Chore: V1.675 Update dependencies to rcsb.utils.dictionary and diagno…

…stic output

HISTORY.txt

@@ -303,4 +303,5 @@
  28-Apr-2021  V1.670 Add content type for mmCIF format validation data
   4-May-2021  V1.671 Remove deprecated schema attribute rcsb_nested_indexing_context.context_attributes.search_paths
  19-May-2021  V1.673 Update dependencies in rcsb.utils.dictionary
- 27-May-2021  V1.674 Update dependencies to rcsb.utils.dictionary
+ 27-May-2021  V1.674 Update dependencies to rcsb.utils.dictionary
+  2-Jun-2021  V1.675 Update dependencies to rcsb.utils.dictionary and diagnostic output

rcsb/db/cli/__init__.py

@@ -2,4 +2,4 @@
 __author__ = "John Westbrook"
 __email__ = "[email protected]"
 __license__ = "Apache 2.0"
-__version__ = "1.674"
+__version__ = "1.675"

rcsb/db/mongo/MongoDbUtil.py

@@ -196,7 +196,8 @@ def insertList(self, databaseName, collectionName, dList, ordered=False, bypassV
             clt = self.__mgObj[databaseName].get_collection(collectionName)
             rV = clt.insert_many(dList, ordered=ordered, bypass_document_validation=bypassValidation)
         except Exception as e:
-            logger.error("Bulk insert failing for document length %d with %s", len(dList), str(e))
+            logger.error("Bulk insert failing for document length %d with %s", len(dList), str(e)[:100])
+
             # for ii, dd in enumerate(dList):
             #    logger.error(" %d error doc %r" % (ii, list(dd.keys())))
         #
@@ -459,6 +460,7 @@ def fetch(self, databaseName, collectionName, selectL, queryD=None, suppressId=F
         query constraints.
         """
         dList = []
+        sD = {}
         try:
             qD = queryD if queryD is not None else None
             if selectL:

requirements.txt

@@ -7,15 +7,15 @@ jsondiff >= 1.2.0
 strict-rfc3339
 mysqlclient >= 1.3.12
 pymongo >= 3.7.0
-mmcif >= 0.63
+mmcif >= 0.70
 rcsb.utils.config >= 0.35
-rcsb.utils.io >= 1.00
-rcsb.utils.multiproc >= 0.17
-rcsb.utils.chemref >= 0.70
+rcsb.utils.io >= 1.12
+rcsb.utils.multiproc >= 0.18
+rcsb.utils.chemref >= 0.72
 scandir; python_version < "3.0"
 configparser; python_version < "3.0"
-rcsb.utils.dictionary >= 0.34
-rcsb.utils.repository >= 0.12
+rcsb.utils.dictionary >= 0.40
+rcsb.utils.repository >= 0.16
 #
 SQLAlchemy; sys_platform == 'linux'
 # For crate and cockroach -

setup.py

@@ -20,21 +20,28 @@
 with open("rcsb/db/cli/__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 Database Access and Loading Utility Classes",
-    long_description="See:  README.md",
+    long_description=longDescription,
     author="John Westbrook",
     author_email="[email protected]",
     url="https://github.com/rcsb/py-rcsb_db",
     #
     license="Apache 2.0",
     classifiers=(
-        "Development Status :: 3 - Alpha",
+        "Development Status :: 4 - Beta",
         # 'Development Status :: 5 - Production/Stable',
         "Intended Audience :: Developers",
         "Natural Language :: English",
@@ -53,29 +60,7 @@
         ]
     },
     #
-    install_requires=[
-        "future",
-        "six",
-        "python-dateutil",
-        "pytz",
-        "jsondiff >= 1.2.0",
-        "jsonschema >= 2.6.0",
-        "strict-rfc3339",
-        "mysqlclient >= 1.3.12",
-        "pymongo >= 3.7.0",
-        "mmcif >= 0.63",
-        'scandir; python_version < "3.0"',
-        # 'configparser; python_version < "3.0"',
-        "rcsb.utils.io >= 1.00",
-        "rcsb.utils.config >= 0.35",
-        "rcsb.utils.multiproc >= 0.17",
-        "rcsb.utils.chemref >= 0.70",
-        "rcsb.utils.dictionary >= 0.34",
-        "rcsb.utils.repository >= 0.12",
-        "SQLAlchemy; sys_platform == 'linux'",
-        "psycopg2-binary",
-        "crate",
-    ],
+    install_requires=packagesRequired,
     packages=find_packages(exclude=["rcsb.db.tests", "rcsb.db.tests-*", "tests.*"]),
     package_data={
         # If any package contains *.md or *.rst ...  files, include them: