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: 9.0.1 Minor Release
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Labels:None
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Sprint:B - Summer 2018
Description
Investigate whether ordering of data providers in IGB preferences JSON file affects their top-to-bottom order in the IGB Available Data Sets section of Data Access tab.
To-Do:
- Update tests in Preferences module to ensure tests do not fail due to trivial reasons such as changing order of data providers in the preferences file.
- Check if order of data sources in Preferences JSON file dictates order in which they appear in Data Access tab. If yes, place new RNA-Seq and BAR data sources above IGB Quickload.
Attachments
Issue Links
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- Closed
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Activity
Fixed Test case as per the suggestions given by Ivory in First level review.
Moving the issue to "First level review" column.
Yes, I liked the idea of modifying the test case in the way Ivory mentioned. Its more clearer and specific. I will change the test case.
Package name was throwing error. Packages are meant for separation. Test file is in com.lorainelab... but it had package name as org.lorain.. So i changed it to the right package it belonged to.
Sneha, I emailed you a note about doing a git rebase.
Please review that and the notes above and make what changes you see fit before passing the issue to the next 1st level reviewer.
(I think we are still doing 2-layers of 1st level review).
We could stand to improve this test. With this new test, we don't really know if the prefs are being read in correctly, just that its reading something, and it got at least one something. We should consider adding something like:
String aName = prefs.getDataProviders().get(0).getName()
assertTrue(!Strings.isNullOrEmpty( aName ) )
int loadPriority = prefs.getDataProviders().get(0).getLoadPriority()
assertTrue(loadPriority instanceof Integer)
Then we would know at least the first one had at least some symptom of being the right data type.
But at least for now, this modified test looks fine.
Digging into the tests here is outside the scope of this issue.
Methods tried:
Interchanging of Load priorities were not changing the load sequence in both Data access Tab and Preferences table.
Change in JSON sequence changed the order but behavior was not consistent
Ex: If RNA-Seq was first element in JSON then it would load before IGB Quickload but if Blueberry is first element, it would not load first so the behavior was inconsistent.
After analyzing, I understood that loadPriority of value "2" was missing. Load priority was 0, 1 ,3, 4, 5...
Issue was fixed when I added load priorities in proper sequence.
Now data providers load according to their Load priority irrespective of their placement in JSON file.
Also fixed test case associated with the same.
Branch link: https://bitbucket.org/swathark/integrated-genome-browser/branch/IGBF-1221-DPOrder
Tested using the IGB-master.dmg downloaded from bitbucket main master...
After reseting preferences, the default data providers appear in this order:
IGB Quickload
RNA-Seq
Bio-analytic Resource
(I think that's wrong)
I also downloaded the latest version of master (with this branch merged in) and when I run it the data providers appear in the correct order.
This baffles me.
The test seem to work. The build fails when I make bad changes to the igbDefaultPrefs.json file.
I'm happy with the code, I'm just baffled by the installer producing a different result.