From c872248e43c1c66e5fed8ef341f7b4ac21d63e6f Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Tue, 10 Nov 2020 17:26:56 -0500
Subject: Valid uploads with sequence_label in PubSeq replaces old one.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
bh20seqanalyzer/main.py | 50 ++++++++++++++++++++++++++++++++++---------------
1 file changed, 35 insertions(+), 15 deletions(-)
(limited to 'bh20seqanalyzer')
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
index 0906958..b54a746 100644
--- a/bh20seqanalyzer/main.py
+++ b/bh20seqanalyzer/main.py
@@ -42,11 +42,11 @@ class SeqAnalyzer:
self.schema_ref = None
def validate_upload(self, collection, revalidate):
- col = arvados.collection.Collection(collection["uuid"], api_client=self.api, keep_client=self.keepclient)
-
if not revalidate and collection["properties"].get("status") in ("validated", "rejected"):
return False
+ col = arvados.collection.Collection(collection["uuid"], api_client=self.api, keep_client=self.keepclient)
+
# validate the collection here. Check metadata, etc.
logging.info("Validating upload '%s' (%s)" % (collection["name"], collection["uuid"]))
@@ -98,19 +98,7 @@ class SeqAnalyzer:
except Exception as v:
errors.append(str(v))
-
- if not errors:
- # Move it to the "validated" project to be included in the next analysis
- if "errors" in collection["properties"]:
- del collection["properties"]["errors"]
- collection["properties"]["status"] = "validated"
- self.api.collections().update(uuid=collection["uuid"], body={
- "owner_uuid": self.validated_project,
- "name": "%s (%s)" % (collection["name"], time.asctime(time.gmtime())),
- "properties": collection["properties"]}).execute()
- logging.info("Added '%s' to validated sequences" % collection["name"])
- return True
- else:
+ if errors:
# It is invalid
logging.warn("'%s' (%s) has validation errors: %s" % (
collection["name"], collection["uuid"], "\n".join(errors)))
@@ -119,6 +107,38 @@ class SeqAnalyzer:
self.api.collections().update(uuid=collection["uuid"], body={"properties": collection["properties"]}).execute()
return False
+ existing = self.api.collections().list(filters=[["owner_uuid", "=", self.validated_project],
+ ["properties.sequence_label", "=", sample_id]]).execute()
+
+ update_from = None
+ if existing["items"]:
+ # "collection" is the newly uploaded one we're looking at
+ update_from = collection
+ collection = existing["items"][0]
+ collection["properties"] = update_from["properties"]
+
+ if "errors" in collection["properties"]:
+ del collection["properties"]["errors"]
+ collection["properties"]["status"] = "validated"
+ collection["properties"]["sequence_label"] = sample_id
+
+ if update_from:
+ self.api.collections().update(uuid=collection["uuid"], body={
+ "properties": collection["properties"],
+ "manifest_text": col.manifest_text()
+ }).execute()
+ self.api.collections().delete(uuid=update_from["uuid"]).execute()
+ logging.info("Updated '%s' in validated sequences" % collection["name"])
+ else:
+ # Move it to the "validated" project to be included in the next analysis
+ self.api.collections().update(uuid=collection["uuid"], body={
+ "owner_uuid": self.validated_project,
+ "name": "%s (%s)" % (collection["name"], time.asctime(time.gmtime())),
+ "properties": collection["properties"]}).execute()
+ logging.info("Added '%s' to validated sequences" % collection["name"])
+
+ return True
+
def run_workflow(self, parent_project, workflow_uuid, name, inputobj):
project = self.api.groups().create(body={
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