Chore: V0.44 Adjust error handling/reporting for atom counts in DictM…

…ethodEntityInstanceHelper(), update GlycanProvider() api in DictMethodResourceProvider()

HISTORY.txt

@@ -1,7 +1,7 @@
 # File: HISTORY.txt
 #
 14-Feb-2021 - V0.11 Created module with content migrated from rcsb.db
-15-Feb-2021 - V0.12 Extend namedtuple "NonpolymerValidationInstance"
+15-Feb-2021 - V0.12 Extend named tuple "NonpolymerValidationInstance"
 18-Feb-2021 - V0.13 Added TargetInteractionProvider() related tests, getNonpolymerInstanceNeighbors() in DictMethodCommonUtils()
 18-Feb-2021 - V0.14 Add further accessors to TargetInteractionProvider()
 21-Feb-2021 - V0.15 Update handling of completeness/disorder in calculating validation scores, add TargetInteractionWorkflow()
@@ -32,4 +32,5 @@
  2-Jun-2021 - V0.40 Add support to filter redundant records in category subsets
  5-Jun-2021 - V0.41 Prune test cases
 10-Jun-2021 - V0.42 Adding calculation of average occupancy __getAtomSiteInfo() in DictMethodCommonUtils()
-10-Jun-2021 - V0.43 Add provenance to the aggregated "is_subject_of_investigation" ligand validation flag.
+10-Jun-2021 - V0.43 Add provenance to the aggregated "is_subject_of_investigation" ligand validation flag.
+30-Jun-2021 - V0.44 Adjust error handling/reporting for atom counts in DictMethodEntityInstanceHelper(), update GlycanProvider() api in DictMethodResourceProvider()

MANIFEST.in

@@ -1,5 +1,7 @@
 #
-# File: py-rcsb_utils_chemref/MANIFEST.in
+# File: py-rcsb_utils_dictionary/MANIFEST.in
 #
 include HISTORY.txt
-#
+include requirements.txt
+include README.md
+#

pylintrc

@@ -142,7 +142,8 @@ disable=missing-docstring,
         xreadlines-attribute,
         deprecated-sys-function,
         exception-escape,
-        comprehension-escape
+        comprehension-escape,
+        W0238
 
 # Enable the message, report, category or checker with the given id(s). You can
 # either give multiple identifier separated by comma (,) or put this option

rcsb/utils/dictionary/DictMethodEntityInstanceHelper.py

@@ -1743,7 +1743,7 @@ def buildInstanceValidationScores(self, dataContainer, catName, **kwargs):
                     else:
                         numReportedAtoms = ligandAtomCountD[asymId]["FL"]
                 except Exception as e:
-                    logger.exception("Failing for entry %s asymId %s altId %r with %s", entryId, asymId, altId, str(e))
+                    logger.warning("Missing ligand atom count for entry %s asymId %s altId %r with %s", entryId, asymId, altId, str(e))
 
                 try:
                     if altId:
@@ -1759,7 +1759,7 @@ def buildInstanceValidationScores(self, dataContainer, catName, **kwargs):
                     else:
                         occupancySum = occupancySumD[asymId]["FL"]
                 except Exception as e:
-                    logger.warning("Failing occupancy for entry %s asymId %s altId %r with %s", entryId, asymId, altId, str(e))
+                    logger.warning("Missing occupancy for entry %s asymId %s altId %r with %s", entryId, asymId, altId, str(e))
                 #
                 avgHeavyOccupancy = round(occupancySum / float(numHeavyAtoms), 4)
                 completeness = self.__calculateModeledCompleteness(

rcsb/utils/dictionary/DictMethodResourceProvider.py

@@ -429,27 +429,15 @@ def __fetchNeighborInteractionProvider(self, cfgOb, configName, cachePath, useCa
     def __fetchGlycanProvider(self, cfgOb, configName, cachePath, useCache=True, **kwargs):
         logger.debug("configName %s cachePath %s kwargs %r", configName, cachePath, kwargs)
         if not self.__glyP:
-            #
             try:
-                minCount = 0
-                userName = cfgOb.get("_STASH_AUTH_USERNAME", sectionName=configName)
-                password = cfgOb.get("_STASH_AUTH_PASSWORD", sectionName=configName)
-                basePath = cfgOb.get("_STASH_SERVER_BASE_PATH", sectionName=configName)
-                url = cfgOb.get("STASH_SERVER_URL", sectionName=configName)
-                urlFallBack = cfgOb.get("STASH_SERVER_FALLBACK_URL", sectionName=configName)
-                #
                 gP = GlycanProvider(cachePath=cachePath, useCache=useCache)
-                ok = gP.fromStash(url, basePath, userName=userName, password=password)
+                gP.restore(cfgOb, configName)
                 ok = gP.reload()
                 ok = gP.testCache(minCount=10)
-                if not ok:
-                    ok = gP.fromStash(urlFallBack, basePath, userName=userName, password=password)
-                    ok = gP.testCache(minCount=minCount)
-                #
                 if gP:
                     self.__glyP = gP
                     riD = gP.getIdentifiers()
-                    logger.info("Fetched glycan mapping dictionary (%d)", len(riD))
+                    logger.info("Fetched glycan mapping dictionary (%r) (%d)", ok, len(riD))
             except Exception as e:
                 logger.exception("Failing with %s", str(e))
             #

