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:None
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Story Points:4
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Epic Link:
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Sprint:Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun
Description
When we first started migrating to OSGi, developer Lance Frohman (Genentech) created a plug-in that drew a sashimi-plot graphic on top of gene models to highlight splicing support.
Recently, we moved the code to a new repository:
https://bitbucket.org/lorainelab/development-apps/src/master/TranscriptIsoform/
Let's revisit this code and investigate what it would be take to implement it now.
Attachments
Issue Links
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IGBF-2373 Move transcript isoform App into a separate repository
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- Closed
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Activity
Progress:
- Initially I was trying to check how the app functions when we install it in IGB.
- When I tried to install the app, nothing was changing in the "VIEW" menu of IGB as written in the code.
- I realized that the bundle activator tag and everything in the POM is changed multiple times in order make it a standalone repo.
- Then as per the discussion, in order to remove activate method and to use @component annotation, I uncommented the @component line which was already there.
- After that I started checking previous commits.
- The TranscriptIsoform app code initially was using "IgbMenuItemProvider". At that time the code had @activate method as well as @component annotation.(I don't know if that was in a working state as IgbMenuItemProvider is not longer supported and I was unable to build that code.)
https://bitbucket.org/pkulka10/developmentplugins/commits/e2b1c688e48d5e40e1e8e8665791605fcc2a4ed5#chg-TranscriptIsoform/src/main/java/com/gene/transcriptisoform/TranscriptIsoFormMenuProvider.java - Later it was changed to implement "MenuBarEntryProvider" in following commit:
https://bitbucket.org/pkulka10/developmentplugins/commits/f74e0b2065ae033950cdbffbf46e1d32749f255d - After above commit, the component part was commented and the activate method along with Optional<List<MenuItem>> getMenuItems() method from "MenuBarEntryProvider" was used to display menuItem with submenu items (menu items which appear after the app installation) in order to introduce app's functionality. Optional<List<MenuItem>> getMenuItems() is just written but the code inside it is commented and is not affecting the IGB Menu manipulation.
- To remove activate method I will have to use Optional<List<MenuItem>> getMenuItems() method properly like other available apps to add a Menu Item dynamically in IGB.
- Then I checked the IGB code as well as other available app's code to make sure if any code uses IGB MenuBarEntryProvider methods to load the menu items with submenu dynamically.
- I found that the repos which I had referred only adds one menu item and not a menu with submenu.
- I tried a few ways to add submenu items using MenuBarEntryProvider but I am not sure how the function given below works:
MenuItem(String menuLabel, Set<MenuItem> subMenuItems)
as this should be used to add submenu items in IGB menu item. - I passed a Set of MenuItems to create submenu but the submenu is not getting rendered on the screen. Only one menuItem without submenu is being displayed even after doing so.
- Also, I wanted to mention that if we are using MenuBarEntryProvider to add submenu dynamically then we don't have enough options to add different type of submenu. The submenu item types which are needed: normal menuItem(available), CheckBoxMenuItem(available) and a group of radioButtonMenuItems(unavailable).
I have assigned available/unavailable tag next to the types which are provide/not provided in "org.lorainelab.igb.menu.api.model" package.
Tested on the latest dev version of IGB on macOS.
IGBF-2373has been resolved, it may be good to try the build again.The app seems to be functioning as expected. Moving to done.