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:Summer 4: 14 Jul - 28 Jul, Summer 5: 3 Aug - 14 Aug
Description
The DAS (version 1) test that relies on this URL - http://genome.cse.ucsc.edu/cgi-bin/das/dsn - is now failing.
We should remove this test or create a mock object that will allow the test of our code to proceed even if the data source is not available.
However, since the UCSC DAS service is no longer actively supported at UCSC, we should eliminate it from the code base. The UCSC DAS1 server was the only DAS service available, so we should probably remove it from the code base.
Note: Removing DAS1 support will affect many places in the code, notably:
- Places where default data sources are configured - see IGB Preferences JSON file
- DAS module itself: "Core - DAS (data source) module"
- POM files that declare dependencies on the DAS module within IGB
Attachments
Issue Links
Activity
| Labels | Beginner |
| Description |
The DAS1 test that relies on this URL - http://genome.cse.ucsc.edu/cgi-bin/das/dsn - is now failing.
We should remove this test or create a mock object that will allow the test of our code to proceed even if the data source is not available. However, since the UCSC DAS1 service is no longer actively supported at UCSC, we should eliminate it from the code base. |
The DAS (version 1) test that relies on this URL - http://genome.cse.ucsc.edu/cgi-bin/das/dsn - is now failing.
We should remove this test or create a mock object that will allow the test of our code to proceed even if the data source is not available. However, since the UCSC DAS service is no longer actively supported at UCSC, we should eliminate it from the code base. The UCSC DAS1 server was the only DAS service available, so we should probably remove it from the code base. Note: Removing DAS1 support will affect many places in the code, notably: * Places where default data sources are configured - see IGB Preferences JSON file * DAS module itself: "Core - DAS (data source) module" * POM files that declare dependencies on the DAS module within IGB |
| Assignee | Ann Loraine [ aloraine ] |
| Summary | Ignore tests that rely on DAS1 server at UC Santa Cruz | Remove DAS v1 support (UCSC DAS v1 service not responding) |
| Epic Link | IGBF-1531 [ 17617 ] |
| Sprint | Summer 4: 14 Jul - 28 Jul [ 99 ] |
| Rank | Ranked higher |
| Assignee | Prutha Kulkarni [ prutha ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | Ignored-Testcases.png [ 14781 ] |
| Comment |
[ Commenting for future reference:
The test cases were already ignored when we try to build IGB using @Ignore annotation. Attaching the screenshot of the same. ] |
Update:
When I removed the DAS plugin and related dependencies from the codebase, the IGB is throwing and exception whenever I am clicking on any Genome to load it.
The exception screenshot is attached to the ticket.
I am investigating the same right now. Looks like the data is not getting loaded after the removal of that dependency.
I am checking the "GeneralLoadUtils" class for the same as it is responsible for loading the data into IGB.
I would mostly continue to work on it tomorrow as I was not able to figure out the cause today.
| Attachment | IGB Exception .png [ 14782 ] |
The code changes are present at :
https://bitbucket.org/pkulka10/igb_prutha/commits/704ebb7507a36fb3595f7d5b802c264e6d5b7fa0
For testing:
Go to the "Downloads" section of my fork and download IGBF-2474 branch installer.
Check if the IGB is functioning properly after removing the DAS v1 support from the codebase.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Prutha Kulkarni [ prutha ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
I have reviewed this ticket. Everything looks fine. Kindly submit a PR for the same Prutha Kulkarni
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] | Prutha Kulkarni [ prutha ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Dr. [~aloraine]
Pull request has been submitted:
https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/813/igbf-2474-remove-das-v1-support/diff
| Sprint | Summer 4: 14 Jul - 28 Jul [ 99 ] | Summer 4: 14 Jul - 28 Jul, Summer 5: 29 Jul - 12 Aug [ 99, 100 ] |
| Rank | Ranked higher |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Prutha Kulkarni [ prutha ] |
PR is merged.
To test, please download master branch installer from the team bitbucket repository.
Request for Prutha Kulkarni:
Could you provide a little more detail on specifics of testing?
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
| Assignee | Prutha Kulkarni [ prutha ] |
Testing steps:
- Go to the "Downloads" section of my fork and download
IGBF-2474branch installer or Master installer(since the code is merged). - Check if the IGB is functioning properly after removing the DAS v1 support from the codebase. Genomes should load properly.
- Check if the name and url for DAS v1 has been removed from 'Data Sources' in IGB Preferences.
- To check if the codebase doesn't have any DAS V1 related functionality, clone my IGB on your system. With the help of CTRL+SHIFT+F search "das" globally in the IGB project. The code should either be commented or removed. Check each and every file that shows up in the search results.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Prutha Kulkarni [ prutha ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Tested this ticket as per the steps mentioned above. Everything is working as expected. Moving to closed.
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] | Prutha Kulkarni [ prutha ] |
To start, turned off tests in DasDataProviderTest. Committed to master branch.