rcsb/utils/dictionary/__init__.py

@@ -2,4 +2,4 @@
 __author__ = "John Westbrook"
 __email__ = "[email protected]"
 __license__ = "Apache 2.0"
-__version__ = "0.43"
+__version__ = "0.44"

rcsb/utils/tests-dictionary/testDictMethodRunner.py

@@ -44,7 +44,7 @@ def setUp(self):
         self.__numProc = 2
         self.__fileLimit = 200
         mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data")
-        self.__cachePath = os.path.join(TOPDIR, "CACHE")
+        self.__cachePath = os.path.join(HERE, "test-output", "CACHE")
         configPath = os.path.join(mockTopPath, "config", "dbload-setup-example.yml")
         configName = "site_info_configuration"
         self.__configName = configName

rcsb/utils/tests-dictionary/testDictionaryApiProvider.py

@@ -36,7 +36,7 @@
 class DictionaryProviderTests(unittest.TestCase):
     def setUp(self):
         mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data")
-        self.__cachePath = os.path.join(TOPDIR, "CACHE")
+        self.__cachePath = os.path.join(HERE, "test-output", "CACHE")
         self.__dirPath = os.path.join(self.__cachePath, "dictionaries")
         configPath = os.path.join(mockTopPath, "config", "dbload-setup-example.yml")
         configName = "site_info_configuration"

rcsb/utils/tests-dictionary/testDictionaryApiProviderWrapper.py

@@ -36,8 +36,8 @@
 class DictionaryProviderTests(unittest.TestCase):
     def setUp(self):
         mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data")
-        self.__cachePath = os.path.join(TOPDIR, "CACHE")
-        configPath = os.path.join(mockTopPath, "config", "dbload-setup-example.yml")
+        self.__cachePath = os.path.join(HERE, "test-output", "CACHE")
+         configPath = os.path.join(mockTopPath, "config", "dbload-setup-example.yml")
         configName = "site_info_configuration"
         self.__configName = configName
         self.__cfgOb = ConfigUtil(configPath=configPath, defaultSectionName=configName, mockTopPath=mockTopPath)

rcsb/utils/tests-dictionary/testNeighborInteractionProvider.py

@@ -38,7 +38,7 @@ class NeighborInteractionProviderTests(unittest.TestCase):
 
     def setUp(self):
         mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data")
-        self.__cachePath = os.path.join(TOPDIR, "CACHE")
+        self.__cachePath = os.path.join(HERE, "test-output", "CACHE")
         configPath = os.path.join(HERE, "test-data", "stash-config-example.yml")
         self.__configName = "site_info_configuration"
         self.__startTime = time.time()

rcsb/utils/tests-dictionary/testNeighborInteractionWorkflow.py

@@ -35,7 +35,7 @@ class NeighborInteractionWorkflowTests(unittest.TestCase):
 
     def setUp(self):
         self.__mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data")
-        self.__cachePath = os.path.join(TOPDIR, "CACHE")
+        self.__cachePath = os.path.join(HERE, "test-output", "CACHE")
         self.__configPath = os.path.join(HERE, "test-data", "stash-config-example.yml")
         self.__configName = "site_info_configuration"
         self.__useCache = False

setup.py

@@ -14,14 +14,22 @@
 with open("rcsb/utils/dictionary/__init__.py", "r") as fd:
     version = re.search(r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]', fd.read(), re.MULTILINE).group(1)
 
+# Load packages from requirements*.txt
+with open("requirements.txt", "r") as ifh:
+    packagesRequired = [ln.strip() for ln in ifh.readlines()]
+
+with open("README.md", "r") as ifh:
+    longDescription = ifh.read()
+
 if not version:
     raise RuntimeError("Cannot find version information")
 
 setup(
     name=thisPackage,
     version=version,
     description="RCSB Python Dictionary Utility Classes",
-    long_description="See:  README.md",
+    long_description_content_type="text/markdown",
+    long_description=longDescription,
     author="John Westbrook",
     author_email="[email protected]",
     url="https://github.com/rcsb/py-rcsb_utils_dictionary",
@@ -39,22 +47,7 @@
     ),
     entry_points={},
     #
-    install_requires=[
-        "scipy",
-        "numpy",
-        "mmcif >= 0.57",
-        "rcsb.utils.io >= 1.12",
-        "rcsb.utils.config >= 0.35",
-        "rcsb.utils.multiproc >= 0.17",
-        "rcsb.utils.validation >= 0.22",
-        "rcsb.utils.chemref >= 0.72",
-        "rcsb.utils.citation >= 0.15",
-        "rcsb.utils.ec >= 0.21",
-        "rcsb.utils.taxonomy >= 0.32",
-        "rcsb.utils.seq >= 0.60",
-        "rcsb.utils.struct >= 0.28",
-        "rcsb.utils.repository >= 0.12",
-    ],
+    install_requires=packagesRequired,
     packages=find_packages(exclude=["rcsb.utils.tests-dictionary", "rcsb.utils.tests-*", "tests.*"]),
     package_data={
         # If any package contains *.md or *.rst ...  files, include them: