dcicutils 8.14.3.1b4__py3-none-any.whl → 8.14.3.2b1__py3-none-any.whl

dcicutils/portal_utils.py

@@ -294,12 +294,6 @@ class Portal:
     def get_health(self) -> OptionalResponse:
         return self.get("/health")
 
-    def get_version(self) -> Optional[str]:
-        try:
-            return self.get_health().json()["project_version"]
-        except Exception:
-            return None
-
     def ping(self) -> bool:
         try:
             return self.get_health().status_code == 200

dcicutils/s3_utils.py

@@ -328,8 +328,10 @@ class s3Utils(s3Base):  # NOQA - This class name violates style rules, but a lot
             # maybe its not json after all
             return auth_text
 
-    def read_s3(self, filename: str):
-        response = self.s3.get_object(Bucket=self.outfile_bucket, Key=filename)
+    def read_s3(self, filename: str, bucket: Optional[str] = None):
+        if (not isinstance(bucket, str)) or (not bucket):
+            bucket = self.outfile_bucket
+        response = self.s3.get_object(Bucket=bucket, Key=filename)
         logger.info(str(response))
         return response['Body'].read()
 

dcicutils/scripts/view_portal_object.py

@@ -360,12 +360,7 @@ def _get_portal_object(portal: Portal, uuid: str,
                 path = f"/{uuid}"
             else:
                 path = uuid
-            if (response := portal.get(path, raw=raw or inserts, database=database)) is not None:
-                if response.status_code == 403:
-                    _exit(f"Permission error getting Portal object from {portal.server}: {uuid}")
-                elif response.status_code == 404:
-                    _exit(f"Not found Portal object from {portal.server}: {uuid}")
-
+            response = portal.get(path, raw=raw or inserts, database=database)
         except Exception as e:
             if "404" in str(e) and "not found" in str(e).lower():
                 _print(f"Portal object not found at {portal.server}: {uuid}")

dcicutils/structured_data.py

@@ -318,7 +318,7 @@ class StructuredDataSet:
         order = {Schema.type_name(key): index for index, key in enumerate(self._order)} if self._order else {}
         for sheet_name in sorted(excel.sheet_names, key=lambda key: order.get(Schema.type_name(key), sys.maxsize)):
             self._load_reader(excel.sheet_reader(sheet_name), type_name=Schema.type_name(sheet_name))
-            if self._validator_sheet_hook and self.data.get(sheet_name):
+            if self._validator_sheet_hook:
                 self._validator_sheet_hook(self, sheet_name, self.data[sheet_name])
         # TODO: Do we really need progress reporting for the below?
         # Check for unresolved reference errors which really are not because of ordering.
@@ -388,7 +388,13 @@ class StructuredDataSet:
             structured_row = structured_row_template.create_row()
             for column_name, value in row.items():
                 if self._validator_hook:
-                    value = self._validator_hook(self, type_name, column_name, reader.row_number, value)
+                    value, validator_error = (
+                        self._validator_hook(self, type_name, column_name, reader.row_number, value))
+                    if validator_error:
+                        self._note_error({
+                            "src": create_dict(type=schema_name, row=reader.row_number),
+                            "error": validator_error
+                        }, "validation")
                 structured_row_template.set_value(structured_row, column_name, value, reader.file, reader.row_number)
                 if self._autoadd_properties:
                     self._add_properties(structured_row, self._autoadd_properties, schema)

{dcicutils-8.14.3.1b4.dist-info → dcicutils-8.14.3.2b1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.14.3.1b4
+Version: 8.14.3.2b1
 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-8.14.3.1b4.dist-info → dcicutils-8.14.3.2b1.dist-info}/RECORD

