Merge pull request #627 from microbiomedata/add-funding-source

Add funding source to `SubmissionPortalTranslator`
microbiomedata · Aug 22, 2024 · c2a7802 · c2a7802
2 parents 8cbd966 + 8f8e92a
commit c2a7802
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Showing 6 changed files with 11 additions and 12 deletions.
diff --git a/nmdc_runtime/site/ops.py b/nmdc_runtime/site/ops.py
@@ -682,7 +682,6 @@ def translate_portal_submission_to_nmdc_schema_database(
     study_category: Optional[str],
     study_doi_category: Optional[str],
     study_doi_provider: Optional[str],
-    study_funding_sources: Optional[List[str]],
     study_pi_image_url: Optional[str],
     biosample_extras: Optional[list[dict]],
     biosample_extras_slot_mapping: Optional[list[dict]],
@@ -701,7 +700,6 @@ def id_minter(*args, **kwargs):
         study_category=study_category,
         study_doi_category=study_doi_category,
         study_doi_provider=study_doi_provider,
-        study_funding_sources=study_funding_sources,
         study_pi_image_url=study_pi_image_url,
         biosample_extras=biosample_extras,
         biosample_extras_slot_mapping=biosample_extras_slot_mapping,

diff --git a/nmdc_runtime/site/repository.py b/nmdc_runtime/site/repository.py
@@ -539,7 +539,6 @@ def biosample_submission_ingest():
                             "study_category": None,
                             "study_doi_category": None,
                             "study_doi_provider": None,
-                            "study_funding_sources": None,
                             "study_pi_image_url": None,
                         }
                     },
@@ -578,7 +577,6 @@ def biosample_submission_ingest():
                             "study_category": None,
                             "study_doi_category": None,
                             "study_doi_provider": None,
-                            "study_funding_sources": None,
                             "study_pi_image_url": None,
                         }
                     },

diff --git a/nmdc_runtime/site/translation/submission_portal_translator.py b/nmdc_runtime/site/translation/submission_portal_translator.py
@@ -404,7 +404,9 @@ def _translate_study(
             description=self._get_from(
                 metadata_submission, ["studyForm", "description"]
             ),
-            funding_sources=self.study_funding_sources,
+            funding_sources=self._get_from(
+                metadata_submission, ["studyForm", "fundingSources"]
+            ),
             # emsl_proposal_identifier=self._get_from(
             #     metadata_submission, ["multiOmicsForm", "studyNumber"]
             # ),

diff --git a/tests/test_data/test_submission_portal_translator.py b/tests/test_data/test_submission_portal_translator.py
@@ -304,7 +304,6 @@ def now(cls, **kwargs):
                 id_minter=test_minter,
                 study_category="research_study",
                 study_doi_provider="jgi",
-                study_funding_sources=["Some award ABC", "Another award XYZ"]
             )
 
             expected = nmdc.Database(**test_data["output"])

diff --git a/tests/test_data/test_submission_portal_translator_data.yaml b/tests/test_data/test_submission_portal_translator_data.yaml
@@ -57,6 +57,9 @@ input:
           annotated. Our findings support that leaf-associated bacterial populations are
           seasonally dynamic and responsive to host cues.
         notes: ''
+        fundingSources: 
+          - Some award ABC
+          - Some award XYZ
         contributors:
         - name: Adina Howe
           orcid: 0000-0002-7705-343X
@@ -806,7 +809,7 @@ output:
       doi_category: dataset_doi
     funding_sources:
       - Some award ABC
-      - Another award XYZ
+      - Some award XYZ
     study_category: research_study
     title: Seasonal activities of the phyllosphere microbiome of perennial crops
     websites:
@@ -867,6 +870,9 @@ input:
             roles:
               - Principal Investigator
         description: This is a test submission
+        fundingSources: 
+          - Some award ABC
+          - Some award XYZ
         linkOutWebpage:
           - http://www.example.com/submission-test
         multiOmicsForm:
@@ -975,7 +981,7 @@ output:
           doi_category: dataset_doi
       funding_sources:
         - Some award ABC
-        - Another award XYZ
+        - Some award XYZ
       has_credit_associations:
         - applies_to_person:
             orcid: 0000-0000-0000-0000

diff --git a/tests/test_graphs/test_submission_portal_graphs.py b/tests/test_graphs/test_submission_portal_graphs.py
@@ -99,10 +99,6 @@ def test_translate_metadata_submission_to_nmdc_schema_database():
                     "study_category": "research_study",
                     "study_doi_category": "dataset_doi",
                     "study_doi_provider": "jgi",
-                    "study_funding_sources": [
-                        "funder 1",
-                        "funder 2",
-                    ],
                     "study_pi_image_url": "http://www.example.com/test.png",
                 }
             },