From d34374f0e822edd1539ea5de6f8522f2b761de3f Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Thu, 16 Jul 2020 14:48:22 -0400
Subject: Improve uploader reporting.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 bh20sequploader/main.py                      | 22 ++++++++++------------
 bh20simplewebuploader/main.py                |  4 ++--
 bh20simplewebuploader/templates/error.html   |  2 +-
 bh20simplewebuploader/templates/success.html |  2 +-
 4 files changed, 14 insertions(+), 16 deletions(-)

diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index f744a8c..6049bf9 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -29,11 +29,10 @@ 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")
+            log.warning("Failed metadata QC")
             failed = True
     except Exception as e:
-        log.debug(e)
-        print(e)
+        log.exception("Failed metadata QC")
         failed = True
 
     target = []
@@ -45,8 +44,7 @@ def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True):
             target[0] = ("reads_1."+target[0][0][6:], target[0][1])
             target[1] = ("reads_2."+target[1][0][6:], target[0][1])
     except Exception as e:
-        log.debug(e)
-        print(e)
+        log.exception("Failed sequence QC")
         failed = True
 
     if failed:
@@ -82,7 +80,7 @@ def main():
     seqlabel = target[0][1]
 
     if args.validate:
-        print("Valid")
+        log.info("Valid")
         exit(0)
 
     col = arvados.collection.Collection(api_client=api)
@@ -91,10 +89,10 @@ def main():
     if args.sequence_p2:
         upload_sequence(col, target[1], args.sequence_p2)
 
-    print("Reading metadata")
+    log.info("Reading metadata")
     with col.open("metadata.yaml", "w") as f:
         r = args.metadata.read(65536)
-        print(r[0:20])
+        log.info(r[0:20])
         while r:
             f.write(r)
             r = args.metadata.read(65536)
@@ -118,7 +116,7 @@ def main():
                                            ["portable_data_hash", "=", col.portable_data_hash()]]).execute()
     if dup["items"]:
         # This exact collection has been uploaded before.
-        print("Duplicate of %s" % ([d["uuid"] for d in dup["items"]]))
+        log.error("Duplicate of %s" % ([d["uuid"] for d in dup["items"]]))
         exit(1)
 
     if args.trusted:
@@ -131,9 +129,9 @@ def main():
                  (seqlabel, properties['upload_user'], properties['upload_ip']),
                  properties=properties, ensure_unique_name=True)
 
-    print("Saved to %s" % col.manifest_locator())
-
-    print("Done")
+    log.info("Saved to %s" % col.manifest_locator())
+    log.info("Done")
+    exit(0)
 
 if __name__ == "__main__":
     main()
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 62b68d9..c814f30 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -445,12 +445,12 @@ def receive_files():
 
         if result.returncode != 0:
             # It didn't work. Complain.
-            error_message="Uploader returned value {} and said:".format(result.returncode) + str(result.stderr.decode('utf-8'))
+            error_message="Uploader returned value {} and said:\n".format(result.returncode) + str(result.stderr.decode('utf-8'))
             print(error_message, file=sys.stderr)
             return (render_template('error.html', error_message=error_message), 403)
         else:
             # It worked. Say so.
-            return render_template('success.html', log=result.stdout.decode('utf-8', errors='replace'))
+            return render_template('success.html', log=result.stderr.decode('utf-8', errors='replace'))
     finally:
         shutil.rmtree(dest_dir)
 
diff --git a/bh20simplewebuploader/templates/error.html b/bh20simplewebuploader/templates/error.html
index b1d9402..fc08aed 100644
--- a/bh20simplewebuploader/templates/error.html
+++ b/bh20simplewebuploader/templates/error.html
@@ -15,7 +15,7 @@
           </pre>
         </p>
         <p>
-            <a href="/">Click here to try again.</a>
+            <a href="/upload">Click here to try again.</a>
         </p>
         <hr>
     </body>
diff --git a/bh20simplewebuploader/templates/success.html b/bh20simplewebuploader/templates/success.html
index 9f0987c..c2302fa 100644
--- a/bh20simplewebuploader/templates/success.html
+++ b/bh20simplewebuploader/templates/success.html
@@ -9,7 +9,7 @@
         <h1>Upload Successful</h1>
         <hr>
         <p>
-            Your files have been uploaded. They should soon appear as output of the <a href="/download">Public SARS-CoV-2 Sequence Resource</a>.
+            Your files have been uploaded. You can track their <a href="/status">QC status</a>, once validated they will be part of the <a href="/download">Public SARS-CoV-2 Sequence Resource</a>.
         </p>
         <p>
             The upload log was:
-- 
cgit v1.2.3