Update existing linked publication(s) rather than creating new.

1 files changed, 18 insertions, 5 deletions

diff --git a/scripts/phenotypes_bulk_edit.py b/scripts/phenotypes_bulk_edit.py
index 7de3347..1d8124e 100644
--- a/scripts/phenotypes_bulk_edit.py
+++ b/scripts/phenotypes_bulk_edit.py
@@ -14,7 +14,7 @@ import uploader.publications.pubmed as pmed
 from uploader.publications.misc import publications_differences
 from uploader.phenotypes.views import BULK_EDIT_COMMON_FIELDNAMES
 from uploader.publications.models import (
-    create_new_publications, fetch_phenotype_publications)
+    update_publications, fetch_phenotype_publications)
 
 logging.basicConfig(
     format="%(asctime)s — %(filename)s:%(lineno)s — %(levelname)s: %(message)s")
@@ -104,15 +104,28 @@ def compute_differences(
 
     #    b. Publications differences
     db_publications = fetch_phenotype_publications(conn, pheno_xref_ids)
-    new_publications = create_new_publications(
-        conn, pmed.fetch_publications(tuple(
+
+    _pubmed_map = {
+        (int(row["PubMed_ID"]) if bool(row["PubMed_ID"]) else None): f"{row['phenotype_id']}::{row['xref_id']}"
+        for row in file_contents
+    }
+    _pub_id_map = {
+        f"{pub['PhenotypeId']}::{pub['xref_id']}": pub["PublicationId"]
+        for pub in db_publications
+    }
+
+    new_publications = update_publications(
+        conn, tuple({
+            **pub, "publication_id": _pub_id_map[_pubmed_map[pub["pubmed_id"]]]
+        } for pub in pmed.fetch_publications(tuple(
             pubmed_id for pubmed_id in pubmed_ids
             if pubmed_id not in
-            tuple(row["PubMed_ID"] for row in db_publications))))
+            tuple(row["PubMed_ID"] for row in db_publications)))))
     logger.debug("New Publications: %s", new_publications)
     pub_diff = publications_differences(
         file_contents, db_publications, {
-            row["PubMed_ID"]: row["PublicationId"]
+            row["PubMed_ID" if "PubMed_ID" in row else "pubmed_id"]: row[
+                "PublicationId" if "PublicationId" in row else "publication_id"]
             for row in db_publications + new_publications})
     logger.debug("Publications diff: %s", pub_diff)
     # 2. Data differences