scout-browser 4.90.1__py3-none-any.whl → 4.91__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (62) hide show
  1. scout/__version__.py +1 -1
  2. scout/adapter/mongo/case.py +27 -38
  3. scout/commands/export/variant.py +14 -4
  4. scout/commands/load/panel.py +2 -1
  5. scout/commands/update/panelapp.py +11 -3
  6. scout/commands/view/case.py +2 -2
  7. scout/constants/__init__.py +1 -2
  8. scout/constants/acmg.py +15 -15
  9. scout/constants/case_tags.py +0 -46
  10. scout/constants/clnsig.py +2 -1
  11. scout/constants/gene_tags.py +0 -6
  12. scout/constants/panels.py +16 -0
  13. scout/constants/variants_export.py +2 -0
  14. scout/demo/__init__.py +4 -1
  15. scout/demo/panelapp_panel.json +463 -0
  16. scout/demo/panelapp_panels_reduced.json +37 -0
  17. scout/load/panel.py +3 -142
  18. scout/load/panelapp.py +138 -0
  19. scout/models/case/case_loading_models.py +5 -4
  20. scout/parse/panel.py +3 -117
  21. scout/parse/panelapp.py +112 -0
  22. scout/parse/variant/clnsig.py +26 -21
  23. scout/parse/variant/genotype.py +6 -5
  24. scout/server/blueprints/alignviewers/controllers.py +7 -5
  25. scout/server/blueprints/alignviewers/templates/alignviewers/utils.html +1 -1
  26. scout/server/blueprints/cases/templates/cases/case_sma.html +49 -42
  27. scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html +27 -12
  28. scout/server/blueprints/cases/views.py +18 -7
  29. scout/server/blueprints/clinvar/templates/clinvar/clinvar_submissions.html +7 -7
  30. scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html +2 -2
  31. scout/server/blueprints/dashboard/controllers.py +128 -165
  32. scout/server/blueprints/dashboard/forms.py +3 -13
  33. scout/server/blueprints/dashboard/templates/dashboard/dashboard_general.html +17 -22
  34. scout/server/blueprints/institutes/forms.py +1 -2
  35. scout/server/blueprints/institutes/templates/overview/cases.html +2 -133
  36. scout/server/blueprints/institutes/templates/overview/utils.html +135 -0
  37. scout/server/blueprints/omics_variants/templates/omics_variants/outliers.html +5 -0
  38. scout/server/blueprints/panels/templates/panels/panel.html +5 -1
  39. scout/server/blueprints/panels/templates/panels/panel_pdf_simple.html +5 -1
  40. scout/server/blueprints/variant/controllers.py +6 -1
  41. scout/server/blueprints/variant/templates/variant/buttons.html +11 -10
  42. scout/server/blueprints/variant/templates/variant/components.html +63 -44
  43. scout/server/blueprints/variant/templates/variant/str-variant-reviewer.html +1 -1
  44. scout/server/blueprints/variant/templates/variant/utils.html +38 -10
  45. scout/server/blueprints/variant/templates/variant/variant.html +1 -1
  46. scout/server/blueprints/variants/controllers.py +9 -4
  47. scout/server/blueprints/variants/templates/variants/cancer-sv-variants.html +9 -5
  48. scout/server/blueprints/variants/templates/variants/cancer-variants.html +6 -17
  49. scout/server/blueprints/variants/templates/variants/str-variants.html +2 -2
  50. scout/server/blueprints/variants/templates/variants/sv-variants.html +8 -1
  51. scout/server/blueprints/variants/templates/variants/utils.html +14 -0
  52. scout/server/extensions/__init__.py +2 -0
  53. scout/server/extensions/panelapp_extension.py +75 -0
  54. scout/server/links.py +19 -1
  55. scout/server/utils.py +25 -33
  56. {scout_browser-4.90.1.dist-info → scout_browser-4.91.dist-info}/METADATA +1 -1
  57. {scout_browser-4.90.1.dist-info → scout_browser-4.91.dist-info}/RECORD +61 -57
  58. {scout_browser-4.90.1.dist-info → scout_browser-4.91.dist-info}/WHEEL +1 -1
  59. scout/demo/panelapp_test_panel.json +0 -79
  60. {scout_browser-4.90.1.dist-info → scout_browser-4.91.dist-info}/LICENSE +0 -0
  61. {scout_browser-4.90.1.dist-info → scout_browser-4.91.dist-info}/entry_points.txt +0 -0
  62. {scout_browser-4.90.1.dist-info → scout_browser-4.91.dist-info}/top_level.txt +0 -0
@@ -1,4 +1,5 @@
1
1
  {% extends "layout.html" %}
2
+ {% from "overview/utils.html" import cases_search_form %}
2
3
 
3
4
  {% block top_nav %}
4
5
  {{ super() }}
@@ -14,7 +15,7 @@
14
15
  <div class="container-float mt-3">
15
16
  <!--filter panel -->
16
17
  <div>
17
- {{ dashboard_search_form() }}
18
+ {{ cases_search_form(dashboard_form, url_for('dashboard.index'), url_for('dashboard.index'), urlnone) }}
18
19
  {% if total_cases == 0 %}
19
20
  <div class="alert alert-danger mt-3">Your search didn't return any results!</div>
20
21
  {% elif not total_cases %}
@@ -133,29 +134,23 @@
133
134
  <script src="{{ url_for('dashboard.static', filename='charts.js') }}"></script>
134
135
  <script type="text/javascript">
135
136
 
136
- // Code taking care of case filtering
137
- var caseSearchTerms = {{ search_terms|safe }};
138
- var searchTerm = document.getElementById('search_term'); // Case search term label
139
- var sel = document.getElementById('search_type'); // Case search term select
140
- document.getElementById("search_type").onchange = function() {
141
- // Change case search term placeholder
142
- selectedKey = sel.options[sel.selectedIndex].value.slice(0, -1);
143
- if(selectedKey){
144
- searchTerm.placeholder=caseSearchTerms[selectedKey]["placeholder"];
145
- searchTerm.disabled = false;
146
- }
147
- else{
148
- searchTerm.disabled = (sel.value == "");
149
- searchTerm.placeholder="Search term";
150
- }
151
- // Reset search
152
- searchTerm.value="";
153
- };
137
+ // Show/hide advanced search options
138
+ let advSearchBlock = $('#advancesSearchOptions');
154
139
 
155
- $(document).ready(function(){
156
- searchTerm.disabled = (sel.value == "");
157
- });
140
+ let advBlockCheckbox = $('#advanced_search');
158
141
 
142
+ window.onload = function(){
143
+ if(!advBlockCheckbox.is(':checked'))
144
+ advSearchBlock.hide();
145
+ }
146
+
147
+ advBlockCheckbox.on('click', function() {
148
+ if($(this).is(':checked')) {
149
+ advSearchBlock.show();
150
+ } else {
151
+ advSearchBlock.hide();
152
+ }
153
+ })
159
154
 
160
155
  {% if cases %}
161
156
  //create analysis type chart ===> general stats
@@ -13,10 +13,9 @@ from wtforms import (
13
13
  )
14
14
  from wtforms.widgets import PasswordInput, TextInput
15
15
 
16
- from scout.constants import CASE_SEARCH_TERMS, PHENOTYPE_GROUPS
16
+ from scout.constants import PHENOTYPE_GROUPS
17
17
  from scout.models.case import STATUS
18
18
 
19
- CASE_SEARCH_KEY = [(value["prefix"], value["label"]) for key, value in CASE_SEARCH_TERMS.items()]
20
19
  CATEGORY_CHOICES = [("snv", "SNV"), ("sv", "SV")]
21
20
 
22
21
 
@@ -1,7 +1,7 @@
1
1
  {% import "bootstrap/wtf.html" as wtf %}
2
2
  {% extends "layout.html" %}
3
3
  {% from "overview/institute_sidebar.html" import institute_actionbar %}
4
- {% from "overview/utils.html" import analysis_type %}
4
+ {% from "overview/utils.html" import analysis_type, cases_search_form %}
5
5
 
6
6
  {% block title %}
7
7
  {{ super() }} - {{ institute.display_name }} - Cases
@@ -20,137 +20,6 @@
20
20
  </li>
21
21
  {% endblock %}
22
22
 
