diff options
Diffstat (limited to 'bh20simplewebuploader')
| -rw-r--r-- | bh20simplewebuploader/main.py | 6 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/form.html | 6 |
2 files changed, 7 insertions, 5 deletions
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 8ce6f6f..afae4c7 100644 --- a/bh20simplewebuploader/templates/form.html +++ b/bh20simplewebuploader/templates/form.html @@ -123,9 +123,9 @@ This tool can be used to upload sequenced genomes of SARS-CoV-2 samples to the <a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca">Public SARS-CoV-2 Sequence Resource</a>. Your uploaded sequence will automatically be processed and incorporated into the public pangenome. </p> <div class="fasta-file-select"> - <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> </div> @@ -181,7 +181,7 @@ </form> </section> <hr> - <small><a href="https://github.com/adamnovak/bh20-simple-web-uploader">Source</a> · Made for <a href="https://github.com/virtual-biohackathons/covid-19-bh20">COVID-19-BH20</a></small> + <small><a href="https://github.com/arvados/bh20-seq-resource">Source</a> · Made for <a href="https://github.com/virtual-biohackathons/covid-19-bh20">COVID-19-BH20</a></small> <script type="text/javascript"> let uploadForm = document.getElementById('metadata_upload_form') |