Fix #4862 - ORPHA inheritance patterns hidden #4863

dnil · 2024-09-17T13:52:05Z

This PR adds a functionality or fixes a bug.

Hide ORPHA inheritance patterns on general report, as they can be misleading. Compare note on variant view.
Also added colored badges for the OMIM inheritance models for consistency with the variant page.

Before:

After:

Testing on cg-vm1 server (Clinical Genomics Stockholm)

Prepare for testing

Make sure the PR is pushed and available on Docker Hub
Fist book your testing time using the Pax software available at https://pax.scilifelab.se/. The resource you are going to call dibs on is scout-stage and the server is cg-vm1.
ssh <USER.NAME>@cg-vm1.scilifelab.se
sudo -iu hiseq.clinical
ssh localhost
(optional) Find out which scout branch is currently deployed on cg-vm1: podman ps
Stop the service with current deployed branch: systemctl --user stop scout.target
Start the scout service with the branch to test: systemctl --user start scout@<this_branch>
Make sure the branch is deployed: systemctl --user status scout.target
After testing is done, repeat procedure at https://pax.scilifelab.se/, which will release the allocated resource (scout-stage) to be used for testing by other users.

Testing on hasta server (Clinical Genomics Stockholm)

Prepare for testing

ssh <USER.NAME>@hasta.scilifelab.se
Book your testing time using the Pax software. us; paxa -u <user> -s hasta -r scout-stage. You can also use the WSGI Pax app available at https://pax.scilifelab.se/.
(optional) Find out which scout branch is currently deployed on cg-vm1: conda activate S_scout; pip freeze | grep scout-browser
Deploy the branch to test: bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_scout -t scout -b <this_branch>
Make sure the branch is deployed: us; scout --version
After testing is done, repeat the paxa procedure, which will release the allocated resource (scout-stage) to be used for testing by other users.

How to test:

how to test it, possibly with real cases/data

Expected outcome:
The functionality should be working
Take a screenshot and attach or copy/paste the output.

Review:

code approved by
tests executed by DN

dnil · 2024-09-17T14:04:28Z

Tested on stage. I was kind of expecting to have to split the general css into a colors part and a more formatting oriented one and only have the colors go to the report, but looks like it works, doesn't it? See if you see anything, and I'll give it another go as well with more rested eyes later.

codecov · 2024-09-17T14:04:44Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 84.78%. Comparing base (c48d621) to head (ae1a94f).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #4863   +/-   ##
=======================================
  Coverage   84.78%   84.78%           
=======================================
  Files         319      319           
  Lines       19289    19290    +1     
=======================================
+ Hits        16354    16355    +1     
  Misses       2935     2935

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

northwestwitch

This changes the code so it will show inheritance only for OMIM terms.

But check for instance at this variant --> https://scout-stage.scilifelab.se/cust002/17083/161ee740fbbc95136ea4c0ff8cc3a916

I think it is safe enough to show that also the ORPHA inhteritance is AR. We could modify both variant page and the report so that whenever OMIM and ORPHA inheritance matches then it's shown in the ORPHA as well, and then we can show other models that appear on ORPHA but not on OMIM apart. Something like this:

OMIM: AR

ORPHA: AR (AD, XR..)

northwestwitch · 2024-09-18T07:32:15Z

scout/server/templates/report_base.html

@@ -6,6 +6,7 @@
 	{% block css %}
  <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-1BmE4kWBq78iYhFldvKuhfTAU6auU8tT94WrHftjDbrCEXSU1oBoqyl2QvZ6jIW3" crossorigin="anonymous">
  <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/all.min.css" integrity="sha512-1ycn6IcaQQ40/MKBW2W4Rhis/DbILU74C1vSrLJxCq57o941Ym01SwNsOMqvEBFlcgUa6xLiPY/NS5R+E6ztJQ==" crossorigin="anonymous" referrerpolicy="no-referrer" />
+  <link rel="stylesheet" href="{{ url_for('static', filename='bs_styles.css') }}">


northwestwitch · 2024-09-18T07:33:54Z

scout/server/blueprints/cases/templates/cases/case_report.html

@@ -712,7 +713,9 @@ <h4>Scout case analysis report</h4> - created on:&nbsp;<strong>{{report_created_
                <td>
                  <ul class="p-0" style="list-style-type: none;">
                  {% for disease_term in gene.disease_terms %}
-                    <li class="d-flex align-items-baseline"><span class="badge bg-secondary m-1">{{ disease_term._id}}</span>&nbsp;<span>{{ disease_term.description }}&nbsp;{{ disease_term.inheritance }}</span></li>
+                    <li class="d-flex align-items-baseline"><span class="badge bg-secondary m-1">{{ disease_term._id}}</span>&nbsp;<span>{{ disease_term.description }}&nbsp;{% if disease_term.source != 'ORPHA' and disease_term.inheritance %}
+                      {% for model in disease_term.inheritance %} {{ inheritance_badge(model,inherit_palette) }}{% endfor %}


Wound't be confusing that variant page shows different values for ORPHA inheritance?

We have modified the variant page to accomodate this, adding a warning. Also, the more clear cut "Gene models" card is nearby. The variant page is used by very or at least somewhat experienced genetics and genomics persons, whereas the reports are often read also by doctors in training, who in particular provide medical input. In the not-yet-specialist case could be confused by an authoritative looking inheritance model, and cannot always be taken to understand the distinction between different database.

