Add a cli command to backfill manifests for all workspaces

I have manually tested this using the db from the test backend. I have
not included automated tests, as a) this is a one off migration command,
b) they would be quite hard to write and c) this is an offline process
that is not mission critical

jobrunner/cli/manifests.py

@@ -0,0 +1,96 @@
+"""
+Ops utility for backfilling manifest.json files from db
+"""
+import argparse
+
+from jobrunner.executors import local
+from jobrunner.lib import database
+from jobrunner.models import Job
+
+
+def main(workspaces=None):
+    conn = database.get_connection()
+    workspaces = [
+        w["workspace"] for w in conn.execute("SELECT DISTINCT(workspace) FROM job;")
+    ]
+
+    n_workspaces = len(workspaces)
+    for i, workspace in enumerate(workspaces):
+        print(f"workspace {i+1}/{n_workspaces}: {workspace}")
+
+        level4_dir = local.get_medium_privacy_workspace(workspace)
+
+        sentinel = level4_dir / ".manifest-backfill"
+        if sentinel.exists():
+            print(" - already done, skipping")
+            continue
+
+        write_manifest(workspace)
+
+        sentinel.touch()
+
+
+def write_manifest(workspace):
+    conn = database.get_connection()
+    workspace_dir = local.get_high_privacy_workspace(workspace)
+    level4_dir = local.get_medium_privacy_workspace(workspace)
+
+    job_ids = conn.execute(
+        """
+        SELECT id FROM job 
+        WHERE workspace = ?
+            AND outputs != '' 
+            AND completed_at IS NOT NULL
+            AND state = 'succeeded'
+        ORDER BY completed_at DESC;
+        """,
+        (workspace,),
+    )
+
+    outputs = {}
+
+    for row in job_ids:
+        job_id = row["id"]
+        job = database.find_one(Job, id=job_id)
+
+        for output, level in job.outputs.items():
+            if output in outputs:
+                # older version of the file, ingnore
+                continue
+
+            abspath = workspace_dir / output
+
+            # testing only
+            abspath.parent.mkdir(parents=True, exist_ok=True)
+            abspath.touch()
+
+            # use presence of message file to detect excluded files
+            message_file = level4_dir / (output + ".txt")
+            excluded = message_file.exists()
+
+            metadata = local.get_output_metadata(
+                abspath,
+                level,
+                job_id=job_id,
+                job_request=job.job_request_id,
+                action=job.action,
+                commit=job.commit,
+                excluded=excluded,
+            )
+
+            outputs[output] = metadata
+
+    manifest = local.read_manifest_file(level4_dir, workspace)
+    manifest["outputs"] = outputs
+    print(f" - writing manifest for {workspace} with {len(outputs)} outputs")
+    local.write_manifest_file(level4_dir, manifest)
+
+
+def run():
+    parser = argparse.ArgumentParser(description=__doc__.partition("\n\n")[0])
+    args = parser.parse_args()
+    main(**vars(args))
+
+
+if __name__ == "__main__":
+    run()