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| author | Frederick Muriuki Muriithi | 2025-04-11 14:59:49 -0500 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2025-04-11 15:18:53 -0500 |
| commit | 5eddcada30e8d6bbc4631103ae3fd96bdc6b134b (patch) | |
| tree | 07e9c5a91de11dd37f7787bb1793a8277bb98aff | |
| parent | 70ecf94d8629d75dfa6ef295ddd18c0f4aa622f8 (diff) | |
| download | gn-uploader-5eddcada30e8d6bbc4631103ae3fd96bdc6b134b.tar.gz | |
Move code to fetch phenotype publications from DB to publications package.
| -rw-r--r-- | scripts/phenotypes_bulk_edit.py | 3 | ||||
| -rw-r--r-- | uploader/publications/models.py | 15 |
2 files changed, 17 insertions, 1 deletions
diff --git a/scripts/phenotypes_bulk_edit.py b/scripts/phenotypes_bulk_edit.py index 488805c..4888924 100644 --- a/scripts/phenotypes_bulk_edit.py +++ b/scripts/phenotypes_bulk_edit.py @@ -13,6 +13,7 @@ from MySQLdb.cursors import DictCursor from gn_libs import jobs, mysqldb, sqlite3 import uploader.publications.pubmed as pmed +from uploader.publications.models import fetch_phenotype_publications logging.basicConfig( format="%(asctime)s — %(filename)s:%(lineno)s — %(levelname)s: %(message)s") logger = logging.getLogger(__name__) @@ -163,7 +164,7 @@ def compute_differences( pub_diff = publications_differences( conn, file_contents, - __fetch_publications__(conn, pheno_xref_ids), + fetch_phenotype_publications(conn, pheno_xref_ids), pubmed_ids) logger.debug("Publications diff: %s", pub_diff) # 2. Data differences diff --git a/uploader/publications/models.py b/uploader/publications/models.py new file mode 100644 index 0000000..89da06c --- /dev/null +++ b/uploader/publications/models.py @@ -0,0 +1,15 @@ +"""Module to handle persistence and retrieval of publication to/from MariaDB""" + +def fetch_phenotype_publications( + conn, ids: tuple[tuple[int, int], ...]) -> tuple[dict, ...]: + """Fetch publication from database by ID.""" + paramstr = ",".join(["(%s, %s)"] * len(ids)) + query = ( + "SELECT " + "pxr.PhenotypeId, pxr.Id AS xref_id, pxr.PublicationId, pub.PubMed_ID " + "FROM PublishXRef AS pxr INNER JOIN Publication AS pub " + "ON pxr.PublicationId=pub.Id " + f"WHERE (pxr.PhenotypeId, pxr.Id) IN ({paramstr})") + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute(query, tuple(item for row in ids for item in row)) + return tuple(dict(row) for row in cursor.fetchall()) |