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:0.5
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Epic Link:
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Sprint:Fall 2
Description
When running UCSCRestSymloaderTest, getting the below error in the log, this isn't an error that fails the test case, but need to be fixed to make the log cleaner:
java.lang.NoClassDefFoundError: org/apache/commons/lang3/StringUtils
at org.lorainelab.igb.synonymlookup.services.impl.SynonymLookup.loadSynonyms(SynonymLookup.java:73)
at org.lorainelab.igb.synonymlookup.services.impl.ChromosomeSynonymLookupImpl.<init>(ChromosomeSynonymLookupImpl.java:28)
and when trying to load a chromosome that's not present for a dataset, UCSC is now throwing a Bad request error, so we have to handle this in the code:
Sep 20, 2024 2:49:43 PM com.affymetrix.genometry.quickload.QuickLoadSymLoader logException
SEVERE: Unexpected response status: 400
org.apache.http.client.ClientProtocolException: Unexpected response status: 400
at org.lorainelab.igb.ucsc.rest.api.service.utils.ApiResponseHandler.handleResponse(ApiResponseHandler.java:33)
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
|
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Nowlan Freese [ nfreese ] |
Code changes look good, and I am no longer seeing the error when building IGB with tests.
Ready for pull request.
| Status | First Level Review in Progress [ 10301 ] | 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 ] |
| Assignee | Nowlan Freese [ nfreese ] | Jaya Sravani Sirigineedi [ jsirigin ] |
Raised the pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1039
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Fix Version/s | 10.1.0 [ 11000 ] |
| Assignee | Ann Loraine [ aloraine ] |
PR is merged. New installers are built and deployed to bioviz.org early access section.
Ready for testing.
| Assignee | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Tested on main branch installer on Mac and main branch through terminal on Mac.
I am no longer seeing the 400 error when loading the T2T annotations for chrM and I am not seeing the error when building IGB with tests.
Closing ticket.
| Assignee | Nowlan Freese [ nfreese ] | Jaya Sravani Sirigineedi [ jsirigin ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Resolved both issues. Fixed the NoClassDefFoundError in the UCSCRestSymloaderTest by adding the required dependencies for the test scope and fixed the Bad request error by updating the code to handle the 400 status response by logging it as a warning message instead of throwing an error. Updated code is present at: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3915. Warning message is taken from the response of UCSC API, below is the warning message that gets logged for the scenario where user tries to load a chromosome that's not present for that dataset:
Please review and let me know if there are any issues.