__ORIGINAL_DATASET_STATE__" type="hidden" value=""/> + <param name="__SET_EXTERNAL_METADATA_COMMAND_LINE__" type="hidden" value=""/> + </inputs> + </tool> + """ + tmp_name = tempfile.NamedTemporaryFile() + tmp_name.write( tool_xml_text ) + tmp_name.flush() + set_meta_tool = toolbox.load_tool( tmp_name.name ) + toolbox.tools_by_id[ set_meta_tool.id ] = set_meta_tool + self.set_external_metadata_tool = set_meta_tool + self.log.debug( "Loaded external metadata tool: %s", self.set_external_metadata_tool.id ) + + def set_default_values( self ): # Default values. if not self.datatypes_by_extension: self.datatypes_by_extension = { @@ -372,236 +667,7 @@ tabular.Sam(), tabular.Eland() ] - def append_to_sniff_order(): - # Just in case any supported data types are not included in the config's sniff_order section. - for ext in self.datatypes_by_extension: - datatype = self.datatypes_by_extension[ext] - included = False - for atype in self.sniff_order: - if isinstance(atype, datatype.__class__): - included = True - break - if not included: - self.sniff_order.append(datatype) - append_to_sniff_order() - def get_datatype_class_by_name( self, name ): - """ - Return the datatype class where the datatype's `type` attribute - (as defined in the datatype_conf.xml file) contains `name`. - """ - #TODO: too roundabout - would be better to generate this once as a map and store in this object - found_class = None - for ext, datatype_obj in self.datatypes_by_extension.items(): - datatype_obj_class = datatype_obj.__class__ - datatype_obj_class_str = str( datatype_obj_class ) - #print datatype_obj_class_str - if name in datatype_obj_class_str: - return datatype_obj_class - return None - # these seem to be connected to the dynamic classes being generated in this file, lines 157-158 - # they appear when a one of the three are used in inheritance with subclass="True" - #TODO: a possible solution is to def a fn in datatypes __init__ for creating the dynamic classes - - #remap = { - # 'galaxy.datatypes.registry.Tabular' : galaxy.datatypes.tabular.Tabular, - # 'galaxy.datatypes.registry.Text' : galaxy.datatypes.data.Text, - # 'galaxy.datatypes.registry.Binary' : galaxy.datatypes.binary.Binary - #} - #datatype_str = str( datatype ) - #if datatype_str in remap: - # datatype = remap[ datatype_str ] - # - #return datatype - - def get_available_tracks(self): - return self.available_tracks - def get_mimetype_by_extension(self, ext, default = 'application/octet-stream' ): - """Returns a mimetype based on an extension""" - try: - mimetype = self.mimetypes_by_extension[ext] - except KeyError: - #datatype was never declared - mimetype = default - self.log.warning('unknown mimetype in data factory %s' % ext) - return mimetype - def get_datatype_by_extension(self, ext ): - """Returns a datatype based on an extension""" - try: - builder = self.datatypes_by_extension[ext] - except KeyError: - builder = data.Text() - return builder - def change_datatype(self, data, ext): - data.extension = ext - # call init_meta and copy metadata from itself. The datatype - # being converted *to* will handle any metadata copying and - # initialization. - if data.has_data(): - data.set_size() - data.init_meta( copy_from=data ) - return data - def old_change_datatype(self, data, ext): - """Creates and returns a new datatype based on an existing data and an extension""" - newdata = factory(ext)(id=data.id) - for key, value in data.__dict__.items(): - setattr(newdata, key, value) - newdata.ext = ext - return newdata - def load_datatype_converters( self, toolbox, installed_repository_dict=None, deactivate=False ): - """ - If deactivate is False, add datatype converters from self.converters or self.proprietary_converters - to the calling app's toolbox. If deactivate is True, eliminates relevant converters from the calling - app's toolbox. - """ - if installed_repository_dict: - # Load converters defined by datatypes_conf.xml included in installed tool shed repository. - converters = self.proprietary_converters - else: - # Load converters defined by local datatypes_conf.xml. - converters = self.converters - for elem in converters: - tool_config = elem[0] - source_datatype = elem[1] - target_datatype = elem[2] - if installed_repository_dict: - converter_path = installed_repository_dict[ 'converter_path' ] - else: - converter_path = self.converters_path - try: - config_path = os.path.join( converter_path, tool_config ) - converter = toolbox.load_tool( config_path ) - if installed_repository_dict: - # If the converter is included in an installed tool shed repository, set the tool - # shed related tool attributes. - converter.tool_shed = installed_repository_dict[ 'tool_shed' ] - converter.repository_name = installed_repository_dict[ 'repository_name' ] - converter.repository_owner = installed_repository_dict[ 'repository_owner' ] - converter.installed_changeset_revision = installed_repository_dict[ 'installed_changeset_revision' ] - converter.old_id = converter.id - # The converter should be included in the list of tools defined in tool_dicts. - tool_dicts = installed_repository_dict[ 'tool_dicts' ] - for tool_dict in tool_dicts: - if tool_dict[ 'id' ] == converter.id: - converter.guid = tool_dict[ 'guid' ] - converter.id = tool_dict[ 'guid' ] - break - if deactivate: - if converter.id in toolbox.tools_by_id: - del toolbox.tools_by_id[ converter.id ] - if source_datatype in self.datatype_converters: - if target_datatype in self.datatype_converters[ source_datatype ]: - del self.datatype_converters[ source_datatype ][ target_datatype ] - self.log.debug( "Deactivated converter: %s", converter.id ) - else: - toolbox.tools_by_id[ converter.id ] = converter - if source_datatype not in self.datatype_converters: - self.datatype_converters[ source_datatype ] = odict() - self.datatype_converters[ source_datatype ][ target_datatype ] = converter - self.log.debug( "Loaded converter: %s", converter.id ) - except Exception, e: - if deactivate: - self.log.exception( "Error deactivating converter from (%s): %s" % ( converter_path, str( e ) ) ) - else: - self.log.exception( "Error loading converter (%s): %s" % ( converter_path, str( e ) ) ) - def load_display_applications( self, installed_repository_dict=None, deactivate=False ): - """ - If deactivate is False, add display applications from self.display_app_containers or - self.proprietary_display_app_containers to appropriate datatypes. If deactivate is - True, eliminates relevant display applications from appropriate datatypes. - """ - if installed_repository_dict: - # Load display applications defined by datatypes_conf.xml included in installed tool shed repository. - datatype_elems = self.proprietary_display_app_containers - else: - # Load display applications defined by local datatypes_conf.xml. - datatype_elems = self.display_app_containers - for elem in datatype_elems: - extension = elem.get( 'extension', None ) - for display_app in elem.findall( 'display' ): - display_file = display_app.get( 'file', None ) - if installed_repository_dict: - display_path = installed_repository_dict[ 'display_path' ] - display_file_head, display_file_tail = os.path.split( display_file ) - config_path = os.path.join( display_path, display_file_tail ) - else: - config_path = os.path.join( self.display_applications_path, display_file ) - try: - inherit = galaxy.util.string_as_bool( display_app.get( 'inherit', 'False' ) ) - display_app = DisplayApplication.from_file( config_path, self ) - if display_app: - if display_app.id in self.display_applications: - if deactivate: - del self.display_applications[ display_app.id ] - else: - # If we already loaded this display application, we'll use the first one loaded. - display_app = self.display_applications[ display_app.id ] - elif installed_repository_dict: - # If the display application is included in an installed tool shed repository, - # set the tool shed related tool attributes. - display_app.tool_shed = installed_repository_dict[ 'tool_shed' ] - display_app.repository_name = installed_repository_dict[ 'repository_name' ] - display_app.repository_owner = installed_repository_dict[ 'repository_owner' ] - display_app.installed_changeset_revision = installed_repository_dict[ 'installed_changeset_revision' ] - display_app.old_id = display_app.id - # The display application should be included in the list of tools defined in tool_dicts. - tool_dicts = installed_repository_dict[ 'tool_dicts' ] - for tool_dict in tool_dicts: - if tool_dict[ 'id' ] == display_app.id: - display_app.guid = tool_dict[ 'guid' ] - display_app.id = tool_dict[ 'guid' ] - break - if deactivate: - if display_app.id in self.display_applications: - del self.display_applications[ display_app.id ] - if extension in self.datatypes_by_extension: - if display_app.id in self.datatypes_by_extension[ extension ].display_applications: - del self.datatypes_by_extension[ extension ].display_applications[ display_app.id ] - if inherit and ( self.datatypes_by_extension[ extension ], display_app ) in self.inherit_display_application_by_class: - self.inherit_display_application_by_class.remove( ( self.datatypes_by_extension[ extension ], display_app ) ) - self.log.debug( "Deactivated display application '%s' for datatype '%s'." % ( display_app.id, extension ) ) - else: - self.display_applications[ display_app.id ] = display_app - self.datatypes_by_extension[ extension ].add_display_application( display_app ) - if inherit and ( self.datatypes_by_extension[ extension ], display_app ) not in self.inherit_display_application_by_class: - self.inherit_display_application_by_class.append( ( self.datatypes_by_extension[ extension ], display_app ) ) - self.log.debug( "Loaded display application '%s' for datatype '%s', inherit=%s." % ( display_app.id, extension, inherit ) ) - except Exception, e: - if deactivate: - self.log.exception( "Error deactivating display application (%s): %s" % ( config_path, str( e ) ) ) - else: - self.log.exception( "Error loading display application (%s): %s" % ( config_path, str( e ) ) ) - # Handle display_application subclass inheritance. - for extension, d_type1 in self.datatypes_by_extension.iteritems(): - for d_type2, display_app in self.inherit_display_application_by_class: - current_app = d_type1.get_display_application( display_app.id, None ) - if current_app is None and isinstance( d_type1, type( d_type2 ) ): - self.log.debug( "Adding inherited display application '%s' to datatype '%s'" % ( display_app.id, extension ) ) - d_type1.add_display_application( display_app ) - def load_external_metadata_tool( self, toolbox ): - """Adds a tool which is used to set external metadata""" - # We need to be able to add a job to the queue to set metadata. The queue will currently only accept jobs with an associated - # tool. We'll create a special tool to be used for Auto-Detecting metadata; this is less than ideal, but effective - # Properly building a tool without relying on parsing an XML file is near impossible...so we'll create a temporary file - tool_xml_text = """ - <tool id="__SET_METADATA__" name="Set External Metadata" version="1.0.1" tool_type="set_metadata"> - <type class="SetMetadataTool" module="galaxy.tools"/> - <action module="galaxy.tools.actions.metadata" class="SetMetadataToolAction"/> - <command>$__SET_EXTERNAL_METADATA_COMMAND_LINE__</command> - <inputs> - <param format="data" name="input1" type="data" label="File to set metadata on."/> - <param name="__ORIGINAL_DATASET_STATE__" type="hidden" value=""/> - <param name="__SET_EXTERNAL_METADATA_COMMAND_LINE__" type="hidden" value=""/> - </inputs> - </tool> - """ - tmp_name = tempfile.NamedTemporaryFile() - tmp_name.write( tool_xml_text ) - tmp_name.flush() - set_meta_tool = toolbox.load_tool( tmp_name.name ) - toolbox.tools_by_id[ set_meta_tool.id ] = set_meta_tool - self.set_external_metadata_tool = set_meta_tool - self.log.debug( "Loaded external metadata tool: %s", self.set_external_metadata_tool.id ) def get_converters_by_datatype(self, ext): """Returns available converters by source type""" converters = odict() @@ -614,12 +680,14 @@ if ext in self.datatype_converters.keys(): converters.update(self.datatype_converters[ext]) return converters + def get_converter_by_target_type(self, source_ext, target_ext): """Returns a converter based on source and target datatypes""" converters = self.get_converters_by_datatype(source_ext) if target_ext in converters.keys(): return converters[target_ext] return None + def find_conversion_destination_for_dataset_by_extensions( self, dataset, accepted_formats, converter_safe = True ): """Returns ( target_ext, existing converted dataset )""" for convert_ext in self.get_converters_by_datatype( dataset.ext ): @@ -633,8 +701,10 @@ ret_data = None return ( convert_ext, ret_data ) return ( None, None ) + def get_composite_extensions( self ): return [ ext for ( ext, d_type ) in self.datatypes_by_extension.iteritems() if d_type.composite_type is not None ] + def get_upload_metadata_params( self, context, group, tool ): """Returns dict of case value:inputs for metadata conditional for upload tool""" rval = {} @@ -650,12 +720,14 @@ if 'auto' not in rval and 'txt' in rval: #need to manually add 'auto' datatype rval[ 'auto' ] = rval[ 'txt' ] return rval + @property def integrated_datatypes_configs( self ): if self.xml_filename and os.path.isfile( self.xml_filename ): return self.xml_filename self.to_xml_file() return self.xml_filename + def to_xml_file( self ): if self.xml_filename is not None: # If persisted previously, attempt to remove https://bitbucket.org/galaxy/galaxy-central/commits/393265d72786/ Changeset: 393265d72786 User: Dave Bouvier Date: 2013-11-12 20:59:02 Summary: Update the tool dependency installation process to mark a tool dependency as installed if the path exists, contains the installation log file, and app.config.running_functional_tests is True. This enables caching of compiled or downloaded tool dependencies when running the EC2 installation and testing framework. Affected #: 1 file diff -r 04663654f82d1f9401749503e321ecda5ce16275 -r 393265d727868689e0f1c14d864a18dab66ea068 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -337,6 +337,18 @@ print '\nSkipping installation of tool dependency', package_name, 'version', package_version, \ 'since it is installed in', install_dir, '\n' can_install_tool_dependency = False + # This tool dependency was previously installed, but the record was missing from the database due to some + # activity outside of the control of the tool shed. Since a new record was created for it and we don't know + # the state of the files on disk, we will set it to an error state. If we are running functional tests, the + # state will be set to Installed, because previously compiled tool dependencies are not deleted by default. + if app.config.running_functional_tests: + tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED + else: + error_message = 'The installation directory for this tool dependency had contents, but the database had no record. ' + error_message += 'The installation log may show this tool dependency to be correctly installed, but due to the ' + error_message += 'missing database record, it is automatically set to Error.' + tool_dependency.status = app.model.ToolDependency.installation_status.ERROR + tool_dependency.error_message = error_message else: error_message = '\nInstallation path %s for tool dependency %s version %s exists, but the expected file %s' % \ ( install_dir, package_name, package_version, fabric_util.INSTALLATION_LOG ) https://bitbucket.org/galaxy/galaxy-central/commits/43231941e970/ Changeset: 43231941e970 User: Dave Bouvier Date: 2013-11-12 20:59:32 Summary: Fix missing blast.py in blast_datatypes repository tarball for tool shed functional tests. Affected #: 1 file diff -r 393265d727868689e0f1c14d864a18dab66ea068 -r 43231941e9705c69b2b6942c27b551ea6c12734c test/tool_shed/test_data/blast/blast_datatypes.tar Binary file test/tool_shed/test_data/blast/blast_datatypes.tar has changed 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: 2 new changesets
by commits-noreply＠bitbucket.org 12 Nov '13

12 Nov '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/480d5127f3ea/ Changeset: 480d5127f3ea User: jmchilton Date: 2013-11-12 15:59:39 Summary: Only show Manage Quotas if quotas are enabled. Affected #: 1 file diff -r cd12bf2ed5475c8c6ab72321e5865441c0805bd2 -r 480d5127f3ea57026b14bb560debdb2356b30b59 templates/webapps/galaxy/admin/index.mako --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -52,7 +52,7 @@ <div class="toolTitle"><a href="${h.url_for( controller='admin', action='users' )}" target="galaxy_main">Manage users</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='groups' )}" target="galaxy_main">Manage groups</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='roles' )}" target="galaxy_main">Manage roles</a></div> - <div class="toolTitle"><a href="${h.url_for( controller='userskeys', action='all_users' )}" target="galaxy_main">Manage users API keys</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='userskeys', action='all_users' )}" target="galaxy_main">Manage users API keys</a></div> %if trans.app.config.allow_user_impersonation: <div class="toolTitle"><a href="${h.url_for( controller='admin', action='impersonate' )}" target="galaxy_main">Impersonate a user</a></div> %endif @@ -62,7 +62,9 @@ <div class="toolSectionTitle">Data</div><div class="toolSectionBody"><div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='quotas' )}" target="galaxy_main">Manage quotas</a></div> + %if trans.app.config.enable_quotas: + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='quotas' )}" target="galaxy_main">Manage quotas</a></div> + %endif <div class="toolTitle"><a href="${h.url_for( controller='library_admin', action='browse_libraries' )}" target="galaxy_main">Manage data libraries</a></div> %if trans.app.config.enable_beta_job_managers: <div class="toolTitle"><a href="${h.url_for( controller='data_admin', action='manage_data' )}" target="galaxy_main">Manage local data</a></div> https://bitbucket.org/galaxy/galaxy-central/commits/41037d908be8/ Changeset: 41037d908be8 User: jmchilton Date: 2013-11-12 20:21:17 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #258) Only show Manage Quotas if quotas are enabled. Affected #: 1 file diff -r 7b60d7eb93520983f9ff1a731f62eac88e2979bc -r 41037d908be82d9790170cbd632924586f45735d templates/webapps/galaxy/admin/index.mako --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -52,7 +52,7 @@ <div class="toolTitle"><a href="${h.url_for( controller='admin', action='users' )}" target="galaxy_main">Manage users</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='groups' )}" target="galaxy_main">Manage groups</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='roles' )}" target="galaxy_main">Manage roles</a></div> - <div class="toolTitle"><a href="${h.url_for( controller='userskeys', action='all_users' )}" target="galaxy_main">Manage