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 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct
Description
Investigate and propose a fix for the following.
The IGB App "Merge Annotation Operation" is currently failing with IGB 9.1.0, even though it can be installed. The problem may be due to a change in the API or possibly an OSGi wiring issue.
The bug:
You execute the usual workflow to install the App to IGB 9.1.0. However, when you try to find the App's menu item under Annotations tab > Multi-Track Operations, it is not there.
To reproduce:
1) Launch IGB 9.1.0
2) Select Arabidopsis genome (click flower picture next to the Mona Lisa)
3) Observe Araport track loads (this is an annotations track)
4) Open another annotations track by selecting its checkbox in the Available Data Sets section (TAIR10 is fine)
5) Load some data for the new track by clicking "Load Data" button or by choosing "Genome" in the Load Mode menu in the Data Management Table.
6) Select Annotations Tab
7) Click "Select All"
8) Now check the Operations menus. If you have installed Merge Annotations Operator, there should be an option "Merge" in this menu.
To install the App:
1) Go to https://bitbucket.org/lorainelab/merge-annotation-operator/src/master/
2) Click Downloads link
3) Copy URL
4) Add this repository as a new App repository in IGB
5) Install the App (it should appear as a new App in the App Manager)
Attachments
Activity
Prof. [~aloraine], I was trying to compare the older version of the plugin with the new one in order to solve the problem. So, I switched to an old branch of IGB which had optionalPlugings code which was created before the separation of optionalPlugins into different repositories because I thought something might have gone wrong after the code separation. So, I tried to run the igb following same steps which are mentioned in the description but instead of adding repository path of downloads section, I added the local path of the target folder and installed the plugin. The "Merge" option was not appearing under the multi-track dropdown. But, when I tried to install the app with "9.0.0" version which is there on "https://bioviz.org/igbserver" then the "Merge" option is appearing under the dropdown. Could you please let me know where I can find the 9.0.0 versioned code of the plugin so that I can compare it with the latest one to check where is it failing?
Thanks.
To locate the 9.0.0 version of the plugin, you would need to check out the 9.0.0 "release" version of the IGB code base.
Normally, to do this, you would look for a release branch here: https://bitbucket.org/lorainelab/integrated-genome-browser/branches/
However, as you can see, it looks like nobody bothered to create such a branch. Boo!!
So I searched the commits for search string "9.0.0" and found this:
You might also look for tags containing string 9.0.0.
Good luck and let me know if there is anything else I can do to help.
I have fixed the issue with Merge Annotation plugin. One line was missing in the configuration of maven bundle plugin because of which the "Merge" option was not appearing in the Multi-Track dropdown of Annotation tab.
The code changes are present at :
https://bitbucket.org/pkulka10/prutha_mergeannotoperator/commits/1841886c80f37e1fe128197e8e1c76bc677d753c
Steps for testing:
1) Go to the downloads section of my fork(if the changes are not merged else use /merge-annotation-operator repository's downloadsection)
2) copy the link of this download section and add this as a new repository in the Plugin Manager of IGB.
3) Follow the "Steps to reproduce" which are mentioned in the description section of the ticket.
4) You would be able to see "Merge" option under Multi-Track dropdown of Annotation Tab which denotes the plugin has been successfully installed and activated and now you can use it.
5) Go ahead and click on Go option which is present next to the combobox.
6) Now, you would see a new track named "merge" which would be above all the tracks.
I followed the steps above and observed the correct behavior. Ready for PR Prutha Kulkarni
Prof. [~aloraine], I have submitted a PR for the same.
Code changes are present at:
https://bitbucket.org/lorainelab/merge-annotation-operator/pull-requests/9/igbf-2010-investigate-why-merge-annotation/diff
Could you please merge it into the master?
Thanks.
Merged. The newly built jar is available from https://bitbucket.org/lorainelab/merge-annotation-operator/downloads/ and ready for testing.
I am able to view the merge option under multi-track option. It is working as expected.
Please work on this after moving the two maven build related issues
IGBF-1945andIGBF-1993to Needs First Level Review.If you have questions or concerns, please let me know!