From f9114879b65a61d68e9f179553b3b0b6c628b260 Mon Sep 17 00:00:00 2001 From: Daniel Nilsson Date: Tue, 22 Oct 2024 09:42:14 +0200 Subject: [PATCH 01/15] Fix #4958 - IGV button names and IGV MT overview link --- CHANGELOG.md | 1 + .../cases/templates/cases/case_sma.html | 79 +++++++++---------- .../cases/collapsible_actionbar.html | 29 ++++--- .../variant/templates/variant/buttons.html | 4 +- .../variant/templates/variant/components.html | 17 ++-- .../variant/str-variant-reviewer.html | 2 +- .../variant/templates/variant/utils.html | 4 +- .../templates/variants/str-variants.html | 4 +- 8 files changed, 75 insertions(+), 65 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index caf70ebe9f..060bcf211b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/) ## [unreleased] ### Changed - On genes panel page and gene panel PDF export, it's more evident which genes were newly introduced into the panel +- Names on IGV buttons, including an overview level IGV MT button ## [4.90.1] ### Fixed diff --git a/scout/server/blueprints/cases/templates/cases/case_sma.html b/scout/server/blueprints/cases/templates/cases/case_sma.html index b3ebcf9839..388795c875 100644 --- a/scout/server/blueprints/cases/templates/cases/case_sma.html +++ b/scout/server/blueprints/cases/templates/cases/case_sma.html @@ -30,61 +30,56 @@

Case: {{case.display_name}}

-
-
{{ smn_individuals_table(case, institute, tissue_types) }}
-
-
-
- {% if case.madeline_info and case.individuals|length > 1 %} - {{ pedigree_panel() }} - {% else %} -

No pedigree picture available.

- {% endif %} -
-
- {{ synopsis_panel() }} -
- {{ comments_panel(institute, case, current_user, comments) }} -
+
{{ smn_individuals_table(case, institute, tissue_types) }}
+
+
+
+ {% if case.madeline_info and case.individuals|length > 1 %} + {{ pedigree_panel() }} + {% else %} +

No pedigree picture available.

+ {% endif %} +
+
+ {{ synopsis_panel() }} +
+ {{ comments_panel(institute, case, current_user, comments) }}
-
+
+
- - {% if case.vcf_files.vcf_snv %} - -
- - - -
- - {% endif %} - {% if case.vcf_files.vcf_sv %} + + {% if case.vcf_files.vcf_snv %} + +
+ + + +
+ + {% endif %} + {% if case.vcf_files.vcf_sv %}
- +
- {% endif %} - {% if case.bam_files %} - IGV viewer SMN1 - IGV viewer SMN2 - {% else %} - BAM file(s) missing - {% endif %} -
+ {% endif %} -
-
{{activity_panel(events)}}
-
+ IGV DNA SMN1 + IGV DNA SMN2 + - {{ modal_synopsis() }} +
+
{{activity_panel(events)}}
+
+ + {{ modal_synopsis() }}
- {% endmacro %} diff --git a/scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html b/scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html index baf4cf73fd..972c7e82c1 100644 --- a/scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html +++ b/scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html @@ -197,22 +197,29 @@ Genome build {{ case.genome_build }} -
- {% if case.bam_files %} +
- +
- {% else %} - Alignment missing - {% endif %} -
-{% if has_rna_tracks %} +
-
- + +
-{% endif %} + {% if has_rna_tracks %} +
+
+ +
+
+ {% endif %} {% endmacro %} {% macro rank_model(case) %} diff --git a/scout/server/blueprints/variant/templates/variant/buttons.html b/scout/server/blueprints/variant/templates/variant/buttons.html index f57fe5ad2e..52a1c5a3a0 100644 --- a/scout/server/blueprints/variant/templates/variant/buttons.html +++ b/scout/server/blueprints/variant/templates/variant/buttons.html @@ -36,10 +36,10 @@ {% macro splice_junctions_button(institute_id, case, variant_id, omics_variant_id) %} {% if omics_variant_id %} RNA splicing + data-bs-toggle="tooltip" data-bs-placement="top" title="Only available in build GRCh{{ case.rna_genome_build or '38' }}">IGV RNA {% else %} RNA splicing + data-bs-toggle="tooltip" data-bs-placement="top" title="Only available in build GRCh{{ case.rna_genome_build or '38' }}">IGV RNA {% endif %} {% endmacro %} diff --git a/scout/server/blueprints/variant/templates/variant/components.html b/scout/server/blueprints/variant/templates/variant/components.html index 565da3abc3..3b5af76516 100644 --- a/scout/server/blueprints/variant/templates/variant/components.html +++ b/scout/server/blueprints/variant/templates/variant/components.html @@ -68,11 +68,18 @@ {% macro alignments(institute, case, variant, current_user, config, igv_tracks, has_rna_tracks=False) %} {% endmacro %} {% macro acmg_form(institute, case, variant, ACMG_OPTIONS, selected=None) %} diff --git a/scout/server/blueprints/variant/templates/variant/utils.html b/scout/server/blueprints/variant/templates/variant/utils.html index 1c708c9610..29d5c144f1 100644 --- a/scout/server/blueprints/variant/templates/variant/utils.html +++ b/scout/server/blueprints/variant/templates/variant/utils.html @@ -92,7 +92,7 @@
Phenotype terms (HPO):
- Settings IGV DNA + Settings IGV DNA
@@ -355,17 +355,31 @@
Phenotype terms (HPO):
{% endif %}
- - - {% else %}"> - {% endif %}IGV - {% if variant.is_mitochondrial %}mt{% else %}g{% endif %}DNA - - + {% if variant.is_mitochondrial and not case.mt_bams %} + + IGV mtDNA + + + {% elif not case.bam_files %} + + IGV gDNA + + + {% else %} + + + IGV {% if variant.is_mitochondrial %}mt{% else %}g{% endif %}DNA + + + {% endif %}
diff --git a/scout/server/blueprints/variant/templates/variant/variant.html b/scout/server/blueprints/variant/templates/variant/variant.html index c5b7cb6aac..8a558118fd 100644 --- a/scout/server/blueprints/variant/templates/variant/variant.html +++ b/scout/server/blueprints/variant/templates/variant/variant.html @@ -21,7 +21,7 @@ {% block top_nav %} {{ super() }} -
  • +
  • Institutes
  • From 6164a5ad6c119c761da15bcaccae90eeb4b1ed02 Mon Sep 17 00:00:00 2001 From: Daniel Nilsson Date: Fri, 15 Nov 2024 10:07:22 +0100 Subject: [PATCH 12/15] ws SMA IGV --- .../blueprints/cases/templates/cases/case_sma.html | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/scout/server/blueprints/cases/templates/cases/case_sma.html b/scout/server/blueprints/cases/templates/cases/case_sma.html index a5442b0c0b..438c0f974a 100644 --- a/scout/server/blueprints/cases/templates/cases/case_sma.html +++ b/scout/server/blueprints/cases/templates/cases/case_sma.html @@ -69,8 +69,18 @@

