From ba38aaf6920b246f6644cfb49730a5e2ee5f9db0 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Tue, 7 Jul 2020 17:17:31 -0400
Subject: --print-status=html creates html report
---
bh20seqanalyzer/main.py | 40 ++++++++++++++++++++++++++++++++++++----
1 file changed, 36 insertions(+), 4 deletions(-)
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
index 2fefa86..1746587 100644
--- a/bh20seqanalyzer/main.py
+++ b/bh20seqanalyzer/main.py
@@ -235,9 +235,10 @@ def upload_schema(api, workflow_def_project):
return "keep:%s/schema.yml" % pdh
-def print_status(api, uploader_project):
+def print_status(api, uploader_project, fmt):
pending = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", uploader_project]])
out = []
+ status = {}
for p in pending:
prop = p["properties"]
out.append(prop)
@@ -245,7 +246,38 @@ def print_status(api, uploader_project):
prop["status"] = "pending"
prop["created_at"] = p["created_at"]
prop["uuid"] = p["uuid"]
- print(json.dumps(out, indent=2))
+ status[prop["status"]] = status.get(prop["status"], 0) + 1
+ if fmt == "html":
+ print(
+"""
+
+
+""")
+ print("Total collections in upload project %s
" % len(out))
+ print("Status %s
" % status)
+ print(
+"""
+
+| Collection |
+Sequence label |
+Status |
+Errors |
|---|
+""")
+ for r in out:
+ print("")
+ print("| %s | " % (r["uuid"], r["uuid"]))
+ print("%s | " % r["sequence_label"])
+ print("%s | " % r["status"])
+ print("%s | " % "\n".join(r.get("errors", [])))
+ print("
")
+ print(
+"""
+
+
+
+""")
+ else:
+ print(json.dumps(out, indent=2))
def main():
parser = argparse.ArgumentParser(description='Analyze collections uploaded to a project')
@@ -264,7 +296,7 @@ def main():
parser.add_argument('--kickoff', action="store_true")
parser.add_argument('--no-start-analysis', action="store_true")
parser.add_argument('--once', action="store_true")
- parser.add_argument('--print-status', action="store_true")
+ parser.add_argument('--print-status', type=str, default=None)
args = parser.parse_args()
api = arvados.api()
@@ -284,7 +316,7 @@ def main():
return
if args.print_status:
- print_status(api, args.uploader_project)
+ print_status(api, args.uploader_project, args.print_status)
exit(0)
logging.info("Starting up, monitoring %s for uploads" % (args.uploader_project))
--
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