users API keys</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='userskeys', action='all_users' )}" target="galaxy_main">Manage users API keys</a></div> %if trans.app.config.allow_user_impersonation: <div class="toolTitle"><a href="${h.url_for( controller='admin', action='impersonate' )}" target="galaxy_main">Impersonate a user</a></div> %endif @@ -62,7 +62,9 @@ <div class="toolSectionTitle">Data</div><div class="toolSectionBody"><div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='quotas' )}" target="galaxy_main">Manage quotas</a></div> + %if trans.app.config.enable_quotas: + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='quotas' )}" target="galaxy_main">Manage quotas</a></div> + %endif <div class="toolTitle"><a href="${h.url_for( controller='library_admin', action='browse_libraries' )}" target="galaxy_main">Manage data libraries</a></div> %if trans.app.config.enable_beta_job_managers: <div class="toolTitle"><a href="${h.url_for( controller='data_admin', action='manage_data' )}" target="galaxy_main">Manage local data</a></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: 2 new changesets
by commits-noreply＠bitbucket.org 12 Nov '13

12 Nov '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fd4b44698aeb/ Changeset: fd4b44698aeb User: guerler Date: 2013-11-12 19:01:17 Summary: Merge stable Affected #: 1 file https://bitbucket.org/galaxy/galaxy-central/commits/7b60d7eb9352/ Changeset: 7b60d7eb9352 User: guerler Date: 2013-11-12 19:02:51 Summary: Merge Affected #: 1 file diff -r fd4b44698aeb0dac0217da7872425552ac390f65 -r 7b60d7eb93520983f9ff1a731f62eac88e2979bc lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -493,7 +493,7 @@ rval = {} # Get the default value for the 'test element' and use it # to determine the current case - test_value = self.test_param.get_initial_value( trans, context, history=None ) + test_value = self.test_param.get_initial_value( trans, context, history=history ) current_case = self.get_current_case( test_value, trans ) # Store the current case in a special value rval['__current_case__'] = current_case @@ -502,7 +502,7 @@ # Fill in state for selected case child_context = ExpressionContext( rval, context ) for child_input in self.cases[current_case].inputs.itervalues(): - rval[ child_input.name ] = child_input.get_initial_value( trans, child_context, history=None ) + rval[ child_input.name ] = child_input.get_initial_value( trans, child_context, history=history ) return rval class ConditionalWhen( object ): 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: jmchilton: Fix bug preventing use of data tools inside of conditionals via API.
by commits-noreply＠bitbucket.org 12 Nov '13

12 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1e7fd56c683c/ Changeset: 1e7fd56c683c User: jmchilton Date: 2013-11-12 18:56:54 Summary: Fix bug preventing use of data tools inside of conditionals via API. Affected #: 1 file diff -r b419cadc12831a2071912d40d1d10413801bf64c -r 1e7fd56c683c9d59784d62e642b1d430edf7e989 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -493,7 +493,7 @@ rval = {} # Get the default value for the 'test element' and use it # to determine the current case - test_value = self.test_param.get_initial_value( trans, context, history=None ) + test_value = self.test_param.get_initial_value( trans, context, history=history ) current_case = self.get_current_case( test_value, trans ) # Store the current case in a special value rval['__current_case__'] = current_case @@ -502,7 +502,7 @@ # Fill in state for selected case child_context = ExpressionContext( rval, context ) for child_input in self.cases[current_case].inputs.itervalues(): - rval[ child_input.name ] = child_input.get_initial_value( trans, child_context, history=None ) + rval[ child_input.name ] = child_input.get_initial_value( trans, child_context, history=history ) return rval class ConditionalWhen( object ): 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: guerler: UI: Fix load order of masthead
by commits-noreply＠bitbucket.org 12 Nov '13

12 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8b60ec04bea6/ Changeset: 8b60ec04bea6 Branch: stable User: guerler Date: 2013-11-12 18:44:04 Summary: UI: Fix load order of masthead Affected #: 1 file diff -r 98a10ba60640eabb7604778a87937aa17e30f73b -r 8b60ec04bea623eeb7ba3b370302cf4e123119d7 templates/webapps/galaxy/galaxy.masthead.mako --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -34,11 +34,13 @@ $('<link href="' + galaxy_config.root + 'static/style/galaxy.frame.masthead.css" rel="stylesheet">').appendTo('head'); ## load galaxy js-modules - require(['galaxy.master', 'galaxy.frame', 'galaxy.modal'], function(master, frame, modal) - { - Galaxy.master = new master.GalaxyMaster(); - Galaxy.frame_manager = new frame.GalaxyFrameManager(); - Galaxy.modal = new modal.GalaxyModal(); + $(function() { + require(['galaxy.master', 'galaxy.frame', 'galaxy.modal'], function(master, frame, modal) + { + Galaxy.master = new master.GalaxyMaster(); + Galaxy.frame_manager = new frame.GalaxyFrameManager(); + Galaxy.modal = new modal.GalaxyModal(); + }); }); </script> 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: 3 new changesets
by commits-noreply＠bitbucket.org 12 Nov '13

12 Nov '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/98a10ba60640/ Changeset: 98a10ba60640 Branch: stable User: jmchilton Date: 2013-11-12 17:51:35 Summary: "Fix" GALAXY_SLOTS for SLURM. Your results with slurm may vary and depending how you allocate things you may want to modify this statement. Affected #: 1 file diff -r 00d8ec60fdc02d3918b6896cf4a8d0cee27f350c -r 98a10ba60640eabb7604778a87937aa17e30f73b lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh --- a/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh +++ b/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh @@ -1,6 +1,9 @@ export GALAXY_SLOTS_CONFIGURED="1" -if [ -n "$SLURM_JOB_NUM_NODES" ]; then - GALAXY_SLOTS="$SLURM_JOB_NUM_NODES" +if [ -n "$SLURM_NTASKS" ]; then + # May want to multiply this by ${SLURM_CPUS_PER_TASK:-1}. + # SLURM_NTASKS is total tasks over all nodes so this is + # shouldn't be used for multi-node requests. + GALAXY_SLOTS="$SLURM_NTASKS" elif [ -n "$NSLOTS" ]; then GALAXY_SLOTS="$NSLOTS" elif [ -f "$PBS_NODEFILE" ]; then