From cc5db1777ad7334243dff0d9a0bbacea417b5ffb Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 29 May 2020 08:29:07 -0500
Subject: Improved error output for the web uploader

---
 bh20sequploader/main.py     | 15 +++++++++++----
 bh20sequploader/qc_fasta.py |  5 ++++-
 2 files changed, 15 insertions(+), 5 deletions(-)

(limited to 'bh20sequploader')

diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index 2cd15c2..a2e62fa 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -31,16 +31,23 @@ def main():
 
     api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True)
 
-    log.debug("Checking metadata")
-    if not qc_metadata(args.metadata.name):
-        log.warning("Failed metadata qc")
+    try:
+        log.debug("Checking metadata")
+        if not qc_metadata(args.metadata.name):
+            log.warning("Failed metadata qc")
+            exit(1)
+    except ValueError as e:
+        log.debug(e)
+        log.debug("Failed metadata qc")
+        print(e)
         exit(1)
 
     try:
         log.debug("Checking FASTA QC")
         target = qc_fasta(args.sequence)
     except ValueError as e:
-        log.warning("Failed FASTA qc")
+        log.debug(e)
+        log.debug("Failed FASTA qc")
         print(e)
         exit(1)
 
diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py
index 16cf2c9..5c8cf3a 100644
--- a/bh20sequploader/qc_fasta.py
+++ b/bh20sequploader/qc_fasta.py
@@ -6,6 +6,8 @@ import tempfile
 import logging
 import re
 
+log = logging.getLogger(__name__ )
+
 def read_fasta(sequence):
     entries = 0
     bases = []
@@ -17,11 +19,12 @@ def read_fasta(sequence):
         else:
             bases.append(line)
         if entries > 1:
+            log.debug("FASTA file contains multiple entries")
             raise ValueError("FASTA file contains multiple entries")
-            break
     return label, bases
 
 def qc_fasta(sequence):
+    log.debug("Starting qc_fasta")
     schema_resource = pkg_resources.resource_stream(__name__, "validation/formats")
     with tempfile.NamedTemporaryFile() as tmp:
         tmp.write(schema_resource.read())
-- 
cgit v1.2.3