Fix end coordinates in ClinVar for indels #4593
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northwestwitch
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northwestwitch
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #4593 +/- ##
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Coverage 84.58% 84.58%
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Files 310 310
Lines 18634 18634
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Hits 15762 15762
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Tested on stage with this variant Main branch:
This branch:
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| @@ -107,7 +107,7 @@ def _get_snv_var_form(variant_obj, case_obj): | |||
| var_form.variations_ids.data = var_ids.split(";")[0] | |||
| var_form.chromosome.data = variant_obj.get("chromosome") | |||
| var_form.start.data = variant_obj.get("position") | |||
| var_form.stop.data = variant_obj.get("position") | |||
| var_form.stop.data = variant_obj.get("end") | |||
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Did you check the docs or test with their stage endpoint to see if this is correct in terms of inclusive coords (off by one or not)?
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Tested using the current submission for cust000 on stage.
Downloaded it as json and used it in a dry-run using preClinVar:
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And before they would have failed it? 😊
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No, the dry run doesn't check that type of things it seems (I tried now). It returns success as well
Checked on their docs and they say:
So we should be fine, no?
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I think so, yes, but I would be a wealthy person if I got a minute amount of currency for every off-by-one error I've had.
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Did you check the JSON summary report from the dry-run? It should be available with that sub nr right?
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Let's try like this. We can fix if they complain. It's not that they make us test better using the test endpoint
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Tested on validate preClinVar endpoint and this fix is effective. There is another error related to the condition that perhaps needs fixing. but this is good to merge
| @@ -276,7 +276,7 @@ def parse_variant_form_fields(form): | |||
| clinvar_var["variations_ids"] = form["dbsnp_id"] | |||
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| if clinvar_var.get("ref_seq") and clinvar_var.get("hgvs"): | |||
| # Variant is described by RefSeq and HGVS already, remove redundanti fields from submission | |||
| # Variant is described by RefSeq and HGVS already, remove redundant fields from submission | |||
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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: