dcicutils 8.14.0.1b7__tar.gz → 8.14.0.1b9__tar.gz

{dcicutils-8.14.0.1b7 → dcicutils-8.14.0.1b9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.14.0.1b7
+Version: 8.14.0.1b9
 Summary: Utility package for interacting with the 4DN Data Portal and other 4DN resources
 Home-page: https://github.com/4dn-dcic/utils
 License: MIT

{dcicutils-8.14.0.1b7 → dcicutils-8.14.0.1b9}/dcicutils/scripts/update_portal_object.py

@@ -38,6 +38,7 @@ class Portal(PortalFromUtils):
 
 _DEFAULT_APP = "smaht"
 _SMAHT_ENV_ENVIRON_NAME = "SMAHT_ENV"
+_DEFAULT_INI_FILE_FOR_LOAD = "development.ini"
 
 # Schema properties to ignore (by default) for the view schema usage.
 _IGNORE_PROPERTIES_ON_UPDATE = [
@@ -120,6 +121,8 @@ def main():
     parser.add_argument("--post", type=str, required=False, default=None, help="POST data.")
     parser.add_argument("--patch", type=str, required=False, default=None, help="PATCH data.")
     parser.add_argument("--upsert", type=str, required=False, default=None, help="Upsert data.")
+    parser.add_argument("--load", type=str, required=False, default=None, help="Load data via snovault.loadxl.")
+    parser.add_argument("--ini", type=str, required=False, default=None, help="INI file for data via snovault.loadxl.")
     parser.add_argument("--delete", type=str, required=False, default=None, help="Delete data.")
     parser.add_argument("--purge", type=str, required=False, default=None, help="Purge data.")
     parser.add_argument("--noignore", action="store_true", required=False, default=False,
@@ -143,6 +146,41 @@ def main():
     else:
         app = APP_SMAHT
 
+    if not (args.post or args.patch or args.upsert or args.delete or args.purge or args.load):
+        usage()
+
+    if args.load:
+        if args.post or args.patch or args.upsert or args.delete or args.purge:
+            _print("Cannot use any other update option"
+                   "when using the --load option (to load data via snovault.loadxl).")
+            exit(1)
+        if args.env:
+            _print("The --env is not used for the --load option (to load data via snovault.loadxl).")
+        if args.schema:
+            _print("The --schema is not used for the --load option (to load data via snovault.loadxl).")
+        from snovault.loadxl import load_data
+        from dcicutils.captured_output import captured_output
+        if args.ini:
+            ini_file = args.ini
+        else:
+            ini_file = _DEFAULT_INI_FILE_FOR_LOAD
+        if not os.path.exists(ini_file):
+            _print(f"The INI file required for --load is not found: {ini_file}")
+            exit(1)
+        if not os.path.isdir(args.load):
+            _print(f"Load directory does not exist: {args.load}")
+            exit(1)
+        portal = None
+        with captured_output(not args.debug):
+            portal = Portal(ini_file)
+        if args.verbose:
+            _print(f"Loading data files into Portal (via snovault.loadxl) from: {args.load}")
+            _print(f"Portal INI file for load is: {ini_file}")
+        load_data(portal.vapp, indir=args.load, overwrite=True, use_master_inserts=False)
+        if args.verbose:
+            _print(f"Done loading data into Portal (via snovault.loadxl) files from: {args.load}")
+        exit(0)
+
     portal = _create_portal(env=args.env, app=app, verbose=args.verbose, debug=args.debug)
 
     if explicit_schema_name := args.schema:
@@ -150,9 +188,6 @@ def main():
         if not schema:
             usage(f"ERROR: Unknown schema name: {args.schema}")
 
-    if not (args.post or args.patch or args.upsert or args.delete or args.purge):
-        usage()
-
     if args.post:
         _post_or_patch_or_upsert(portal=portal,
                                  file_or_directory=args.post,

{dcicutils-8.14.0.1b7 → dcicutils-8.14.0.1b9}/dcicutils/scripts/view_portal_object.py

@@ -330,6 +330,8 @@ def _get_portal_object(portal: Portal, uuid: str,
             results_total = len(results)
             for result in results:
                 results_index += 1
+                if debug:
+                    print(f"Processing result: {results_index}")
                 result.pop("schema_version", None)
                 result = prune_data(result)
                 if (subtypes and one_or_more_objects_of_types_exists(portal, subtypes, debug=debug) and
@@ -374,14 +376,7 @@ def _get_portal_object(portal: Portal, uuid: str,
 
 def one_or_more_objects_of_types_exists(portal: Portal, schema_types: List[str], debug: bool = False) -> bool:
     for schema_type in schema_types:
-        try:
-            if one_or_more_objects_of_type_exists(portal, schema_type, debug=debug):
-                return True
-            response = portal.get(f"/{schema_type}")
-            if response and response.status_code == 404:
-                _print(f"There are no objects of sub-type: {schema_type}")
-                return False
-        except Exception:
+        if one_or_more_objects_of_type_exists(portal, schema_type, debug=debug):
             return True
     return False
 
@@ -393,14 +388,15 @@ def one_or_more_objects_of_type_exists(portal: Portal, schema_type: str, debug:
             _print(f"Checking if there are actually any objects of type: {schema_type}")
         if portal.get(f"/{schema_type}").status_code == 404:
             if debug:
-                _print(f"No any objects of type exist: {schema_type}")
+                _print(f"No objects of type actually exist: {schema_type}")
+            return False
         else:
             if debug:
                 _print(f"One or more objects of type exist: {schema_type}")
     except Exception as e:
-        _print(f"ERROR: Checking if there are actually any objects of type: {schema_type}")
+        _print(f"ERROR: Cannot determine if there are actually any objects of type: {schema_type}")
         _print(e)
-    return False
+    return True
 
 
 @lru_cache(maxsize=1)

{dcicutils-8.14.0.1b7 → dcicutils-8.14.0.1b9}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.14.0.1b7"  # TODO: To become 8.14.1
+version = "8.14.0.1b9"  # TODO: To become 8.14.1
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"