https://bitbucket.org/galaxy/galaxy-central/commits/4dbb6209fe78/ Changeset: 4dbb6209fe78 User: jmchilton Date: 2013-11-12 17:54:26 Summary: Merge latest stable. Affected #: 1 file diff -r 5e4174bee7de7e29eb6021b2097568a4c8f597b9 -r 4dbb6209fe789752bf0bb587350b024fe8d74e6c lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh --- a/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh +++ b/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh @@ -1,6 +1,9 @@ export GALAXY_SLOTS_CONFIGURED="1" -if [ -n "$SLURM_JOB_NUM_NODES" ]; then - GALAXY_SLOTS="$SLURM_JOB_NUM_NODES" +if [ -n "$SLURM_NTASKS" ]; then + # May want to multiply this by ${SLURM_CPUS_PER_TASK:-1}. + # SLURM_NTASKS is total tasks over all nodes so this is + # shouldn't be used for multi-node requests. + GALAXY_SLOTS="$SLURM_NTASKS" elif [ -n "$NSLOTS" ]; then GALAXY_SLOTS="$NSLOTS" elif [ -f "$PBS_NODEFILE" ]; then https://bitbucket.org/galaxy/galaxy-central/commits/b419cadc1283/ Changeset: b419cadc1283 User: jmchilton Date: 2013-11-12 17:55:56 Summary: Automated merge. Affected #: 1 file diff -r 4dbb6209fe789752bf0bb587350b024fe8d74e6c -r b419cadc12831a2071912d40d1d10413801bf64c templates/webapps/galaxy/galaxy.masthead.mako --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -72,38 +72,40 @@ $('<link href="' + galaxy_config.root + 'static/style/galaxy.frame.masthead.css" rel="stylesheet">').appendTo('head'); ## load galaxy js-modules - require(['galaxy.masthead', 'galaxy.menu', 'galaxy.modal', 'galaxy.frame', 'galaxy.upload'], - function(mod_masthead, mod_menu, mod_modal, mod_frame, mod_upload) - { - ## check if masthead is available - if (Galaxy.masthead) - return; + $(function() { + require(['galaxy.masthead', 'galaxy.menu', 'galaxy.modal', 'galaxy.frame', 'galaxy.upload'], + function(mod_masthead, mod_menu, mod_modal, mod_frame, mod_upload) + { + ## check if masthead is available + if (Galaxy.masthead) + return; - ## get configuration - var masthead_config = ${ h.to_json_string( masthead_config ) }; + ## get configuration + var masthead_config = ${ h.to_json_string( masthead_config ) }; - ## set up the quota meter (And fetch the current user data from trans) - Galaxy.currUser = new User(masthead_config.user.json); + ## set up the quota meter (And fetch the current user data from trans) + Galaxy.currUser = new User(masthead_config.user.json); - ## load global galaxy objects - Galaxy.masthead = new mod_masthead.GalaxyMasthead(masthead_config); - Galaxy.modal = new mod_modal.GalaxyModal(); - Galaxy.frame = new mod_frame.GalaxyFrame(); + ## load global galaxy objects + Galaxy.masthead = new mod_masthead.GalaxyMasthead(masthead_config); + Galaxy.modal = new mod_modal.GalaxyModal(); + Galaxy.frame = new mod_frame.GalaxyFrame(); - ## construct default menu options - Galaxy.menu = new mod_menu.GalaxyMenu({ - masthead: Galaxy.masthead, - config: masthead_config + ## construct default menu options + Galaxy.menu = new mod_menu.GalaxyMenu({ + masthead: Galaxy.masthead, + config: masthead_config + }); + + ## add upload plugin + ##Galaxy.upload = new mod_upload.GalaxyUpload(); + + ## add quota meter to masthead + Galaxy.quotaMeter = new UserQuotaMeter({ + model : Galaxy.currUser, + el : $(Galaxy.masthead.el).find('.quota-meter-container') + }).render(); }); - - ## add upload plugin - ##Galaxy.upload = new mod_upload.GalaxyUpload(); - - ## add quota meter to masthead - Galaxy.quotaMeter = new UserQuotaMeter({ - model : Galaxy.currUser, - el : $(Galaxy.masthead.el).find('.quota-meter-container') - }).render(); }); </script></%def> 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: guerler: UI: Fix load order of masthead
by commits-noreply＠bitbucket.org 12 Nov '13

12 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/efe68bbfec73/ Changeset: efe68bbfec73 User: guerler Date: 2013-11-12 17:51:36 Summary: UI: Fix load order of masthead Affected #: 1 file diff -r 5e4174bee7de7e29eb6021b2097568a4c8f597b9 -r efe68bbfec73e8367314c7751cfe24d8c515b778 templates/webapps/galaxy/galaxy.masthead.mako --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -72,38 +72,40 @@ $('<link href="' + galaxy_config.root + 'static/style/galaxy.frame.masthead.css" rel="stylesheet">').appendTo('head'); ## load galaxy js-modules - require(['galaxy.masthead', 'galaxy.menu', 'galaxy.modal', 'galaxy.frame', 'galaxy.upload'], - function(mod_masthead, mod_menu, mod_modal, mod_frame, mod_upload) - { - ## check if masthead is available - if (Galaxy.masthead) - return; + $(function() { + require(['galaxy.masthead', 'galaxy.menu', 'galaxy.modal', 'galaxy.frame', 'galaxy.upload'], + function(mod_masthead, mod_menu, mod_modal, mod_frame, mod_upload) + { + ## check if masthead is available + if (Galaxy.masthead) + return; - ## get configuration - var masthead_config = ${ h.to_json_string( masthead_config ) }; + ## get configuration + var masthead_config = ${ h.to_json_string( masthead_config ) }; - ## set up the quota meter (And fetch the current user data from trans) - Galaxy.currUser = new User(masthead_config.user.json); + ## set up the quota meter (And fetch the current user data from trans) + Galaxy.currUser = new User(masthead_config.user.json); - ## load global galaxy objects - Galaxy.masthead = new mod_masthead.GalaxyMasthead(masthead_config); - Galaxy.modal = new mod_modal.GalaxyModal(); - Galaxy.frame = new mod_frame.GalaxyFrame(); + ## load global galaxy objects + Galaxy.masthead = new mod_masthead.GalaxyMasthead(masthead_config); + Galaxy.modal = new mod_modal.GalaxyModal(); + Galaxy.frame = new mod_frame.GalaxyFrame(); - ## construct default menu options - Galaxy.menu = new mod_menu.GalaxyMenu({ - masthead: Galaxy.masthead, - config: masthead_config + ## construct default menu options + Galaxy.menu = new mod_menu.GalaxyMenu({ + masthead: Galaxy.masthead, + config: masthead_config + }); + + ## add upload plugin + ##Galaxy.upload = new mod_upload.GalaxyUpload(); + + ## add quota meter to masthead + Galaxy.quotaMeter = new UserQuotaMeter({ + model : Galaxy.currUser, + el : $(Galaxy.masthead.el).find('.quota-meter-container') + }).render(); }); - - ## add upload plugin - ##Galaxy.upload = new mod_upload.GalaxyUpload(); - - ## add quota meter to masthead - Galaxy.quotaMeter = new UserQuotaMeter({ - model : Galaxy.currUser, - el : $(Galaxy.masthead.el).find('.quota-meter-container') - }).render(); }); </script></%def> 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: 2 new changesets