23
-
24
- {% macro search_form() %}
25
-
26
- <!-- Collect advanced search key/values -->
27
- {% set search = {} %}
28
- {% for field in form._fields %}
29
- {% if field not in ["search", "csrf_token", "advanced_search"] and form._fields[field].data %}
30
- {% do search.update({field: form._fields[field].data}) %}
31
- {% endif %}
32
- {% endfor %}
33
-
34
- <form action="{{ url_for('overview.cases', institute_id=institute._id) }}" method="POST" accept-charset="utf-8">
35
- {{ form.hidden_tag() }}
36
-
37
- <div class="row">
38
- <div class="col-md-3 mb-3">
39
- {{ form.case.label(class="form-label") }}
40
- {{ form.case(class="form-control", placeholder="example:18201", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
41
- </div>
42
- <div class="col-md-1 mb-3">
43
- {{ form.search_limit.label(class="form-label") }}
44
- {{ form.search_limit(class="form-control") }}
45
- </div>
46
- <div class="d-grid btn-sm mb-3 col-md-2 mx-auto">
47
- {{ form.search(class="btn btn-lg btn-primary mt-4") }}
48
- </div>
49
- <div class="d-grid btn-sm mb-3 col-md-2 mx-auto">
50
- <a href="{{ url_for('overview.cases', institute_id=institute._id) }}" class="btn btn-lg btn-secondary mt-4 text-white" role="button">Reset search</a>
51
- </div>
52
- <div class="col-md-3 mb-3 form-check align-self-center mt-3 ms-3" data-bs-toggle="tooltip" title="Using multiple search criteria will narrow down your results as returned cases will contain all your searched conditions.">
53
- {{ form.advanced_search(class="form-check-input") }}
54
- {{ form.advanced_search.label(class="form-check-label") }}
55
- </div>
56
- </div>
57
- <div class="row">
58
- <div class="col-md-2 mb-3 form-check ms-3">
59
- {{ form.skip_assigned(class="form-check-input") }}
60
- {{ form.skip_assigned.label(class="form-check-label") }}
61
- </div>
62
- <div class="col-md-2 mb-3 form-check">
63
- {{ form.is_research(class="form-check-input") }}
64
- {{ form.is_research.label(class="form-check-label") }}
65
- </div>
66
- <div class="col-md-2 mb-3 form-check">
67
- {{ form.clinvar_submitted(class="form-check-input") }}
68
- {{ form.clinvar_submitted.label(class="form-check-label") }}
69
- </div>
70
- <div class="col-md-2 mb-3 form-check">
71
- {{ form.has_rna(class="form-check-input") }}
72
- {{ form.has_rna.label(class="form-check-label") }}
73
- </div>
74
- <div class="col-md-2 mb-3 form-check">
75
- {{ form.validation_ordered(class="form-check-input") }}
76
- {{ form.validation_ordered.label(class="form-check-label") }}
77
- </div>
78
- </div>
79
- <!-- This div contains the advances search options -->
80
- <div id="advancesSearchOptions">
81
- <div class="row">
82
- <div class="col-md-4 mb-3">
83
- {{ form.exact_pheno.label(class="form-label") }}
84
- {{ form.exact_pheno(class="form-control", placeholder="example:HP:0001298, HP:0001250,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
85
- </div>
86
- <div class="col-md-4 mb-3">
87
- {{ form.exact_dia.label(class="form-label") }}
88
- {{ form.exact_dia(class="form-control", placeholder="example:OMIM:125310, ORPHA:585,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
89
- </div>
90
- </div>
91
- <div class="row">
92
- <div class="col-md-4 mb-3">
93
- {{ form.synopsis.label(class="form-label") }}
94
- {{ form.synopsis(class="form-control", placeholder="example:epilepsy", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
95
- </div>
96
- <div class="col-md-4 mb-3">
97
- {{ form.panel.label(class="form-label") }}
98
- {{ form.panel(class="form-control", placeholder="example:NMD", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
99
- </div>
100
- <div class="col-md-4 mb-3">
101
- {{ form.status.label(class="form-label") }}
102
- {{ form.status(class="form-control", placeholder="example:active", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
103
- </div>
104
- </div>
105
- <div class="row">
106
- <div class="col-md-4 mb-3">
107
- {{ form.tags.label(class="form-label") }}
108
- {{ form.tags(class="form-control", placeholder="example:medical", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
109
- </div>
110
- <div class="col-md-4 mb-3">
111
- {{ form.track.label(class="form-label") }}
112
- {{ form.track(class="form-control", placeholder="rare or cancer", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
113
- </div>
114
- <div class="col-md-4 mb-3">
115
- {{ form.pheno_group.label(class="form-label") }}
116
- {{ form.pheno_group(class="form-control", placeholder="example:HP:0001166", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
117
- </div>
118
- </div>
119
- <div class="row">
120
- <div class="col-md-4 mb-3">
121
- {{ form.cohort.label(class="form-label") }}
122
- {{ form.cohort(class="form-control", placeholder="example:pedhep", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
123
- </div>
124
- <div class="col-md-4 mb-3">
125
- {{ form.similar_case.label(class="form-label") }}
126
- {{ form.similar_case(class="form-control", placeholder="example:18201", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
127
- </div>
128
- <div class="col-md-4 mb-3">
129
- {{ form.similar_pheno.label(class="form-label") }}
130
- {{ form.similar_pheno(class="form-control", placeholder="example:HP:0001298, HP:0001250,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
131
- </div>
132
- </div>
133
- <div class="row">
134
- <div class="col-md-4 mb-3">
135
- {{ form.pinned.label(class="form-label") }}
136
- {{ form.pinned(class="form-control", placeholder="example:POT1", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
137
- </div>
138
- <div class="col-md-4 mb-3">
139
- {{ form.causative.label(class="form-label") }}
140
- {{ form.causative(class="form-control", placeholder="example:POT1", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
141
- </div>
142
- <div class="col-md-4 mb-3">
143
- {{ form.user.label(class="form-label") }}
144
- {{ form.user(class="form-control", placeholder="John Doe", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
145
- </div>
146
- </div>
147
- </div> <!--End of advancedSearchOptions div -->
148
- </form>
149
- <div>
150
- <span class="text-muted">The following search criteria were used: {{search}}</span>
151
- </div>
152
- {% endmacro %}
153
-
154
23
  {% macro cases_table(group_name, cases) %}
155
24
  {% if sort_order == 'asc' %}
156
25
  {% set sort_option = 'desc'%}
@@ -333,7 +202,7 @@
333
202
  <div class="container-float">
334
203
  <div class="card panel-default">
335
204
  <div class="card-body">
336
- {{ search_form() }}
205
+ {{ cases_search_form(form, url_for('overview.cases', institute_id=institute._id), url_for('overview.cases', institute_id=institute._id), institute) }}
337
206
  </div>
338
207
  <div class="card-footer text-center">
339
208
  Showing {{ found_cases }} / {{ nr_cases }} cases
@@ -1,5 +1,140 @@
1
1
  {% from "variants/components.html" import variant_gene_symbols_cell, variant_funct_anno_cell, fusion_variant_gene_symbols_cell %}
2
2
 
