mats-sql-bundle / code /utils /db_utils.py
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Push code: scripts, slurm sbatch, recipes, utils (v3 + selector series)
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import os
import sqlite3
from pyserini.search.lucene import LuceneSearcher
import json
from func_timeout import func_set_timeout, FunctionTimedOut
import time
import multiprocessing
from multiprocessing.pool import ThreadPool
import requests
# get the database cursor for a sqlite database path
def get_cursor_from_path(sqlite_path):
try:
if not os.path.exists(sqlite_path):
print("Openning a new connection %s" % sqlite_path)
connection = sqlite3.connect(sqlite_path, check_same_thread = False)
except Exception as e:
print(sqlite_path)
raise e
connection.text_factory = lambda b: b.decode(errors="ignore")
cursor = connection.cursor()
return cursor
# execute predicted sql with a time limitation
@func_set_timeout(30)
def execute_sql(cursor, sql):
cursor.execute(sql)
return cursor.fetchall()
# execute predicted sql with a long time limitation (for buiding content index)
@func_set_timeout(2000)
def execute_sql_long_time_limitation(cursor, sql):
cursor.execute(sql)
return cursor.fetchall()
def check_sql_executability(generated_sql, db):
if not os.path.exists(db):
raise Exception("Database file not found: %s" % db)
connection = sqlite3.connect(db, check_same_thread = False)
connection.text_factory = lambda b: b.decode(errors="ignore")
cursor = connection.cursor()
if generated_sql.strip() == "":
return "Error: empty string"
try:
execute_sql(cursor, "EXPLAIN QUERY PLAN " + generated_sql)
execution_error = None
except FunctionTimedOut as fto:
print("SQL execution time out error: {}.".format(fto))
execution_error = "SQL execution times out."
except Exception as e:
# print("SQL execution runtime error: {}.".format(e))
execution_error = str(e)
cursor.close()
connection.close()
return execution_error
def is_number(s):
try:
float(s)
return True
except ValueError:
return False
def detect_special_char(name):
for special_char in ['(', '-', ')', ' ', '/']:
if special_char in name:
return True
return False
def add_quotation_mark(s):
return "`" + s + "`"
def get_column_contents(column_name, table_name, cursor):
select_column_sql = "SELECT DISTINCT `{}` FROM `{}` WHERE `{}` IS NOT NULL LIMIT 2;".format(column_name, table_name, column_name)
results = execute_sql_long_time_limitation(cursor, select_column_sql)
column_contents = [str(result[0]).strip() for result in results]
# remove empty and extremely-long contents
column_contents = [content for content in column_contents if len(content) != 0 and len(content) <= 25]
return column_contents
def get_db_schema_sequence(schema):
"""Build a CHESS-style DDL schema string with inline -- comments.
Each column line follows the format:
col_name TYPE, -- Example Values: `v1`, `v2` | Column Description: ... | Value Description: ...
Falls back gracefully when description fields are absent.
"""
schema_sequence = "database schema:\n"
for table in schema["schema_items"]:
table_name_raw = table["table_name"]
table_name = add_quotation_mark(table_name_raw) if detect_special_char(table_name_raw) else table_name_raw
column_defs = []
cols = zip(
table["column_names"],
table["column_types"],
table["column_comments"],
table["column_contents"],
table["pk_indicators"],
table.get("column_descriptions", [""] * len(table["column_names"])),
table.get("value_descriptions", [""] * len(table["column_names"])),
)
for col_name, col_type, col_comment, col_content, pk_indicator, col_desc, val_desc in cols:
display_name = add_quotation_mark(col_name) if detect_special_char(col_name) else col_name
type_str = col_type.upper() if col_type else "TEXT"
suffix = "," if True else "" # always add comma for DDL style
comment_parts = []
if col_content:
examples = ", ".join(f"`{v}`" for v in col_content[:3])
comment_parts.append(f"Example Values: {examples}")
if col_desc:
comment_parts.append(f"Column Description: {col_desc}")
elif col_comment:
comment_parts.append(f"Column Description: {col_comment}")
if val_desc:
comment_parts.append(f"Value Description: {val_desc}")
if pk_indicator != 0:
comment_parts.append("Primary Key")
if comment_parts:
column_defs.append(
f" {display_name} {type_str}, -- {' | '.join(comment_parts)}"
)
else:
column_defs.append(f" {display_name} {type_str},")
col_block = "\n".join(column_defs)
schema_sequence += f"CREATE TABLE {table_name}\n(\n{col_block}\n);\n"
if len(schema["foreign_keys"]) != 0:
schema_sequence += "-- Foreign keys:\n"
for foreign_key in schema["foreign_keys"]:
fk = [add_quotation_mark(p) if detect_special_char(p) else p for p in foreign_key]
schema_sequence += f"-- {fk[0]}.{fk[1]} = {fk[2]}.{fk[3]}\n"
return schema_sequence.strip()
def retrieve_most_similar_column_content(question, db_id, table_name, column_name):
# requests to retrieval api to get most similar column content
pass
def get_db_schema_sequence_with_matched_examples(schema, question):
schema_sequence = "database schema:\n"
for table in schema["schema_items"]:
table_name, table_comment = table["table_name"], table["table_comment"]
if detect_special_char(table_name):
table_name = add_quotation_mark(table_name)
# if table_comment != "":
# table_name += " ( comment : " + table_comment + " )"
column_info_list = []
for column_name, column_type, column_comment, pk_indicator in \
zip(table["column_names"], table["column_types"], table["column_comments"], table["pk_indicators"]):
if detect_special_char(column_name):
column_name = add_quotation_mark(column_name)
additional_column_info = []
# column type
# pk indicator
if pk_indicator != 0:
additional_column_info.append("primary key")
additional_column_info.append(f"type: {column_type}")
# column comment
if column_comment != "":
additional_column_info.append("meaning: " + column_comment)
# representive column values
if len(column_content) != 0:
additional_column_info.append("values: " + " , ".join(column_content))
column_info_list.append(column_name + " | " + " ; ".join(additional_column_info))
schema_sequence += "table "+ table_name + " , columns = [\n " + "\n ".join(column_info_list) + "\n]\n"
if len(schema["foreign_keys"]) != 0:
schema_sequence += "foreign keys:\n"
for foreign_key in schema["foreign_keys"]:
for i in range(len(foreign_key)):
if detect_special_char(foreign_key[i]):
foreign_key[i] = add_quotation_mark(foreign_key[i])
schema_sequence += "{}.{} = {}.{}\n".format(foreign_key[0], foreign_key[1], foreign_key[2], foreign_key[3])
else:
schema_sequence += "foreign keys: None\n"
return schema_sequence.strip()
def get_matched_content_sequence(matched_contents):
content_sequence = ""
if len(matched_contents) != 0:
content_sequence += "matched contents:\n"
for tc_name, contents in matched_contents.items():
table_name = tc_name.split(".")[0]
column_name = tc_name.split(".")[1]
if detect_special_char(table_name):
table_name = add_quotation_mark(table_name)
if detect_special_char(column_name):
column_name = add_quotation_mark(column_name)
content_sequence += table_name + "." + column_name + " ( " + " , ".join(contents) + " )\n"
else:
content_sequence = "matched contents: None"
return content_sequence.strip()
def get_most_similar_column_contents(args):
base_url, source, question, db_id, table_name, column_name = args
# base_url = "http://localhost:8005"
url = f"{base_url}/search_column_content"
payload = {
"source": source,
"db_id": db_id,
"table": table_name,
"column": column_name,
"query": question,
"k": 2
}
response = requests.post(url, json=payload)
if response.status_code == 200:
return response.json()["results"]
else:
print("No results: ", source, db_id, table_name, column_name)
return []
def get_db_schema(api_url, source, question, db_path, db_comments, db_id,
db_descriptions=None):
"""Build the schema dict for a database.
Args:
api_url: URL of the BM25 column-content retrieval service.
source: Dataset identifier ('bird', 'spider', …).
question: Natural-language question (used for BM25 retrieval).
db_path: Path to the SQLite file.
db_comments: Legacy tables.json comment dict {db_id: {table: …}}.
db_id: Database identifier string.
db_descriptions: Optional BIRD CSV descriptions loaded via
bird_csv_utils.load_db_descriptions(). When provided, each
schema item gets ``column_descriptions`` and
``value_descriptions`` lists for CHESS-style DDL rendering.
"""
if db_id in db_comments:
db_comment = db_comments[db_id]
else:
db_comment = None
cursor = get_cursor_from_path(db_path)
results = execute_sql(cursor, "SELECT name FROM sqlite_master WHERE type='table';")
table_names = [result[0].lower() for result in results]
schema = dict()
schema["schema_items"] = []
foreign_keys = []
for table_name in table_names:
if table_name == "sqlite_sequence":
continue
results = execute_sql(cursor, "SELECT name, type, pk FROM PRAGMA_TABLE_INFO('{}')".format(table_name))
column_names_in_one_table = [result[0].lower() for result in results]
column_types_in_one_table = [result[1].lower() for result in results]
pk_indicators_in_one_table = [result[2] for result in results]
with ThreadPool(processes=16) as pool:
column_contents = pool.map(
get_most_similar_column_contents,
[(api_url, source, question, db_id, table_name, col) for col in column_names_in_one_table],
)
results = execute_sql(cursor, "SELECT * FROM pragma_foreign_key_list('{}');".format(table_name))
for result in results:
if None not in [result[3], result[2], result[4]]:
foreign_keys.append([table_name.lower(), result[3].lower(), result[2].lower(), result[4].lower()])
if db_comment is not None:
if table_name in db_comment:
table_comment = db_comment[table_name]["table_comment"]
column_comments = [
db_comment[table_name]["column_comments"].get(col, "")
for col in column_names_in_one_table
]
else:
table_comment = ""
column_comments = ["" for _ in column_names_in_one_table]
else:
table_comment = ""
column_comments = ["" for _ in column_names_in_one_table]
has_none_indicators = []
for col in column_names_in_one_table:
cursor.execute(f"SELECT COUNT(*) FROM `{table_name}` WHERE `{col}` IS NULL")
count = cursor.fetchone()[0]
has_none_indicators.append(1 if count > 0 else 0)
# Enrich with BIRD CSV descriptions when available
table_csv = {}
if db_descriptions:
table_csv = db_descriptions.get(table_name, {})
column_descriptions = []
value_descriptions = []
for col in column_names_in_one_table:
col_info = table_csv.get(col, {})
column_descriptions.append(col_info.get("column_description", ""))
value_descriptions.append(col_info.get("value_description", ""))
schema["schema_items"].append({
"table_name": table_name,
"table_comment": table_comment,
"column_names": column_names_in_one_table,
"column_types": column_types_in_one_table,
"column_comments": column_comments,
"column_contents": column_contents,
"pk_indicators": pk_indicators_in_one_table,
"has_none_indicators": has_none_indicators,
"column_descriptions": column_descriptions,
"value_descriptions": value_descriptions,
})
schema["foreign_keys"] = foreign_keys
return schema