cocluto v1.0.27 - fixes bug in returned table of SshAccessedMysqlDb.query('select...') and SshAccessedMysqlDb.get_last_insert_id()

- splitted  ISqlDatabaseBackend.query() into ISqlDatabaseBackend.query() and the more specialized SqlDatabaseBackend.query_select ()
- this way the return type of query_select is explicit (a Table).
- it also allows robust sql query parsing (usin json).
- replaced calls to ISqlDatabaseBackend.query('select ...') with calls to ISqlDatabaseBackend.query_select()

work related to [https://bugzilla.ipr.univ-rennes.fr/show_bug.cgi?id=3093]

cocluto/SimpaDbUtil.py

@@ -1,6 +1,7 @@
-from typing import Union, List
+from typing import Union, List, Optional, Tuple
 from pathlib import Path
 from enum import Enum
+import json
 import logging
 import MySQLdb  # sudo port install py-mysql; sudo apt install python-mysqldb or pip install mysqlclient
 import time
@@ -43,6 +44,7 @@ def is_machine_responding(machineName):
 
 
 SqlQuery = str
+Table = List[Tuple]
 
 
 class SqlTableField():
@@ -68,6 +70,10 @@ class SqlTableField():
         self.is_autoinc_index = is_autoinc_index
 
 
+ColumnId = str  # eg 'matrix_size'
+TableId = str   # eg 'benchmark_results'
+
+
 class ISqlDatabaseBackend(object):
     def __init__(self):
         pass
@@ -79,6 +85,19 @@ class ISqlDatabaseBackend(object):
         """
         raise NotImplementedError()
 
+    def query_select(self, columns: List[ColumnId], table: TableId, where_clause: Optional[str] = None, join_clause: Optional[str] = None, distinct: bool = False) -> Table:
+        """
+        performs a select query on the sql database and returns the results in the form of a list of tuples (one tuple per row, tuple values are the column values)
+
+        :param List[ColumnId] columns: the columns to select
+        :param TableId table: the name of the table to query
+        :param Optional[str] where_clause: the where clause for the query, eg "matrix_size > 100"
+        :param Optional[str] join_clause: the join clause for the query, eg "disables ON log.id = disables.disable_request_id"
+        :param bool distinct: whether to return distinct rows
+        :return: the results of the query
+        """
+        raise NotImplementedError()
+
     @abc.abstractmethod
     def get_last_insert_id(self) -> int:
         """
@@ -142,10 +161,20 @@ class RemoteMysqlDb(ISqlDatabaseBackend):
         """
         :param str sql_query: the sql query to perform
         """
-        self._conn.query(sql_query)
+        cursor = self._conn.cursor()
-        rows = self._conn.store_result()
+        cursor.execute(sql_query)
+        rows = cursor.fetchall()
+        logging.debug("RemoteMysqlDb.query:: results of query using cursor '%s': %s", sql_query, rows)
         return rows
 
+    def query_select(self, columns: List[str], table: str, where_clause: Optional[str] = None, join_clause: Optional[str] = None, distinct: bool = False) -> Table:
+        sql_query = f"SELECT {('DISTINCT ' if distinct else '')}{', '.join(columns)} FROM {table}"
+        if join_clause:
+            sql_query += f" JOIN {join_clause}"
+        if where_clause:
+            sql_query += f" WHERE {where_clause}"
+        return self.query(sql_query)
+
     def get_last_insert_id(self) -> int:
         """
         :return: the id of the last inserted row
@@ -167,6 +196,26 @@ class RemoteMysqlDb(ISqlDatabaseBackend):
         raise NotImplementedError()
 
 
+def json_to_table(json_str: str) -> Table:
+    # logging.debug("json_to_table:: json_str = '%s'", json_str)
+    if json_str == 'NULL':
+        return []
+    try:
+        json_data = json.loads(json_str)
+    except json.JSONDecodeError:
+        logging.error("json_to_table:: invalid json string: '%s'", json_str)
+        raise
+    assert isinstance(json_data, list), f'Expected a list of rows in the json string but got {type(json_data)}'
+    table = []
+    for row in json_data:
+        values = []
+        for column_value in row.values():
+            assert isinstance(column_value, (str, int, float)), f'Expected a string, int or float value for each column value in the json string but got {type(column_value)}'
+            values.append(column_value)
+        table.append(tuple(values))
+    return table
+
+
 class SshAccessedMysqlDb(ISqlDatabaseBackend):
 
     """a mysql database server accessed using ssh instead of a remote mysql client
@@ -200,14 +249,58 @@ class SshAccessedMysqlDb(ISqlDatabaseBackend):
         if completed_process.returncode != 0:
             logging.error(completed_process.stderr.decode(encoding='utf-8'))
             assert False
-        rows = completed_process.stdout.decode('utf-8').split('\n')
+        stdout = completed_process.stdout.decode('utf-8')
+        logging.debug("SshAccessedMysqlDb.query:: results of query '%s': %s", sql_query, stdout)
+        rows = stdout.split('\n') if stdout != '' else []
+        logging.debug("SshAccessedMysqlDb.query:: split results of query '%s' by new lines: %s", sql_query, rows)
         return rows
 
