dcicutils 8.8.1.1b27__tar.gz → 8.8.1.1b29__tar.gz

{dcicutils-8.8.1.1b27 → dcicutils-8.8.1.1b29}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.8.1.1b27
+Version: 8.8.1.1b29
 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-8.8.1.1b29/dcicutils/submitr/ref_lookup_strategy.py

@@ -0,0 +1,67 @@
+import re
+from typing import Optional
+from dcicutils.structured_data import Portal
+
+
+def ref_lookup_strategy(portal: Portal, type_name: str, schema: dict, value: str) -> (int, Optional[str]):
+    #
+    # FYI: Note this situation WRT object lookups ...
+    #
+    # /{submitted_id}                # NOT FOUND
+    # /UnalignedReads/{submitted_id} # OK
+    # /SubmittedFile/{submitted_id}  # OK
+    # /File/{submitted_id}           # NOT FOUND
+    #
+    # /{accession}                   # OK
+    # /UnalignedReads/{accession}    # NOT FOUND
+    # /SubmittedFile/{accession}     # NOT FOUND
+    # /File/{accession}              # OK
+    #
+    def ref_validator(schema: Optional[dict],
+                      property_name: Optional[str], property_value: Optional[str]) -> Optional[bool]:
+        """
+        Returns False iff the type represented by the given schema, can NOT be referenced by
+        the given property name with the given property value, otherwise returns None.
+
+        For example, if the schema is for the UnalignedReads type and the property name
+        is accession, then we will return False iff the given property value is NOT a properly
+        formatted accession ID. Otherwise, we will return None, which indicates that the
+        caller (in dcicutils.structured_data.Portal.ref_exists) will continue executing
+        its default behavior, which is to check other ways in which the given type can NOT
+        be referenced by the given value, i.e. it checks other identifying properties for
+        the type and makes sure any patterns (e.g. for submitted_id or uuid) are ahered to.
+
+        The goal (in structured_data) being to detect if a type is being referenced in such
+        a way that cannot possibly be allowed, i.e. because none of its identifying types
+        are in the required form (if indeed there any requirements). Note that it is guaranteed
+        that the given property name is indeed an identifying property for the given type.
+        """
+        if property_format := schema.get("properties", {}).get(property_name, {}).get("format"):
+            if (property_format == "accession") and (property_name == "accession"):
+                if not _is_accession_id(property_value):
+                    return False
+        return None
+
+    DEFAULT_RESPONSE = (Portal.LOOKUP_DEFAULT, ref_validator)
+
+    if not value:
+        return DEFAULT_RESPONSE
+    if not schema:
+        if not isinstance(portal, Portal) or not (schema := portal.get_schema(type_name)):
+            return DEFAULT_RESPONSE
+    if schema_properties := schema.get("properties"):
+        if schema_properties.get("accession") and _is_accession_id(value):
+            # Case: lookup by accession (only by root).
+            return Portal.LOOKUP_ROOT, ref_validator
+        elif schema_property_info_submitted_id := schema_properties.get("submitted_id"):
+            if schema_property_pattern_submitted_id := schema_property_info_submitted_id.get("pattern"):
+                if re.match(schema_property_pattern_submitted_id, value):
+                    # Case: lookup by submitted_id (only by specified type).
+                    return Portal.LOOKUP_SPECIFIED_TYPE, ref_validator
+    return DEFAULT_RESPONSE
+
+
+# This is here for now because of problems with circular dependencies.
+# See: smaht-portal/.../schema_formats.py
+def _is_accession_id(value: str) -> bool:
+    return isinstance(value, str) and re.match(r"^SMA[1-9A-Z]{9}$", value) is not None

{dcicutils-8.8.1.1b27 → dcicutils-8.8.1.1b29}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.1.1b27"  # TODO: To become 8.8.2
+version = "8.8.1.1b29"  # TODO: To become 8.8.2
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"