rcsb.exdb 1.23__tar.gz → 1.24__tar.gz

{rcsb_exdb-1.23 → rcsb_exdb-1.24}/HISTORY.txt

@@ -103,3 +103,4 @@
 13-May-2024 V1.21 Update requirements; fix linting
 17-Jul-2024 V1.22 Adjust LigandNeighborMappingExtractor
 20-Aug-2024 V1.23 Add support for target cofactor data loading
+27-Aug-2024 V1.24 Update tree loading for CARD ontology data

{rcsb_exdb-1.23/rcsb.exdb.egg-info → rcsb_exdb-1.24}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: rcsb.exdb
-Version: 1.23
+Version: 1.24
 Summary: RCSB Python ExDB data extraction and loading workflows
 Home-page: https://github.com/rcsb/py-rcsb_exdb
 Author: John Westbrook
@@ -28,11 +28,11 @@ Requires-Dist: rcsb.utils.ec>=0.25
 Requires-Dist: rcsb.utils.go>=0.18
 Requires-Dist: rcsb.utils.seq>=0.82
 Requires-Dist: rcsb.utils.seqalign>=0.29
-Requires-Dist: rcsb.utils.targets>=0.80
+Requires-Dist: rcsb.utils.targets>=0.82
 Requires-Dist: rcsb.utils.struct>=0.47
 Requires-Dist: rcsb.utils.taxonomy>=0.43
-Requires-Dist: rcsb.utils.dictionary>=1.26
-Requires-Dist: rcsb.workflow>=0.44
+Requires-Dist: rcsb.utils.dictionary>=1.27
+Requires-Dist: rcsb.workflow>=0.45
 Requires-Dist: statistics; python_version < "3.0"
 Provides-Extra: dev
 Requires-Dist: check-manifest; extra == "dev"

{rcsb_exdb-1.23 → rcsb_exdb-1.24}/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__ = "1.23"
+__version__ = "1.24"

{rcsb_exdb-1.23 → rcsb_exdb-1.24}/rcsb/exdb/tree/TreeNodeListWorker.py

@@ -8,6 +8,7 @@
 #  9-Sep-2019 jdw add AtcProvider() and ChemrefExtractor() for ATC tree.
 # 12-Apr-2023 dwp add CARD ontology tree
 #  8-Aug-2023 dwp Load full (unfiltered) taxonomy tree node list, and stop loading GO tree (will be loaded in DW instead)
+# 27-Aug-2024 dwp Update CARD ontology tree loading
 #
 ##
 __docformat__ = "google en"
@@ -181,13 +182,30 @@ class TreeNodeListWorker(object):
                 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)
+            okCou = True
+            cou = CARDTargetOntologyProvider(cachePath=self.__cachePath, useCache=useCache)
+            if not cou.testCache():
+                ok = cou.buildOntologyData()
+                cou.reload()
+                if not (ok and cou.testCache()):
+                    logger.error("Skipping load of CARD Target Ontology tree data because it is missing.")
+                    okCou = False
+            if okCou:
+                nL = cou.getTreeNodeList()
+                logger.info("Starting load of CARD ontology 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
             tU = TaxonomyProvider(cachePath=self.__cachePath, useCache=useCache)
             if self.__useFilteredLists:

{rcsb_exdb-1.23 → rcsb_exdb-1.24/rcsb.exdb.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: rcsb.exdb
-Version: 1.23
+Version: 1.24
 Summary: RCSB Python ExDB data extraction and loading workflows
 Home-page: https://github.com/rcsb/py-rcsb_exdb
 Author: John Westbrook
@@ -28,11 +28,11 @@ Requires-Dist: rcsb.utils.ec>=0.25
 Requires-Dist: rcsb.utils.go>=0.18
 Requires-Dist: rcsb.utils.seq>=0.82
 Requires-Dist: rcsb.utils.seqalign>=0.29
-Requires-Dist: rcsb.utils.targets>=0.80
+Requires-Dist: rcsb.utils.targets>=0.82
 Requires-Dist: rcsb.utils.struct>=0.47
 Requires-Dist: rcsb.utils.taxonomy>=0.43
-Requires-Dist: rcsb.utils.dictionary>=1.26
-Requires-Dist: rcsb.workflow>=0.44
+Requires-Dist: rcsb.utils.dictionary>=1.27
+Requires-Dist: rcsb.workflow>=0.45
 Requires-Dist: statistics; python_version < "3.0"
 Provides-Extra: dev
 Requires-Dist: check-manifest; extra == "dev"

{rcsb_exdb-1.23 → rcsb_exdb-1.24}/rcsb.exdb.egg-info/requires.txt

@@ -11,11 +11,11 @@ rcsb.utils.ec>=0.25
 rcsb.utils.go>=0.18
 rcsb.utils.seq>=0.82
 rcsb.utils.seqalign>=0.29
-rcsb.utils.targets>=0.80
+rcsb.utils.targets>=0.82
 rcsb.utils.struct>=0.47
 rcsb.utils.taxonomy>=0.43
-rcsb.utils.dictionary>=1.26
-rcsb.workflow>=0.44
+rcsb.utils.dictionary>=1.27
+rcsb.workflow>=0.45
 
 [:python_version < "3.0"]
 statistics

{rcsb_exdb-1.23 → rcsb_exdb-1.24}/requirements.txt

@@ -12,9 +12,9 @@ rcsb.utils.ec >= 0.25
 rcsb.utils.go >= 0.18
 rcsb.utils.seq >= 0.82
 rcsb.utils.seqalign >= 0.29
-rcsb.utils.targets >= 0.80
+rcsb.utils.targets >= 0.82
 rcsb.utils.struct >= 0.47
 rcsb.utils.taxonomy >= 0.43
-rcsb.utils.dictionary >= 1.26
-rcsb.workflow >= 0.44
+rcsb.utils.dictionary >= 1.27
+rcsb.workflow >= 0.45
 statistics; python_version < "3.0"