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: 10.1.0
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Labels:None
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Story Points:1
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Epic Link:
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Sprint:Fall 1, Fall 2
Description
Situation: In IGB 10.1.0 we are adding the UCSC REST API data provider to replace the UCSC DAS data provider. On the current IGB main branch we have set the DAS data provider to be disabled. If IGB 10.1.0 is installed on a new system, DAS is disabled. However, if a user goes from 10.0.1 to 10.1.0 the DAS data provider remains enabled. Having both DAS and UCSC REST enabled slows IGB down it requires additional API calls.
Task: Remove the DAS data provider from the igbDefaultPrefs.json file. This will work to remove DAS from both new installs of IGB as well as updates from a previous version of IGB to the new version.
Attachments
Activity
After going through the code a bit more for this ticket, I understood that this part of the code is only executed when the user creates a custom data provider, which won't have the option to specify datasetLinkoutUrl and also won't have any defaultDataProviderId. So, the if condition will always be false and isn't required at all. That's why I have removed it and it's the code I added when adding the datasetLinkoutUrl to the constructors.
Ah gotcha, thank you!
Please go ahead and create a PR.
Raised the pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1036
PR is merged and new installers built and copied to "early access" section of Bioviz.org website.
Ready for testing.
Testing using main branch installer on Mac.
After running 10.0.1 and then switching to 10.1.0 the DAS data provider is no longer a Data Source.
I am able to add back the DAS data provider in the Data Sources tab.
The UCSC REST data provider id now appears in the "info" window in the Data Source tab.
Closing ticket.
The UCSC DAS data provider has been disabled as far back as release-9.0.1 in the igbDefaultPrefs.json (9.0.1 was as far back as I tested). In release-9.1.6 we removed DAS v1 support (
IGBF-2474) and also removed DAS from igbDefaultPrefs.json. The removal of the DAS v1 module in IGB caused a few features to fail in IGB (external view tab), and this is what we received user requests for (HELP-374). We then restored DAS v1 support in IGB for release-9.1.8 (IGBF-2793), but we kept the DAS data provider as disabled. We then switched the DAS data provider to be on by default in release-9.1.10 (IGBF-3068).For testing, I went back to the release-9.1.0 branch (DAS disabled by default), enabled DAS, closed IGB, started release-9.1.2 branch (DAS disabled by default), and DAS remained enabled.
My conclusion is that if a data provider is enabled, switching the data provider to disabled in igbDefaultPrefs.json will not override the enabled status of the data provider when a user switches to a new version of IGB. The user help issues related to DAS were due to a previous reliance on DAS for the external view tab, that has since been updated to use the UCSC REST API endpoint (
IGBF-2863).My recommendation would be to remove the DAS data provider from igbDefaultPrefs.json. The UCSC REST API is providing all of the functionality that DAS provided, and we have only had das enabled by default for the last two releases (9.1.10 and 10.0.0). We can add documentation to the IGB user's guide for how to re-enable the DAS data provider, should a user need it.