internlm/SWE-Fixer-Train-110K huggingface dataset:
Repository: rucio/rucio

Issue:
throttler releases less requests than the available quota
Motivation
----------
```
conveyor-throttler[8b7233a:0/4]: limit to UKI-NORTHGRID-LANCS-HEP-CEPH_DATADISK activity Data rebalancing: can release 41853 out of 1628126 waiting requests. Account share:
 {ddmadmin: {'waiting': 1627436, 'active': 42723, 'residual_capacity': 0}, panda: {'waiting': 690, 'active': 15424, 'residual_capacity': 690}}
```
this is due to the code which splits the quota per account to achieve fair share




Discussion:

Resolving patch:
diff --git a/lib/rucio/daemons/conveyor/throttler.py b/lib/rucio/daemons/conveyor/throttler.py
--- a/lib/rucio/daemons/conveyor/throttler.py
+++ b/lib/rucio/daemons/conveyor/throttler.py
@@ -334,17 +334,11 @@ def _split_threshold_per_account(per_account_stats, total_to_release):
     nr_accounts = len(per_account_stats)
     remaining_to_release = total_to_release
     remaining_accounts = nr_accounts
-    for account, account_stat in sorted(per_account_stats.items(), key=lambda i: i[1]['active']):
+    for account, account_stat in sorted(per_account_stats.items(), key=lambda i: i[1]['waiting']):
         threshold_per_account = math.ceil(remaining_to_release / remaining_accounts)
 
         waiting = account_stat['waiting']
-        active = account_stat['active']
-        if active > threshold_per_account:
-            to_release_for_account = 0
-        elif active + waiting <= threshold_per_account:
-            to_release_for_account = waiting
-        else:
-            to_release_for_account = threshold_per_account - active
+        to_release_for_account = min(waiting, threshold_per_account)
 
         yield account, to_release_for_account
 


Test patch:
Repository: rucio/rucio

Issue:
remove traces endpoint from the default list in flask
Motivation
----------
By default, we activate the `traces` endpoint
https://github.com/rucio/rucio/blob/03f26f683d23fd4acbafac22465840b857e4bc10/lib/rucio/web/rest/flaskapi/v1/main.py#L48

but it expects quite some configuration and most people don't use it. 

Modification
------------
Remove the endpoint from the default list.




Discussion:

Resolving patch:
diff --git a/lib/rucio/web/rest/flaskapi/v1/main.py b/lib/rucio/web/rest/flaskapi/v1/main.py
--- a/lib/rucio/web/rest/flaskapi/v1/main.py
+++ b/lib/rucio/web/rest/flaskapi/v1/main.py
@@ -45,7 +45,6 @@
     'rules',
     'scopes',
     'subscriptions',
-    'traces',
 ]
 
 


Test patch:
Repository: rucio/rucio

Issue:
globus RSE protocol silently ignores errors
This will potentially result in dark data. 

To avoid this, just throw an exception which will be picked by reaper and skip removing the replicas 


Discussion:

Resolving patch:
diff --git a/lib/rucio/rse/protocols/globus.py b/lib/rucio/rse/protocols/globus.py
--- a/lib/rucio/rse/protocols/globus.py
+++ b/lib/rucio/rse/protocols/globus.py
@@ -198,13 +198,14 @@ def delete(self, path):
             try:
                 delete_response = send_delete_task(endpoint_id=self.globus_endpoint_id, path=path, logger=self.logger)
             except TransferAPIError as err:
-                print(err)
+                self.logger(logging.WARNING, str(err))
+                raise exception.RucioException(err)
         else:
-            print('No rse attribute found for globus endpoint id.')
+            raise exception.RucioException('No rse attribute found for globus endpoint id.')
 
         if delete_response['code'] != 'Accepted':
-            print('delete_task not accepted by Globus')
-            print('delete_response: %s' % delete_response)
+            self.logger(logging.DEBUG, 'delete_response: %s' % delete_response)
+            raise exception.RucioException('delete_task not accepted by Globus')
 
     def bulk_delete(self, pfns):
         """
@@ -218,13 +219,13 @@ def bulk_delete(self, pfns):
             try:
                 bulk_delete_response = send_bulk_delete_task(endpoint_id=self.globus_endpoint_id, pfns=pfns, logger=self.logger)
             except TransferAPIError as err:
-                self.logger(logging.WARNING, str(err))
+                raise exception.RucioException(err)
         else:
-            self.logger(logging.WARNING, 'No rse attribute found for globus endpoint id.')
+            raise exception.RucioException('No rse attribute found for globus endpoint id.')
 
         if bulk_delete_response['code'] != 'Accepted':
-            self.logger(logging.WARNING, 'delete_task not accepted by Globus')
-            self.logger(logging.WARNING, 'delete_response: %s' % bulk_delete_response)
+            self.logger(logging.DEBUG, 'delete_response: %s' % bulk_delete_response)
+            raise exception.RucioException('delete_task not accepted by Globus')
 
     def connect(self):
         """


Test patch:
Repository: rucio/rucio

Issue:
bad-str-strip-call errors in pylint
### Description

Pylint found 3 occurrences of E1310 bad-str-strip-call in the codebase.

### Steps to reproduce

1. run donkeyrider with `-d centos7 -s syntax --build`
2. examine output of `running pylint`

### Rucio Version

_No response_

### Additional Information

_No response_


Discussion:

Resolving patch:
diff --git a/lib/rucio/rse/protocols/rclone.py b/lib/rucio/rse/protocols/rclone.py
--- a/lib/rucio/rse/protocols/rclone.py
+++ b/lib/rucio/rse/protocols/rclone.py
@@ -195,7 +195,7 @@ def stat(self, path):
 
             if status_query == 0:
                 chsum = 'md5'
-                val = out.strip('  ').split()
+                val = out.strip(' ').split()
                 ret[chsum] = val[0]
 
         except Exception as e:
diff --git a/lib/rucio/rse/protocols/ssh.py b/lib/rucio/rse/protocols/ssh.py
--- a/lib/rucio/rse/protocols/ssh.py
+++ b/lib/rucio/rse/protocols/ssh.py
@@ -110,7 +110,7 @@ def stat(self, path):
 
             if status_query == 0:
                 chsum = 'md5'
-                val = out.strip('  ').split()
+                val = out.strip(' ').split()
                 ret[chsum] = val[0]
 
         except Exception as e:
@@ -324,7 +324,7 @@ def stat(self, path):
 
             if status_query == 0:
                 chsum = 'md5'
-                val = out.strip('  ').split()
+                val = out.strip(' ').split()
                 ret[chsum] = val[0]
 
         except Exception as e:


Test patch:
Repository: rucio/rucio

Issue:
temporary table attach_dids doesn't tolerate duplicate entries in children
This seems to be a change in behavioral change from the version without temporary tables:

```
DatabaseException in rucio.web.rest.flaskapi.v1.dids Attachment POST
Database exception.
Details: (cx_Oracle.IntegrityError) ORA-00001: unique constraint (ATLAS_RUCIO.TEMPORARY_SCOPE_NAME_0_PK) violated
[SQL: INSERT INTO atlas_rucio."TEMPORARY_SCOPE_NAME_0" (scope, name) VALUES (:scope, :name)]
[parameters: [{'scope': 'data22_13p6TeV', 'name': 'data22_13p6TeV.00440497.physics_Main.merge.AOD.f1321_m2153._lb0036._0001.1'}, {'scope': 'data22_13p6TeV', 'name': 'data22_13p6TeV.00440497.physics_Main.merge.AOD.f1321_m2153._lb0056._0001.1'}, {'scope': 'data22_13p6TeV', 'name': 'data22_13p6TeV.00440497.physics_Main.merge.AOD.f1321_m2153._lb0036._0001.1'}]]
```


Discussion:

Resolving patch:
diff --git a/lib/rucio/core/did.py b/lib/rucio/core/did.py
--- a/lib/rucio/core/did.py
+++ b/lib/rucio/core/did.py
@@ -328,7 +328,7 @@ def _attach_dids_to_dids(
             parent_did = session.execute(stmt).scalar_one()
             if not first_iteration:
                 session.query(children_temp_table).delete()
-            session.bulk_insert_mappings(children_temp_table, [{'scope': file['scope'], 'name': file['name']} for file in attachment['dids']])
+            session.bulk_insert_mappings(children_temp_table, [{'scope': s, 'name': n} for s, n in children])
 
             if parent_did.did_type == DIDType.FILE:
                 # check if parent file has the archive extension


Test patch:
Repository: rucio/rucio

Issue:
Use GFAL’s create_parent transfer parameter
Motivation
----------

The implementation here can be simplified:
https://github.com/rucio/rucio/blob/master/lib/rucio/rse/protocols/gfal.py#L398

*This should not be done until GFAL 2.16.4 reaches EPEL.*

Modification
------------

Do not make a separate call to GFAL to create the destination path. Use the `create_parent` transfer parameter instead.


