reformWeb

A reform web UI implemented by Flask

Installation

Installation script found at ./INSTALL/install.sh

Using the Site

• Fill the form with the required parameters
  • email Email address to have notifications sent to
  • chrom ID of the chromsome to modify
  • position Position in chromosome at which to insert <in_fasta>. Can use -1 to add to end of chromosome. Note: Either position, or upstream AND downstream sequence must be provided.
  • upstream_fasta Path to Fasta file with upstream sequence. Note: Either position, or upstream AND downstream sequence must be provided.
  • downstream_fasta Path to Fasta file with downstream sequence. Note: Either position, or upstream AND downstream sequence must be provided.
  • in_fasta Path to new sequence to be inserted into reference genome in FASTA format.
  • in_gff Path to GFF file describing new fasta sequence to be inserted.
  • ref_fasta Path to reference fasta file.
  • ref_gff Path to reference gff file.
• After submission, the data and files will be gathered and submitted to a message queue to run reform
• If sucessful or failure, an e-mail will be sent to the e-mail address provided

Using the Test Site

Test site is designed to help developers and researchers test updates more easily and quickly by using local files and default populated addresses. Files used for testing need to be uploaded in advance according to the requirements in INSTALL/install.sh.

• Fill the form with the required parameters
  • email Use the default test email address.
  • chrom Default is 1.
  • position User-provided.
  • upstream_fasta If no file is uploaded, use the local upstream_fasta file.
  • downstream_fasta If no file is uploaded, use the local downstream_fasta file.
  • in_fasta If no file is uploaded, use the local in_fasta file.
  • in_gff If no file is uploaded, use the local in_gff file.
  • ref_fasta Use the example FTP link or the local ref_fasta file.
  • ref_gff Use the example FTP link or the local ref_gff file.

Troubleshooting

Error or Unexepected behavior when submitting form

Check the logic here in app.py

reformWeb/app.py

Lines 24 to 37 in a6b7e75

	if request.method == 'POST' and form.validate():
	if (request.files['downstream_fasta'].filename or request.files['upstream_fasta'].filename) and request.form[
	'position']:
	flash("Error: You must provide either the position, or the upstream and downstream sequences.", 'error')
	return redirect(url_for('submit'))
	if (request.files['downstream_fasta'].filename or request.files['upstream_fasta'].filename):
	if not (request.files['downstream_fasta'].filename and request.files['upstream_fasta'].filename):
	flash("Error: Must enter both upstream and downstream", 'error')
	return redirect(url_for('submit'))
	if not (request.files['downstream_fasta'].filename or request.files['upstream_fasta'].filename) and not \
	request.form['position']:
	flash("Error: You must provide either the position, or the upstream and downstream sequences.", 'error')
	return redirect(url_for('submit'))
	else:

No Activity or Emails

Check that reform (gunicorn) and rq workers services running with supervisorctl.

[root@reform ~]# supervisorctl status
reform                           STOPPED   Feb 15 10:36 AM
worker                           STOPPED   Feb 15 10:36 AM

Start or restart if needed

[root@reform ~]# supervisorctl start all
worker: started
reform: started

How to monitor logs

Logs are written to /var/log/reform. Most of the echo outs are controlled in run.sh. Edit as needed for debugging.

• reform.err.log Contains errors from Flask (e.g., errors in app.py) and ERROR, INFO logs from Gunicorn.
• reform.out.log Contains standard output from Gunicorn.
• worker.out.log Contains echo outputs from run.sh, indicating the current task of the worker.
• worker.err.log Contains errors from reform.py and FTP download records.

Receive an Email with a Zip of an Empty Download Folder

An empty download folder means reform didn't finish, resulting in empty result and download folders. To debug this error, please check /var/log/reform for more information. Here are some common issues:

In worker.err.log:

1. OSError: [Errno 28] No space left on device:
   • There is no free space on the server. Please clean up files in /data/downloads/, /data/results/, and /data/uploads/.
2. FileNotFoundError: [Errno 2] No such file or directory:
   • Please check the corresponding folder, especially when using the test site.

In worker.err.log:

1. ./run.sh: line XX: syntax error near unexpected token:
   • An invalid input has been passed into run.sh, usually an invalid FTP link.

Get Error Status Code when access reform web

Error status code usually represent the web service has not run as expectly.

1. 502 Bad Gateway: This error typically occurs due to communication problems between servers. It might be helpful to check app.py for any unhandled routes.
2. 500 Internal Server Error: This error indicates that the server encountered an unexpected condition that prevented it from fulfilling the request. Check /var/log/reform/reform.err.log for detailed information.

Cannot SSH

SSH is only accessible on NYU VPN