dcicutils 8.8.3.1b7__py3-none-any.whl → 8.8.3.1b8__py3-none-any.whl

dcicutils/structured_data.py

@@ -154,7 +154,32 @@ class StructuredDataSet:
 
     @property
     def resolved_refs_with_uuids(self) -> List[str]:
-        return list([{"path": resolved_ref[0], "uuid": resolved_ref[1]} for resolved_ref in self._resolved_refs])
+        return list([{"path": resolved_ref[0],
+                      "uuid": resolved_ref[1] if len(resolved_ref) >= 2 else None}
+                     for resolved_ref in self._resolved_refs])
+
+    @property
+    def unchecked_refs(self) -> List[str]:
+        """
+        Returns list of unchecked (for existence) references, grouped by reference path;
+        each object in the list has a path property and a srcs property which is a list of
+        src objects containing the type, column and row of the reference to the reference.
+        Note that this is only populated if the norefs option is specified.
+        """
+        def load_json(value: str) -> Optional[dict]:
+            try:
+                return json.loads(value)
+            except Exception:
+                return None
+        result = []
+        if self._norefs:
+            for ref in self._resolved_refs:
+                if len(ref) >= 3 and (ref_path := ref[0]) and (ref_src := load_json(ref[2])):
+                    if existing_ref := [item for item in result if item.get("path") == ref_path]:
+                        existing_ref[0]["srcs"].append(ref_src)
+                    else:
+                        result.append({"path": ref_path, "srcs": [ref_src]})
+        return result
 
     @property
     def upload_files(self) -> List[str]:
@@ -653,10 +678,14 @@ class Schema(SchemaBase):
         def map_ref(value: str, link_to: str, portal: Optional[Portal], src: Optional[str]) -> Any:
             nonlocal self, typeinfo
             if self._norefs:
+                # Here the caller has specified the (StructuredDataSet) norefs option
+                # which means we do not check for the existence of references at all.
                 if value:
-                    # Dump the src because this cannot add dictionary to a set; note that
-                    # this is ONLY used for smaht-submitr/submit-metadata-bundle --info --refs.
-                    self._resolved_refs.add((f"/{link_to}/{value}", json.dumps(src) if isinstance(src, dict) else None))
+                    # Dump the src as a JSON string because a dictionary cannot be added to a set; note
+                    # that this is ONLY used for smaht-submitr/submit-metadata-bundle --info --refs.
+                    # This info can be gotten at using StructureDataSet.unchecked_refs.
+                    self._resolved_refs.add((f"/{link_to}/{value}", None,
+                                             json.dumps(src) if isinstance(src, dict) else None))
                 return value
             if not value:
                 if (column := typeinfo.get("column")) and column in self.data.get("required", []):

{dcicutils-8.8.3.1b7.dist-info → dcicutils-8.8.3.1b8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.8.3.1b7
+Version: 8.8.3.1b8
 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-8.8.3.1b7.dist-info → dcicutils-8.8.3.1b8.dist-info}/RECORD

@@ -63,7 +63,7 @@ dcicutils/secrets_utils.py,sha256=8dppXAsiHhJzI6NmOcvJV5ldvKkQZzh3Fl-cb8Wm7MI,19
 dcicutils/sheet_utils.py,sha256=VlmzteONW5VF_Q4vo0yA5vesz1ViUah1MZ_yA1rwZ0M,33629
 dcicutils/snapshot_utils.py,sha256=ymP7PXH6-yEiXAt75w0ldQFciGNqWBClNxC5gfX2FnY,22961
 dcicutils/ssl_certificate_utils.py,sha256=F0ifz_wnRRN9dfrfsz7aCp4UDLgHEY8LaK7PjnNvrAQ,9707
-dcicutils/structured_data.py,sha256=YCLGtjsCMXCm5ZM96aiTRQ9OPUuj0lK8O9vSkLx1gv8,58450
+dcicutils/structured_data.py,sha256=Ho97KAqPgfn9QVfIMpjp0gS1FXLAnEJu6usdVi2lGHc,59927
 dcicutils/submitr/progress_constants.py,sha256=5bxyX77ql8qEJearfHEvsvXl7D0GuUODW0T65mbRmnE,2895
 dcicutils/submitr/ref_lookup_strategy.py,sha256=Js2cVznTmgjciLWBPLCvMiwLIHXjDn3jww-gJPjYuFw,3467
 dcicutils/task_utils.py,sha256=MF8ujmTD6-O2AC2gRGPHyGdUrVKgtr8epT5XU8WtNjk,8082
@@ -72,8 +72,8 @@ 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=rnjNv_k6L9jT2SjDSgVXp4BEJYLtz9XN6Cl2Fy-tqnM,2027
-dcicutils-8.8.3.1b7.dist-info/LICENSE.txt,sha256=qnwSmfnEWMl5l78VPDEzAmEbLVrRqQvfUQiHT0ehrOo,1102
-dcicutils-8.8.3.1b7.dist-info/METADATA,sha256=v8fZzOT3EWHNMI-R_bT-jbA1LTjKnGd1LOGD_oLn1Yg,3356
-dcicutils-8.8.3.1b7.dist-info/WHEEL,sha256=7Z8_27uaHI_UZAc4Uox4PpBhQ9Y5_modZXWMxtUi4NU,88
-dcicutils-8.8.3.1b7.dist-info/entry_points.txt,sha256=51Q4F_2V10L0282W7HFjP4jdzW4K8lnWDARJQVFy_hw,270
-dcicutils-8.8.3.1b7.dist-info/RECORD,,
+dcicutils-8.8.3.1b8.dist-info/LICENSE.txt,sha256=qnwSmfnEWMl5l78VPDEzAmEbLVrRqQvfUQiHT0ehrOo,1102
+dcicutils-8.8.3.1b8.dist-info/METADATA,sha256=saFsKdu4mbE4RBPh2331yy2nC-ZUcE5n3fT740wn9iY,3356
+dcicutils-8.8.3.1b8.dist-info/WHEEL,sha256=7Z8_27uaHI_UZAc4Uox4PpBhQ9Y5_modZXWMxtUi4NU,88
+dcicutils-8.8.3.1b8.dist-info/entry_points.txt,sha256=51Q4F_2V10L0282W7HFjP4jdzW4K8lnWDARJQVFy_hw,270
+dcicutils-8.8.3.1b8.dist-info/RECORD,,