Discussion:
2.18 now on EPEL; this can be done now; Possibly for summer student.
See #3681
that would be https://github.com/rucio/rucio/blob/d7e04cb2cd46aca683bb5372faf50ba158c8de26/lib/rucio/rse/protocols/gfal.py#L398

Resolving patch:
diff --git a/lib/rucio/rse/protocols/gfal.py b/lib/rucio/rse/protocols/gfal.py
--- a/lib/rucio/rse/protocols/gfal.py
+++ b/lib/rucio/rse/protocols/gfal.py
@@ -445,13 +445,8 @@ def __gfal2_copy(self, src, dest, src_spacetoken=None, dest_spacetoken=None, tra
             params.timeout = int(transfer_timeout)
             watchdog = Timer(params.timeout + 60, self.__gfal2_cancel)
 
-        if not (self.renaming and dest[:5] == 'https'):
-            dir_name = os.path.dirname(dest)
-            # This function will be removed soon. gfal2 will create parent dir automatically.
-            try:
-                ctx.mkdir_rec(str(dir_name), 0o775)
-            except:
-                pass
+        if not (self.renaming and dest.startswith('https')):
+            params.create_parent = True
 
         if not self.renaming:
             params.strict_copy = True


Test patch:
Repository: rucio/rucio

Issue:
cancelled job_state + failed file_state multi-source transfers never handled by poller
the issue is, again, in this state transition : 
https://github.com/rucio/rucio/blob/2b23466beec4372ae6ae25b1e3e2a69501788a27/lib/rucio/transfertool/fts3.py#L596

There were so many bugs already with it that I'm afraid to touch anything here :cry: 


Discussion:

Resolving patch:
diff --git a/lib/rucio/transfertool/fts3.py b/lib/rucio/transfertool/fts3.py
--- a/lib/rucio/transfertool/fts3.py
+++ b/lib/rucio/transfertool/fts3.py
@@ -593,7 +593,7 @@ def initialize(self, session, logger=logging.log):
         if file_state_is_final:
             if file_state == FTS_STATE.FINISHED:
                 new_state = RequestState.DONE
-            elif file_state == FTS_STATE.FAILED and job_state == FTS_STATE.FAILED or \
+            elif file_state == FTS_STATE.FAILED and job_state_is_final or \
                     file_state == FTS_STATE.FAILED and not self._multi_sources:  # for multi-source transfers we must wait for the job to be in a final state
                 if self._is_recoverable_fts_overwrite_error(self.request(session), reason, self._file_metadata):
                     new_state = RequestState.DONE


Test patch:
Repository: rucio/rucio

Issue:
move_rule does not convert account string to InternAccount type
### Description

An attempt to change the account of the rule in move_rule would result in HTTP 500:

The user gets:
```
rucio.common.exception.RucioException: An unknown exception occurred.
Details: no error information passed (HTTP status code: 500)
```
And we have the following stack trace in the server:
```
File "/usr/local/lib/python3.6/site-packages/rucio/core/rule.py", line 1603, in move_rule
    new_rule_id = add_rule(**options)
File "/usr/local/lib/python3.6/site-packages/rucio/db/sqla/session.py", line 444, in new_funct
    result = function(*args, session=session, **kwargs)
File "/usr/local/lib/python3.6/site-packages/rucio/core/rule.py", line 126, in add_rule
    vo = account.vo
AttributeError: 'str' object has no attribute 'vo'
```




### Steps to reproduce

1. Move the rule to a different account using the python client and set account attribute in the override dict
```
from rucio.client import client
rucio_client = Client()
......
.......
override = { "account" : "new_account" }
rucio_client.move_replication_rule(
                    rule_id = rule_id,
                    rse_expression = rse_expression,
                    override = override
                    )
```

### Rucio Version

_No response_

### Additional Information

The account is passed as a  string to the `add_rule` function. 
https://github.com/rucio/rucio/blob/ea4d2c7e2702b85a86a8668b2d852971f42fceb4/lib/rucio/core/rule.py#L1604-L1607

It needs to be converted into an `InternalAccount` type.


Discussion:

Resolving patch:
diff --git a/lib/rucio/api/rule.py b/lib/rucio/api/rule.py
--- a/lib/rucio/api/rule.py
+++ b/lib/rucio/api/rule.py
@@ -318,6 +318,9 @@ def move_replication_rule(rule_id, rse_expression, override, issuer, vo='def', *
     :param vo:                         The VO to act on.
     :raises:                           RuleNotFound, RuleReplaceFailed, InvalidRSEExpression, AccessDenied
     """
+    override = override.copy()
+    if 'account' in override:
+        override['account'] = InternalAccount(override['account'], vo=vo)
     kwargs = {
         'rule_id': rule_id,
         'rse_expression': rse_expression,


Test patch:
Repository: rucio/rucio

Issue:
Unused `key` parameter in post account attribute API
Motivation
----------
The `key` parameter in the path to post an account attribute is not used.
https://github.com/rucio/rucio/blob/d19db9eeb09440ae97477840fff57112f9b25620/lib/rucio/web/rest/flaskapi/v1/accounts.py#L72-L90

Modification
------------
Set the path parameter as default and override it with the json parameter if necessary.


Discussion:
Hi @joeldierkes  and @bari12 , can I work on this issue as a part of Google summer of code 2023 evaluation for Rucio project ?
Also the code which is being mentioned is not from master branch where their is a small difference default = key) is present (https://github.com/rucio/rucio/blob/ea4d2c7e2702b85a86a8668b2d852971f42fceb4/lib/rucio/web/rest/flaskapi/v1/accounts.py#L134). So, is this issue solved or there is still something that I can work with ? Thanks!

Resolving patch:
diff --git a/lib/rucio/web/rest/flaskapi/v1/accounts.py b/lib/rucio/web/rest/flaskapi/v1/accounts.py
--- a/lib/rucio/web/rest/flaskapi/v1/accounts.py
+++ b/lib/rucio/web/rest/flaskapi/v1/accounts.py
@@ -131,7 +131,6 @@ def post(self, account, key):
             description: Attribute already exists
         """
         parameters = json_parameters()
-        key = param_get(parameters, 'key', default=key)
         value = param_get(parameters, 'value')
         try:
             add_account_attribute(key=key, value=value, account=account, issuer=request.environ.get('issuer'), vo=request.environ.get('vo'))


Test patch:
Repository: rucio/rucio

Issue:
Keyword `type` gets overwritten
Motivation
----------
The keyword `type` in identities.py gets overwritten, this is a bad practice.
https://github.com/rucio/rucio/blob/1b68bbf6d44013b193db3f668b1e4b608e488bce/lib/rucio/web/rest/flaskapi/v1/identities.py#L134

Modification
------------
Use another variable name.
Keyword `type` gets overwritten
Motivation
----------
The keyword `type` in identities.py gets overwritten, this is a bad practice.
https://github.com/rucio/rucio/blob/1b68bbf6d44013b193db3f668b1e4b608e488bce/lib/rucio/web/rest/flaskapi/v1/identities.py#L134

Modification
------------
Use another variable name.


Discussion:
Should be replaced by `type_`
Should be replaced by `type_`

Resolving patch:
diff --git a/lib/rucio/web/rest/flaskapi/v1/identities.py b/lib/rucio/web/rest/flaskapi/v1/identities.py
--- a/lib/rucio/web/rest/flaskapi/v1/identities.py
+++ b/lib/rucio/web/rest/flaskapi/v1/identities.py
@@ -200,7 +200,7 @@ class Accounts(ErrorHandlingMethodView):
     """ Retrieve list of accounts mapped to an identity. """
 
     @check_accept_header_wrapper_flask(['application/json'])
-    def get(self, identity_key, type):
+    def get(self, identity_key, type_):
         """
         ---
         summary: List
@@ -236,7 +236,7 @@ def get(self, identity_key, type):
           401:
             description: Not acceptable
         """
-        accounts = list_accounts_for_identity(identity_key, type)
+        accounts = list_accounts_for_identity(identity_key, type_)
         return jsonify(accounts)
 
 


Test patch:
Repository: rucio/rucio

Issue:
Propagate the timeout parameter to gfal
### Description

When using the downloadclient, one can specify a timeout. This timeout is used by the watchdog to stop unresponsive transfers. But if the timeout is set to a large value, the download might first hits the gfal internal timeout. It would be better to have the same timeout for both.

