[ARVADOS] created: 1.3.0-831-g889cdaf5d

[Git user]

        at  889cdaf5db96d87f14cff6a232408ab55e1226b6 (commit)


commit 889cdaf5db96d87f14cff6a232408ab55e1226b6
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Tue Apr 30 18:06:54 2019 -0400

    15112: Script to re-run containers
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/tools/rerun/keep-rerun.py b/tools/rerun/keep-rerun.py
new file mode 100755
index 000000000..58372064e
--- /dev/null
+++ b/tools/rerun/keep-rerun.py
@@ -0,0 +1,73 @@
+#!/usr/bin/env python
+from __future__ import print_function, absolute_import
+import argparse
+import arvados
+import arvados.util
+
+"""
+Given a list of collections missing blocks (as produced by
+keep-balance), delete the collections and re-run associated containers.
+"""
+
+def rerun_request(arv, container_requests_to_rerun, ct):
+    requests = arvados.util.list_all(arv.container_requests().list, filters=[["container_uuid", "=", ct["uuid"]]])
+    for cr in requests:
+        if cr["requesting_container_uuid"]:
+            rerun_request(arv, container_requests_to_rerun, arv.containers().get(uuid=cr["requesting_container_uuid"]).execute())
+        else:
+            container_requests_to_rerun.append(cr)
+
+
+def main():
+    parser = argparse.ArgumentParser(description='Re-run containers associated with missing blocks')
+    parser.add_argument('--dry-run', action='store_true', default=False)
+    parser.add_argument('inp')
+    args = parser.parse_args()
+
+    arv = arvados.api('v1')
+
+    busted_collections = set()
+
+    # Get the list of bad collection PDHs
+    blocksfile = open(args.inp, "rt")
+    for line in blocksfile:
+        # Ignore the first item, that's the block id
+        collections = line.rstrip().split(" ")[1:]
+        for c in collections:
+            busted_collections.add(c)
+
+    collections_to_delete = {}
+    container_requests_to_rerun = []
+    # Get containers that produced these collections
+    for b in busted_collections:
+        collections_to_delete = arvados.util.list_all(arv.collections().list, filters=[["portable_data_hash", "=", b]])
+        for d in collections_to_delete:
+            print("Will delete %s" % d["uuid"])
+            if not args.dry_run:
+                arv.collections().delete(uuid=d["uuid"]).execute()
+        maybe_containers_to_rerun = arvados.util.list_all(arv.containers().list, filters=[["output", "=", b]])
+        for ct in maybe_containers_to_rerun:
+            rerun_request(arv, container_requests_to_rerun, ct)
+
+    for cr in container_requests_to_rerun:
+        new_cr = {}
+        for f in ("command",
+                  "cwd",
+                  "environment",
+                  "output_path",
+                  "container_image",
+                  "mounts",
+                  "runtime_constraints",
+                  "scheduling_parameters",
+                  "owner_uuid"):
+            new_cr[f] = cr[f]
+        new_cr["name"] = cr["name"] + " rerun"
+        new_cr["state"] = "Committed"
+        new_cr["priority"] = 500
+        print("Will re-run %s" % cr["uuid"])
+        if not args.dry_run:
+            new_cr = arv.container_requests().create(body=new_cr).execute()
+            print("Submitted %s" % new_cr["uuid"])
+
+if __name__ == "__main__":
+    main()

-----------------------------------------------------------------------


hooks/post-receive
--