src/db_utils/__main__.py

src/db_utils/__main__.py

@@ -6,19 +6,22 @@
 Description: Populate the gin database
 """
 
-from .config import Config, logging_def
-from .creation_of_exon_table import get_ctrl, get_exon_table
-from .create_freq_table import create_freq_table
-from .populate_database import populate
+from .config import Config
+from ..logging_conf import logging_def
+from .db_creation import main_create_db
+# from .creation_of_exon_table import get_ctrl, get_exon_table
+# from .create_freq_table import create_freq_table
+# from .populate_database import populate
 import logging
 
 
 def launcher(logging_level: str = "INFO"):
     """
-    Fill the database
+    Create and fill the database
     """
-    logging_def(Config.output, "INFO")
-    Config.output.mkdir(exist_ok=True)
+    logging_def(Config.output, __file__, logging_level)
+    logging.info('Database creation')
+    main_create_db()
     # logging.info(f"Creation of {Config.ctrl_exon_file} file")
     # get_ctrl(Config.exon_intern)
     # logging.info(f"Creation of {Config.exon_file} file")
@@ -27,13 +30,13 @@ def launcher(logging_level: str = "INFO"):
     # create_freq_table(Config.bed_orf, Config.bed_exon, Config.ctrl_exon_file,
     #                   logging_level)
     #
-    mpopulate = populate.__wrapped__
+    # mpopulate = populate.__wrapped__
     # logging.info(f"Filling {Config.tables[0]} table")
     # mpopulate(Config.tables[0], Config.gene_file, "y", logging_level)
     # logging.info(f"Filling {Config.tables[1]} table")
     # mpopulate(Config.tables[1], Config.exon_file, "y", logging_level)
-    logging.info(f"Filling {Config.tables[2]} table")
-    mpopulate(Config.tables[2], Config.frequency_file, "y", logging_level)
+    # logging.info(f"Filling {Config.tables[2]} table")
+    # mpopulate(Config.tables[2], Config.frequency_file, "y", logging_level)
 
 
 launcher(logging_level = "DEBUG")
\ No newline at end of file