Merge pull request #3534 from OpenNeuroOrg/annex-fsck-tasks

nellh · web-flow · commit 37dc4dec8cbc · 2025-08-12T11:51:32.000-07:00
Add git-annex fsck checks for datasets
diff --git a/services/datalad/datalad_service/common/git.py b/services/datalad/datalad_service/common/git.py
@@ -10,6 +10,8 @@
 import pygit2
 from charset_normalizer import from_bytes
 
+from datalad_service.common.onchange import on_head
+
 tag_ref = re.compile('^refs/tags/')
 
 COMMITTER_NAME = 'Git Worker'
@@ -130,7 +132,7 @@ def git_rename_master_to_main(repo):
         repo.references['HEAD'].set_target('refs/heads/main')
 
 
-def git_commit(
+async def git_commit(
     repo, file_paths, author=None, message='[OpenNeuro] Recorded changes', parents=None
 ):
     """Commit array of paths at HEAD."""
@@ -161,10 +163,10 @@ def git_commit(
         sentry_sdk.capture_exception(e)
         logger.error(f'Failed to read index after git-annex add: {e}')
         raise OpenNeuroGitError(f'Failed to read index: {e}') from e
-    return git_commit_index(repo, author, message, parents)
+    return await git_commit_index(repo, author, message, parents)
 
 
-def git_commit_index(
+async def git_commit_index(
     repo, author=None, message='[OpenNeuro] Recorded changes', parents=None
 ):
     """Commit any existing index changes."""
@@ -180,4 +182,5 @@ def git_commit_index(
         'refs/heads/main', author, committer, message, tree, parent_commits
     )
     repo.head.set_target(commit)
+    await on_head(repo.workdir)
     return commit
diff --git a/services/datalad/datalad_service/common/onchange.py b/services/datalad/datalad_service/common/onchange.py
@@ -0,0 +1,11 @@
+from datalad_service.tasks.fsck import git_annex_fsck_local, git_annex_fsck_remote
+
+
+async def on_head(dataset_path):
+    """Called after any change to HEAD."""
+    await git_annex_fsck_local.kiq(dataset_path)
+
+
+async def on_tag(dataset_path, tag):
+    """Called after any new tag."""
+    await git_annex_fsck_remote.kiq(dataset_path, tag)
diff --git a/services/datalad/datalad_service/handlers/dataset.py b/services/datalad/datalad_service/handlers/dataset.py
@@ -41,7 +41,7 @@ async def on_post(self, req, resp, dataset):
                 author = pygit2.Signature(name, email)
             else:
                 author = None
-            hexsha = create_dataset(self.store, dataset, author)
+            hexsha = await create_dataset(self.store, dataset, author)
             resp.media = {'hexsha': hexsha}
             resp.status = falcon.HTTP_OK
 
diff --git a/services/datalad/datalad_service/handlers/draft.py b/services/datalad/datalad_service/handlers/draft.py
@@ -53,9 +53,9 @@ async def on_post(self, req, resp, dataset):
                 # Add all changes to the index
                 if name and email:
                     author = pygit2.Signature(name, email)
-                    media_dict['ref'] = str(git_commit(repo, ['.'], author))
+                    media_dict['ref'] = str(await git_commit(repo, ['.'], author))
                 else:
-                    media_dict['ref'] = str(git_commit(repo, ['.']))
+                    media_dict['ref'] = str(await git_commit(repo, ['.']))
                 resp.media = media_dict
                 resp.status = falcon.HTTP_OK
             except:
diff --git a/services/datalad/datalad_service/handlers/files.py b/services/datalad/datalad_service/handlers/files.py
@@ -6,7 +6,6 @@
 import pygit2
 
 from datalad_service.common.git import (
-    git_show,
     git_show_content,
     git_tree,
     OpenNeuroGitError,
@@ -125,7 +124,7 @@ async def on_delete(self, req, resp, dataset):
                     media_dict['email'] = email
                 try:
                     if len(dirs_to_delete) > 0:
-                        remove_files(
+                        await remove_files(
                             self.store,
                             dataset,
                             dirs_to_delete,
@@ -135,7 +134,7 @@ async def on_delete(self, req, resp, dataset):
                         )
                         resp.status = falcon.HTTP_INTERNAL_SERVER_ERROR
                     if len(files_to_delete) > 0:
-                        remove_files(
+                        await remove_files(
                             self.store,
                             dataset,
                             files_to_delete,
diff --git a/services/datalad/datalad_service/handlers/git.py b/services/datalad/datalad_service/handlers/git.py
@@ -6,6 +6,7 @@
 
 from datalad_service.common.events import log_git_event
 from datalad_service.common.const import CHUNK_SIZE_BYTES
+from datalad_service.common.onchange import on_head
 
 
 cache_control = ['no-cache', 'max-age=0', 'must-revalidate']
@@ -137,11 +138,12 @@ async def on_post(self, req, resp, worker, dataset):
             resp.status = falcon.HTTP_OK
 
