Simplify handling of publications: Assume a maximum of one.

Adding publication details in the R/qtl2 bundle might not be an easy
thing, so for now, assume all the phenotypes uploaded in a particular
session are all published in one publication.

1 files changed, 3 insertions, 34 deletions

diff --git a/scripts/load_phenotypes_to_db.py b/scripts/load_phenotypes_to_db.py
index 8ff8ab4..7e1112e 100644
--- a/scripts/load_phenotypes_to_db.py
+++ b/scripts/load_phenotypes_to_db.py
@@ -21,29 +21,6 @@ logging.basicConfig(
 logger = logging.getLogger(__name__)
 
 
-def save_publications(
-        conn: mysqldb.Connection,
-        pubfiles,
-        standalone_publication_id=Optional[int] = None
-) -> tuple[dict[str, Union[int, str]]]:
-    """Read the `pubfiles` and save the publications therein."""
-    _publications = tuple()
-    if standalone_publication_id:
-        # HACK: This is a hack. Remove once we update bundle creation to include
-        #       publication(s) in the bundle
-        _publications = _publications + (
-            fetch_publication_by_id(conn, standalone_publication_id),)
-    # -> check whether the publication-id exists?
-    # -> perhaps setup the bundle with the appropriate publications
-    # -> gn-data -> (phenotypes-se, phenotypes-n)
-    # -> gn-metadata -> (pheno, geno)
-    if len(pubfiles) > 0:# TODO: check for presence of data — improve this check.
-        logger.info("Saving publications.")
-        _publications = _publication + create_new_publications(conn, pubs)
-    # Check for PubMed IDs, perhaps?
-    return _publications
-
-
 def save_phenotypes(
         cursor: mysqldb.Connection,
         control_data: dict[str, Any]
@@ -261,17 +238,9 @@ def load_data(conn, job):
         }
         for dataid, row in enumerate(_phenos, start=__fetch_next_dataid__(conn))
     }
-    # 2. Save any new publications (in multi-file bundle):
-    #     -> return publication IDS: TODO: Figure out how to link file IDs to
-    #        DB IDs.
-    publications = save_publications(cursor,
-                                     _control_data.get(
-                                         "metadata", {}).get(
-                                             "publications"),
-                                     _job_metadata.get("publicationid"))
-    _pubidmap = {
-        # TODO: Map the pheno ids to the publication ids
-    }
+    # 2. Just retrive the publication: Don't create publications for now.
+    publication = fetch_publication_by_id(
+        conn, int(_job_metadata.get("publicationid", "0"))) or {"Id": 0}
     # 3. a. Fetch the strain names and IDS: create name->ID map
     samples = {
         row["Name"]: row