From 4f30e506055acb788a1ff1bbcb6359c4413a4eab Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Sun, 5 Jul 2020 21:33:26 +0000
Subject: Add bh20-seq-analyzer --print-status

Get status from new property "status: validated/rejected"

Also store QC fail error message.
---
 bh20sequploader/main.py        |  9 +++------
 bh20sequploader/qc_metadata.py | 21 +++++++--------------
 2 files changed, 10 insertions(+), 20 deletions(-)

(limited to 'bh20sequploader')

diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index cdc4c3f..8555e2b 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -26,11 +26,9 @@ def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True):
     try:
         log.debug("Checking metadata" if do_qc else "Skipping metadata check")
         if do_qc and not qc_metadata(metadata.name):
-            log.warning("Failed metadata qc")
-            exit(1)
-    except ValueError as e:
+            raise Exception("Failed metadata qc")
+    except Exception as e:
         log.debug(e)
-        log.debug("Failed metadata qc")
         print(e)
         exit(1)
 
@@ -42,9 +40,8 @@ def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True):
             target.append(qc_fasta(sequence_p2))
             target[0] = ("reads_1."+target[0][0][6:], target[0][1])
             target[1] = ("reads_2."+target[1][0][6:], target[0][1])
-    except ValueError as e:
+    except Exception as e:
         log.debug(e)
-        log.debug("Failed FASTA qc")
         print(e)
         exit(1)
 
diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py
index 9122ace..2b57991 100644
--- a/bh20sequploader/qc_metadata.py
+++ b/bh20sequploader/qc_metadata.py
@@ -21,20 +21,13 @@ def qc_metadata(metadatafile):
     shex = pkg_resources.resource_stream(__name__, "bh20seq-shex.rdf").read().decode("utf-8")
 
     if not isinstance(avsc_names, schema_salad.avro.schema.Names):
-        print(avsc_names)
-        return False
+        raise Exception(avsc_names)
 
-    try:
-        doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True)
-        g = schema_salad.jsonld_context.makerdf("workflow", doc, document_loader.ctx)
-        rslt, reason = evaluate(g, shex, doc["id"], "https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-shex.rdf#submissionShape")
+    doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True)
+    g = schema_salad.jsonld_context.makerdf("workflow", doc, document_loader.ctx)
+    rslt, reason = evaluate(g, shex, doc["id"], "https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-shex.rdf#submissionShape")
 
-        if not rslt:
-            log.debug(reason)
-            print(reason)
+    if not rslt:
+        raise Exception(reason)
 
-        return rslt
-    except Exception as e:
-        traceback.print_exc()
-        log.warn(e)
-    return False
+    return True
-- 
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