Merge pull request #317 from 4dn-dcic/dmichaels-misc-updates-20240823

Minor changes to view-portal-object utility script.

CHANGELOG.rst

@@ -6,6 +6,15 @@ dcicutils
 Change Log
 ----------
 
+8.16.0
+======
+
+* Minor changes to view_portal_object utility script.
+* Minor changes to validators hooks in structured_data.
+* Added portal_utils.Portal.get_version method.
+* Minor fix in misc_utils.format_duration.
+
+
 8.15.0
 ======
 * 2024-10-04 (dmichaels)

dcicutils/misc_utils.py

@@ -2802,7 +2802,7 @@ def format_duration(seconds: Union[int, float]) -> str:
     durations = [("year", 31536000), ("day", 86400), ("hour", 3600), ("minute", 60), ("second", 1)]
     parts = []
     for name, duration in durations:
-        if seconds >= duration:
+        if (seconds == 0) or (seconds >= duration):
             count = seconds // duration
             seconds %= duration
             if count != 1:

dcicutils/portal_utils.py

@@ -294,6 +294,12 @@ def head(self, url: str, follow: bool = True, raise_exception: bool = False, **k
     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/scripts/view_portal_object.py

@@ -360,7 +360,12 @@ def write_insert_files(response: dict) -> None:
                 path = f"/{uuid}"
             else:
                 path = uuid
-            response = portal.get(path, raw=raw or inserts, database=database)
+            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}")
+
         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 @@ def get_counts() -> Tuple[int, int]:
         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:
+            if self._validator_sheet_hook and self.data.get(sheet_name):
                 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.
@@ -388,13 +388,7 @@ def _load_reader(self, reader: RowReader, type_name: str) -> None:
             structured_row = structured_row_template.create_row()
             for column_name, value in row.items():
                 if self._validator_hook:
-                    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")
+                    value = self._validator_hook(self, type_name, column_name, reader.row_number, value)
                 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)

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.15.0"
+version = "8.16.0"
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"