3
+ {% macro cases_search_form(form, form_action, reset_action, institute = none) %}
4
+ <!-- Collect advanced search key/values -->
5
+ {% set search = {} %}
6
+ {% for field in form._fields %}
7
+ {% if field not in ["search", "csrf_token", "advanced_search"] and form._fields[field].data %}
8
+ {% do search.update({field: form._fields[field].data}) %}
9
+ {% endif %}
10
+ {% endfor %}
11
+
12
+ <form action="{{ form_action }}" method="POST" accept-charset="utf-8">
13
+ {{ form.hidden_tag() }}
14
+
15
+ <div class="row">
16
+ {% if not institute %} <!-- used only on dashboard page, when search might return results from many institutes -->
17
+ <div class="col-md-2 mb-3">
18
+ {{ form.search_institute.label(class="form-label") }}
19
+ {{ form.search_institute(class="form-control") }}
20
+ </div>
21
+ {% endif %}
22
+ <div class="col-md-3 mb-3">
23
+ {{ form.case.label(class="form-label") }}
24
+ {{ form.case(class="form-control", placeholder="example:18201", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
25
+ </div>
26
+ <div class="col-md-1 mb-3">
27
+ {{ form.search_limit.label(class="form-label") }}
28
+ {{ form.search_limit(class="form-control") }}
29
+ </div>
30
+ <div class="btn-sm mb-2 col-md-2 mx-auto">
31
+ {{ form.search(class="btn btn-lg btn-primary mt-4") }}
32
+ <a href="{{ reset_action }}" class="btn btn-lg btn-secondary mt-4 text-white">Reset search</a>
33
+ </div>
34
+ <div class="col-md-2 mb-3 form-check align-self-center mt-3 ms-3" data-bs-toggle="tooltip" title="Using multiple search criteria will narrow down your results as returned cases will contain all your searched conditions.">
35
+ {{ form.advanced_search(class="form-check-input") }}
36
+ {{ form.advanced_search.label(class="form-check-label") }}
37
+ </div>
38
+ </div>
39
+ {% if institute %} <!-- The following checkboxes will be displayed when the form is used on institute caseS page only, not on the dashboard -->
40
+ <div class="row">
41
+ <div class="col-md-2 mb-3 form-check ms-3">
42
+ {{ form.skip_assigned(class="form-check-input") }}
43
+ {{ form.skip_assigned.label(class="form-check-label") }}
44
+ </div>
45
+ <div class="col-md-2 mb-3 form-check">
46
+ {{ form.is_research(class="form-check-input") }}
47
+ {{ form.is_research.label(class="form-check-label") }}
48
+ </div>
49
+ <div class="col-md-2 mb-3 form-check">
50
+ {{ form.clinvar_submitted(class="form-check-input") }}
51
+ {{ form.clinvar_submitted.label(class="form-check-label") }}
52
+ </div>
53
+ <div class="col-md-2 mb-3 form-check">
54
+ {{ form.has_rna(class="form-check-input") }}
55
+ {{ form.has_rna.label(class="form-check-label") }}
56
+ </div>
57
+ <div class="col-md-2 mb-3 form-check">
58
+ {{ form.validation_ordered(class="form-check-input") }}
59
+ {{ form.validation_ordered.label(class="form-check-label") }}
60
+ </div>
61
+ </div>
62
+ {% endif %}
63
+ <!-- This div contains the advances search options -->
64
+ <div id="advancesSearchOptions">
65
+ <div class="row">
66
+ <div class="col-md-4 mb-3">
67
+ {{ form.exact_pheno.label(class="form-label") }}
68
+ {{ form.exact_pheno(class="form-control", placeholder="example:HP:0001298, HP:0001250,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
69
+ </div>
70
+ <div class="col-md-4 mb-3">
71
+ {{ form.exact_dia.label(class="form-label") }}
72
+ {{ form.exact_dia(class="form-control", placeholder="example:OMIM:125310, ORPHA:585,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
73
+ </div>
74
+ </div>
75
+ <div class="row">
76
+ <div class="col-md-4 mb-3">
77
