src/db_utils/populate_database.py - src/db_utils/config.py: modification of...

src/db_utils/populate_database.py - src/db_utils/config.py: modification of check_table_name, it now checks if the table name given exists in the database, not if it presents in Config.tables (so, this last variable was removed)

src/db_utils/config.py

@@ -13,8 +13,11 @@ class Config:
     """
     A class containing every parameters used in the submodule db_utils
     """
-    db_file = Path(__file__).parents[2] / "results" / 'chia_pet_database.db'
-    tables = ["cin_gene", "cin_exon", "cin_frequency", "cin_interaction"]
-    bed_exon = Path(__file__).parents[2] / 'data' / 'bed' / 'exon.bed'
-    bed_gene = Path(__file__).parents[2] / 'data' / 'bed' / 'gene.bed'
-
+    data = Path(__file__).parents[2] / 'data'
+    results = Path(__file__).parents[2] / "results"
+    db_file = results / 'chia_pet_database.db'
+    bed_exon = data / 'bed' / 'exon.bed'
+    bed_gene = data / 'bed' / 'gene.bed'
+    ase_event_file = data / 'splicing_lore_data' / 'ase_event.txt'
+    splicing_projects = data / 'splicing_lore_data' / \
+        'splicing_lore_projects.txt'

src/db_utils/populate_database.py

@@ -113,16 +113,31 @@ def insert_data(table: str, content: List[Tuple], cnx: sqlite3.Connection
     cursor.close()
 
 
-def check_table_name(table : str):
+def get_table_names(cnx: sqlite3.Connection) -> List[str]:
+    """
+    Get the list of available table names.
+
+    :param cnx: The connection to ChIA-PET database.
+
+    :return: The list of availbale tables
+    """
+    c = cnx.cursor()
+    c.execute("""SELECT name FROM sqlite_master WHERE type = 'table';""")
+    res = c.fetchall()
+    res = [r[0] for r in res]
+    return res
+
+
+def check_table_name(cnx: sqlite3.Connection, table: str):
     """
     Check if we can use the table name `table`.
 
+    :param cnx: Connection to ChIA-PET database
     :param table: The name of the table to fille
     :return: The same name with the prefix gin if it wasn't here.
     """
-    if "cin" not in table:
-        table = f"cin_{table.lower()}"
-    if table not in Config.tables:
+    tables = get_table_names(cnx)
+    if table not in tables:
         msg = f"The name {table} is not available." \
               f" If the table exist in the database, " \
               f"change the config file to add the table name " \
@@ -175,8 +190,8 @@ def populate_df(table: str, df: pd.DataFrame, clean: str):
     tab.
     :param clean: y to remove the data in the table, n else.
     """
-    table = check_table_name(table)
     cnx = sqlite3.connect(Config.db_file)
+    table = check_table_name(cnx, table)
     check_content_clean_and_insert(table, df, cnx, clean)
 
 
@@ -195,8 +210,8 @@ def populate(table: str, file: str, clean: str, logging_level: str =
     """
     logging_def(Config.db_file.parent, __file__, logging_level)
     mfile = Path(file)
-    table = check_table_name(table)
     cnx = sqlite3.connect(Config.db_file)
+    table = check_table_name(cnx, table)
     check_content_clean_and_insert(table, mfile, cnx, clean)