Fix issues reported by flake8-bugbear

bioblend/_tests/TestGalaxyInvocations.py

@@ -53,7 +53,7 @@ def invocation_steps_by_order_index():
             invocation = self.gi.invocations.show_invocation(invocation_id)
             return dict((s["order_index"], s) for s in invocation["steps"])
 
-        for i in range(20):
+        for _ in range(20):
             if 2 in invocation_steps_by_order_index():
                 break
             time.sleep(.5)
@@ -64,7 +64,7 @@ def invocation_steps_by_order_index():
             self.gi.invocations.show_invocation_step(invocation_id, pause_step["id"])["action"])
         self.gi.invocations.run_invocation_step_action(invocation_id, pause_step["id"], action=True)
         self.assertTrue(self.gi.invocations.show_invocation_step(invocation_id, pause_step["id"])["action"])
-        for i in range(20):
+        for _ in range(20):
             invocation = self.gi.invocations.show_invocation(invocation_id)
             if invocation["state"] == "scheduled":
                 break

bioblend/_tests/TestGalaxyWorkflows.py

@@ -34,7 +34,7 @@ def invocation_steps_by_order_index():
             invocation = self.gi.workflows.show_invocation(workflow_id, invocation_id)
             return dict((s["order_index"], s) for s in invocation["steps"])
 
-        for i in range(20):
+        for _ in range(20):
             if 2 in invocation_steps_by_order_index():
                 break
             time.sleep(.5)
@@ -48,7 +48,7 @@ def invocation_steps_by_order_index():
             self.gi.workflows.show_invocation_step(workflow_id, invocation_id, pause_step["id"])["action"])
         self.gi.workflows.run_invocation_step_action(workflow_id, invocation_id, pause_step["id"], action=True)
         self.assertTrue(self.gi.workflows.show_invocation_step(workflow_id, invocation_id, pause_step["id"])["action"])
-        for i in range(20):
+        for _ in range(20):
             invocation = self.gi.workflows.show_invocation(workflow_id, invocation_id)
             if invocation["state"] == "scheduled":
                 break

bioblend/cloudman/__init__.py

@@ -73,7 +73,7 @@ def __init__(self,
                  galaxy_data_option='',
                  initial_storage_size=10,
                  key_name='cloudman_key_pair',
-                 security_groups=['CloudMan'],
+                 security_groups=None,
                  placement='',
                  kernel_id=None,
                  ramdisk_id=None,
@@ -160,6 +160,8 @@ def __init__(self,
                                  extra parameters to the ``CloudManInstance.launch_instance``
                                  method.
         """
+        if security_groups is None:
+            security_groups = ['CloudMan']
         self.set_connection_parameters(access_key, secret_key, cloud_metadata)
         self.set_pre_launch_parameters(
             cluster_name, image_id, instance_type,
@@ -176,8 +178,9 @@ def set_connection_parameters(self, access_key, secret_key, cloud_metadata=None)
     def set_pre_launch_parameters(
             self, cluster_name, image_id, instance_type, password,
             kernel_id=None, ramdisk_id=None, key_name='cloudman_key_pair',
-            security_groups=['CloudMan'], placement='',
-            block_until_ready=False):
+            security_groups=None, placement='', block_until_ready=False):
+        if security_groups is None:
+            security_groups = ['CloudMan']
         self.cluster_name = cluster_name
         self.image_id = image_id
         self.instance_type = instance_type
@@ -711,14 +714,16 @@ def terminate(self, terminate_master_instance=True, delete_cluster=False):
                                         timeout=15)
         return result
 
-    def _make_get_request(self, url, parameters={}, timeout=None):
+    def _make_get_request(self, url, parameters=None, timeout=None):
         """
         Private function that makes a GET request to the nominated ``url``,
         with the provided GET ``parameters``. Optionally, set the ``timeout``
         to stop waiting for a response after a given number of seconds. This is
         particularly useful when terminating a cluster as it may terminate
         before sending a response.
         """
+        if parameters is None:
+            parameters = {}
         req_url = '/'.join((self.cloudman_url, 'root', url))
         r = requests.get(req_url, params=parameters, auth=("", self.password), timeout=timeout)
         try:

bioblend/cloudman/launch.py

@@ -117,7 +117,7 @@ def __repr__(self):
 