             # After this request finishes successfully, log it to the OpenNeuro API
-            def schedule_git_event():
+            async def schedule_git_event():
+                await on_head(dataset_path)
                 for new_commit, new_ref in refs_updated:
                     log_git_event(dataset, new_commit, new_ref, req.context['token'])
 
-            resp.schedule_sync(schedule_git_event)
+            resp.schedule(schedule_git_event)
         else:
             resp.status = falcon.HTTP_UNPROCESSABLE_ENTITY
 
diff --git a/services/datalad/datalad_service/handlers/upload.py b/services/datalad/datalad_service/handlers/upload.py
@@ -34,9 +34,9 @@ async def move_files_into_repo(
     await move_files(upload_path, dataset_path)
     if name and email:
         author = pygit2.Signature(name, email)
-        hexsha = str(git_commit(repo, unlock_files, author))
+        hexsha = str(await git_commit(repo, unlock_files, author))
     else:
-        hexsha = str(git_commit(repo, unlock_files))
+        hexsha = str(await git_commit(repo, unlock_files))
 
 
 class UploadResource:
diff --git a/services/datalad/datalad_service/tasks/dataset.py b/services/datalad/datalad_service/tasks/dataset.py
@@ -42,7 +42,7 @@ def create_datalad_config(dataset_path):
         configfile.write(config)
 
 
-def create_dataset(store, dataset, author=None, initial_head='main'):
+async def create_dataset(store, dataset, author=None, initial_head='main'):
     """Create a DataLad git-annex repo for a new dataset.
 
     initial_head is only meant for tests and is overridden by the implementation of git_commit
@@ -61,7 +61,7 @@ def create_dataset(store, dataset, author=None, initial_head='main'):
     # Set a datalad UUID
     create_datalad_config(dataset_path)
     repo.index.add('.datalad/config')
-    git_commit(
+    await git_commit(
         repo,
         ['.gitattributes', '.datalad/config'],
         author,
diff --git a/services/datalad/datalad_service/tasks/description.py b/services/datalad/datalad_service/tasks/description.py
@@ -32,7 +32,7 @@ async def update_description(store, dataset, description_fields, name=None, emai
             path, description, json.dumps(updated, indent=4, ensure_ascii=False)
         )
         # Commit new content, run validator
-        commit_files(store, dataset, ['dataset_description.json'])
+        await commit_files(store, dataset, ['dataset_description.json'])
         return updated
     else:
         return description_json
diff --git a/services/datalad/datalad_service/tasks/files.py b/services/datalad/datalad_service/tasks/files.py
@@ -21,7 +21,7 @@
 from datalad_service.config import AWS_S3_PUBLIC_BUCKET
 
 
-def commit_files(store, dataset, files, name=None, email=None, cookies=None):
+async def commit_files(store, dataset, files, name=None, email=None, cookies=None):
     """
     Commit a list of files with the email and name provided.
 
@@ -35,9 +35,9 @@ def commit_files(store, dataset, files, name=None, email=None, cookies=None):
         and pygit2.Signature(name, email)
         or pygit2.Signature(COMMITTER_NAME, COMMITTER_EMAIL)
     )
-    ref = git_commit(repo, files, author)
+    ref = await git_commit(repo, files, author)
     # Run the validator but don't block on the request
-    asyncio.create_task(validate_dataset.kiq(dataset, dataset_path, str(ref), cookies))
+    await validate_dataset.kiq(dataset, dataset_path, str(ref), cookies)
     return ref
 
 
@@ -47,7 +47,7 @@ def get_tree(store, dataset, tree):
     return get_repo_files(dataset, dataset_path, tree)
 
