eo300/apbs-web

Developmental front-end UI for the APBS/PDB2PQR server. Using React with the Ant Design component library

apbs-web's Issues

Add optional email field for so user can be notified when a job is finished

A space to enter an email address would be useful so that a user wouldn't need to continually visit job status page to check status of job.

The start/end times for a job should be in a readable format.

The timestamps displayed appear to be a raw integer, either in seconds, milliseconds, etc. A user should be able to view this in a more readable form (e.g. local time + date)

Affix "Submit" button to some footer overlay

Job submission button currently just floats over the form. A better look may be to have it within it's own footer-like component.

Display past jobs within submenu utilizing webstorage

Since there's no account system at the moment, it'd be useful to display the associated job IDs for jobs launched from a user's browser in case they...

1. Didn't record the job ID
2. Would like to easily navigate without copy/pasting the respective job status URL

(APBS) A user's input should be validated as they fill form items

As user fills APBS form, we should dynamically check form item values.
This can be addressed within the onChange handler for form fields

(PDB2PQR) A user's input should be validated as they fill form items

We should dynamically check form item values as the user fills PDB2PQR form.
This can be addressed within the onChange handler for form fields

Submit button gives no feedback when pressed on-submit

After submitting the form, an onSubmit handler should change appearance of "Start Job" button so that user sees that submission is made.

This expected behavior works for the APBS config page, but not for PDB2QPR.

Remake Job Status page to indicate and treat each APBS/PDB2PQR task as individual jobs

Previously (as with the old website), an APBS task spawned from the results of the PDB2PQR task are kept within the same job ID. Since we are now allowing APBS to be launched without a previous PDB2PQR job, it would be useful to treat both as individuals, even if the user is using the PQR file from another PDB2PQR task.

As such, the Job Status page should reflect this. Namely:

• Don't display both PDB2PQR and APBS columns. Show only the one related to the job requested
• Restyle the page to show the progress of the job.
  • For now this includes the states "RUNNING", "COMPLETE", and "ERROR"
  • Later states should include
    • "QUEUE" - for tasks in TESK but not running
    • "DOWNLOADING" - when tasks are downloading input files into respective volume in cluster
    • "UPLOADING" - when uploading respective output files to storage service

Duplicating page does not trigger fetch for new job ID

On Chrome, duplicating a tab while on the configuration page does not trigger another job ID to be fetched from the server.

This carries the dangerous effect of potentially conflicting with/overwriting the results of an existing job, with the backend's current implementation.

Implement long-polling when checking for job status from server

Current method to check job status client side is a naive implementation of a fetch request. Obviously this can pose an issue with scale.

(will need corresponding issue in backend to support this)

Possible approach from off the dome

• client: sends status request
• server: if job running, send a "running" response
• client: updates timer displays to reflect elapsed time and that job is running
• client: sends a long-poll request
• server: waits on to respond until job is in a finished state. Then send response

Refill fields in APBS after uploading new PQR file

While the items in the APBS form autofill after uploading a PQR file, uploading a new PQR file doesn't refill the fields with new values

Disable "Submit" button until validation checks pass

Add a state flag to disable the submit button until all validation checks are passed. At the very least, this would serve as a first gate to preventing user from submitting an invalid form. Of course, validate in the backend as well (will create related issue)

A search field to navigate to an existing job would be nice in case user doesn't have the link on hand

If a user navigates away from the job status page mid-job without saving the URL, there isn't a way to navigate to a running/completed job. Having a search field on the homepage or navigation bar, like a USPS/Fedex tracking number, would help in requiring the user to only have to save an ID number rather than an entire URL.

This should be in addition to the option to supplying an email address for notification as described in #5

Send APBS form data as JSON

After a user hits submits a job, the form values should be sent to the server as JSON data rather than the default HTML form

APBS job autofill warns user of field overwriting only if they previously used the auto-fill

If the user starts manually filling in the fields for an APBS job configuration but then decides to auto-fill them through a PQR upload, they are not warned that uploading will potentially overwrite all the fields.

This is unlike the current case where a warning is emitted only if an auto-fill was already used

Proposed solution

• raise a flag upon change to any form item. Ensure warning mechanism acknowledges it

Allow user to to choose the input file type on the interface

At the moment, the core APBS software supports various input file types within its READ section including keywords "mol", "charge", "diel". Because we are porting this from the old interface which supported only the "mol" keyword with *.pqr files, this is all that is supported for now.

Expanding this would be a nice feature to add in the future. Will require adjustments to backend (will create related issue for that)

Navigating to an APBS job from the job status page would be useful

Under the assumption that an ABPS calculation would often occur after a PDB2PQR run (as with the old server), we should include a button on the job status page that would go the the respective APBS config page for the job ID

Send PDB2PQR form data as JSON

Currently the APBS job config form consolidates form data and sends as a JSON request. This ought to be the case for PDB2PQR.

Noteworthy Obstacles

• Handling uploads for PDB, User forcefield/names, and Ligand MOL2 files