    Case: {{case.display_name}}

    {% endif %} - IGV DNA SMN1 - IGV DNA SMN2 + + IGV DNA SMN1 + + + + IGV DNA SMN2 + +
    From d457357e41be3bc8230a1a86df80dc9811f6a01a Mon Sep 17 00:00:00 2001 From: Daniel Nilsson Date: Fri, 15 Nov 2024 10:13:47 +0100 Subject: [PATCH 13/15] actionbar ws --- .../templates/cases/collapsible_actionbar.html | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html b/scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html index c48b67aba1..10c4e378e7 100644 --- a/scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html +++ b/scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html @@ -197,7 +197,8 @@ Genome build {{ case.genome_build }}
    • -
    +
    -
    +
    - +
    {% if has_rna_tracks %} From 881d680a930086aa2fd513c8598a2e2a99019add Mon Sep 17 00:00:00 2001 From: Daniel Nilsson Date: Fri, 15 Nov 2024 10:40:00 +0100 Subject: [PATCH 14/15] Again, mt vars have their own bams. --- .../server/blueprints/variant/templates/variant/components.html | 2 +- scout/server/blueprints/variant/templates/variant/utils.html | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/scout/server/blueprints/variant/templates/variant/components.html b/scout/server/blueprints/variant/templates/variant/components.html index 71e1f57b31..4262bd8770 100644 --- a/scout/server/blueprints/variant/templates/variant/components.html +++ b/scout/server/blueprints/variant/templates/variant/components.html @@ -76,7 +76,7 @@ disabled" title="Alignment file(s) missing" data-bs-toggle="tooltip" aria-disabled="true">IGV mtDNA - {% elif not case.bam_files %} + {% elif not case.bam_files and not variant.is_mitochondrial %} Phenotype terms (HPO): disabled" title="Alignment file(s) missing" data-bs-toggle="tooltip" aria-disabled="true">IGV mtDNA - {% elif not case.bam_files %} + {% elif not case.bam_files and not variant.is_mitochondrial%} Date: Fri, 15 Nov 2024 11:03:04 +0100 Subject: [PATCH 15/15] SMA... --- .../blueprints/cases/templates/cases/case_sma.html | 10 ++++++---- .../variant/templates/variant/components.html | 7 +++---- 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/scout/server/blueprints/cases/templates/cases/case_sma.html b/scout/server/blueprints/cases/templates/cases/case_sma.html index 438c0f974a..583a6ee060 100644 --- a/scout/server/blueprints/cases/templates/cases/case_sma.html +++ b/scout/server/blueprints/cases/templates/cases/case_sma.html @@ -71,14 +71,16 @@

    Case: {{case.display_name}}

    -     IGV DNA SMN1 + + IGV DNA SMN1     - IGV DNA SMN2 + + IGV DNA SMN2 diff --git a/scout/server/blueprints/variant/templates/variant/components.html b/scout/server/blueprints/variant/templates/variant/components.html index 4262bd8770..4a930447f8 100644 --- a/scout/server/blueprints/variant/templates/variant/components.html +++ b/scout/server/blueprints/variant/templates/variant/components.html @@ -72,16 +72,15 @@ IGV mtDNA + class="btn btn-secondary btn-sm text-white disabled" aria-disabled="true">IGV mtDNA {% elif not case.bam_files and not variant.is_mitochondrial %} IGV DNA + class="btn btn-secondary btn-sm text-white disabled" + aria-disabled="true">IGV gDNA {% else %}