1 files changed, 17 insertions, 4 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index bfc7762..f5324a5 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -3,12 +3,18 @@ import tempfile
 import shutil
 import subprocess
 import os
+import sys
 import re
 import string
 import yaml
 import urllib.request
 from flask import Flask, request, redirect, send_file, send_from_directory, render_template
 
+import os.path
+
+if not os.path.isfile('bh20sequploader/mainx.py'):
+    print("WARNING: run FLASK from the root of the source repository!", file=sys.stderr)
+
 app = Flask(__name__, static_url_path='/static', static_folder='static')
 
 # Limit file upload size. We shouldn't be working with anything over 1 MB; these are small genomes.
@@ -126,6 +132,7 @@ def generate_form(schema):
 
     return list(walk_fields(root_name))
 
+
 # At startup, we need to load the current metadata schema so we can make a form for it
 METADATA_SCHEMA = yaml.safe_load(urllib.request.urlopen('https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml'))
 FORM_ITEMS = generate_form(METADATA_SCHEMA)
@@ -184,15 +191,17 @@ def receive_files():
 
     # We're going to work in one directory per request
     dest_dir = tempfile.mkdtemp()
+    # The uploader will happily accept a FASTQ with this name
     fasta_dest = os.path.join(dest_dir, 'fasta.fa')
     metadata_dest = os.path.join(dest_dir, 'metadata.json')
     try:
         if 'fasta' not in request.files:
             return (render_template('error.html',
-                error_message="You did not include a FASTA file."), 403)
+                error_message="You did not include a FASTA or FASTQ file."), 403)
         try:
             with open(fasta_dest, 'wb') as out_stream:
-                copy_with_limit(request.files.get('fasta').stream, out_stream)
+                # Use a plausible file size limit for a little FASTQ
+                copy_with_limit(request.files.get('fasta').stream, out_stream, limit=50*1024*1024)
         except FileTooBigError as e:
             # Delegate to the 413 error handler
             return handle_large_file(e)
@@ -247,12 +256,16 @@ def receive_files():
                     error_message="You did not include metadata."), 403)
 
         # Try and upload files to Arvados using the sequence uploader CLI
-        result = subprocess.run(['bh20-seq-uploader', fasta_dest, metadata_dest],
+
+        cmd = ['python3','bh20sequploader/main.py', fasta_dest, metadata_dest]
+        print(" ".join(cmd),file=sys.stderr)
+        result = subprocess.run(cmd,
             stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 
         if result.returncode != 0:
             # It didn't work. Complain.
-            error_message="Upload failed. Uploader returned {} and said:\n{}".format(result.returncode, result.stderr)
+            error_message="Uploader returned value {} and said:".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.