We are currently solving the following issue within our repository. Here is the issue text:
--- BEGIN ISSUE ---
Enable management command to fix file issues on published resource
Currently, running `repair_resource` on published resources will fail.

Reproduce by:
* Create a resource and add some files
* Use the database or shell to remove some of the files from django to put the resource in a "broken" state
* Publish the resource
* Run the repair_resource --published management command and see that the published resource cannot be fixed by this script

**Additional context**
HS v2.11.3


--- END ISSUE ---

Below are some code segments, each from a relevant file. One or more of these files may contain bugs.
--- BEGIN FILES ---
Path: `hs_core/management/commands/repair_resource.py`
Content:
```
1 # -*- coding: utf-8 -*-
2 
3 """
4 Check synchronization between iRODS and Django for multiple resources
5 
6 This checks that:
7 
8 1. every ResourceFile corresponds to an iRODS file
9 2. every iRODS file in {short_id}/data/contents corresponds to a ResourceFile
10 3. every iRODS directory {short_id} corresponds to a Django resource
11 """
12 
13 from django.core.management.base import BaseCommand, CommandError
14 from hs_core.models import BaseResource
15 from hs_core.management.utils import repair_resource
16 from hs_core.views.utils import get_default_admin_user
17 from hs_core import hydroshare
18 from django.utils import timezone
19 from django.db.models import F
20 from datetime import timedelta
21 
22 import logging
23 
24 
25 class Command(BaseCommand):
26     help = "Check synchronization between iRODS and Django."
27 
28     def add_arguments(self, parser):
29         parser.add_argument('resource_ids', nargs='*', type=str)
30         parser.add_argument('--days', type=int, dest='days', help='include resources updated in the last X days')
31         parser.add_argument(
32             '--admin',
33             action='store_true',  # True for presence, False for absence
34             dest='admin',  # value is options['dry_run']
35             help='run process as admin user - this allows published resources to be modified',
36         )
37         parser.add_argument(
38             '--dryrun',
39             action='store_true',  # True for presence, False for absence
40             dest='dry_run',  # value is options['dry_run']
41             help='run process without saving changes',
42         )
43         parser.add_argument(
44             '--published',
45             action='store_true',  # True for presence, False for absence
46             dest='published',  # value is options['published']
47             help='filter to just published resources',
48         )
49 
50     def handle(self, *args, **options):
51         logger = logging.getLogger(__name__)
52         resources_ids = options['resource_ids']
53         resources = BaseResource.objects.all()
54         days = options['days']
55         admin = options['admin']
56         dry_run = options['dry_run']
57         published = options['published']
58         site_url = hydroshare.utils.current_site_url()
59 
60         if resources_ids:  # an array of resource short_id to check.
61             print("CHECKING RESOURCES PROVIDED")
62             resources = resources.filter(short_id__in=resources_ids)
63         if published:
64             if not dry_run:
65                 print("WARNING: Executing with --published arg without --dryrun. Published resources will be modified.")
66             print("FILTERING TO INCLUDE PUBLISHED RESOURCES ONLY")
67             resources = resources.filter(raccess__published=True)
68 
69         if days:
70             print(f"FILTERING TO INCLUDE RESOURCES UPDATED IN LAST {days} DAYS")
71             if resources_ids:
72                 print("Your supplied resource_ids will be filtered by the --days that you provided. ")
73             cuttoff_time = timezone.now() - timedelta(days)
74             resources = resources.filter(updated__gte=cuttoff_time)
75 
76         if dry_run:
77             print("CONDUCTING A DRY RUN: FIXES WILL NOT BE SAVED")
78 
79         if not resources:
80             print("NO RESOURCES FOUND MATCHING YOUR FILTER ARGUMENTS")
81             return
82 
83         if admin:
84             print("PROCESSES WILL BE RUN AS ADMIN USER. ALLOWS DELETING DJANGO RESOURCE FILES ON PUBLISHED RESOURCES")
85             user = get_default_admin_user()
86         else:
87             user = None
88 
89         resources = resources.order_by(F('updated').asc(nulls_first=True))
90 
91         total_res_to_check = resources.count()
92         current_resource = 0
93         impacted_resources = 0
94         total_files_missing_in_django = 0
95         total_files_dangling_in_django = 0
96         resources_with_missing_django = []
97         resources_with_missing_irods = []
98         for resource in resources.iterator():
99             current_resource += 1
100             res_url = site_url + resource.absolute_url
101             print("*" * 100)
102             print(f"{current_resource}/{total_res_to_check}: Checking resource {res_url}")
103             if resource.raccess.published:
104                 print("This Resource is published")
105                 if admin:
106                     print("Command running with --admin. Published resources will be repaired if needed.")
107                 else:
108                     print("Command running without --admin. Fixing a published resource raise ValidationError")
109             _, missing_in_django, dangling_in_django = repair_resource(resource, logger, dry_run=dry_run, user=user)
110             if dangling_in_django > 0 or missing_in_django > 0:
111                 impacted_resources += 1
112                 total_files_missing_in_django += missing_in_django
113                 total_files_dangling_in_django += dangling_in_django
114                 if missing_in_django > 0:
115                     resources_with_missing_django.append(res_url)
116                 if dangling_in_django > 0:
117                     resources_with_missing_irods.append(res_url)
118                 print(f"{dangling_in_django} files dangling in Django for this resource.")
119                 print(f"{missing_in_django} files missing in Django for this resource.")
120                 print(f"Resources thus far with at least one missing django file: {len(resources_with_missing_django)}")
121                 print(f"Resources thus far with at least one dangling django file: {len(resources_with_missing_irods)}")
122                 print(f"Total resources with discrepancies thus far: {impacted_resources}")
123         print("*" * 100)
124         print("*" * 100)
125         print(f"Number of resources that had at least one file issue: {impacted_resources}")
126 
127         print("*" * 100)
128         print(f"Total number of files missing in Django (across all checked resources): \
129               {total_files_missing_in_django}")
130         print(f"Number of resources with at least one missing django file: {len(resources_with_missing_django)}")
131         for res in resources_with_missing_django:
132             print(res)
133 
134         print("*" * 100)
135         print(f"Total number of files dangling in Django (across all checked resources): \
136               {total_files_dangling_in_django}")
137         print(f"Number of resources with at least one dangling Django file: {len(resources_with_missing_irods)}")
138         for res in resources_with_missing_irods:
139             print(res)
140 
141         # Make it simple to detect clean/fail run in Jenkins
142         if impacted_resources:
143             raise CommandError("repair_resources detected problems")
144         else:
145             print("Completed run without detecting issues")
146
```
--- END FILES ---

Please first localize the bug based on the issue statement, and then generate a patch according to the `git diff` format fenced by three backticks.

Here is an example:

```diff
diff --git a/examples/server_async.py b/examples/server_async.py
--- a/examples/server_async.py
+++ b/examples/server_async.py
@@ -313,4 +313,4 @@
 
 
 if __name__ == "__main__":
-    asyncio.run(run_async_server("."), debug=True)
+    asyncio.run(run_async_server(), debug=True)
diff --git a/examples/server_sync.py b/examples/server_sync.py
--- a/examples/server_sync.py
+++ b/examples/server_sync.py
@@ -313,5 +313,5 @@
 
 
 if __name__ == "__main__":
-    server = run_sync_server(".")
+    server = run_sync_server()
     server.shutdown()

```

diff --git a/hs_core/management/commands/repair_resource.py b/hs_core/management/commands/repair_resource.py
--- a/hs_core/management/commands/repair_resource.py
+++ b/hs_core/management/commands/repair_resource.py
@@ -11,6 +11,7 @@
 """
 
 from django.core.management.base import BaseCommand, CommandError
+from django.core.exceptions import ValidationError
 from hs_core.models import BaseResource
 from hs_core.management.utils import repair_resource
 from hs_core.views.utils import get_default_admin_user
@@ -95,6 +96,7 @@
         total_files_dangling_in_django = 0
         resources_with_missing_django = []
         resources_with_missing_irods = []
+        failed_resources = []
         for resource in resources.iterator():
             current_resource += 1
             res_url = site_url + resource.absolute_url
@@ -106,7 +108,13 @@
                     print("Command running with --admin. Published resources will be repaired if needed.")
                 else:
                     print("Command running without --admin. Fixing a published resource raise ValidationError")
-            _, missing_in_django, dangling_in_django = repair_resource(resource, logger, dry_run=dry_run, user=user)
+            try:
+                _, missing_in_django, dangling_in_django = repair_resource(resource, logger, dry_run=dry_run, user=user)
+            except ValidationError as ve:
+                failed_resources.append(res_url)
+                print("Exception while attempting to repair resource:")
+                print(ve)
+                continue
             if dangling_in_django > 0 or missing_in_django > 0:
                 impacted_resources += 1
                 total_files_missing_in_django += missing_in_django
@@ -139,7 +147,13 @@
             print(res)
 
         # Make it simple to detect clean/fail run in Jenkins
-        if impacted_resources:
-            raise CommandError("repair_resources detected problems")
+        if impacted_resources and dry_run:
+            raise CommandError("repair_resources detected resources in need of repair during dry run")
         else:
-            print("Completed run without detecting issues")
+            print("Completed run of repair_resource")
+        if failed_resources:
+            print("*" * 100)
+            print("Repair was attempted but failed for the following resources:")
+            for res in resources_with_missing_irods:
+                print(res)
+            raise CommandError("Repair was attempted but failed on at least one resource")

{"golden_diff": "diff --git a/hs_core/management/commands/repair_resource.py b/hs_core/management/commands/repair_resource.py\n--- a/hs_core/management/commands/repair_resource.py\n+++ b/hs_core/management/commands/repair_resource.py\n@@ -11,6 +11,7 @@\n \"\"\"\n \n from django.core.management.base import BaseCommand, CommandError\n+from django.core.exceptions import ValidationError\n from hs_core.models import BaseResource\n from hs_core.management.utils import repair_resource\n from hs_core.views.utils import get_default_admin_user\n@@ -95,6 +96,7 @@\n         total_files_dangling_in_django = 0\n         resources_with_missing_django = []\n         resources_with_missing_irods = []\n+        failed_resources = []\n         for resource in resources.iterator():\n             current_resource += 1\n             res_url = site_url + resource.absolute_url\n@@ -106,7 +108,13 @@\n                     print(\"Command running with --admin. Published resources will be repaired if needed.\")\n                 else:\n                     print(\"Command running without --admin. Fixing a published resource raise ValidationError\")\n-            _, missing_in_django, dangling_in_django = repair_resource(resource, logger, dry_run=dry_run, user=user)\n+            try:\n+                _, missing_in_django, dangling_in_django = repair_resource(resource, logger, dry_run=dry_run, user=user)\n+            except ValidationError as ve:\n+                failed_resources.append(res_url)\n+                print(\"Exception while attempting to repair resource:\")\n+                print(ve)\n+                continue\n             if dangling_in_django > 0 or missing_in_django > 0:\n                 impacted_resources += 1\n                 total_files_missing_in_django += missing_in_django\n@@ -139,7 +147,13 @@\n             print(res)\n \n         # Make it simple to detect clean/fail run in Jenkins\n-        if impacted_resources:\n-            raise CommandError(\"repair_resources detected problems\")\n+        if impacted_resources and dry_run:\n+            raise CommandError(\"repair_resources detected resources in need of repair during dry run\")\n         else:\n-            print(\"Completed run without detecting issues\")\n+            print(\"Completed run of repair_resource\")\n+        if failed_resources:\n+            print(\"*\" * 100)\n+            print(\"Repair was attempted but failed for the following resources:\")\n+            for res in resources_with_missing_irods:\n+                print(res)\n+            raise CommandError(\"Repair was attempted but failed on at least one resource\")\n", "issue": "Enable management command to fix file issues on published resource\nCurrently, running `repair_resource` on published resources will fail.\r\n\r\nReproduce by:\r\n* Create a resource and add some files\r\n* Use the database or shell to remove some of the files from django to put the resource in a \"broken\" state\r\n* Publish the resource\r\n* Run the repair_resource --published management command and see that the published resource cannot be fixed by this script\r\n\r\n**Additional context**\r\nHS v2.11.3\r\n\n", "before_files": [{"content": "# -*- coding: utf-8 -*-\n\n\"\"\"\nCheck synchronization between iRODS and Django for multiple resources\n\nThis checks that:\n\n1. every ResourceFile corresponds to an iRODS file\n2. every iRODS file in {short_id}/data/contents corresponds to a ResourceFile\n3. every iRODS directory {short_id} corresponds to a Django resource\n\"\"\"\n\nfrom django.core.management.base import BaseCommand, CommandError\nfrom hs_core.models import BaseResource\nfrom hs_core.management.utils import repair_resource\nfrom hs_core.views.utils import get_default_admin_user\nfrom hs_core import hydroshare\nfrom django.utils import timezone\nfrom django.db.models import F\nfrom datetime import timedelta\n\nimport logging\n\n\nclass Command(BaseCommand):\n    help = \"Check synchronization between iRODS and Django.\"\n\n    def add_arguments(self, parser):\n        parser.add_argument('resource_ids', nargs='*', type=str)\n        parser.add_argument('--days', type=int, dest='days', help='include resources updated in the last X days')\n        parser.add_argument(\n            '--admin',\n            action='store_true',  # True for presence, False for absence\n            dest='admin',  # value is options['dry_run']\n            help='run process as admin user - this allows published resources to be modified',\n        )\n        parser.add_argument(\n            '--dryrun',\n            action='store_true',  # True for presence, False for absence\n            dest='dry_run',  # value is options['dry_run']\n            help='run process without saving changes',\n        )\n        parser.add_argument(\n            '--published',\n            action='store_true',  # True for presence, False for absence\n            dest='published',  # value is options['published']\n            help='filter to just published resources',\n        )\n\n    def handle(self, *args, **options):\n        logger = logging.getLogger(__name__)\n        resources_ids = options['resource_ids']\n        resources = BaseResource.objects.all()\n        days = options['days']\n        admin = options['admin']\n        dry_run = options['dry_run']\n        published = options['published']\n        site_url = hydroshare.utils.current_site_url()\n\n        if resources_ids:  # an array of resource short_id to check.\n            print(\"CHECKING RESOURCES PROVIDED\")\n            resources = resources.filter(short_id__in=resources_ids)\n        if published:\n            if not dry_run:\n                print(\"WARNING: Executing with --published arg without --dryrun. Published resources will be modified.\")\n            print(\"FILTERING TO INCLUDE PUBLISHED RESOURCES ONLY\")\n            resources = resources.filter(raccess__published=True)\n\n        if days:\n            print(f\"FILTERING TO INCLUDE RESOURCES UPDATED IN LAST {days} DAYS\")\n            if resources_ids:\n                print(\"Your supplied resource_ids will be filtered by the --days that you provided. \")\n            cuttoff_time = timezone.now() - timedelta(days)\n            resources = resources.filter(updated__gte=cuttoff_time)\n\n        if dry_run:\n            print(\"CONDUCTING A DRY RUN: FIXES WILL NOT BE SAVED\")\n\n        if not resources:\n            print(\"NO RESOURCES FOUND MATCHING YOUR FILTER ARGUMENTS\")\n            return\n\n        if admin:\n            print(\"PROCESSES WILL BE RUN AS ADMIN USER. ALLOWS DELETING DJANGO RESOURCE FILES ON PUBLISHED RESOURCES\")\n            user = get_default_admin_user()\n        else:\n            user = None\n\n        resources = resources.order_by(F('updated').asc(nulls_first=True))\n\n        total_res_to_check = resources.count()\n        current_resource = 0\n        impacted_resources = 0\n        total_files_missing_in_django = 0\n        total_files_dangling_in_django = 0\n        resources_with_missing_django = []\n        resources_with_missing_irods = []\n        for resource in resources.iterator():\n            current_resource += 1\n            res_url = site_url + resource.absolute_url\n            print(\"*\" * 100)\n            print(f\"{current_resource}/{total_res_to_check}: Checking resource {res_url}\")\n            if resource.raccess.published:\n                print(\"This Resource is published\")\n                if admin:\n                    print(\"Command running with --admin. Published resources will be repaired if needed.\")\n                else:\n                    print(\"Command running without --admin. Fixing a published resource raise ValidationError\")\n            _, missing_in_django, dangling_in_django = repair_resource(resource, logger, dry_run=dry_run, user=user)\n            if dangling_in_django > 0 or missing_in_django > 0:\n                impacted_resources += 1\n                total_files_missing_in_django += missing_in_django\n                total_files_dangling_in_django += dangling_in_django\n                if missing_in_django > 0:\n                    resources_with_missing_django.append(res_url)\n                if dangling_in_django > 0:\n                    resources_with_missing_irods.append(res_url)\n                print(f\"{dangling_in_django} files dangling in Django for this resource.\")\n                print(f\"{missing_in_django} files missing in Django for this resource.\")\n                print(f\"Resources thus far with at least one missing django file: {len(resources_with_missing_django)}\")\n                print(f\"Resources thus far with at least one dangling django file: {len(resources_with_missing_irods)}\")\n                print(f\"Total resources with discrepancies thus far: {impacted_resources}\")\n        print(\"*\" * 100)\n        print(\"*\" * 100)\n        print(f\"Number of resources that had at least one file issue: {impacted_resources}\")\n\n        print(\"*\" * 100)\n        print(f\"Total number of files missing in Django (across all checked resources): \\\n              {total_files_missing_in_django}\")\n        print(f\"Number of resources with at least one missing django file: {len(resources_with_missing_django)}\")\n        for res in resources_with_missing_django:\n            print(res)\n\n        print(\"*\" * 100)\n        print(f\"Total number of files dangling in Django (across all checked resources): \\\n              {total_files_dangling_in_django}\")\n        print(f\"Number of resources with at least one dangling Django file: {len(resources_with_missing_irods)}\")\n        for res in resources_with_missing_irods:\n            print(res)\n\n        # Make it simple to detect clean/fail run in Jenkins\n        if impacted_resources:\n            raise CommandError(\"repair_resources detected problems\")\n        else:\n            print(\"Completed run without detecting issues\")\n", "path": "hs_core/management/commands/repair_resource.py"}], "after_files": [{"content": "# -*- coding: utf-8 -*-\n\n\"\"\"\nCheck synchronization between iRODS and Django for multiple resources\n\nThis checks that:\n\n1. every ResourceFile corresponds to an iRODS file\n2. every iRODS file in {short_id}/data/contents corresponds to a ResourceFile\n3. every iRODS directory {short_id} corresponds to a Django resource\n\"\"\"\n\nfrom django.core.management.base import BaseCommand, CommandError\nfrom django.core.exceptions import ValidationError\nfrom hs_core.models import BaseResource\nfrom hs_core.management.utils import repair_resource\nfrom hs_core.views.utils import get_default_admin_user\nfrom hs_core import hydroshare\nfrom django.utils import timezone\nfrom django.db.models import F\nfrom datetime import timedelta\n\nimport logging\n\n\nclass Command(BaseCommand):\n    help = \"Check synchronization between iRODS and Django.\"\n\n    def add_arguments(self, parser):\n        parser.add_argument('resource_ids', nargs='*', type=str)\n        parser.add_argument('--days', type=int, dest='days', help='include resources updated in the last X days')\n        parser.add_argument(\n            '--admin',\n            action='store_true',  # True for presence, False for absence\n            dest='admin',  # value is options['dry_run']\n            help='run process as admin user - this allows published resources to be modified',\n        )\n        parser.add_argument(\n            '--dryrun',\n            action='store_true',  # True for presence, False for absence\n            dest='dry_run',  # value is options['dry_run']\n            help='run process without saving changes',\n        )\n        parser.add_argument(\n            '--published',\n            action='store_true',  # True for presence, False for absence\n            dest='published',  # value is options['published']\n            help='filter to just published resources',\n        )\n\n    def handle(self, *args, **options):\n        logger = logging.getLogger(__name__)\n        resources_ids = options['resource_ids']\n        resources = BaseResource.objects.all()\n        days = options['days']\n        admin = options['admin']\n        dry_run = options['dry_run']\n        published = options['published']\n        site_url = hydroshare.utils.current_site_url()\n\n        if resources_ids:  # an array of resource short_id to check.\n            print(\"CHECKING RESOURCES PROVIDED\")\n            resources = resources.filter(short_id__in=resources_ids)\n        if published:\n            if not dry_run:\n                print(\"WARNING: Executing with --published arg without --dryrun. Published resources will be modified.\")\n            print(\"FILTERING TO INCLUDE PUBLISHED RESOURCES ONLY\")\n            resources = resources.filter(raccess__published=True)\n\n        if days:\n            print(f\"FILTERING TO INCLUDE RESOURCES UPDATED IN LAST {days} DAYS\")\n            if resources_ids:\n                print(\"Your supplied resource_ids will be filtered by the --days that you provided. \")\n            cuttoff_time = timezone.now() - timedelta(days)\n            resources = resources.filter(updated__gte=cuttoff_time)\n\n        if dry_run:\n            print(\"CONDUCTING A DRY RUN: FIXES WILL NOT BE SAVED\")\n\n        if not resources:\n            print(\"NO RESOURCES FOUND MATCHING YOUR FILTER ARGUMENTS\")\n            return\n\n        if admin:\n            print(\"PROCESSES WILL BE RUN AS ADMIN USER. ALLOWS DELETING DJANGO RESOURCE FILES ON PUBLISHED RESOURCES\")\n            user = get_default_admin_user()\n        else:\n            user = None\n\n        resources = resources.order_by(F('updated').asc(nulls_first=True))\n\n        total_res_to_check = resources.count()\n        current_resource = 0\n        impacted_resources = 0\n        total_files_missing_in_django = 0\n        total_files_dangling_in_django = 0\n        resources_with_missing_django = []\n        resources_with_missing_irods = []\n        failed_resources = []\n        for resource in resources.iterator():\n            current_resource += 1\n            res_url = site_url + resource.absolute_url\n            print(\"*\" * 100)\n            print(f\"{current_resource}/{total_res_to_check}: Checking resource {res_url}\")\n            if resource.raccess.published:\n                print(\"This Resource is published\")\n                if admin:\n                    print(\"Command running with --admin. Published resources will be repaired if needed.\")\n                else:\n                    print(\"Command running without --admin. Fixing a published resource raise ValidationError\")\n            try:\n                _, missing_in_django, dangling_in_django = repair_resource(resource, logger, dry_run=dry_run, user=user)\n            except ValidationError as ve:\n                failed_resources.append(res_url)\n                print(\"Exception while attempting to repair resource:\")\n                print(ve)\n                continue\n            if dangling_in_django > 0 or missing_in_django > 0:\n                impacted_resources += 1\n                total_files_missing_in_django += missing_in_django\n                total_files_dangling_in_django += dangling_in_django\n                if missing_in_django > 0:\n                    resources_with_missing_django.append(res_url)\n                if dangling_in_django > 0:\n                    resources_with_missing_irods.append(res_url)\n                print(f\"{dangling_in_django} files dangling in Django for this resource.\")\n                print(f\"{missing_in_django} files missing in Django for this resource.\")\n                print(f\"Resources thus far with at least one missing django file: {len(resources_with_missing_django)}\")\n                print(f\"Resources thus far with at least one dangling django file: {len(resources_with_missing_irods)}\")\n                print(f\"Total resources with discrepancies thus far: {impacted_resources}\")\n        print(\"*\" * 100)\n        print(\"*\" * 100)\n        print(f\"Number of resources that had at least one file issue: {impacted_resources}\")\n\n        print(\"*\" * 100)\n        print(f\"Total number of files missing in Django (across all checked resources): \\\n              {total_files_missing_in_django}\")\n        print(f\"Number of resources with at least one missing django file: {len(resources_with_missing_django)}\")\n        for res in resources_with_missing_django:\n            print(res)\n\n        print(\"*\" * 100)\n        print(f\"Total number of files dangling in Django (across all checked resources): \\\n              {total_files_dangling_in_django}\")\n        print(f\"Number of resources with at least one dangling Django file: {len(resources_with_missing_irods)}\")\n        for res in resources_with_missing_irods:\n            print(res)\n\n        # Make it simple to detect clean/fail run in Jenkins\n        if impacted_resources and dry_run:\n            raise CommandError(\"repair_resources detected resources in need of repair during dry run\")\n        else:\n            print(\"Completed run of repair_resource\")\n        if failed_resources:\n            print(\"*\" * 100)\n            print(\"Repair was attempted but failed for the following resources:\")\n            for res in resources_with_missing_irods:\n                print(res)\n            raise CommandError(\"Repair was attempted but failed on at least one resource\")\n", "path": "hs_core/management/commands/repair_resource.py"}]}