by commits-noreply＠bitbucket.org 12 Nov '13

12 Nov '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/00d8ec60fdc0/ Changeset: 00d8ec60fdc0 Branch: stable User: carlfeberhard Date: 2013-11-12 17:10:04 Summary: History grid: fix logic to prevent deleting/purging a shared history Affected #: 1 file diff -r 56b077b51694fba1dcb37044dc8f2c0ea8d8b9bf -r 00d8ec60fdc02d3918b6896cf4a8d0cee27f350c lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -17,10 +17,12 @@ log = logging.getLogger( __name__ ) + class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, history ): return history.get_display_name() + class HistoryListGrid( grids.Grid ): # Custom column types @@ -303,32 +305,33 @@ if history.users_shared_with: message_parts.append( "History (%s) has been shared with others, unshare it before deleting it. " % history.name ) status = ERROR - elif not history.deleted: - # We'll not eliminate any DefaultHistoryPermissions in case we undelete the history later - history.deleted = True - # If deleting the current history, make a new current. - if history == trans.get_history(): - deleted_current = True - trans.log_event( "History (%s) marked as deleted" % history.name ) - n_deleted += 1 - if purge and trans.app.config.allow_user_dataset_purge: - for hda in history.datasets: - if trans.user: - trans.user.total_disk_usage -= hda.quota_amount( trans.user ) - hda.purged = True - trans.sa_session.add( hda ) - trans.log_event( "HDA id %s has been purged" % hda.id ) - trans.sa_session.flush() - if hda.dataset.user_can_purge: - try: - hda.dataset.full_delete() - trans.log_event( "Dataset id %s has been purged upon the the purge of HDA id %s" % ( hda.dataset.id, hda.id ) ) - trans.sa_session.add( hda.dataset ) - except: - log.exception( 'Unable to purge dataset (%s) on purge of hda (%s):' % ( hda.dataset.id, hda.id ) ) - history.purged = True - self.sa_session.add( history ) - self.sa_session.flush() + else: + if not history.deleted: + # We'll not eliminate any DefaultHistoryPermissions in case we undelete the history later + history.deleted = True + # If deleting the current history, make a new current. + if history == trans.get_history(): + deleted_current = True + trans.log_event( "History (%s) marked as deleted" % history.name ) + n_deleted += 1 + if purge and trans.app.config.allow_user_dataset_purge: + for hda in history.datasets: + if trans.user: + trans.user.total_disk_usage -= hda.quota_amount( trans.user ) + hda.purged = True + trans.sa_session.add( hda ) + trans.log_event( "HDA id %s has been purged" % hda.id ) + trans.sa_session.flush() + if hda.dataset.user_can_purge: + try: + hda.dataset.full_delete() + trans.log_event( "Dataset id %s has been purged upon the the purge of HDA id %s" % ( hda.dataset.id, hda.id ) ) + trans.sa_session.add( hda.dataset ) + except: + log.exception( 'Unable to purge dataset (%s) on purge of hda (%s):' % ( hda.dataset.id, hda.id ) ) + history.purged = True + self.sa_session.add( history ) + self.sa_session.flush() trans.sa_session.flush() if n_deleted: part = "Deleted %d %s" % ( n_deleted, iff( n_deleted != 1, "histories", "history" ) ) https://bitbucket.org/galaxy/galaxy-central/commits/5e4174bee7de/ Changeset: 5e4174bee7de User: carlfeberhard Date: 2013-11-12 17:11:01 Summary: Merge stable Affected #: 1 file diff -r 1479c52c26e2bbc1fa4b367d1e718be966f5eb63 -r 5e4174bee7de7e29eb6021b2097568a4c8f597b9 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -17,10 +17,12 @@ log = logging.getLogger( __name__ ) + class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, history ): return history.get_display_name() + class HistoryListGrid( grids.Grid ): # Custom column types @@ -303,32 +305,33 @@ if history.users_shared_with: message_parts.append( "History (%s) has been shared with others, unshare it before deleting it. " % history.name ) status = ERROR - elif not history.deleted: - # We'll not eliminate any DefaultHistoryPermissions in case we undelete the history later - history.deleted = True - # If deleting the current history, make a new current. - if history == trans.get_history(): - deleted_current = True - trans.log_event( "History (%s) marked as deleted" % history.name ) - n_deleted += 1 - if purge and trans.app.config.allow_user_dataset_purge: - for hda in history.datasets: - if trans.user: - trans.user.total_disk_usage -= hda.quota_amount( trans.user ) - hda.purged = True - trans.sa_session.add( hda ) - trans.log_event( "HDA id %s has been purged" % hda.id ) - trans.sa_session.flush() - if hda.dataset.user_can_purge: - try: - hda.dataset.full_delete() - trans.log_event( "Dataset id %s has been purged upon the the purge of HDA id %s" % ( hda.dataset.id, hda.id ) ) - trans.sa_session.add( hda.dataset ) - except: - log.exception( 'Unable to purge dataset (%s) on purge of hda (%s):' % ( hda.dataset.id, hda.id ) ) - history.purged = True - self.sa_session.add( history ) - self.sa_session.flush() + else: + if not history.deleted: + # We'll not eliminate any DefaultHistoryPermissions in case we undelete the history later + history.deleted = True + # If deleting the current history, make a new current. + if history == trans.get_history(): + deleted_current = True + trans.log_event( "History (%s) marked as deleted" % history.name ) + n_deleted += 1 + if purge and trans.app.config.allow_user_dataset_purge: + for hda in history.datasets: + if trans.user: + trans.user.total_disk_usage -= hda.quota_amount( trans.user ) + hda.purged = True + trans.sa_session.add( hda ) + trans.log_event( "HDA id %s has been purged" % hda.id ) + trans.sa_session.flush() + if hda.dataset.user_can_purge: + try: + hda.dataset.full_delete() + trans.log_event( "Dataset id %s has been purged upon the the purge of HDA id %s" % ( hda.dataset.id, hda.id ) ) + trans.sa_session.add( hda.dataset ) + except: + log.exception( 'Unable to purge dataset (%s) on purge of hda (%s):' % ( hda.dataset.id, hda.id ) ) + history.purged = True + self.sa_session.add( history ) + self.sa_session.flush() trans.sa_session.flush() if n_deleted: part = "Deleted %d %s" % ( n_deleted, iff( n_deleted != 1, "histories", "history" ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: More Trackster CSS cleanup.
