Fix liftover #5326
Fix liftover #5326
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #5326 +/- ##
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Coverage 84.46% 84.46%
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Files 326 326
Lines 19961 19958 -3
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- Hits 16860 16858 -2
+ Misses 3101 3100 -1 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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| @@ -10,23 +10,18 @@ | |||
| LOG = logging.getLogger(__name__) | |||
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| HEADERS = {"Content-type": "application/json"} | |||
| RESTAPI_37 = "https://grch37.rest.ensembl.org" | |||
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Back in the day we had this distinction because we had more REST API functions. This is no longer needed now, I think
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Ah wait a sec, there is one functionality that is not liftover. I'll convert this to a draft again
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Ah no, it's just a test, nothing used in the code. I think I'll just remove it
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| @responses.activate | ||
| def test_send_gene_request(ensembl_gene_response, ensembl_rest_client_37): | ||
| """Test send request with correct params and endpoint""" | ||
| url = f"{RESTAPI_37}/overlap/id/ENSG00000103591?feature=gene" |
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This overlap functionality is not even used in Scout so the test is pointless
This PR adds a functionality or fixes a bug.
Testing on cg-vm1 server (Clinical Genomics Stockholm)
Prepare for testing
scout-stageand the server iscg-vm1.ssh <USER.NAME>@cg-vm1.scilifelab.sesudo -iu hiseq.clinicalssh localhostpodman pssystemctl --user stop scout.targetsystemctl --user start scout@<this_branch>systemctl --user status scout.targetscout-stage) to be used for testing by other users.Testing on hasta server (Clinical Genomics Stockholm)
Prepare for testing
ssh <USER.NAME>@hasta.scilifelab.seus; paxa -u <user> -s hasta -r scout-stage. You can also use the WSGI Pax app available at https://pax.scilifelab.se/.conda activate S_scout; pip freeze | grep scout-browserbash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_scout -t scout -b <this_branch>us; scout --versionpaxaprocedure, which will release the allocated resource (scout-stage) to be used for testing by other users.How to test:
Expected outcome:
The functionality should be working
Take a screenshot and attach or copy/paste the output.
Review: