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- ```python
- import sys
- import os.path
- import pandas as pd
- import sqlite3
- def compare_causal(c, d, e):
- #Read a tsv file into pandas.dataframe
- os.chdir(c)
- patient_df = pd.read_csv(d, sep='t')
- patient_table = d[0:-4]
- patient_db_path = os.path.join(e, "PID_patients_data.db")
- #Build a connection
- pat_connect = sqlite3.connect(patient_db_path, timeout=10.0)
- pat_connect.isolation_level = None
- #Import the pandas.dataframe to sql database
- patient_df.to_sql(name=patient_table, con=pat_connect, if_exists='replace')
- # There are other subsequent codes but they are all in the definition of the function compare_causal.
- ```
- ```python
- import sys
- import os.path
- import pandas as pd
- import apsw
- def compare_causal(c, d, e):
- #Read a tsv file into pandas.dataframe
- os.chdir(c)
- patient_df = pd.read_csv(d, sep='t')
- patient_table = d[0:-4]
- patient_db_path = os.path.join(e, "PID_patients_data.db")
- #Build a connection
- pat_connect = apsw.Connection(patient_db_path)
- pat_connect.setbusytimeout(10000)
- #Import the pandas.dataframe to sql database
- patient_df.to_sql(name=patient_table, con=pat_connect, if_exists='replace')
- # There are other subsequent codes but they are all in the definition of the function compare_causal.
- ```
- Traceback (most recent call last):
- File "/Users/skyxt/anaconda3/lib/python3.7/site-packages/pandas/io/sql.py", line 1431, in execute
- cur.execute(*args)
- sqlite3.OperationalError: database is locked
- During handling of the above exception, another exception occurred:
- Traceback (most recent call last):
- File "/Users/skyxt/Google Drive/HKU_YANG_LAB/HKU_Academic_Issue/Python Learning/Python scripts/Database_related scripts/Compare_PID_causal_genes_sqlite.py", line 207, in <module>
- "/Users/skyxt/Google Drive/HKU_YANG_LAB/HKU_Academic_Issue/Project PID WES/Patients_Database")
- File "/Users/skyxt/Google Drive/HKU_YANG_LAB/HKU_Academic_Issue/Python Learning/Python scripts/Database_related scripts/Compare_PID_causal_genes_sqlite.py", line 37, in compare_causal
- patient_df.to_sql(name=patient_table, con=patient_connect, if_exists='replace')
- File "/Users/skyxt/anaconda3/lib/python3.7/site-packages/pandas/core/generic.py", line 2531, in to_sql
- dtype=dtype, method=method)
- File "/Users/skyxt/anaconda3/lib/python3.7/site-packages/pandas/io/sql.py", line 460, in to_sql
- chunksize=chunksize, dtype=dtype, method=method)
- File "/Users/skyxt/anaconda3/lib/python3.7/site-packages/pandas/io/sql.py", line 1546, in to_sql
- table.create()
- File "/Users/skyxt/anaconda3/lib/python3.7/site-packages/pandas/io/sql.py", line 577, in create
- self.pd_sql.drop_table(self.name, self.schema)
- File "/Users/skyxt/anaconda3/lib/python3.7/site-packages/pandas/io/sql.py", line 1566, in drop_table
- self.execute(drop_sql)
- File "/Users/skyxt/anaconda3/lib/python3.7/site-packages/pandas/io/sql.py", line 1445, in execute
- raise_with_traceback(ex)
- File "/Users/skyxt/anaconda3/lib/python3.7/site-packages/pandas/compat/__init__.py", line 420, in raise_with_traceback
- raise exc.with_traceback(traceback)
- File "/Users/skyxt/anaconda3/lib/python3.7/site-packages/pandas/io/sql.py", line 1431, in execute
- cur.execute(*args)
- pandas.io.sql.DatabaseError: Execution failed on sql 'DROP TABLE "sorted_A170618_Wang_PathwayCommons11_All_network_search_results"': database is locked
- Traceback (most recent call last):
- File "/Users/skyxt/anaconda3/lib/python3.7/site-packages/pandas/io/sql.py", line 1431, in execute
- cur.execute(*args)
- File "src/cursor.c", line 236, in resetcursor
- apsw.BusyError: BusyError: database is locked
- During handling of the above exception, another exception occurred:
- Traceback (most recent call last):
- File "/Users/skyxt/anaconda3/lib/python3.7/site-packages/pandas/io/sql.py", line 1435, in execute
- self.con.rollback()
- AttributeError: 'apsw.Connection' object has no attribute 'rollback'
- During handling of the above exception, another exception occurred:
- Traceback (most recent call last):
- File "/Users/skyxt/Google Drive/HKU_YANG_LAB/HKU_Academic_Issue/Python Learning/Python scripts/Database_related scripts/Compare_PID_causal_genes_sqlite.py", line 207, in <module>
- "/Users/skyxt/Google Drive/HKU_YANG_LAB/HKU_Academic_Issue/Project PID WES/Patients_Database")
- File "/Users/skyxt/Google Drive/HKU_YANG_LAB/HKU_Academic_Issue/Python Learning/Python scripts/Database_related scripts/Compare_PID_causal_genes_sqlite.py", line 37, in compare_causal
- patient_df.to_sql(name=patient_table, con=patient_connect, if_exists='replace')
- File "/Users/skyxt/anaconda3/lib/python3.7/site-packages/pandas/core/generic.py", line 2531, in to_sql
- dtype=dtype, method=method)
- File "/Users/skyxt/anaconda3/lib/python3.7/site-packages/pandas/io/sql.py", line 460, in to_sql
- chunksize=chunksize, dtype=dtype, method=method)
- File "/Users/skyxt/anaconda3/lib/python3.7/site-packages/pandas/io/sql.py", line 1546, in to_sql
- table.create()
- File "/Users/skyxt/anaconda3/lib/python3.7/site-packages/pandas/io/sql.py", line 577, in create
- self.pd_sql.drop_table(self.name, self.schema)
- File "/Users/skyxt/anaconda3/lib/python3.7/site-packages/pandas/io/sql.py", line 1566, in drop_table
- self.execute(drop_sql)
- File "/Users/skyxt/anaconda3/lib/python3.7/site-packages/pandas/io/sql.py", line 1440, in execute
- raise_with_traceback(ex)
- File "/Users/skyxt/anaconda3/lib/python3.7/site-packages/pandas/compat/__init__.py", line 420, in raise_with_traceback
- raise exc.with_traceback(traceback)
- File "/Users/skyxt/anaconda3/lib/python3.7/site-packages/pandas/io/sql.py", line 1435, in execute
- self.con.rollback()
- pandas.io.sql.DatabaseError: Execution failed on sql: DROP TABLE "sorted_A170618_Wang_PathwayCommons11_All_network_search_results"
- BusyError: database is locked
- unable to rollback
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