+ {{ form.synopsis.label(class="form-label") }}
78
+ {{ form.synopsis(class="form-control", placeholder="example:epilepsy", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
79
+ </div>
80
+ <div class="col-md-4 mb-3">
81
+ {{ form.panel.label(class="form-label") }}
82
+ {{ form.panel(class="form-control", placeholder="example:NMD", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
83
+ </div>
84
+ <div class="col-md-4 mb-3">
85
+ {{ form.status.label(class="form-label") }}
86
+ {{ form.status(class="form-control", placeholder="example:active", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
87
+ </div>
88
+ </div>
89
+ <div class="row">
90
+ <div class="col-md-4 mb-3">
91
+ {{ form.tags.label(class="form-label") }}
92
+ {{ form.tags(class="form-control", placeholder="example:medical", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
93
+ </div>
94
+ <div class="col-md-4 mb-3">
95
+ {{ form.track.label(class="form-label") }}
96
+ {{ form.track(class="form-control", placeholder="rare or cancer", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
97
+ </div>
98
+ <div class="col-md-4 mb-3">
99
+ {{ form.pheno_group.label(class="form-label") }}
100
+ {{ form.pheno_group(class="form-control", placeholder="example:HP:0001166", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
101
+ </div>
102
+ </div>
103
+ <div class="row">
104
+ <div class="col-md-4 mb-3">
105
+ {{ form.cohort.label(class="form-label") }}
106
+ {{ form.cohort(class="form-control", placeholder="example:pedhep", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
107
+ </div>
108
+ <div class="col-md-4 mb-3">
109
+ {{ form.similar_case.label(class="form-label") }}
110
+ {{ form.similar_case(class="form-control", placeholder="example:18201", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
111
+ </div>
112
+ <div class="col-md-4 mb-3">
113
+ {{ form.similar_pheno.label(class="form-label") }}
114
+ {{ form.similar_pheno(class="form-control", placeholder="example:HP:0001298, HP:0001250,..", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
115
+ </div>
116
+ </div>
117
+ <div class="row">
118
+ <div class="col-md-4 mb-3">
119
+ {{ form.pinned.label(class="form-label") }}
120
+ {{ form.pinned(class="form-control", placeholder="example:POT1", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
121
+ </div>
122
+ <div class="col-md-4 mb-3">
123
+ {{ form.causative.label(class="form-label") }}
124
+ {{ form.causative(class="form-control", placeholder="example:POT1", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
125
+ </div>
126
+ <div class="col-md-4 mb-3">
127
+ {{ form.user.label(class="form-label") }}
128
+ {{ form.user(class="form-control", placeholder="John Doe", pattern="[^\\\<\>\?\!\=\/]*", title="Characters \<>?!=/ are not allowed") }}
129
+ </div>
130
+ </div>
131
+ </div> <!--End of advancedSearchOptions div -->
132
+ </form>
133
+ <div>
134
+ <span class="text-muted">The following search criteria were used: {{search}}</span>
135
+ </div>
136
+ {% endmacro %}
137
+
3
138
  {% macro analysis_type(analysis_types) %}
4
139
  {% for analysis_type in analysis_types %}
5
140
  {% if analysis_type == 'wgs' %}
@@ -5,6 +5,7 @@
5
5
  {% from "variants/components.html" import external_scripts, external_stylesheets, gene_cell %}
6
6
  {% from "variant/buttons.html" import splice_junctions_button %}
7
7
  {% from "variants/utils.html" import filter_script_main, pagination_footer, pagination_hidden_div, stash_filter_buttons, update_stash_filter_button_status%}
8
+ {% from "variant/components.html" import variant_scripts %}
8
9
 
