Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:0.5
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Epic Link:
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Sprint:Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun
Description
BioViz Connect has a feature that lets users run analysis algorithms on files using CyVerse cloud resources. This is super useful because often people want to see output of visual analytics functions that are too compute or data intensive to run on a personal computer.
So we (IGB CyVerse core team) have created and published analysis "apps" within CyVerse itself, thus making them available for users to run and then view the output in IGB.
Recently we published an App for generating scaled coverage graphs. This uses a tool from the DeepTools suite.
Currently, the documentation for the App within BioViz Connect contains a weird-looking string - %INPUT%bam. (Please see attached screen capture.) It is not clear what this means and so this could be a bit confusing for users.
For this task, investigate why this is being shown. If feasible, propose a way to remove it, unless it is trying to convey some kind of useful information, in which case we should probably try to think of better wording.
Note: We might leave it – depends on the level of difficulty involved! Thus the goal of this task is to "investigate" only.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2376 [ 18533 ] |
| Rank | Ranked higher |
| Assignee | Ann Loraine [ aloraine ] |
| Description |
BioViz Connect has a feature that lets users run analysis algorithms on files using CyVerse cloud resources. This is super useful because often people want to see output of visual analytics functions that are too compute or data intensive to run on a personal computer.
So we (IGB CyVerse core team) have created and published analysis "apps" within CyVerse itself, thus making them available for users to run and then view the output in IGB. Recently we published an App for generating scaled coverage graphs. This uses a tool from the DeepTools suite. Currently, the documentation for the App within BioViz Connect contains a weird-looking string - %INPUT%bam. (Please see attached screen capture.) It is not clear what this means and so this could be a bit confusing for users. For this task, investigate why this is being shown. If feasible, propose a way to remove it, unless it is trying to convey some kind of useful information, in which case we should probably try to think of better wording. |
BioViz Connect has a feature that lets users run analysis algorithms on files using CyVerse cloud resources. This is super useful because often people want to see output of visual analytics functions that are too compute or data intensive to run on a personal computer.
So we (IGB CyVerse core team) have created and published analysis "apps" within CyVerse itself, thus making them available for users to run and then view the output in IGB. Recently we published an App for generating scaled coverage graphs. This uses a tool from the DeepTools suite. Currently, the documentation for the App within BioViz Connect contains a weird-looking string - %INPUT%bam. (Please see attached screen capture.) It is not clear what this means and so this could be a bit confusing for users. For this task, investigate why this is being shown. If feasible, propose a way to remove it, unless it is trying to convey some kind of useful information, in which case we should probably try to think of better wording. Note: We might leave it -- depends on the level of difficulty involved! Thus the goal of this task is to "investigate" only. |
| Sprint | Spring 8 : 24 Apr to 8 May [ 93 ] | Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May [ 93, 94 ] |
| Rank | Ranked higher |
The %INPUT% is how BioViz Connect determines what input files an analysis can be run on. Unfortunately CyVerse does not provide additional fields that we can populate with this information.
The only option to remove this so that the user does not see it would be to apply a filtering on BioViz Connect to remove any text starting with and following %INPUT% for the description field.
I think it would be a good idea to filter out this information, as it is not beneficial to the user.
| Sprint | Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May [ 93, 94 ] | Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun [ 93, 94, 95 ] |
| Rank | Ranked higher |
| Assignee | Chaitanya Kintali [ chaitanya ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
I have made the code changes to remove the %input% information from the description.
However, it would not affect the current functionality or the flow, since, we are using the description from the Cyverse API to manage and show the list of apps at the backend, Doing any changes at the UI would not affect this flow.
Moving it to Needs First Level Review.
Nowlan Freese, Could you please test the above code changes at chaitanya.bioviz.org. I have my code changes pushed onto my ec2 and let me know if I can raise a pull request if everything looks good.
https://bitbucket.org/ckintali/latest-ck-django-cyversedev/commits/9e152a6000e40211323d3f2f200bb7a55f660531
https://bitbucket.org/ckintali/latest-ck-django-cyversedev/commits/bd23ea42549d1907a06df58063c05908d82a98bb
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Chaitanya Kintali [ chaitanya ] | Nowlan Freese [ nfreese ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Working correctly for the three analyses, the %input% is not visible and the coverage graph analysis is still working.
Moving to ready for pull request.
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Nowlan Freese [ nfreese ] | Chaitanya Kintali [ chaitanya ] |
Merged https://bitbucket.org/nfreese/django-cyversedev/pull-requests/165/igbf-2377/diff
Chaitanya Kintali pull master onto your EC2 and I will test.
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Chaitanya Kintali [ chaitanya ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Nowlan Freese [ nfreese ] |
Working correctly.
Closing issue.
| Assignee | Nowlan Freese [ nfreese ] | Chaitanya Kintali [ chaitanya ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
cc: Nowlan Freese to keep you in the loop.