Merge pull request #174 from cgat-developers/JS-sqlalchemy

sqlalchemy 2.0 fix

cgatcore/database.py

@@ -45,6 +45,9 @@ def executewait(dbhandle, statement, regex_error="locked",
     while 1:
         try:
             cc = dbhandle.execute(statement)
+        except AttributeError:
+            with dbhandle.begin() as conn:
+                cc = conn.execute(sqlalchemy.text(statement))
         except Exception as msg:
             if retries == 0:
                 raise

cgatcore/experiment.py

@@ -482,7 +482,7 @@ def convert_value(self, opt, value):
     # they could be accessed as self.action and self.dest?
     def take_action(self, action, dest, opt, value, values, parser):
 
-        if action == "append" and type(value) == list:
+        if action == "append" and isinstance(value, list):
             values.ensure_value(dest, []).extend(value)
         else:
             optparse.Option.take_action(

cgatcore/iotools.py

@@ -1282,7 +1282,7 @@ def write_table(outfile, table, columns=None, fillvalue=""):
 
     '''
 
-    if type(table) == dict:
+    if isinstance(table, dict):
         if columns is None:
             columns = list(table.keys())
         outfile.write("\t".join(columns) + "\n")

cgatcore/pipeline/control.py

@@ -49,7 +49,7 @@
 from cgatcore.pipeline.parameters import input_validation, get_params, get_parameters
 from cgatcore.experiment import get_header, MultiLineFormatter
 from cgatcore.pipeline.utils import get_caller, get_caller_locals, is_test
-from cgatcore.pipeline.execution import execute, start_session,\
+from cgatcore.pipeline.execution import execute, start_session, \
     close_session
 
 

cgatcore/pipeline/parameters.py

@@ -510,7 +510,7 @@ def as_list(value):
     list
 
     '''
-    if type(value) == str:
+    if isinstance(value, str):
         try:
             values = [x.strip() for x in value.strip().split(",")]
         except AttributeError: