rcsb.exdb 0.95__tar.gz → 0.96__tar.gz

{rcsb.exdb-0.95 → rcsb.exdb-0.96}/HISTORY.txt

@@ -88,4 +88,5 @@
  9-Jan-2023 V0.93 Configuration changes to support tox 4
  9-Mar-2023 V0.94 Update ExDbWorkflow to make use of multiple processors for 'upd_ref_seq' operation;
                   Lower refChunkSize to 10 for requests to UniProt API
-13-Mar-2023 V0.95 Updates to PubChem workflow to use multiprocess count, disable git stash testing, remove obsolete entries from test data
+13-Mar-2023 V0.95 Updates to PubChem workflow to use multiprocess count, disable git stash testing, remove obsolete entries from test data
+12-Apr-2023 V0.96 Add CARD ontology data to tree builder

{rcsb.exdb-0.95/rcsb.exdb.egg-info → rcsb.exdb-0.96}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: rcsb.exdb
-Version: 0.95
+Version: 0.96
 Summary: RCSB Python ExDB data extraction and loading workflows
 Home-page: https://github.com/rcsb/py-rcsb_exdb
 Author: John Westbrook

{rcsb.exdb-0.95 → rcsb.exdb-0.96}/rcsb/exdb/cli/__init__.py

@@ -2,4 +2,4 @@ __docformat__ = "google en"
 __author__ = "John Westbrook"
 __email__ = "john.westbrook@rcsb.org"
 __license__ = "Apache 2.0"
-__version__ = "0.95"
+__version__ = "0.96"

{rcsb.exdb-0.95 → rcsb.exdb-0.96}/rcsb/exdb/tree/TreeNodeListWorker.py

@@ -6,7 +6,8 @@
 #
 # Updates:
 #  9-Sep-2019 jdw add AtcProvider() and ChemrefExtractor() for ATC tree.
-# JDW TODO TEST
+# 12-Apr-2023 dwp add CARD ontology tree
+#
 ##
 __docformat__ = "google en"
 __author__ = "John Westbrook"
@@ -23,6 +24,7 @@ from rcsb.exdb.seq.AnnotationExtractor import AnnotationExtractor
 from rcsb.exdb.seq.TaxonomyExtractor import TaxonomyExtractor
 from rcsb.utils.chemref.AtcProvider import AtcProvider
 from rcsb.utils.ec.EnzymeDatabaseProvider import EnzymeDatabaseProvider
+from rcsb.utils.targets.CARDTargetOntologyProvider import CARDTargetOntologyProvider
 from rcsb.utils.go.GeneOntologyProvider import GeneOntologyProvider
 from rcsb.utils.struct.CathClassificationProvider import CathClassificationProvider
 from rcsb.utils.struct.EcodClassificationProvider import EcodClassificationProvider
@@ -172,6 +174,14 @@ class TreeNodeListWorker(object):
                 collectionName = "tree_ec_node_list"
                 ok = dl.load(databaseName, collectionName, loadType=loadType, documentList=nL, indexAttributeList=["update_id"], keyNames=None, addValues=addValues, schemaLevel=None)
                 self.__updateStatus(updateId, databaseName, collectionName, ok, statusStartTimestamp)
+            # ---- CARD
+            cou = CARDTargetOntologyProvider(cachePath=self.__cachePath, useCache=False)
+            nL = cou.getTreeNodeList()
+            logger.info("Starting load of EC node tree length %d", len(nL))
+            if doLoad:
+                collectionName = "tree_card_node_list"
+                ok = dl.load(databaseName, collectionName, loadType=loadType, documentList=nL, indexAttributeList=["update_id"], keyNames=None, addValues=addValues, schemaLevel=None)
+                self.__updateStatus(updateId, databaseName, collectionName, ok, statusStartTimestamp)
             # ---- Taxonomy
             # Get the taxon coverage in the current data set -
             epe = TaxonomyExtractor(self.__cfgOb)

{rcsb.exdb-0.95 → rcsb.exdb-0.96/rcsb.exdb.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: rcsb.exdb
-Version: 0.95
+Version: 0.96
 Summary: RCSB Python ExDB data extraction and loading workflows
 Home-page: https://github.com/rcsb/py-rcsb_exdb
 Author: John Westbrook