dcicutils 8.14.3.1b3__tar.gz → 8.14.3.2b1__tar.gz

{dcicutils-8.14.3.1b3 → dcicutils-8.14.3.2b1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.14.3.1b3
+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-8.14.3.1b3 → dcicutils-8.14.3.2b1}/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-8.14.3.1b3 → dcicutils-8.14.3.2b1}/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-8.14.3.1b3 → dcicutils-8.14.3.2b1}/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-8.14.3.1b3 → dcicutils-8.14.3.2b1}/dcicutils/structured_data.py

@@ -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-8.14.3.1b3 → dcicutils-8.14.3.2b1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.14.3.1b3"  # TODO: To become 8.14.4
+version = "8.14.3.2b1"  # TODO: To become 8.15.0
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"