9
10
  {% block title %}
10
11
  {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - {{ form.variant_type.data|capitalize }} omics outlier variants
@@ -117,6 +118,9 @@
117
118
  </td>
118
119
  <td class="text-end">{{ variant.chromosome }}</td>
119
120
  <td class="text-end"><span style="white-space: nowrap;">{{ variant.position|human_longint|safe }}</span>-<span style="white-space: nowrap;">{{ variant.end|human_longint|safe }}</span>
121
+ <button type="button" class="fa fa-copy btn-xs js-tooltip js-copy"
122
+ style="background-color: Transparent;outline:none; border: none;" data-bs-toggle="tooltip" data-bs-placement="bottom" data-copy="{{ variant.chromosome }}:{{ variant.position }}-{{ variant.end }}" title="Copy to clipboard">
123
+ </button>
120
124
  {% if case.has_rna_tracks %}
121
125
  {{ splice_junctions_button(institute._id, case, None, variant.omics_variant_id) }}
122
126
  {% endif %}
@@ -142,6 +146,7 @@
142
146
  {% block scripts %}
143
147
  {{ super() }}
144
148
  {{ external_scripts() }}
149
+ {{ variant_scripts() }}
145
150
  <script src="{{ url_for('variants.static', filename='form_scripts.js') }}"></script>
146
151
  {{ filter_script_main(cytobands) }}
147
152
  <script type="text/javascript">
@@ -180,7 +180,11 @@
180
180
  <td>{{ gene.disease_associated_transcripts|join(', ') }}</td>
181
181
  <td>{{ 'Yes' if gene.reduced_penetrance }}</td>
182
182
  <td>{{ 'Yes' if gene.mosaicism }}</td>
183
- <td>{{ gene.database_entry_version }}</td>
183
+ <td class="d-flex justify-content-center">
184
+ {% if gene.database_entry_version and gene.database_entry_version|string == panel.version|string %}
185
+ <span class="badge bg-success rounded-pill" data-bs-toggle="tooltip" data-bs-placement="right" data-bs-html="true" title="This gene has been introduced in the panel starting from version {{gene.database_entry_version}}.">new</span>
186
+ {% endif %}
187
+ </td>
184
188
  <td>{{ gene.inheritance_models|join(', ') }}</td>
185
189
  <td>{{ gene.custom_inheritance_models|join(', ') }}</td>
186
190
  <td>{{ gene.comment }}</td>
@@ -69,7 +69,11 @@
69
69
  <td>{{ gene.disease_associated_transcripts|join(', ') }}</td>
70
70
  <td>{{ 'Reduced penetrance' if gene.reduced_penetrance }}</td>
71
71
  <td>{{ 'Mosaicism' if gene.mosaicism }}</td>
72
- <td>{{ gene.database_entry_version }}</td>
72
+ <td>
73
+ {% if gene.database_entry_version and gene.database_entry_version|string == panel.version|string %}
74
+ <span class="badge bg-success rounded-pill">new</span>
75
+ {% endif %}
76
+ </td>
73
77
  <td>{{ gene.inheritance_models|join(', ') }}</td>
74
78
  <td>{{ gene.custom_inheritance_models|join(', ') }}</td>
75
79
  <td>{{ gene.comment }}</td>
@@ -63,6 +63,7 @@ def tx_overview(variant_obj: dict):
63
63
  variant_obj(dict)
64
64
  """
65
65
  overview_txs = [] # transcripts to be shown in transcripts overview
66
+ ensembl_txid_mane_transcripts = {}
66
67
  if variant_obj.get("genes") is None:
67
68
  variant_obj["overview_transcripts"] = []
68
69
  return
@@ -89,7 +90,6 @@ def tx_overview(variant_obj: dict):
89
90
  ovw_tx["muted_refseq_ids"] = []
90
91
 
91
92
  for refseq_id in tx.get("refseq_identifiers", []):
92
- decorated_tx = None
93
93
  if ovw_tx["mane"] and ovw_tx["mane"].startswith(refseq_id):
94
94
  decorated_tx = ovw_tx["mane"]
95
95
  elif ovw_tx["mane_plus"] and ovw_tx["mane_plus"].startswith(refseq_id):
@@ -121,12 +121,17 @@ def tx_overview(variant_obj: dict):
121
121
  ovw_tx["cbioportal_link"] = tx.get("cbioportal_link")
122
122
  ovw_tx["mycancergenome_link"] = tx.get("mycancergenome_link")
123
123
 
124
+ ensembl_txid_mane_transcripts[tx.get("transcript_id")] = {
125
+ "mane": ovw_tx["mane"],
126
+ "mane_plus": ovw_tx["mane_plus"],
127
+ }
124
128
  overview_txs.append(ovw_tx)
125
129
 
126
130
  # sort txs for the presence of "mane_select_transcript" and "mane_plus_clinical_transcript"
127
131
  variant_obj["overview_transcripts"] = sorted(
128
132
  overview_txs, key=lambda tx: (tx["mane"], tx["mane_plus"]), reverse=True
129
133
  )
134
+ variant_obj["mane_transcripts"] = ensembl_txid_mane_transcripts
130
135
 
