diff options
| -rw-r--r-- | README.md | 4 | ||||
| -rw-r--r-- | bh20simplewebuploader/main.py | 6 | ||||
| -rw-r--r-- | 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> |