diff --git a/src/db_utils/populate_database.py b/src/db_utils/populate_database.py
index 2fb89619d9a9e34b1d04ac701ed1ae6caf886cd2..56ff2750217e745a2cf2131d62fe80a65d563950 100755
--- a/src/db_utils/populate_database.py
+++ b/src/db_utils/populate_database.py
@@ -8,9 +8,10 @@ Description: This file can be used to populate the database of the website.
import sqlite3
-from .config import Config, logging_def
+from .config import Config
+from ..logging_conf import logging_def
from pathlib import Path
-from typing import List, Tuple
+from typing import List, Tuple, Union
import lazyparser as lp
import logging
import pandas as pd
@@ -46,7 +47,8 @@ def get_number_columns(table: str, cnx: sqlite3.Connection) -> List[str]:
return col_name
-def check_file(table: str, file: Path, cnx: sqlite3.Connection) -> List[Tuple]:
+def check_file(table: str, file: Union[Path, pd.DataFrame],
+ cnx: sqlite3.Connection) -> List[Tuple]:
"""
Check is the file has alwas the same nu_mber of columns and if \
it match the number of columns find in the table ``table``.
@@ -54,12 +56,15 @@ def check_file(table: str, file: Path, cnx: sqlite3.Connection) -> List[Tuple]:
:param table: The name of the table in the database in which we want \
to add data.
:param file: A tabulated file containing the data to insert in the table \
- tab.
+ tab or a pandas dataframe.
:param cnx: Connection to the database
:return: The row in file.
"""
column_names = get_number_columns(table, cnx)
- df = pd.read_csv(file, sep="\t")
+ if isinstance(file, Path):
+ df = pd.read_csv(file, sep="\t")
+ else:
+ df = file
if len(df.columns) != len(column_names):
msg = "Wrong number of columns"
logging.exception(msg)
@@ -70,7 +75,7 @@ def check_file(table: str, file: Path, cnx: sqlite3.Connection) -> List[Tuple]:
f"and the columns name of the database table {table} : " \
f"{df.columns} differs"
logging.exception(msg)
- raise ColumnsNameError(msg)
+ raise ColumnsNameError(msg)
df = df[column_names]
return df.values
@@ -108,23 +113,15 @@ def insert_data(table: str, content: List[Tuple], cnx: sqlite3.Connection
cursor.close()
-@lp.parse(file="file", clean=["y", "Y", "n", "N"])
-def populate(table: str, file: str, clean: str, logging_level: str =
- "DISABLE"):
+def check_table_name(table : str):
"""
- Update the content of the database of the web interface.
+ Check if we can use the table name `table`.
- :param table: The name of the table in the database in which we want \
- to add data.
- :param file: A tabulated file containing the data to insert in the table \
- tab.
- :param clean: y to remove the data in the table, n else.
- :param logging_level: The level of information to display
+ :param table: The name of the table to fille
+ :return: The same name with the prefix gin if it wasn't here.
"""
- logging_def(Config.output, logging_level)
- mfile = Path(file)
- if "gin" not in table:
- table = f"gin_{table.lower()}"
+ if "cin" not in table:
+ table = f"cin_{table.lower()}"
if table not in Config.tables:
msg = f"The name {table} is not available." \
f" If the table exist in the database, " \
@@ -132,15 +129,76 @@ def populate(table: str, file: str, clean: str, logging_level: str =
f"wanted in 'tables' field"
logging.exception(msg)
raise TableNameError(msg)
- cnx = sqlite3.connect(Config.db_file)
- logging.debug("Checking file ...")
- content = check_file(table, mfile, cnx)
+ return table
+
+
+def cleaning(cnx: sqlite3.Connection, clean: str, table: str) -> None:
+ """
+ Clean the table ``table`` if asked.
+
+ :param cnx: Connection to ChIA-PET database
+ :param clean: Y to clean the database
+ :param table: The name of the table to fill in the database
+ """
if clean.upper() == "Y":
logging.debug("Cleaning table")
clean_table(table, cnx)
+
+
+def check_content_clean_and_insert(table: str, df: Union[Path, pd.DataFrame],
+ cnx: sqlite3.Connection, clean: str):
+ """
+ Check content of df, clean database if needed and fill database.
+
+ :param table: The name of the table in the database in which we want \
+ to add data.
+ :param df: A tabulated file containing the data to insert in the table \
+ tab or a pandas dataframe.
+ :param cnx: Connection to ChIA-PET database
+ :param clean: y to remove the data in the table, n else.
+ :return:
+ """
+ logging.debug("Checking file ...")
+ content = check_file(table, df, cnx)
+ cleaning(cnx, clean, table)
logging.debug("Inserting data ...")
insert_data(table, content, cnx)
+def populate_df(table: str, df: pd.DataFrame, clean: str):
+ """
+ Update the content of the database of the web interface.
+
+ :param table: The name of the table in the database in which we want \
+ to add data.
+ :param df: A tabulated file containing the data to insert in the table \
+ tab.
+ :param clean: y to remove the data in the table, n else.
+ """
+ table = check_table_name(table)
+ cnx = sqlite3.connect(Config.db_file)
+ check_content_clean_and_insert(table, df, cnx, clean)
+
+
+@lp.parse(file="file", clean=["y", "Y", "n", "N"])
+def populate(table: str, file: str, clean: str, logging_level: str =
+ "DISABLE"):
+ """
+ Update the content of the database of the web interface.
+
+ :param table: The name of the table in the database in which we want \
+ to add data.
+ :param file: A tabulated file containing the data to insert in the table \
+ tab.
+ :param clean: y to remove the data in the table, n else.
+ :param logging_level: The level of information to display
+ """
+ logging_def(Config.db_file.parent, __file__, logging_level)
+ mfile = Path(file)
+ table = check_table_name(table)
+ cnx = sqlite3.connect(Config.db_file)
+ check_content_clean_and_insert(table, mfile, cnx, clean)
+
+
if __name__ == "__main__":
populate()