Yes I remember this problem and our solution.

northwestwitch · 2024-09-18T07:42:08Z

Good that it's a thing that can be fixed without modifying the disease terms code by the way! 😆

dnil · 2024-09-18T08:14:05Z

This changes the code so it will show inheritance only for OMIM terms.

But check for instance at this variant --> https://scout-stage.scilifelab.se/cust002/17083/161ee740fbbc95136ea4c0ff8cc3a916

I think it is safe enough to show that also the ORPHA inhteritance is AR. We could modify both variant page and the report so that whenever OMIM and ORPHA inheritance matches then it's shown in the ORPHA as well, and then we can show other models that appear on ORPHA but not on OMIM apart. Something like this:
OMIM: AR

ORPHA: AR (AD, XR..)

I considered something like that, but rejected it since I would have to explain that the OMIM data is used to select which of the ORPHA models are not in parenthesis. I do not like this unclear path of information.

I rejected the idea to show them if identical, since it might lead to confusion as to why ORPHA models are missing for other disorders

I also rejected the option to show the ORPHA model if there are no OMIM disorders for the gene, as it is not really clear to me from ORPHA that they then really say the inheritance pattern is for that gene. Not only that cases with that disorder have been seen with that gene, plus another which has this shown inheritance model.

northwestwitch

I think this solution will be OK for our users. Consider adding a popover in the report page explaining that ORPHA inheritance is not accounted for Or perhaps modify the existing popover on the variant page adding that ORPHA models will be not shown on the case report?

northwestwitch · 2024-09-18T08:16:43Z

scout/server/blueprints/cases/templates/cases/case_report.html

@@ -712,7 +713,9 @@ <h4>Scout case analysis report</h4> - created on:&nbsp;<strong>{{report_created_
                <td>
                  <ul class="p-0" style="list-style-type: none;">
                  {% for disease_term in gene.disease_terms %}
-                    <li class="d-flex align-items-baseline"><span class="badge bg-secondary m-1">{{ disease_term._id}}</span>&nbsp;<span>{{ disease_term.description }}&nbsp;{{ disease_term.inheritance }}</span></li>
+                    <li class="d-flex align-items-baseline"><span class="badge bg-secondary m-1">{{ disease_term._id}}</span>&nbsp;<span>{{ disease_term.description }}&nbsp;{% if disease_term.source != 'ORPHA' and disease_term.inheritance %}
+                      {% for model in disease_term.inheritance %} {{ inheritance_badge(model,inherit_palette) }}{% endfor %}


Yes I remember this problem and our solution.

dnil · 2024-09-18T08:44:39Z

Right, it's a bit of a corollary to #4443. I didn't quite think about the non-specialists reading the report then and was happy with the OMIM and ORPHA being on different lines. Updating the tooltip is a nice suggestion - will do! The reports occasionally live their life on paper, so tooltips there are not always read.

northwestwitch · 2024-09-18T08:49:28Z

scout/server/blueprints/variant/templates/variant/gene_disease_relations.html

@@ -50,7 +50,7 @@
              {% if gene.common and gene.disease_terms %}
                {% for disease_term in gene.disease_terms %}
                  {% if disease_term.source == 'ORPHA' %}
-                    <tr data-bs-toggle="tooltip" title="Some ORPHA disorders are phenotypic umbrella terms for multiple genetic entities. The inheritance models are in this case a set derived from all those entities, not necessarily the inheritance mode known for this gene.">
+                    <tr data-bs-toggle="tooltip" title="Some ORPHA disorders are phenotypic umbrella terms for multiple genetic entities. The inheritance models are in this case a set derived from all those entities, not necessarily modes of inheritance known for this gene. ORPHA inheritance modes will not be shown on the general case report.">


sonarcloud · 2024-09-18T08:53:07Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

…cal-Genomics#4863) * Fix Clinical-Genomics#4862 - ORPHA inheritance patterns hidden * use import only for css colors * whitespace * update tooltip --------- Co-authored-by: Chiara Rasi <rasi.chiara@gmail.com>

dnil added 2 commits September 17, 2024 15:48

Fix #4862 - ORPHA inheritance patterns hidden

53670a6

use import only for css colors

8bf5db3

dnil marked this pull request as ready for review September 17, 2024 14:02

dnil and others added 3 commits September 17, 2024 16:06

whitespace

2ba0691

Merge branch 'main' into silence_orpha_report_inheritance

5603caa

Merge branch 'main' into silence_orpha_report_inheritance

ae1a94f

northwestwitch reviewed Sep 18, 2024

View reviewed changes

northwestwitch approved these changes Sep 18, 2024

View reviewed changes

update tooltip

9ea3024

northwestwitch reviewed Sep 18, 2024

View reviewed changes

Merge branch 'main' into silence_orpha_report_inheritance

2f9e5ff

dnil merged commit 0bc179b into main Sep 18, 2024
25 checks passed

dnil deleted the silence_orpha_report_inheritance branch September 18, 2024 09:03

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Fix #4862 - ORPHA inheritance patterns hidden #4863

Fix #4862 - ORPHA inheritance patterns hidden #4863

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Fix #4862 - ORPHA inheritance patterns hidden #4863

Fix #4862 - ORPHA inheritance patterns hidden #4863

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