+    def query_select(self, columns: List[str], table: str, where_clause: Optional[str] = None, join_clause: Optional[str] = None, distinct: bool = False) -> Table:
+        # MariaDB [quman]> SELECT JSON_ARRAYAGG(JSON_OBJECT('toto', timestamp, 'iddd', user_id)) FROM log;
+        # +-------------------------------------------------------------------------------------------------------+
+        # | JSON_ARRAYAGG(JSON_OBJECT('toto', timestamp, 'iddd', user_id))                                        |
+        # +-------------------------------------------------------------------------------------------------------+
+        # | [{"toto": "2026-05-21 15:11:58", "iddd": "graffy"},{"toto": "2026-05-22 15:55:39", "iddd": "graffy"}] |
+        # +-------------------------------------------------------------------------------------------------------+
+        # 1 row in set (0,006 sec)
+        # columns_list_str = ', '.join([f'"{col}"' for col in columns])
+        columns_list_str = ', '.join([f"'{col}', {col}" for col in columns])
+        columns_statement = f'JSON_ARRAYAGG(JSON_OBJECT({columns_list_str}))'
+        sql_query = f"SELECT {('DISTINCT ' if distinct else '')}{columns_statement} FROM {table}"
+        if join_clause:
+            sql_query += f" JOIN {join_clause}"
+        if where_clause:
+            sql_query += f" WHERE {where_clause}"
+        stdout = self.query(sql_query)
+        json_str = stdout[-2]  # eg '[{"queue_machine": "gpuonly.q@alambix104.ipr.univ-rennes1.fr"}]'
+        assert isinstance(json_str, str), f'Expected a string as data line in the query output but got {type(json_str)}'
+        logging.debug("SshAccessedMysqlDb.query_select:: data line of query '%s': '%s'", sql_query, json_str)
+        # match = re.match(r'^\s*(?P<json_data>{[^}]*})\s*$', data_line)
+        # assert match, 'Unexpected output format for query "%s" : %s' % (sql_query, stdout)
+        # json_data = json.loads(match.group('json_data'))
+
+        table = json_to_table(json_str)
+        return table
+
     def get_last_insert_id(self) -> int:
         """
         :return: the id of the last inserted row
         """
-        return int(self.query("SELECT last_insert_id();")[0][0])
+        # MariaDB [quman]> SELECT JSON_OBJECT('toto', last_insert_id());
+        # +---------------------------------------+
+        # | JSON_OBJECT('toto', last_insert_id()) |
+        # +---------------------------------------+
+        # | {"toto": 0}                           |
+        # +---------------------------------------+
+        # 1 row in set (0,002 sec)
+        stdout = self.query("SELECT JSON_OBJECT('toto', last_insert_id());")
+        data_line = stdout[-2]
+        match = re.match(r'^\s*(?P<json_data>{\s*"toto"\s*:\s*(\d+)\s*})\s*$', data_line)
+        assert match
+        json_data = json.loads(match.group('json_data'))
+        last_insert_id = int(json_data['toto'])
+        assert last_insert_id > 0, f'Unexpected last insert id : {last_insert_id}'
+        return last_insert_id
 
     def table_exists(self, table_name: str) -> bool:
         rows = self.query(f"SHOW TABLES LIKE '{table_name}';")
@@ -293,6 +386,14 @@ class SqliteDb(ISqlDatabaseBackend):
         self._con.commit()
         return rows
 
+    def query_select(self, columns: List[str], table: str, where_clause: Optional[str] = None, join_clause: Optional[str] = None, distinct: bool = False) -> Table:
+        sql_query = f"SELECT {('DISTINCT ' if distinct else '')}{', '.join(columns)} FROM {table}"
+        if join_clause:
+            sql_query += f" JOIN {join_clause}"
+        if where_clause:
+            sql_query += f" WHERE {where_clause}"
+        return self.query(sql_query)
+
     def get_last_insert_id(self) -> int:
         """
         :return: the id of the last inserted row

cocluto/quman.py

@@ -263,8 +263,7 @@ class QueueManager:
         return log_id
 
     def get_disable_requests(self, queue_machine: QueueMachineId) -> Dict[int, DisableRequest]:
-        sql_query = f"SELECT log.id, log.user_id, log.host_fqdn, log.queue_machines, log.reason, log.disable_id, log.timestamp FROM log JOIN disables ON log.id = disables.disable_request_id WHERE disables.queue_machine = '{queue_machine}' AND log.action = 'disable';"
+        results = self.db_backend.query_select(['log.id', 'log.user_id', 'log.host_fqdn', 'log.queue_machines', 'log.reason', 'log.disable_id', 'log.timestamp'], join_clause="disables ON log.id = disables.disable_request_id", table="log", where_clause=f"disables.queue_machine = '{queue_machine}' AND log.action = 'disable'")
-        results = self.db_backend.query(sql_query)
         disable_requests = []
         for row in results:
             log_id = row[0]
@@ -324,10 +323,10 @@ class QueueManager:
         qs = self.grid_engine.get_status()
 
         db_queues = set()
-        sql_query = "SELECT queue_machine FROM queues;"
+        results = self.db_backend.query_select(columns=["queue_machine"], table="queues")
-        results = self.db_backend.query(sql_query)
+        logging.debug("synchronize_with_grid_engine: results of query': %s", results)
         for row in results:
-            assert len(row) == 1, "Each row should have only one column (queue_machine)"
+            assert len(row) == 1, "Each row should have only one column (queue_machine) but got row='%s' (len=%d)" % (str(row), len(row))
             db_queues.add(row[0])
 
         for queue_machine, is_enabled in qs.is_enabled.items():
@@ -355,8 +354,7 @@ class QueueManager:
     def get_state(self) -> QueueDisableState:
         """returns the state of the queues."""
         # get the list of queue names from the disables table in the database
-        sql_query = "SELECT DISTINCT queue_machine FROM disables;"
+        results = self.db_backend.query_select(columns=["queue_machine"], table="disables", distinct=True)
-        results = self.db_backend.query(sql_query)
         for row in results:
             assert len(row) == 1, "Each row should have only one column (queue_machine)"
         queue_machines = [row[0] for row in results]

cocluto/version.py

@@ -1,4 +1,4 @@
-__version__ = '1.0.26'
+__version__ = '1.0.27'
 
 
 class Version(object):