     def launch(self, cluster_name, image_id, instance_type, password,
                kernel_id=None, ramdisk_id=None, key_name='cloudman_key_pair',
-               security_groups=['CloudMan'], placement='', subnet_id=None,
+               security_groups=None, placement='', subnet_id=None,
                ebs_optimized=False, **kwargs):
         """
         Check all the prerequisites (key pair and security groups) for
@@ -139,6 +139,8 @@ def launch(self, cluster_name, image_id, instance_type, password,
         ``instance_id`` containing the ID of a started instance, and
         ``error`` containing an error message if there was one.
         """
+        if security_groups is None:
+            security_groups = ['CloudMan']
         ret = {'sg_names': [],
                'sg_ids': [],
                'kp_name': '',
@@ -215,7 +217,7 @@ def launch(self, cluster_name, image_id, instance_type, password,
             ret['rs'] = rs
         except EC2ResponseError as e:
             err_msg = "Problem launching an instance: {0} (code {1}; status {2})" \
-                      .format(e.message, e.error_code, e.status)
+                      .format(str(e), e.error_code, e.status)
             bioblend.log.exception(err_msg)
             ret['error'] = err_msg
             return ret
@@ -228,7 +230,7 @@ def launch(self, cluster_name, image_id, instance_type, password,
                 except EC2ResponseError as e:
                     err_msg = "Problem with the launched instance object: {0} " \
                               "(code {1}; status {2})" \
-                              .format(e.message, e.error_code, e.status)
+                              .format(str(e), e.error_code, e.status)
                     bioblend.log.exception(err_msg)
                     ret['error'] = err_msg
             else:
@@ -281,7 +283,7 @@ def create_cm_security_group(self, sg_name='CloudMan', vpc_id=None):
             err_msg = ("Problem getting security groups. This could indicate a "
                        "problem with your account credentials or permissions: "
                        "{0} (code {1}; status {2})"
-                       .format(e.message, e.error_code, e.status))
+                       .format(str(e), e.error_code, e.status))
             bioblend.log.exception(err_msg)
             progress['error'] = err_msg
             return progress
@@ -300,7 +302,7 @@ def create_cm_security_group(self, sg_name='CloudMan', vpc_id=None):
             except EC2ResponseError as e:
                 err_msg = "Problem creating security group '{0}': {1} (code {2}; " \
                           "status {3})" \
-                          .format(sg_name, e.message, e.error_code, e.status)
+                          .format(sg_name, str(e), e.error_code, e.status)
                 bioblend.log.exception(err_msg)
                 progress['error'] = err_msg
         if cmsg:
@@ -322,7 +324,7 @@ def create_cm_security_group(self, sg_name='CloudMan', vpc_id=None):
                 except EC2ResponseError as e:
                     err_msg = "A problem adding security group authorizations: {0} " \
                               "(code {1}; status {2})" \
-                              .format(e.message, e.error_code, e.status)
+                              .format(str(e), e.error_code, e.status)
                     bioblend.log.exception(err_msg)
                     progress['error'] = err_msg
             # Add ICMP (i.e., ping) rule required by HTCondor
@@ -340,7 +342,7 @@ def create_cm_security_group(self, sg_name='CloudMan', vpc_id=None):
             except EC2ResponseError as e:
                 err_msg = "A problem with security ICMP rule authorization: {0} " \
                           "(code {1}; status {2})" \
-                          .format(e.message, e.error_code, e.status)
+                          .format(str(e), e.error_code, e.status)
                 bioblend.log.exception(err_msg)
                 progress['err_msg'] = err_msg
             # Add rule that allows communication between instances in the same
@@ -365,7 +367,7 @@ def create_cm_security_group(self, sg_name='CloudMan', vpc_id=None):
                 except EC2ResponseError as e:
                     err_msg = "A problem with security group group " \
                               "authorization: {0} (code {1}; status {2})" \
-                              .format(e.message, e.error_code, e.status)
+                              .format(str(e), e.error_code, e.status)
                     bioblend.log.exception(err_msg)
                     progress['err_msg'] = err_msg
             bioblend.log.info("Done configuring '%s' security group", cmsg.name)
@@ -414,7 +416,7 @@ def create_key_pair(self, key_name='cloudman_key_pair'):
             kps = self.ec2_conn.get_all_key_pairs()
         except EC2ResponseError as e:
             err_msg = "Problem getting key pairs: {0} (code {1}; status {2})" \
-                      .format(e.message, e.error_code, e.status)
+                      .format(str(e), e.error_code, e.status)
             bioblend.log.exception(err_msg)
             progress['error'] = err_msg
             return progress
@@ -427,7 +429,7 @@ def create_key_pair(self, key_name='cloudman_key_pair'):
             kp = self.ec2_conn.create_key_pair(key_name)
         except EC2ResponseError as e:
             err_msg = "Problem creating key pair '{0}': {1} (code {2}; status {3})" \
-                      .format(key_name, e.message, e.error_code, e.status)
+                      .format(key_name, str(e), e.error_code, e.status)
             bioblend.log.exception(err_msg)
             progress['error'] = err_msg
             return progress

bioblend/galaxy/dataset_collections/__init__.py

@@ -1,6 +1,6 @@
 class HasElements(object):
 
