From d1910f722988e4affdfd0fccce1101179fb9aef7 Mon Sep 17 00:00:00 2001 From: MarvinDo Date: Mon, 26 Feb 2024 11:15:10 +0100 Subject: [PATCH] bugfixes in assay length --- .../annotation_jobs/annotate_from_vcf_job.py | 2 ++ src/common/db_IO.py | 2 +- src/frontend_celery/webapp/templates/index.html | 14 ++++++++++++-- .../webapp/templates/variant/variant_base.html | 8 +++++++- 4 files changed, 22 insertions(+), 4 deletions(-) diff --git a/src/annotation_service/annotation_jobs/annotate_from_vcf_job.py b/src/annotation_service/annotation_jobs/annotate_from_vcf_job.py index 31434d9b..0273826f 100644 --- a/src/annotation_service/annotation_jobs/annotate_from_vcf_job.py +++ b/src/annotation_service/annotation_jobs/annotate_from_vcf_job.py @@ -153,6 +153,8 @@ def save_to_db(self, info, variant_id, conn): #submissions = functions.decode_vcf(submission)#.replace('\\', ',').replace('_', ' ').replace(',', ', ').replace(' ', ' ').replace('&', ';').split('|') conn.insert_clinvar_submission(clinvar_variant_annotation_id, submissions[1], submissions[2], submissions[3], submissions[4], submissions[5], submissions[6]) + + assay_type_dict = conn.get_assay_type_id_dict() conn.delete_assays(variant_id = variant_id,user_id = None) # delete only automatically annotated assays # CSpec splicing assays diff --git a/src/common/db_IO.py b/src/common/db_IO.py index ac6f7469..af2dc6ed 100644 --- a/src/common/db_IO.py +++ b/src/common/db_IO.py @@ -1246,7 +1246,7 @@ def preprocess_submission_condition(self, submission_condition): submission_condition.append("missing") elif len(submission_condition) > 2: functions.eprint("WARNING: the clinvar submission condition: " + str(submission_condition) + " has more than two entries. Although it should only have 2: id and description. Will be neglecting everything after the first two entries.") - submission_condition = submission_condition[0:2] + submission_condition = [submission_condition[0], ':'.join(submission_condition[1:])] return submission_condition def get_variant_consequences(self, variant_id): diff --git a/src/frontend_celery/webapp/templates/index.html b/src/frontend_celery/webapp/templates/index.html index e537056e..bf928995 100644 --- a/src/frontend_celery/webapp/templates/index.html +++ b/src/frontend_celery/webapp/templates/index.html @@ -92,9 +92,20 @@

Overview

Changelog

-
v 1.8.1 (23.02.2024)
+ +
v 1.8.2 (26.02.2024)
!! The automatic classification algorithm is currently under construction. HerediVar is already prepared for it. Thus, you might encounter disabled buttons or dummy data. It will be enabled in a future update
!! Scores from likelihood ratio tests are currently under construction. A simple reannotation is required to show them on HerediVar once they are ready to be downloaded from HerediCaRe.
+
+ Bugfixes: +
    +
  • Fixed a bug where the SpliceAI score was not shown correctly when it is "."
    • +
  • In rare cases the submission condition in ClinVar submissions is na with a description. This case is now handled properly and does not produce erroneous links.
    • +
  • Fixed a bug when the assay comment for splicing assays could not be inserted due to length
    • +
+
+ +
v 1.8.1 (23.02.2024)
General changes:
    @@ -107,7 +118,6 @@

    Changelog

  • Fixed default strength for supporting criteria in ACMG standard scheme
  • Fixed wrapping of PVS1_mod criterium
  • Fixed a bug where the SpliceAI scores would not show on longer indels
    • -
  • Fixed a bug where the SpliceAI score was not shown correctly when it is "."
v 1.8 (21.02.2024)
diff --git a/src/frontend_celery/webapp/templates/variant/variant_base.html b/src/frontend_celery/webapp/templates/variant/variant_base.html index b05f3c16..3898326e 100644 --- a/src/frontend_celery/webapp/templates/variant/variant_base.html +++ b/src/frontend_celery/webapp/templates/variant/variant_base.html @@ -301,9 +301,15 @@

ClinVar classifications

{{ submission.review_status }} {% for clinvar_submission_condition in submission.conditions %} + {% if clinvar_submission_condition.condition_id == 'na' %} +
+ {{clinvar_submission_condition.title}} +
+ {% else %}
{{ macros.external_link(clinvar_submission_condition.title, "https://www.ncbi.nlm.nih.gov/medgen/" + clinvar_submission_condition.condition_id) }}
+ {% endif %} {% endfor %} {{ submission.submitter }} @@ -434,7 +440,7 @@

Assays

{% for assay_metadata_title in assay.metadata %}
{{assay.metadata[assay_metadata_title].metadata_type.display_title}}
-
{{assay.metadata[assay_metadata_title].value}}
+
{{assay.metadata[assay_metadata_title].value}}
{% endfor %}