 
-def remove_files(store, dataset, paths, name=None, email=None, cookies=None):
+async def remove_files(store, dataset, paths, name=None, email=None, cookies=None):
     dataset_path = store.get_dataset_path(dataset)
     repo = pygit2.Repository(dataset_path)
     if name and email:
@@ -57,7 +57,9 @@ def remove_files(store, dataset, paths, name=None, email=None, cookies=None):
     repo.index.remove_all(paths)
     repo.index.write()
     repo.checkout_index()
-    hexsha = str(git_commit_index(repo, author, message='[OpenNeuro] Files removed'))
+    hexsha = str(
+        await git_commit_index(repo, author, message='[OpenNeuro] Files removed')
+    )
 
 
 def parse_s3_annex_url(url, bucket_name=AWS_S3_PUBLIC_BUCKET):
diff --git a/services/datalad/datalad_service/tasks/fsck.py b/services/datalad/datalad_service/tasks/fsck.py
@@ -0,0 +1,117 @@
+import json
+import io
+import logging
+import subprocess
+
+import pygit2
+import requests
+
+from datalad_service.broker import broker
+from datalad_service.config import GRAPHQL_ENDPOINT
+
+
+def get_head_commit_and_references(repo):
+    """
+    Returns the current HEAD commit and any references (tags) pointing to it.
+    """
+    head_commit = repo[repo.head.target]
+    references = []
+    for ref in repo.references:
+        if (
+            ref.startswith('refs/tags/')
+            and repo.lookup_reference(ref).target == head_commit.id
+        ):
+            references.append(ref)
+    return head_commit, references
+
+
+@broker.task
+def git_annex_fsck_local(dataset_path):
+    """Run git-annex fsck for local annexed objects in the draft. Runs on commits, verifies checksums."""
+    try:
+        commit, references = get_head_commit_and_references(
+            pygit2.Repository(dataset_path)
+        )
+    except pygit2.GitError:
+        logging.error(f'Could not open git repository for {dataset_path}')
+        return
+    annex_command = (
+        'git-annex',
+        'fsck',
+        '--json',
+        '--json-error-messages',
+        '--incremental-schedule',
+        '7d',
+    )
+    annex_process = subprocess.Popen(
+        annex_command, cwd=dataset_path, stdout=subprocess.PIPE
+    )
+    bad_files = []
+    for annexed_file_json in io.TextIOWrapper(annex_process.stdout, encoding='utf-8'):
+        annexed_file = json.loads(annexed_file_json)
+        if not annexed_file['success']:
+            bad_files.append(annexed_file)
+    if len(bad_files) > 0:
+        logging.error(f'missing or corrupt annexed objects found in {dataset_path}')
+    # Send any bad files to updateFileCheck
+    requests.post(
+        url=GRAPHQL_ENDPOINT,
+        json={
+            'query': 'mutation ($datasetId: ID!, $hexsha: String!, $refs: [String], $annexFsck: [AnnexFsck]) { updateFileChecks(datasetId: $datasetId, hexsha: $hexsha, refs: $refs, annexFsck: $annexFsck) { datasetId, hexsha } }',
+            'variables': {
+                'datasetId': dataset_path.split('/')[-1],
+                'hexsha': str(commit.id),
+                'refs': references,
+                'annexFsck': bad_files,
+            },
+        },
+    )
+
+
+@broker.task
+def git_annex_fsck_remote(dataset_path, branch=None, remote='s3-PUBLIC'):
+    """Run incremental fsck for one branch (tag) and remote."""
+    try:
+        # Basic sanity check opening the repo before running git-annex
+        repo = pygit2.Repository(dataset_path)
+    except pygit2.GitError:
+        logging.error(f'Could not open git repository for {dataset_path}')
+        return
+    if not branch:
+        # Find the newest tag chronologically
+        all_tags = sorted(
+            [tag for tag in repo.references if tag.startswith('refs/tags/')],
+            key=lambda tag: repo.lookup_reference(tag).target.commit_time,
+            reverse=True,
+        )
+        if all_tags:
+            branch = all_tags[0]
+        else:
+            logging.info(
+                f'No tags found for dataset: {dataset_path}. Skipping remote fsck.'
+            )
+            return
+
+    # Run at most once per month per dataset
+    annex_command = (
+        'git-annex',
+        'fsck',
+        f'--branch={branch}',
+        '--from={remote}',
+        '--fast',
+        '--json',
+        '--json-error-messages',
+        '--incremental-schedule=7d',
+    )
+    annex_process = subprocess.Popen(
+        annex_command, cwd=dataset_path, stdout=subprocess.PIPE
+    )
+    bad_files = []
+    for annexed_file_json in io.TextIOWrapper(annex_process.stdout, encoding='utf-8'):
+        annexed_file = json.loads(annexed_file_json)
+        if not annexed_file['success']:
+            bad_files.append(annexed_file)
+    if len(bad_files) > 0:
+        logging.error(
+            f'{dataset_path} remote {remote} has missing or corrupt annexed objects'
+        )
diff --git a/services/datalad/datalad_service/tasks/snapshots.py b/services/datalad/datalad_service/tasks/snapshots.py
@@ -9,6 +9,7 @@
 from datalad_service.tasks.dataset import create_datalad_config
 from datalad_service.tasks.description import update_description
 from datalad_service.tasks.files import commit_files
+from datalad_service.common.onchange import on_tag
 
 
 class SnapshotExistsException(Exception):
@@ -119,7 +120,7 @@ async def update_changes(store, dataset, tag, new_changes):
         current_date = datetime.today().strftime('%Y-%m-%d')
         updated = await write_new_changes(dataset_path, tag, new_changes, current_date)
         # Commit new content, run validator
-        commit_files(store, dataset, ['CHANGES'])
+        await commit_files(store, dataset, ['CHANGES'])
         return updated
     else:
         return await get_head_changes(dataset_path)
@@ -133,20 +134,22 @@ def validate_snapshot_name(store, dataset, snapshot):
         raise SnapshotExistsException(f'Tag "{snapshot}" already exists, name conflict')
 
 
-def validate_datalad_config(store, dataset):
+async def validate_datalad_config(store, dataset):
     """Add a .datalad/config file if one does not exist."""
     dataset_path = store.get_dataset_path(dataset)
     repo = store.get_dataset_repo(dataset)
     try:
         git_show(repo, 'HEAD', '.datalad/config')
     except KeyError:
         create_datalad_config(dataset_path)
-        commit_files(store, dataset, ['.datalad/config'])
+        await commit_files(store, dataset, ['.datalad/config'])
 
 
-def save_snapshot(store, dataset, snapshot):
-    repo = pygit2.Repository(store.get_dataset_path(dataset))
+async def save_snapshot(store, dataset, snapshot):
+    ds_path = store.get_dataset_path(dataset)
+    repo = pygit2.Repository(ds_path)
     repo.references.create(f'refs/tags/{snapshot}', str(repo.head.target))
+    await on_tag(ds_path, snapshot)
 
 
 async def create_snapshot(
@@ -158,8 +161,8 @@ async def create_snapshot(
     Raises an exception if the tag already exists.
     """
     validate_snapshot_name(store, dataset, snapshot)
-    validate_datalad_config(store, dataset)
+    await validate_datalad_config(store, dataset)
     await update_description(store, dataset, description_fields)
     await update_changes(store, dataset, snapshot, snapshot_changes)
-    save_snapshot(store, dataset, snapshot)
+    await save_snapshot(store, dataset, snapshot)
     return get_snapshot(store, dataset, snapshot)
diff --git a/services/datalad/tests/test_bids.py b/services/datalad/tests/test_bids.py
@@ -70,10 +70,10 @@ def test_read_dataset_description(new_dataset):
     assert description['Name'] == 'Test fixture new dataset'
 
 
-def test_read_dataset_description_invalid_json(new_dataset):
+async def test_read_dataset_description_invalid_json(new_dataset):
     repo = Repository(new_dataset.path)
     open(os.path.join(new_dataset.path, 'dataset_description.json'), 'w').close()
-    git_commit(repo, ['dataset_description.json'])
+    await git_commit(repo, ['dataset_description.json'])
     description = read_dataset_description(new_dataset.path, 'HEAD')
     assert description is None
 
diff --git a/services/datalad/tests/test_datalad.py b/services/datalad/tests/test_datalad.py

Original file line number	Diff line number	Diff line change
`@@ -32,7 +32,7 @@ async def update_description(store, dataset, description_fields, name=None, emai`
`32`	`32`	`path, description, json.dumps(updated, indent=4, ensure_ascii=False)`
`33`	`33`	`)`
`34`	`34`	`# Commit new content, run validator`
`35`		`- commit_files(store, dataset, ['dataset_description.json'])`
	`35`	`+ await commit_files(store, dataset, ['dataset_description.json'])`
`36`	`36`	`return updated`
`37`	`37`	`else:`
`38`	`38`	`return description_json`