-    def __init__(self, name, type="list", elements=[]):
+    def __init__(self, name, type="list", elements=None):
         self.name = name
         self.type = type
         if isinstance(elements, dict):

bioblend/galaxy/groups/__init__.py

@@ -49,7 +49,7 @@ def show_group(self, group_id):
         """
         return self._get(id=group_id)
 
-    def create_group(self, group_name, user_ids=[], role_ids=[]):
+    def create_group(self, group_name, user_ids=None, role_ids=None):
         """
         Create a new group.
 
@@ -71,14 +71,18 @@ def create_group(self, group_name, user_ids=[], role_ids=[]):
               'name': 'My Group Name',
               'url': '/api/groups/7c9636938c3e83bf'}]
         """
+        if user_ids is None:
+            user_ids = []
+        if role_ids is None:
+            role_ids = []
         payload = {
             'name': group_name,
             'user_ids': user_ids,
             'role_ids': role_ids
         }
         return self._post(payload)
 
-    def update_group(self, group_id, group_name=None, user_ids=[], role_ids=[]):
+    def update_group(self, group_id, group_name=None, user_ids=None, role_ids=None):
         """
         Update a group.
 
@@ -100,6 +104,10 @@ def update_group(self, group_id, group_name=None, user_ids=[], role_ids=[]):
         :rtype: None
         :return: None
         """
+        if user_ids is None:
+            user_ids = []
+        if role_ids is None:
+            role_ids = []
         payload = {
             'name': group_name,
             'user_ids': user_ids,

bioblend/galaxy/quotas/__init__.py

@@ -60,7 +60,7 @@ def show_quota(self, quota_id, deleted=False):
         return self._get(id=quota_id, deleted=deleted)
 
     def create_quota(self, name, description, amount, operation,
-                     default='no', in_users=[], in_groups=[]):
+                     default='no', in_users=None, in_groups=None):
         """
         Create a new quota
 
@@ -113,7 +113,7 @@ def create_quota(self, name, description, amount, operation,
         return self._post(payload)
 
     def update_quota(self, quota_id, name=None, description=None, amount=None, operation=None,
-                     default='no', in_users=[], in_groups=[]):
+                     default='no', in_users=None, in_groups=None):
         """
         Update an existing quota
 

bioblend/galaxy/roles/__init__.py

@@ -49,7 +49,7 @@ def show_role(self, role_id):
         """
         return self._get(id=role_id)
 
-    def create_role(self, role_name, description, user_ids=[], group_ids=[]):
+    def create_role(self, role_name, description, user_ids=None, group_ids=None):
         """
         Create a new role.
 
@@ -76,6 +76,10 @@ def create_role(self, role_name, description, user_ids=[], group_ids=[]):
               'id': 'ebfb8f50c6abde6d',
               'name': 'Foo'}]
         """
+        if user_ids is None:
+            user_ids = []
+        if group_ids is None:
+            group_ids = []
         payload = {
             'name': role_name,
             'description': description,

docs/examples/objects/w5_galaxy_api.py

@@ -57,7 +57,7 @@
 
 # Select the blastn step
 
-ws = [_ for _ in iw_details['steps'].itervalues()
+ws = [_ for _ in iw_details['steps'].values()
       if _['tool_id'] and 'blastn' in _['tool_id']]
 assert len(ws) == 1
 ws = ws[0]
@@ -66,7 +66,7 @@
 # Get (a copy of) the parameters dict for the selected step
 
 ws_parameters = ws['tool_inputs'].copy()
-for k, v in ws_parameters.iteritems():
+for k, v in ws_parameters.items():
     ws_parameters[k] = json.loads(v)
 
 # Run the workflow on a new history with the selected dataset

tox.ini

@@ -8,6 +8,7 @@ commands =
 deps =
     flake8: flake8
     flake8: flake8-import-order>=0.9
+    flake8: flake8-bugbear
     py{35,36,37,38}: pytest
 passenv =
     py{35,36,37,38}: BIOBLEND_GALAXY_API_KEY BIOBLEND_GALAXY_MASTER_API_KEY BIOBLEND_GALAXY_URL BIOBLEND_GALAXY_USER_EMAIL BIOBLEND_TEST_JOB_TIMEOUT GALAXY_VERSION