by commits-noreply＠bitbucket.org 12 Nov '13

12 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1479c52c26e2/ Changeset: 1479c52c26e2 User: jgoecks Date: 2013-11-12 16:10:13 Summary: More Trackster CSS cleanup. Affected #: 3 files diff -r cd12bf2ed5475c8c6ab72321e5865441c0805bd2 -r 1479c52c26e2bbc1fa4b367d1e718be966f5eb63 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1016,9 +1016,9 @@ } this.zo_link = $("<a/>").attr("id", "zoom-out").attr("title", "Zoom out").tooltip( {placement: 'bottom'} ) - .click(function() { view.zoom_out(); view.request_redraw(); }).appendTo(this.nav_controls); + .click(function() { view.zoom_out(); }).appendTo(this.nav_controls); this.zi_link = $("<a/>").attr("id", "zoom-in").attr("title", "Zoom in").tooltip( {placement: 'bottom'} ) - .click(function() { view.zoom_in(); view.request_redraw(); }).appendTo(this.nav_controls); + .click(function() { view.zoom_in(); }).appendTo(this.nav_controls); // Get initial set of chroms. this.load_chroms_deferred = this.load_chroms({low: 0}); @@ -1097,14 +1097,9 @@ // Dragging in the top label track allows selecting a region // to zoom in this.top_labeltrack.bind( "dragstart", function( e, d ) { - return $("<div />").css( { - "height": view.browser_content_div.height() + view.top_labeltrack.height() + view.nav_labeltrack.height() + 1, - "top": "0px", - "position": "absolute", - "background-color": "#ccf", - "opacity": 0.5, - "z-index": 1000 - } ).appendTo( $(this) ); + return $("<div/>").addClass('zoom-area').css( + "height", view.browser_content_div.height() + view.top_labeltrack.height() + view.nav_labeltrack.height() + 1 + ).appendTo( $(this) ); }).bind( "drag", function( e, d ) { $( d.proxy ).css({ left: Math.min( e.pageX, d.startX ) - view.container.offset().left, width: Math.abs( e.pageX - d.startX ) }); var min = Math.min(e.pageX, d.startX ) - view.container.offset().left, @@ -1549,6 +1544,7 @@ } this.low = Math.round(cur_center - new_half); this.high = Math.round(cur_center + new_half); + this.changed(); this.request_redraw(); }, @@ -3079,7 +3075,7 @@ // Step (c) for (re)moving tiles when clear_after is false. if (!clear_after) { this.tiles_div.children(".remove").removeClass("remove").remove(); } - // Use interval to check if tiles have been drawn. When all tiles are drawn, call post-draw actions. + // When all tiles are drawn, call post-draw actions. var track = this; $.when.apply($, tile_promises).then(function() { // Step (c) for (re)moving tiles when clear_after is true: @@ -3373,7 +3369,7 @@ if (this.left_offset) { left -= this.left_offset; } - tile_element.css({ position: 'absolute', top: 0, left: left }); + tile_element.css('left', left); if ( tile_element.hasClass("remove") ) { // Step (b) for (re)moving tiles. See _draw() function for description of algorithm @@ -3528,13 +3524,12 @@ tickDistance = Math.floor( Math.pow( 10, Math.floor( Math.log( range ) / Math.log( 10 ) ) ) ), position = Math.floor( view.low / tickDistance ) * tickDistance, width = this.view.container.width(), - new_div = $("<div style='position: relative; height: 1.3em;'></div>"); + new_div = $("<div/>").addClass('label-container'); while ( position < view.high ) { var screenPosition = ( position - view.low ) / range * width; - new_div.append( $("<div class='label'>" + commatize( position ) + "</div>").css( { - position: "absolute", + new_div.append( $("<div/>").addClass('label').text(commatize( position )).css( { // Reduce by one to account for border - left: screenPosition - 1 + left: screenPosition })); position += tickDistance; } diff -r cd12bf2ed5475c8c6ab72321e5865441c0805bd2 -r 1479c52c26e2bbc1fa4b367d1e718be966f5eb63 static/style/blue/trackster.css --- a/static/style/blue/trackster.css +++ b/static/style/blue/trackster.css @@ -26,14 +26,15 @@ .track-name{float:left;margin-top:2px} .tiles{background:url('../images/tracks/diag_bg.gif');position:relative;overflow:hidden} .overlay{position:absolute;left:0;top:0} -.track-tile{background:white}.track-tile canvas{position:relative;z-index:1} +.track-tile{position:absolute;background:white}.track-tile canvas{position:relative;z-index:1} .tile-message{border-bottom:solid 1px red;text-align:center;color:red;background-color:white} .track{border-bottom:1px solid #bbb}.track.error{background-color:#ECB4AF;background-image:none} .track.nodata .track-content{background-color:white;background-image:none} .track.pending .track-content{background-color:white;background-image:none} .track-content{text-align:center;position:relative;min-height:20px;padding:0px 0px 1px 0px} .loading{min-height:100px} -.label-track{font-size:10px;border:none;padding:0;margin:0;height:1.5em;overflow:hidden}.label-track .label{border-left:solid #999 1px;padding:1px;padding-bottom:2px;display:inline-block} +.label-track{font-size:10px;border:none;padding:0;margin:0;height:1.5em;overflow:hidden}.label-track .label-container{position:relative;height:1.3em} +.label-track .label{position:absolute;border-left:solid #999 1px;padding:1px;padding-bottom:2px;display:inline-block} .label-track .track-content{border:none;background:white} .reference-track{border:none;margin:0;padding:0;line-height:1}.reference-track .track-content{min-height:0px} .right-float{float:right;margin-left:5px} @@ -75,3 +76,4 @@ .icon.more-across{background:url('../images/fugue/arrow-transition-bw.png') no-repeat 0 0} .feature-popup{position:absolute;z-index:2;padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);background-position:top center} .feature-popup-inner{padding:5px 8px 4px 8px;background-color:black;color:white} +.zoom-area{position:absolute;top:0px;background-color:#ccf;opacity:0.5;z-index:2} diff -r cd12bf2ed5475c8c6ab72321e5865441c0805bd2 -r 1479c52c26e2bbc1fa4b367d1e718be966f5eb63 static/style/src/less/trackster.less --- a/static/style/src/less/trackster.less +++ b/static/style/src/less/trackster.less @@ -227,6 +227,7 @@ } .track-tile { + position: absolute; background: white; canvas { @@ -285,7 +286,13 @@ height: 1.5em; overflow: hidden; + .label-container { + position: relative; + height: 1.3em; + } + .label { + position: absolute; border-left: solid #999 1px; padding: 1px; padding-bottom: 2px; @@ -509,3 +516,11 @@ background-color: black; color: white; } + +.zoom-area { + position: absolute; + top: 0px; + background-color: #ccf; + opacity: 0.5; + z-index: @overlay-index; +} \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: Dave Bouvier: Add more informative logging for repository installation errors when installing and testing repositories. Limit uninstallation of tool dependencies in an error state to those that are displayed on the "Uninstall tool dependencies" page.
by commits-noreply＠bitbucket.org 12 Nov '13

12 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cd12bf2ed547/ Changeset: cd12bf2ed547 User: Dave Bouvier Date: 2013-11-12 15:25:32 Summary: Add more informative logging for repository installation errors when installing and testing repositories. Limit uninstallation of tool dependencies in an error state to those that are displayed on the "Uninstall tool dependencies" page. Affected #: 2 files diff -r e12a10e5418d53c9440982ddc935e1b7d647bd07 -r cd12bf2ed5475c8c6ab72321e5865441c0805bd2 test/install_and_test_tool_shed_repositories/base/twilltestcase.py --- a/test/install_and_test_tool_shed_repositories/base/twilltestcase.py +++ b/test/install_and_test_tool_shed_repositories/base/twilltestcase.py @@ -163,6 +163,8 @@ url = '/admin_toolshed/uninstall_tool_dependencies?repository_id=%s&inst_td_ids=%s&operation=uninstall' % \ ( encoded_repository_id, tool_dependency_ids ) self.visit_url( url ) - tc.fv( 'uninstall_tool_dependencies', 'tool_dependency_ids', tool_dependency_ids ) - tc.submit( 'uninstall_tool_dependencies_button' ) + html = self.last_page() + if 'uninstall_tool_dependencies' in html: + tc.fv( 'uninstall_tool_dependencies', 'tool_dependency_ids', tool_dependency_ids ) + tc.submit( 'uninstall_tool_dependencies_button' ) \ No newline at end of file diff -r e12a10e5418d53c9440982ddc935e1b7d647bd07 -r cd12bf2ed5475c8c6ab72321e5865441c0805bd2 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 @@ -1037,16 +1037,20 @@ # If a tool dependency fails to install correctly, this should be considered an installation error, # and functional tests should be skipped, since the tool dependency needs to be correctly installed # for the test to be considered reliable. - log.error( 'One or more tool dependencies of this repository are marked as missing.' ) + log.error( 'One or more dependencies of this repository are marked as missing.' ) log.error( 'Updating repository and skipping functional tests.' ) # In keeping with the standard display layout, add the error message to the dict for each tool individually. for dependency in failed_tool_dependencies: + log.error( 'Missing tool dependency %s of type %s version %s: %s' % \ + ( str( dependency.name ), str( dependency.type ), str( dependency.version ), str( dependency.error_message ) ) ) test_result = dict( type=dependency.type, name=dependency.name, version=dependency.version, error_message=dependency.error_message ) repository_status[ 'installation_errors' ][ 'tool_dependencies' ].append( test_result ) for dependency in repository.repository_dependencies_with_installation_errors: + log.error( 'Missing repository dependency %s changeset revision %s owned by %s: %s' % \ + ( str( dependency.name ), str( dependency.changeset_revision ), str( dependency.owner ), str( dependency.error_message ) ) ) test_result = dict( tool_shed=dependency.tool_shed, name=dependency.name, owner=dependency.owner, 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: guerler: UI: Fix tooltip placement for masthead icons
by commits-noreply＠bitbucket.org 11 Nov '13

11 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e12a10e5418d/ Changeset: e12a10e5418d User: guerler Date: 2013-11-11 22:00:10 Summary: UI: Fix tooltip placement for masthead icons Affected #: 1 file diff -r 28469a503b56c374f8ec4730e276a89a6323cef9 -r e12a10e5418d53c9440982ddc935e1b7d647bd07 static/scripts/galaxy.masthead.js --- a/static/scripts/galaxy.masthead.js +++ b/static/scripts/galaxy.masthead.js @@ -226,7 +226,7 @@ // configure icon var self = this; - $(this.el).find('.icon').tooltip({title: this.options.tooltip}) + $(this.el).find('.icon').tooltip({title: this.options.tooltip, placement: 'bottom'}) .on('mouseup', self.options.on_click); // visiblity 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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