### Motivation

_No response_

### Change

_No response_


Discussion:

Resolving patch:
diff --git a/lib/rucio/rse/protocols/gfal.py b/lib/rucio/rse/protocols/gfal.py
--- a/lib/rucio/rse/protocols/gfal.py
+++ b/lib/rucio/rse/protocols/gfal.py
@@ -436,14 +436,16 @@ def __gfal2_copy(self, src, dest, src_spacetoken=None, dest_spacetoken=None, tra
         :raises RucioException: if it failed to copy the file.
         """
         ctx = self.__ctx
+        if transfer_timeout:
+            ctx.set_opt_integer("HTTP PLUGIN", "OPERATION_TIMEOUT", transfer_timeout)
+            ctx.set_opt_integer("SRM PLUGIN", "OPERATION_TIMEOUT", transfer_timeout)
+            ctx.set_opt_integer("GRIDFTP PLUGIN", "OPERATION_TIMEOUT", transfer_timeout)
+            watchdog = Timer(int(transfer_timeout) + 60, self.__gfal2_cancel)
         params = ctx.transfer_parameters()
         if src_spacetoken:
             params.src_spacetoken = str(src_spacetoken)
         if dest_spacetoken:
             params.dst_spacetoken = str(dest_spacetoken)
-        if transfer_timeout:
-            params.timeout = int(transfer_timeout)
-            watchdog = Timer(params.timeout + 60, self.__gfal2_cancel)
 
         if not (self.renaming and dest.startswith('https')):
             params.create_parent = True
@@ -453,6 +455,7 @@ def __gfal2_copy(self, src, dest, src_spacetoken=None, dest_spacetoken=None, tra
 
         try:
             if transfer_timeout:
+                params.timeout = int(transfer_timeout)
                 watchdog.start()
             ret = ctx.filecopy(params, str(src), str(dest))
             if transfer_timeout:


Test patch:
Repository: rucio/rucio

Issue:
list_dids_by_meta function probably redundant 
Investigate the function https://github.com/rucio/rucio/blob/f9d52b7c7afbc1cfa41076f1d24f85299aa06cb8/bin/rucio#L1240 and the associated client one. Remove them if `list-dids` with the `filter` attribute can cover this use-case


Discussion:

Resolving patch:
diff --git a/lib/rucio/client/didclient.py b/lib/rucio/client/didclient.py
--- a/lib/rucio/client/didclient.py
+++ b/lib/rucio/client/didclient.py
@@ -14,7 +14,7 @@
 # limitations under the License.
 
 from datetime import datetime
-from json import dumps, loads
+from json import dumps
 
 from requests.status_codes import codes
 from urllib.parse import quote_plus
@@ -715,22 +715,3 @@ def list_archive_content(self, scope, name):
             return self._load_json_data(r)
         exc_cls, exc_msg = self._get_exception(headers=r.headers, status_code=r.status_code, data=r.content)
         raise exc_cls(exc_msg)
-
-    def list_dids_by_meta(self, scope=None, select={}):
-        """
-        Gets all dids matching the values of the provided metadata keys
-        :param scope: the scope of the search
-        :param select: the key value pairs to search with(query in json format)
-        """
-        path = '/'.join([self.DIDS_BASEURL, 'list_dids_by_meta'])
-        payload = {}
-        if scope is not None:
-            payload['scope'] = scope
-        payload['select'] = dumps(select)
-        url = build_url(choice(self.list_hosts), path=path, params=payload)
-        r = self._send_request(url, type_='GET')
-        if r.status_code == codes.ok:
-            return loads(next(self._load_json_data(r)))
-        else:
-            exc_cls, exc_msg = self._get_exception(headers=r.headers, status_code=r.status_code, data=r.content)
-            raise exc_cls(exc_msg)


Test patch:
Repository: rucio/rucio

Issue:
Use of bulk_insert_mappings in reaper causes issue with Hermes
### Description

The use of `bulk_insert_mappings` to the `Messages` table in the `delete_replicas` used by the `reaper` leads to empty `services` that can cause issue in `Hermes`

### Steps to reproduce

-

### Rucio Version

_No response_

### Additional Information

_No response_


Discussion:

Resolving patch:
diff --git a/lib/rucio/core/replica.py b/lib/rucio/core/replica.py
--- a/lib/rucio/core/replica.py
+++ b/lib/rucio/core/replica.py
@@ -47,6 +47,7 @@
 from rucio.common.constants import SuspiciousAvailability
 from rucio.core.credential import get_signed_url
 from rucio.core import config as config_core
+from rucio.core.message import add_messages
 from rucio.core.monitor import MetricManager
 from rucio.core.rse import get_rse, get_rse_name, get_rse_attribute, get_rse_vo, list_rses
 from rucio.core.rse_counter import decrease, increase
@@ -2149,7 +2150,7 @@ def __cleanup_after_replica_deletion(scope_name_temp_table, scope_name_temp_tabl
         session.execute(stmt)
 
     for chunk in chunks(messages, 100):
-        session.bulk_insert_mappings(models.Message, chunk)
+        add_messages(chunk, session=session)
 
     # Delete dids
     dids_to_delete_filter = exists(select(1)
@@ -2598,7 +2599,7 @@ def __cleanup_after_replica_deletion_without_temp_table(rse_id, files, *, sessio
             delete(synchronize_session=False)
 
     for chunk in chunks(messages, 100):
-        session.bulk_insert_mappings(models.Message, chunk)
+        add_messages(chunk, session=session)
 
     for chunk in chunks(deleted_dids, 100):
         stmt = delete(models.DataIdentifier).\


Test patch:
Repository: rucio/rucio

Issue:
incorrect availability filter direction in conveyor query
This filter is applied to the destination rse, so it should check availability_write

https://github.com/rucio/rucio/blob/a86e74e9a3ee45bf8ffd2c040dd1e2eb4e28ea17/lib/rucio/core/request.py#L429


Discussion:

Resolving patch:
diff --git a/lib/rucio/core/request.py b/lib/rucio/core/request.py
--- a/lib/rucio/core/request.py
+++ b/lib/rucio/core/request.py
@@ -426,7 +426,7 @@ def list_transfer_requests_and_source_replicas(
     )
 
     if not ignore_availability:
-        sub_requests = sub_requests.where(models.RSE.availability_read == true())
+        sub_requests = sub_requests.where(models.RSE.availability_write == true())
 
     if isinstance(older_than, datetime.datetime):
         sub_requests = sub_requests.where(models.Request.requested_at < older_than)


Test patch:
Repository: rucio/rucio

Issue:
incorrect distance logged in conveyor logs
All distances are shifted by 10 (the hop_penalty). This has absolutely no impact on the final outcome, because absolutely all paths get an additional +10. But this is confusing for people who try to investigate problems and see that numbers don't match. 


Discussion:

Resolving patch:
diff --git a/lib/rucio/core/topology.py b/lib/rucio/core/topology.py
--- a/lib/rucio/core/topology.py
+++ b/lib/rucio/core/topology.py
@@ -161,10 +161,12 @@ def search_shortest_paths(
                 if adjacent_node not in remaining_sources and adjacent_node not in self.multihop_rses:
                     continue
 
-                try:
-                    hop_penalty = int(self.rse_collection[adjacent_node].attributes.get('hop_penalty', HOP_PENALTY))
-                except ValueError:
-                    hop_penalty = HOP_PENALTY
+                hop_penalty = 0
+                if current_node != dest_rse_id:
+                    try:
+                        hop_penalty = int(self.rse_collection[current_node].attributes.get('hop_penalty', HOP_PENALTY))
+                    except ValueError:
+                        hop_penalty = HOP_PENALTY
                 new_adjacent_distance = current_distance + link_distance + hop_penalty
                 if next_hop.get(adjacent_node, {}).get('cumulated_distance', 9999) <= new_adjacent_distance:
                     continue


Test patch: