A basic user should be able to import simple files (i.e. single-file directory formats) without having to create a directory or using a particular file naming requirement.

The job inputs are within a form, so Enter/Return is linked to submitting that form, however the job submission currently doesn't use that same method, so it'll need to have an event listener added and route the enter key to the proper onSubmit() function instead of "submitting" the form itself.

It seems like it'll actually be possible to hook the function in as both the submit button and the form submission action, so potentially no listener would be needed. <form onsubmit={}> might do the trick, and allow removing the onClick from the Submit button, and moving both Go as type="submit" and Cancel back into the form wrapper.

Artifact/Visualization saving code can likely be simplified. See qiime2/qiime2#135

This was recently added to the framework: qiime2/qiime2#116

At the time of this issue being filed, q2studio has a fallen behind q2cli in terms of supported features. We would like to be more transparent about this with users (since we are bundling this in the VBox image, for example).

At minimum, we would like to display a warning on the main application window, as some kind of permanent alert (e.g. Bootstrap warning/error). If the banner shows up on all application windows, that is okay, too (whatever is quickest/easiest).

If it is straightforward, it would be great to see this warning also show up in a splash screen, but this is just a "nice-to-have."

Since we are moving to an Electron-based app, we don't need to worry about versioning the API anymore, which will simplify the handshake code quite a bit.

Currently in #32 I can create artifacts that get missed by the UI because they don't end in .qzf. Also I can overwrite artifacts (which share a filepath and delete) but the old artifact is still present in the UI, so if I delete the old one, I end up deleting the new one.

See setup.py for the content.

Currently q2-types shows up, but it isn't relevant to the panel.

I ran a visualizer with q2-dada2's plot_qualities. After it completed I hit "Run again" and got the following error:

I'm running this in dev mode.

References
Related to qiime2/qiime2#269

It would also be nice to get Hot Module Reloading working.

Improvement Description
Story:
A user should be able to start the studio without thinking that the program has hung or crashed.

Comments
Not sure what is causing this. I think @thermokarst noticed this initially. It is definitely worse than before.

They get shuffled in state as they get modified during artifact validation. This looks really bad.

Show currently running jobs.

Improvement Description
If a user tries to add a new artifact but runs into an error, all their typed out params are lost. A better behavior would be to not clear the values so they could just edit whichever they think is responsible for the error and try again.

This will probably have to be handled through the server using something like:

os.path.split(os.getcwd())[1]

and sending it along either in the initial connection hash, or on one of the first contacts between the two, as using Node's __dirname is just placing a '/' as the title of the page, and assuming they'll launch the server from different directories while the UI stays in place it makes more sense to come from the backend.

Comments
This will certainly simplify the install process.

Right now the field names are in-{ name }, param-{ name }, out-{ name }. These end up masking each other, we just need to fix this so that name is interpolated into the string correctly.

Right now a Google search for "qiime 2" yields these top hits:

The description for q2studio could stand to be updated with a more accurate summary, or dropped altogether.

In order to support backwards navigation in Electron, a cancel button would allow the user to travel back to the main page without having to execute the job.

q2cli users have the ability to specify the source_format when importing data, it would be great to have feature parity in q2studio.

See qiime2/q2cli#57 for more details on the q2cli implementation.

Check here. I think we should alert(error.error); instead.

This came up on a new install of the the studio --- instead of alerting the error (in this case, it was a matplotlib backend error on mac), it displayed [object Object] 🦂 .

This would be like the react-router middleware, expect instead of pages, it would handle open windows. This way there is a single store for the app and each render process is a view of some section of the shared store.

Output handling code can likely be simplified. See qiime2/qiime2#131

Match q2cli functionality to export data from an artifact.

If the list of formats or types returned by QIIME 2 to the studio is empty, the drop down lists say

FORMAT
FORMAT
FORMAT
FORMAT
... etc

... or ....

TYPE
TYPE
TYPE
TYPE
... etc

... respectively.

Instead they should just be empty, and maybe default to a value such as N/A, None, or NULL.

Related to qiime2/qiime2#267

The framework and CLI now support default values for parameters (qiime2/qiime2#125, qiime2/q2cli#54). It would be great to support default values in the studio.

When the studio encounters an internal error (on the Python side) while processing a job, the job status pane keeps the job as "active" indefinitely. It'd be great to handle this sort of issue (if feasible) on the client side so that it can be reported to users, because it isn't clear right now that the server errored (I thought I just had a long-running job). This is analogous to an internal server error (status code 500) being reported to website users.

Here's some example output for the specific issue I ran into (which I'm about to fix, but it may help illustrate where this could be handled):

[1] API: 127.0.0.1 - - [2016-08-31 12:44:50] "OPTIONS /api/jobs/5834205a-ebf2-45e2-9f3c-af2c3be6bfe9 HTTP/1.1" 200 330 0.001631
[1] API: 127.0.0.1 - - [2016-08-31 12:44:50] "GET /api/jobs/5834205a-ebf2-45e2-9f3c-af2c3be6bfe9 HTTP/1.1" 200 3682 0.002653
[1] API (error): ERROR:concurrent.futures:exception calling callback for <Future at 0x11127d1d0 state=finished returned Results>
[1] Traceback (most recent call last):
[1]   File "/Users/jairideout/miniconda3/envs/qiime2/lib/python3.5/concurrent/futures/_base.py", line 297, in _invoke_callbacks
[1]     callback(self)
[1]   File "/Users/jairideout/dev/qiime2/qiime-studio/qiime_studio/api/jobs.py", line 153, in callback
[1]     result.save(path)
[1] AttributeError: 'Results' object has no attribute 'save'
[1] API: 127.0.0.1 - - [2016-08-31 12:44:51] "GET /api/jobs/5834205a-ebf2-45e2-9f3c-af2c3be6bfe9 HTTP/1.1" 200 3682 0.001878
[1] API: 127.0.0.1 - - [2016-08-31 12:44:52] "GET /api/jobs/5834205a-ebf2-45e2-9f3c-af2c3be6bfe9 HTTP/1.1" 200 3682 0.001785
[1] API: 127.0.0.1 - - [2016-08-31 12:44:53] "GET /api/jobs/5834205a-ebf2-45e2-9f3c-af2c3be6bfe9 HTTP/1.1" 200 3682 0.001880

Examples can be seen here. Basically the goal is to keep the length of this pane under control. We'll need something more robust in the future, but this should work fine for the alpha release.

https://github.com/qiime2/q2studio/blob/master/q2studio/api/workspace.py#L184

Improvement Description
Investigate options for packaging q2studio for user installs.

Actions with long descriptions can take up a majority of the page just with the heading. Possibly break them apart into two pieces, with the description being small.

We need to attach Go to an Executor in the QIIME SDK so that work can be done by the interface.

This will need to be non-blocking, so we can either get the WSGI server to spawn a new flask process for each request OR, set up a non-blocking process call that we can poll periodically OR, we could create something like SSE to actually push the notification to the interface.

For now this could just be a file-browser to choose a single directory, but we could expand this to something more like an IDE's project list.

Steps to Reproduce Behavior
@ebolyen I used the electron-packager to create an executable for q2studio.

I did this by running the command electron-packager . --overwrite --platform=linux --arch=x64 --icon=icons/qiime2_logo.png --prune=true --out=release-builds

This successfully created an executable of the application and when I run the executable named q2studio by running ./q2studio the program boots properly. However, whenever I go to the executable file via the file manager and click on the q2studio executable it gives me an error:

Screenshots

Comments
I am not sure when you click on a file it is opened differently than when it is run in the shell or not.

I added "main": "build/main.js" to the package.json file for the electron-packager. Maybe I did this incorrectly.

• NEW_ARTIFACT
• EXPECTING_ARTIFACT
• DELETE_ARTIFACT
• REFRESH_ARTIFACTS
• LOAD_PLUGINS
• LOAD_WORKFLOWS
• CREATE_JOB
• START_JOB

Subprocesses are seemingly being ran by the default Python install and not the current environment, so job execution is failing due to QIIME 2 not existing in the default Python path.

Improvement Description
Story:
As a developer, I need setup.py to accurately reflect the current release so that I can install qiime2 and plugins.

Current Behavior
Currently Metadata shows just as the filename, with no other functionality (link to view the data, etc).

This results in very unhelpful errors on the UI side. The MacOSX matplotlib backend that now throws the OSError just isn't being passed on to the UI by a try-except.