131
136
 
132
137
  def get_igv_tracks(build: str = "37") -> set:
@@ -1,33 +1,34 @@
1
1
  {% macro database_buttons(variant) %}
2
2
  <div class="mt-3">
3
- <a class="btn btn-sm btn-info text-white me-1 mb-1" role="button" href="{{ variant.swegen_link }}" target="_blank">SweGen</a>
4
- <a class="btn btn-sm btn-info text-white me-1 mb-1" role="button" href="{{ variant.beacon_link }}" target="_blank">Beacon</a>
3
+ <a class="btn btn-sm btn-info text-white me-1 mb-1" href="{{ variant.swegen_link }}" rel="noreferrer noopener" target="_blank">SweGen</a>
4
+ <a class="btn btn-sm btn-info text-white me-1 mb-1" href="{{ variant.beacon_link }}" rel="noreferrer noopener" target="_blank">Beacon</a>
5
+ <a class="btn btn-sm btn-info text-white me-1 mb-1" href="{{ variant.franklin_link }}" rel="noreferrer noopener" target="_blank">Franklin</a>
5
6
  {% if variant.cosmic_links %} <!-- This is a list of tuples : [(id1, link1), (id2, link2), ..] -->
6
7
  {% for cosmic_link in variant.cosmic_links %}
7
- <a data-bs-toggle="tooltip" title="COSMIC" class="btn btn-sm btn-info text-white me-1 mb-1" role="button" href="{{cosmic_link[1]}}" target="_blank">{{cosmic_link[0]}}</a>
8
+ <a data-bs-toggle="tooltip" title="COSMIC" class="btn btn-sm btn-info text-white me-1 mb-1" rel="noreferrer noopener" href="{{cosmic_link[1]}}" target="_blank">{{cosmic_link[0]}}</a>
8
9
  {% endfor %}
9
10
  {% endif %}
10
11
  {% if variant.dbsnp_id %}
11
12
  {% for snp in variant.dbsnp_id.split(';') %}
12
- <a class="btn btn-sm btn-info text-white me-1 mb-1" role="button" target="_blank" href="{{variant.snp_links[snp]}}">dbSNP ({{ snp }})</a>
13
+ <a class="btn btn-sm btn-info text-white me-1 mb-1" target="_blank" rel="noreferrer noopener" href="{{variant.snp_links[snp]}}">dbSNP ({{ snp }})</a>
13
14
  {% endfor %}
14
15
  {% endif %}
15
16
  </div>
16
17
  <div class="btn-group">
17
18
  {% if primary_transcript and primary_transcript.varsome_link %}
18
- <a href="{{ primary_transcript.varsome_link }}" class="btn btn-sm btn-info text-white me-1 mb-1" role="button" target="_blank"
19
+ <a href="{{ primary_transcript.varsome_link }}" class="btn btn-sm btn-info text-white me-1 mb-1" rel="noreferrer noopener" target="_blank"
19
20
  data-bs-toggle="tooltip" title="Varsome">V</a>
20
21
  {% endif %}
21
22
  {% if primary_transcript and primary_transcript.tp53_link %}
22
- <a href="{{ primary_transcript.tp53_link }}" class="btn btn-sm btn-info text-white me-1 mb-1" role="button" target="_blank"
23
+ <a href="{{ primary_transcript.tp53_link }}" class="btn btn-sm btn-info text-white me-1 mb-1" rel="noreferrer noopener" target="_blank"
23
24
  data-bs-toggle="tooltip" title="MutanTP53">TP53</a>
24
25
  {% endif %}
25
26
  {% if primary_transcript and primary_transcript.cbioportal_link %}
26
- <a href="{{ primary_transcript.cbioportal_link }}" class="btn btn-sm btn-info text-white me-1 mb-1" role="button" target="_blank"
27
+ <a href="{{ primary_transcript.cbioportal_link }}" class="btn btn-sm btn-info text-white me-1 mb-1" rel="noreferrer noopener" target="_blank"
27
28
  data-bs-toggle="tooltip" title="cBioPortal">CBP</a>
28
29
  {% endif %}
29
30
  {% if primary_transcript and primary_transcript.mycancergenome_link %}
30
- <a href="{{ primary_transcript.mycancergenome_link }}" class="btn btn-sm btn-info text-white me-1 mb-1" role="button" target="_blank"
31
+ <a href="{{ primary_transcript.mycancergenome_link }}" class="btn btn-sm btn-info text-white me-1 mb-1" rel="noreferrer noopener" target="_blank"
31
32
  data-bs-toggle="tooltip" title="MyCancerGenome">MCG</a>
32
33
  {% endif %}
33
34
  </div>
@@ -36,10 +37,10 @@
36
37
  {% macro splice_junctions_button(institute_id, case, variant_id, omics_variant_id) %}
37
38
  {% if omics_variant_id %}
38
39
  <a class="btn btn-sm btn-secondary text-white" href="{{url_for('alignviewers.sashimi_igv', institute_id=institute_id, case_name=case.display_name, omics_variant_id=omics_variant_id)}}" target="_blank"
39
- data-bs-toggle="tooltip" data-bs-placement="top" title="Only available in build GRCh{{ case.rna_genome_build or '38' }}">RNA splicing</a>
40
+ data-bs-toggle="tooltip" data-bs-placement="top" title="Only available in build GRCh{{ case.rna_genome_build or '38' }}"><span class="fa fa-magnifying-glass fa-fw me-1"></span>IGV RNA</a>
40
41
  {% else %}
41
42
  <a class="btn btn-sm btn-secondary text-white" href="{{url_for('alignviewers.sashimi_igv', institute_id=institute_id, case_name=case.display_name, variant_id=variant_id)}}" target="_blank"
42
- data-bs-toggle="tooltip" data-bs-placement="top" title="Only available in build GRCh{{ case.rna_genome_build or '38' }}">RNA splicing</a>
43
+ data-bs-toggle="tooltip" data-bs-placement="top" title="Only available in build GRCh{{ case.rna_genome_build or '38' }}"><span class="fa fa-magnifying-glass fa-fw me-1"></span>IGV RNA</a>
43
44
  {% endif %}
44
45
  {% endmacro %}
45
46