Put JGI proposal ID in jgi_portal_study_identifiers slot on Study

microbiomedata · Nov 14, 2024 · 7c8719f · 7c8719f
1 parent 001f54f
commit 7c8719f
Show file tree

Hide file tree

Showing 2 changed files with 23 additions and 5 deletions.
diff --git a/nmdc_runtime/site/translation/submission_portal_translator.py b/nmdc_runtime/site/translation/submission_portal_translator.py
@@ -191,6 +191,20 @@ def _get_gold_study_identifiers(
 
         return [self._ensure_curie(gold_study_id, default_prefix="gold")]
 
+    def _get_jgi_study_identifiers(
+        self, metadata_submission: JSON_OBJECT
+    ) -> Union[List[str], None]:
+        """Construct a JGI proposal CURIE from the multiomics from data
+
+        :param metadata_submission: submission portal entry
+        :return: JGI proposal CURIE
+        """
+        jgi_study_id = get_in(["multiOmicsForm", "JGIStudyId"], metadata_submission)
+        if not jgi_study_id:
+            return None
+
+        return [self._ensure_curie(jgi_study_id, default_prefix="jgi.proposal")]
+
     def _get_quantity_value(
         self, raw_value: Optional[str], unit: Optional[str] = None
     ) -> Union[nmdc.QuantityValue, None]:
@@ -410,9 +424,6 @@ def _translate_study(
         :return: nmdc:Study object
         """
         return nmdc.Study(
-            alternative_identifiers=self._get_from(
-                metadata_submission, ["multiOmicsForm", "JGIStudyId"]
-            ),
             alternative_names=self._get_from(
                 metadata_submission, ["multiOmicsForm", "alternativeNames"]
             ),
@@ -436,6 +447,9 @@ def _translate_study(
             insdc_bioproject_identifiers=self._get_from(
                 metadata_submission, ["multiOmicsForm", "NCBIBioProjectId"]
             ),
+            jgi_portal_study_identifiers=self._get_jgi_study_identifiers(
+                metadata_submission
+            ),
             name=self._get_from(metadata_submission, ["studyForm", "studyName"]),
             notes=self._get_from(metadata_submission, ["studyForm", "notes"]),
             principal_investigator=self._get_pi(metadata_submission),

diff --git a/tests/test_data/test_submission_portal_translator_data.yaml b/tests/test_data/test_submission_portal_translator_data.yaml
@@ -83,8 +83,8 @@ input:
       multiOmicsForm:
         alternativeNames: []
         studyNumber: ''
-        GOLDStudyId: ''
-        JGIStudyId: ''
+        GOLDStudyId: 'Gs0123456'
+        JGIStudyId: '123456'
         NCBIBioProjectId: ''
         omicsProcessingTypes:
         - mg
@@ -991,6 +991,10 @@ output:
       - Principal Investigator
       - Funding acquisition
       type: nmdc:CreditAssociation
+    gold_study_identifiers:
+    - gold:Gs0123456
+    jgi_portal_study_identifiers:
+    - jgi.proposal:123456
 ---
 input:
   metadata_submission: