Fix pylinting; fix assignment logic of Pharos data for rcsb_chem_comp…

…_related.related_mapping_method in DictMethodChemRefHelper
rcsb · Jul 25, 2024 · 13afe11 · 13afe11
1 parent 1960971
commit 13afe11
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Showing 5 changed files with 13 additions and 4 deletions.
diff --git a/pylintrc b/pylintrc
@@ -573,5 +573,5 @@ min-public-methods=2
 
 # Exceptions that will emit a warning when being caught. Defaults to
 # "BaseException, Exception".
-overgeneral-exceptions=BaseException,
-                       Exception
+# overgeneral-exceptions=builtins.BaseException,
+#                       builtins.Exception
diff --git a/rcsb/utils/dictionary/DictMethodAssemblyHelper.py b/rcsb/utils/dictionary/DictMethodAssemblyHelper.py
@@ -608,7 +608,8 @@ def __getAssemblyComposition(self, dataContainer):
         epTypeD = self.__commonU.getEntityPolymerTypes(dataContainer)
         eTypeD = self.__commonU.getEntityTypes(dataContainer)
         epTypeFilteredD = self.__commonU.getPolymerEntityFilteredTypes(dataContainer)
-
+        #
+        methodL = []
         if dataContainer.exists("exptl"):
             xObj = dataContainer.getObj("exptl")
             methodL = xObj.getAttributeValueList("method")

diff --git a/rcsb/utils/dictionary/DictMethodChemRefHelper.py b/rcsb/utils/dictionary/DictMethodChemRefHelper.py
@@ -9,6 +9,7 @@
 #    5-Apr-2023 dwp Stop loading rcsb_chem_comp_synonyms for rcsb_chem_comp_synonyms.type 'Brand Name' (to be loaded to new separate data item later)
 #   18-Sep-2023 dwp Load COD references separately from CCDC/CSD references
 #    3-May-2024 dwp Change BIRD citation method to copy categories instead of just renaming, and only apply to BIRD entries
+#   25-Jul-2024 dwp Fix assignment logic of Pharos data for rcsb_chem_comp_related.related_mapping_method in addChemCompRelated()
 ##
 """
 Helper class implements external method references supporting chemical
@@ -200,12 +201,16 @@ def addChemCompRelated(self, dataContainer, catName, **kwargs):
 
                     #
                     for rName, rIdS in xD.items():
-                        if rName in ["PubChem", "Pharos"]:
+                        aMethod = None
+                        if rName in ["PubChem"]:
                             aMethod = "matching InChIKey in PubChem"
                         elif rName in ["CAS", "ChEMBL", "ChEBI"]:
                             aMethod = "assigned by PubChem resource"
                         elif rName in ["Pharos"]:
                             aMethod = "matching ChEMBL ID in Pharos"
+                        if not aMethod:
+                            logger.error("No matching condition for rName %r", rName)
+                            continue
                         for rId in rIdS:
                             iRow = wObj.getRowCount()
                             wObj.setValue(ccId, "comp_id", iRow)

diff --git a/rcsb/utils/dictionary/DictMethodCompModelHelper.py b/rcsb/utils/dictionary/DictMethodCompModelHelper.py
@@ -312,6 +312,8 @@ def consolidateGlobalQAScores(self, dataContainer, catName, **kwargs):
 
             if dataContainer.exists("ma_qa_metric_global"):
                 bObj = dataContainer.getObj("ma_qa_metric_global")
+            else:
+                return False
 
             maQaMetricTypeD = self.__commonU.getMaQaMetricType(dataContainer)
             maQaMetricGlobalTypeD = maQaMetricTypeD["maQaMetricGlobalTypeD"]

diff --git a/rcsb/utils/dictionary/DictMethodResourceProvider.py b/rcsb/utils/dictionary/DictMethodResourceProvider.py
@@ -720,6 +720,7 @@ def syncCache(self, providerName, cfgOb, configName, cachePath, remotePrefix=Non
         logger.debug("%r classArgs %r", providerName, classArgs)
         #
         useCache = True
+        ok = okB = True
         try:
             if sourceCache == "stash":
                 prI = self.__providerD[providerName]["class"](cachePath=cachePath, useCache=useCache, **classArgs)