From 04912c58cdab27962429be56971afde189d702c4 Mon Sep 17 00:00:00 2001
From: Adam Novak
Date: Fri, 10 Apr 2020 16:43:05 -0700
Subject: Clarify supported formats and make web UI take FASTQ

---
 README.md                                 | 4 ++--
 bh20simplewebuploader/main.py             | 6 ++++--
 bh20simplewebuploader/templates/form.html | 4 ++--
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 2a1657d..db4fe52 100644
--- a/README.md
+++ b/README.md
@@ -126,10 +126,10 @@ For running/developing the uploader with GNU Guix see [INSTALL.md](./doc/INSTALL
 
 # Usage
 
-Run the uploader with a FASTA file and accompanying metadata file in [JSON-LD format](https://json-ld.org/):
+Run the uploader with a FASTA or FASTQ file and accompanying metadata file in JSON or YAML:
 
 ```sh
-bh20-seq-uploader example/sequence.fasta example/metadata.json
+bh20-seq-uploader example/sequence.fasta example/metadata.yaml
 ```
 
 ## Workflow for Generating a Pangenome
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index bfc7762..383ef84 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -184,15 +184,17 @@ 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)
diff --git a/bh20simplewebuploader/templates/form.html b/bh20simplewebuploader/templates/form.html
index 2934a7c..e722ab3 100644
--- a/bh20simplewebuploader/templates/form.html
+++ b/bh20simplewebuploader/templates/form.html
@@ -13,9 +13,9 @@
         </p>
         <hr>
         <form action="/submit" method="POST" enctype="multipart/form-data" id="main_form">
-            <label for="fasta">Select FASTA file for assembled genome (max 1MB):</label>
+            <label for="fasta">Select FASTA file of assembled genome, or FASTQ of reads (max 50MB):</label>
             <br>
-            <input type="file" id="fasta" name="fasta" accept=".fa,.fasta,.fna" required>
+            <input type="file" id="fasta" name="fasta" accept=".fa,.fasta,.fna,.fq" required>
             <br>
             
             <label>Select metadata submission method:</label>
-- 
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