@@ -49,24 +49,24 @@ dcicutils/misc_utils.py,sha256=mO-5i0IUZ2U-P7rnQcC9VURzQ35pz7jFsMZdq6BB_QM,11592
 dcicutils/obfuscation_utils.py,sha256=fo2jOmDRC6xWpYX49u80bVNisqRRoPskFNX3ymFAmjw,5963
 dcicutils/opensearch_utils.py,sha256=V2exmFYW8Xl2_pGFixF4I2Cc549Opwe4PhFi5twC0M8,1017
 dcicutils/portal_object_utils.py,sha256=Az3n1aL-PQkN5gOFE6ZqC2XkYsqiwKlq7-tZggs1QN4,11062
-dcicutils/portal_utils.py,sha256=4mHNdMcaQDUVPfiDYwGeIqjerNuDRnNloUDIZl41r9g,45439
+dcicutils/portal_utils.py,sha256=Ub4rlG6Ir4JVSH1KHQRRtJTU_5yBGzVOKrdIkhqJMLQ,45268
 dcicutils/progress_bar.py,sha256=R3bWLMYM3Xq9PY7U0JadcFT1m7QmCbrbDp9qs9_Kf_c,19472
 dcicutils/project_utils.py,sha256=qPdCaFmWUVBJw4rw342iUytwdQC0P-XKpK4mhyIulMM,31250
 dcicutils/qa_checkers.py,sha256=j0kzo_T5VduKTxgsMTp7xjneyNokumZzI_iz55Y0Jjs,20505
 dcicutils/qa_utils.py,sha256=tMvsMX0fXmE0BAaw34ulDw0f2twqgWnYcNQFBXHtAM0,160179
 dcicutils/redis_tools.py,sha256=qkcSNMtvqkpvts-Cm9gWhneK523Q_oHwhNUud1be1qk,7055
 dcicutils/redis_utils.py,sha256=VJ-7g8pOZqR1ZCtdcjKz3-6as2DMUcs1b1zG6wSprH4,6462
-dcicutils/s3_utils.py,sha256=h2B9ftOo-kxqfiKth5ZDC_cAUFy1Pbu7BrVanFnE5Iw,28839
+dcicutils/s3_utils.py,sha256=Nft1H6ohkYTYpO6Q42bldfEWPtZARqhv_ZGvWme2lj0,28955
 dcicutils/schema_utils.py,sha256=GmRm-XqZKJ6qine16SQF1txcby9WougDav_sYmKNs9E,12400
 dcicutils/scripts/publish_to_pypi.py,sha256=sMd4WASQGlxlh7uLrt2eGkFRXYgONVmvIg8mClMS5RQ,13903
 dcicutils/scripts/run_license_checker.py,sha256=z2keYnRDZsHQbTeo1XORAXSXNJK5axVzL5LjiNqZ7jE,4184
 dcicutils/scripts/update_portal_object.py,sha256=BwZw1cZx2zhzp1ivn_DXUxfnmUyC5A9fAotjHV0fXf4,41875
-dcicutils/scripts/view_portal_object.py,sha256=uu1w2sPCjrztA_OZAzo-HiPJhju9mICHf-lJ5RC_Ak0,41573
+dcicutils/scripts/view_portal_object.py,sha256=mfaWIjVD_dtLNl8Gfue-9Xo1zBrfChe2Tr9J6aoA7sA,41274
 dcicutils/secrets_utils.py,sha256=8dppXAsiHhJzI6NmOcvJV5ldvKkQZzh3Fl-cb8Wm7MI,19745
 dcicutils/sheet_utils.py,sha256=VlmzteONW5VF_Q4vo0yA5vesz1ViUah1MZ_yA1rwZ0M,33629
 dcicutils/snapshot_utils.py,sha256=YDeI3vD-MhAtHwKDzfEm2q-n3l-da2yRpRR3xp0Ah1M,23021
 dcicutils/ssl_certificate_utils.py,sha256=F0ifz_wnRRN9dfrfsz7aCp4UDLgHEY8LaK7PjnNvrAQ,9707
-dcicutils/structured_data.py,sha256=PbsdEdeC01RvBq9SB7ozMu3oNDJrMlVyHQcBnwAzAkU,66382
+dcicutils/structured_data.py,sha256=75f03o6a3LwsP_AA3fN-RVJKwdVjVEsXxCisZvMQBXg,66662
 dcicutils/submitr/progress_constants.py,sha256=5bxyX77ql8qEJearfHEvsvXl7D0GuUODW0T65mbRmnE,2895
 dcicutils/submitr/ref_lookup_strategy.py,sha256=VJN-Oo0LLna6Vo2cu47eC-eU-yUC9NFlQP29xajejVU,4741
 dcicutils/task_utils.py,sha256=MF8ujmTD6-O2AC2gRGPHyGdUrVKgtr8epT5XU8WtNjk,8082
@@ -75,8 +75,8 @@ dcicutils/trace_utils.py,sha256=g8kwV4ebEy5kXW6oOrEAUsurBcCROvwtZqz9fczsGRE,1769
 dcicutils/validation_utils.py,sha256=cMZIU2cY98FYtzK52z5WUYck7urH6JcqOuz9jkXpqzg,14797
 dcicutils/variant_utils.py,sha256=2H9azNx3xAj-MySg-uZ2SFqbWs4kZvf61JnK6b-h4Qw,4343
 dcicutils/zip_utils.py,sha256=_Y9EmL3D2dUZhxucxHvrtmmlbZmK4FpSsHEb7rGSJLU,3265
-dcicutils-8.14.3.1b4.dist-info/LICENSE.txt,sha256=qnwSmfnEWMl5l78VPDEzAmEbLVrRqQvfUQiHT0ehrOo,1102
-dcicutils-8.14.3.1b4.dist-info/METADATA,sha256=Rn9ZoIveSCzsgMWbLZgKaakQCKHRKYUKGRmNMZNmJus,3446
-dcicutils-8.14.3.1b4.dist-info/WHEEL,sha256=7Z8_27uaHI_UZAc4Uox4PpBhQ9Y5_modZXWMxtUi4NU,88
-dcicutils-8.14.3.1b4.dist-info/entry_points.txt,sha256=W6kEWdUJk9tQ4myAgpehPdebcwvCAZ7UgB-wyPgDUMg,335
-dcicutils-8.14.3.1b4.dist-info/RECORD,,
+dcicutils-8.14.3.2b1.dist-info/LICENSE.txt,sha256=qnwSmfnEWMl5l78VPDEzAmEbLVrRqQvfUQiHT0ehrOo,1102
+dcicutils-8.14.3.2b1.dist-info/METADATA,sha256=ZFbqt8tPihlmZmmJdjGlj8OYEv78noSFf4ll8AHiyXM,3446
+dcicutils-8.14.3.2b1.dist-info/WHEEL,sha256=7Z8_27uaHI_UZAc4Uox4PpBhQ9Y5_modZXWMxtUi4NU,88
+dcicutils-8.14.3.2b1.dist-info/entry_points.txt,sha256=W6kEWdUJk9tQ4myAgpehPdebcwvCAZ7UgB-wyPgDUMg,335
+dcicutils-8.14.3.2b1.dist-info/RECORD,,