From 6bfefe984a84fb215d61e045c49a4ab123bb7339 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Thu, 16 Jul 2020 12:32:43 -0400
Subject: Catch exceptions

Add script to cleanup bad uploads.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 scripts/cleanup.py | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 scripts/cleanup.py

(limited to 'scripts/cleanup.py')

diff --git a/scripts/cleanup.py b/scripts/cleanup.py
new file mode 100644
index 0000000..f4bd0b4
--- /dev/null
+++ b/scripts/cleanup.py
@@ -0,0 +1,20 @@
+import arvados
+import arvados.util
+
+api = arvados.api()
+
+patterns = [
+    "%missing%`collection_location`%",
+    "%missing%`technology`%",
+    "%missing%`host_species`%",
+    "%QC fail: alignment%",
+    "%does not look like a valid URI%",
+    ]
+
+for p in patterns:
+    c = arvados.util.list_all(api.collections().list, filters=[
+        ["owner_uuid", "=", "lugli-j7d0g-n5clictpuvwk8aa"],
+        ["properties.errors", "like", p]])
+    for i in c:
+        print("trashing %s %s" % (i["uuid"], i["properties"].get("sequence_label")))
+        api.collections().delete(uuid=i["uuid"]).execute()
-- 
cgit v1.2.3


From 474d15e17be63046a091615e89ba63adecdb109b Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Thu, 16 Jul 2020 14:28:02 -0400
Subject: Cleanup script also clears errors for revalidate

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 scripts/cleanup.py | 22 ++++++++++++++++++++--
 1 file changed, 20 insertions(+), 2 deletions(-)

(limited to 'scripts/cleanup.py')

diff --git a/scripts/cleanup.py b/scripts/cleanup.py
index f4bd0b4..6a82659 100644
--- a/scripts/cleanup.py
+++ b/scripts/cleanup.py
@@ -3,18 +3,36 @@ import arvados.util
 
 api = arvados.api()
 
-patterns = [
+delete_patterns = [
     "%missing%`collection_location`%",
     "%missing%`technology`%",
     "%missing%`host_species`%",
     "%QC fail: alignment%",
     "%does not look like a valid URI%",
+    "%Duplicate of%"
     ]
 
-for p in patterns:
+revalidate_patterns = [
+    "%missing%`license`%"
+]
+
+for p in delete_patterns:
     c = arvados.util.list_all(api.collections().list, filters=[
         ["owner_uuid", "=", "lugli-j7d0g-n5clictpuvwk8aa"],
         ["properties.errors", "like", p]])
     for i in c:
         print("trashing %s %s" % (i["uuid"], i["properties"].get("sequence_label")))
         api.collections().delete(uuid=i["uuid"]).execute()
+
+for p in revalidate_patterns:
+    c = arvados.util.list_all(api.collections().list, filters=[
+        ["owner_uuid", "=", "lugli-j7d0g-n5clictpuvwk8aa"],
+        ["properties.errors", "like", p]])
+    for i in c:
+        print("clearing status %s %s" % (i["uuid"], i["properties"].get("sequence_label")))
+        pr = i["properties"]
+        if "status" in pr:
+            del pr["status"]
+        if "errors" in pr:
+            del pr["errors"]
+        api.collections().update(uuid=i["uuid"], body={"properties": pr}).execute()
-- 
cgit v1.2.3