Initialise `install_phenos` script.

1 files changed, 57 insertions, 0 deletions

diff --git a/scripts/rqtl2/install_phenos.py b/scripts/rqtl2/install_phenos.py
new file mode 100644
index 0000000..b532dad
--- /dev/null
+++ b/scripts/rqtl2/install_phenos.py
@@ -0,0 +1,57 @@
+"""Load pheno from R/qtl2 bundle into the database."""
+import sys
+import logging
+# import traceback
+from pathlib import Path
+
+import MySQLdb as mdb
+
+from scripts.rqtl2.entry import build_main
+from scripts.cli_parser import init_cli_parser
+from scripts.rqtl2.cli_parser import add_common_arguments
+
+stderr_handler = logging.StreamHandler(stream=sys.stderr)
+logger = logging.getLogger("install_phenos")
+logger.addHandler(stderr_handler)
+
+def install_pheno_files(_dbconn: mdb.Connection,
+                        _speciesid: int,
+                        _populationid: int,
+                        _platformid: int,
+                        _studyid: int,
+                        _datasetid: int,
+                        _rqtl2bundle: Path) -> int:
+    """Load data in `pheno` files and other related files into the database."""
+    logger.debug("WE ARE HERE!!!")
+    return 5
+
+if __name__ == "__main__":
+
+    def cli_args():
+        """Process command-line arguments for install_genotypes"""
+        parser = init_cli_parser(
+            "install_genotypes",
+            "Parse genotypes from R/qtl2 bundle into the database.")
+
+        parser.add_argument(
+            "platformid",
+            help="The platform from which the data was generated.")
+        parser.add_argument("studyid",
+                            help="The study to which the data belongs.")
+
+        parser = add_common_arguments(parser)
+
+        return parser.parse_args()
+
+    main = build_main(
+        cli_args,
+        lambda dbconn, args: install_pheno_files(dbconn,
+                                                 args.speciesid,
+                                                 args.populationid,
+                                                 args.platformid,
+                                                 args.studyid,
+                                                 args.datasetid,
+                                                 args.rqtl2bundle),
+        logger,
+        "DEBUG")
+    sys.exit(main())