1 files changed, 0 insertions, 142 deletions
diff --git a/scripts/phenotypes_bulk_edit.py b/scripts/phenotypes_bulk_edit.py
deleted file mode 100644
index 1d6689e..0000000
--- a/scripts/phenotypes_bulk_edit.py
+++ /dev/null
@@ -1,142 +0,0 @@
-import sys
-import uuid
-import logging
-import argparse
-from pathlib import Path
-from typing import Iterator
-
-from MySQLdb.cursors import DictCursor
-
-from gn_libs import jobs, mysqldb, sqlite3
-
-logging.basicConfig(
-    format="%(asctime)s — %(filename)s:%(lineno)s — %(levelname)s: %(message)s")
-logger = logging.getLogger(__name__)
-
-
-def check_ids(conn, contents):
-    """Verify that all the `UniqueIdentifier` values are valid."""
-    logger.info("Checking the 'UniqueIdentifier' values.")
-    with conn.cursor(cursorclass=DictCursor) as cursor:
-        ids = tuple((row["phenotype_id"], row["xref_id"]) for row in contents)
-        paramstr = ",".join(["(%s, %s)"] * len(ids))
-        cursor.execute(
-            "SELECT PhenotypeId AS phenotype_id, Id AS xref_id "
-            "FROM PublishXRef "
-            f"WHERE (PhenotypeId, Id) IN ({paramstr})",
-            tuple(item for row in ids for item in row))
-        mysqldb.debug_query(cursor, logger)
-        found = tuple((str(row["phenotype_id"]), str(row["xref_id"]))
-                 for row in cursor.fetchall())
-
-    not_found = tuple(item for item in ids if item not in found)
-    if len(not_found) == 0:
-        logger.info("All 'UniqueIdentifier' are valid.")
-        return True
-
-    for item in not_found:
-        logger.error(f"Invalid 'UniqueIdentifier' value: phId:%s::xrId:%s", item[0], item[1])
-
-    return False
-
-
-def check_for_mandatory_fields():
-    """Verify that mandatory fields have values."""
-    pass
-
-
-def compute_differences():
-    """Compute differences between data in DB and edited data."""
-    logger.info("Computing differences.")
-    pass
-
-
-def update_descriptions():
-    """Update descriptions in the database"""
-    logger.info("Updating descriptions")
-    # Compute differences between db data and uploaded file
-    # Only run query for changed descriptions
-    pass
-
-
-def link_publications():
-    """Link phenotypes to relevant publications."""
-    logger.info("Linking phenotypes to publications.")
-    # Create publication if PubMed_ID doesn't exist in db
-    pass
-
-
-def update_values():
-    """Update the phenotype values."""
-    logger.info("Updating phenotypes values.")
-    # Compute differences between db data and uploaded file
-    # Only run query for changed data
-    pass
-
-
-def parse_args():
-    parser = argparse.ArgumentParser(
-        prog="Phenotypes Bulk-Edit Processor",
-        description="Process the bulk-edits to phenotype data and descriptions.")
-    parser.add_argument("db_uri", type=str, help="MariaDB/MySQL connection URL")
-    parser.add_argument(
-        "jobs_db_path", type=Path, help="Path to jobs' SQLite database.")
-    parser.add_argument("job_id", type=uuid.UUID, help="ID of the running job")
-    parser.add_argument(
-        "--log-level",
-        type=str,
-        help="Determines what is logged out.",
-        choices=("debug", "info", "warning", "error", "critical"),
-        default="info")
-    return parser.parse_args()
-
-
-def read_file(filepath: Path) -> Iterator[str]:
-    """Read the file, one line at a time."""
-    with filepath.open(mode="r", encoding="utf-8") as infile:
-        count = 0
-        headers = None
-        for line in infile:
-            if line.startswith("#"): # ignore comments
-                continue;
-
-            fields = line.strip().split("\t")
-            if count == 0:
-                headers = fields
-                count = count + 1
-                continue
-
-            _dict = dict(zip(headers, fields))
-            _pheno, _xref = _dict.pop("UniqueIdentifier").split("::")
-            _dict["phenotype_id"] = _pheno.split(":")[1]
-            _dict["xref_id"] = _xref.split(":")[1]
-            yield _dict
-            count = count + 1
-
-
-def run(conn, job):
-    """Process the data and update it."""
-    file_contents = tuple(read_file(Path(job["metadata"]["edit-file"])))
-    check_ids(conn, file_contents)
-    check_for_mandatory_fields()
-    # stop running here if any errors are found.
-    compute_differences()
-    update_descriptions()
-    link_publications()
-    update_values()
-    return 0
-
-
-def main():
-    """Entry-point for this script."""
-    args = parse_args()
-    logger.setLevel(args.log_level.upper())
-    logger.debug("Arguments: %s", args)
-
-    with (mysqldb.database_connection(args.db_uri) as conn,
-          sqlite3.connection(args.jobs_db_path) as jobs_conn):
-        return run(conn, jobs.job(jobs_conn, args.job_id))
-
-
-if __name__ == "__main__":
-    sys.exit(main())