Details
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Type:
Bug
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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:
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Story Points:0.5
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Epic Link:
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Sprint:Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8
Description
We now have a new IGB App that creates graphs from BAM files using only the soft clips.
The repository is here:
https://bitbucket.org/lorainelab/softclip_track_operation/src/master/
The POM.xml is configured to ensure that when you build the project, the file AppDescription.md gets base64-encoded and included in the repository.xml file.
This is required so that the information contained in the file gets shown to the user when they click on the app in the App Manager window within IGB.
However, this encoding is not happening for some reason.
Investigate why not.
For an example of this correctly working, see the other Apps in the IGB Apps Project.
Attachments
Activity
Fork link: https://bitbucket.org/Inaylor01/softclip_track_operation/src/IGBF-2581/
Change is done according to Supreeth's suggestion above
Please submit a PR when ready.
App description is not getting to the repository.xml. Kindly check.
Some observations -
I read through the pom.xml file in full again to try and narrow down where the issue could be and I settled in around the sourceEncoding variable (currently set to UTF-8).
I figured the issue potentially might be solved by changing this variable to base64 to switch the encoding so the description will work but I ran into a few Maven compiler errors when I did some local testing, so I don't think I've got that quite yet.
I've done a bit of googling about UTF-8 and base64 to see if I maybe had a syntactical issue and will continue to work at it.
Am I in the right ballpark, however?
Suggestion:
- To understand the wrong behavior & fix it, it's helpful to examine a similar system that is working as expected.
We have an app that is super simple that is working as expected - https://bitbucket.org/lorainelab/super-simple-igb-app/src/master/
Build the app either on your local machine or in a bitbucket repo (using the pipeline script). Review the output of the build process to observe the correct behavior. Then look at what happens when you build the (broken) soft clip app. This may give you some ideas.
Some background:
Our Loraine Lab maven plugin bundle-markdown-encoder is supposed to take the file indicated by parameter "markdownFile" and base64-encode it for inclusion in the "repository.xml" file bundled with the app jar file. This is the step that appears to not be working properly with the soft clip app. Something about how the soft-clip app is configured is preventing this from happening.
Also look at the implementation of the plugin. This may also give you some ideas on what to do: https://bitbucket.org/lorainelab/bundlemarkdownencoder/src/master/
Everything works fine. But I am not sure if this is how the soft-clip option should appear if I select operations for a BAM file.
Please submit PR when ready.
For testing, try loading the App from team repo downloads section:
https://bitbucket.org/lorainelab/softclip_track_operation/downloads/
To do this:
- Add the above link as a new App Repository (Tools > App Manager > Manage Repositories)
- The soft clip app should appear in the list of available apps within App Manager
- When you select the soft clip app, you should see the description of the app shown in the App manager
If the above occurs, move to Done.
The softclip app appears as `Graph Soft Clips` application in the list of available apps and shows the description in the app manager
The soft Clip app installs as expected... There are no errors in the logs.
Tested on Mac OS Catalina 10.15.7
GroupId is given as com.igb instead of org.lorainelab.igb
cc: [~aloraine] and Noor Zahara