add provisional 10X expression parser with pandas

scirexport/airr_import.py

@@ -31,7 +31,8 @@ from argparse import RawTextHelpFormatter
 from scirexport.logger import logger
 import scirexport.sr_tools as sr
 from scirexport.importools import (
-    import_expression,
+    import_FACS_expression,
+    import_10X_expression,
     import_repertoires,
     import_rearrangements,
     import_receptors,
@@ -91,7 +92,7 @@ def main():
 
     if DB_ARGS["ssh_group"] and "test" not in DB_ARGS["ssh_group"]:
         try:
-            # first toplevel connection for shh tunneling
+            # first top-level connection for shh tunneling
             server, db = sr.connect(conf_db=config_db, ssh_group=DB_ARGS["ssh_group"])
             safe_create_schema(db, project_name)
             server.stop()
@@ -105,6 +106,7 @@ def main():
 
         except Exception as error:
             logger.error(f"MariaDB ERROR {error}")
+            raise (error)
 
     elif DB_ARGS["ssh_group"] and "test" in DB_ARGS["ssh_group"]:
         mode = "test"
@@ -126,6 +128,7 @@ def main():
     # Create database tables from templates/igdb_project.sql
     c = db.cursor()
     c.execute(sr.mysql_as_string(mysql_file))
+    db.commit()
 
     # @@@@ get files @@@@@ #
     # 1  rearrangements DF
@@ -137,15 +140,18 @@ def main():
             receptors_json = json.load(json_file)
         import_receptors(receptors_json, db, mode=mode)
     else:
-        logger.warning("receptors file was not provided no receptors will be imported")
+        logger.warning("No receptors file was provided. No receptors will be imported")
 
         # 5 expression DF/s
     if "expression" in files_dictionary:
-        expression_hdf = pd.read_csv(files_dictionary["expression"], sep="\t")
-        import_expression(expression_hdf, project_name, db)
+        if "facs" in files_dictionary["expression"].lower():
+            # expression_hdf = pd.read_csv(files_dictionary["expression"], sep="\t")
+            import_FACS_expression(files_dictionary["expression"], project_name, db)
+        elif "10x" in files_dictionary["expression"].lower():
+            import_10X_expression(files_dictionary["expression"], project_name, db)
     else:
         logger.warning(
-            "expression file was not provided no expression data will be imported"
+            "No expression file was provided. No expression data will be imported"
         )
 
     # 3 cells DF