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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 13 Nov '13

13 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 13 Nov '13

13 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 13 Nov '13

13 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. 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