@molgenis/vip-report-template 2.7.3 → 3.0.0-beta

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 (593) hide show
  1. package/.eslintignore +4 -0
  2. package/.eslintrc.js +16 -22
  3. package/.gitattributes +1 -0
  4. package/.husky/pre-commit +4 -0
  5. package/.prettierignore +4 -0
  6. package/.prettierrc.json +3 -0
  7. package/.travis.yml +14 -11
  8. package/README.md +7 -29
  9. package/index.html +12 -0
  10. package/package.json +42 -55
  11. package/src/Api.ts +12 -0
  12. package/src/App.tsx +101 -0
  13. package/src/__tests__/decisionTreeUtils.test.ts +75 -0
  14. package/src/__tests__/field.test.ts +107 -0
  15. package/src/__tests__/query.test.ts +99 -0
  16. package/src/__tests__/sortUtils.test.ts +83 -0
  17. package/src/__tests__/utils.test.ts +24 -0
  18. package/src/__tests__/viewUtils.test.ts +125 -0
  19. package/src/assets/sass/main.scss +113 -0
  20. package/src/components/Abbr.tsx +20 -0
  21. package/src/components/Anchor.tsx +12 -0
  22. package/src/components/Breadcrumb.tsx +33 -0
  23. package/src/components/Checkbox.tsx +32 -0
  24. package/src/components/ConsequenceTable.tsx +38 -0
  25. package/src/components/DatasetDropdown.tsx +44 -0
  26. package/src/components/Error.tsx +9 -0
  27. package/src/components/FieldHeader.tsx +26 -0
  28. package/src/components/GenomeBrowser.tsx +114 -0
  29. package/src/components/InfoCollapsablePane.tsx +68 -0
  30. package/src/components/Loader.tsx +5 -0
  31. package/src/components/SampleTable.tsx +118 -0
  32. package/src/components/SearchBox.tsx +44 -0
  33. package/src/components/Sort.tsx +58 -0
  34. package/src/components/VariantInfoNestedTable.tsx +117 -0
  35. package/src/components/VariantInfoTable.tsx +30 -0
  36. package/src/components/VariantSampleTable.tsx +56 -0
  37. package/src/components/VariantTable.tsx +71 -0
  38. package/src/components/VariantsSampleTable.tsx +87 -0
  39. package/src/components/VariantsTable.tsx +135 -0
  40. package/src/components/VcfHeaderRow.tsx +15 -0
  41. package/src/components/filter/Filter.tsx +34 -0
  42. package/src/components/filter/FilterCategorical.tsx +66 -0
  43. package/src/components/filter/FilterIntegerDp.tsx +24 -0
  44. package/src/components/filter/FilterIntegerVid.tsx +28 -0
  45. package/src/components/filter/FilterIntegerVim.tsx +24 -0
  46. package/src/components/filter/Filters.tsx +27 -0
  47. package/src/components/filter/InfoFilter.tsx +36 -0
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  49. package/src/components/filter/SampleFilters.tsx +44 -0
  50. package/src/components/filter/SamplesFilters.tsx +31 -0
  51. package/src/components/record/Allele.tsx +38 -0
  52. package/src/components/record/AlleleBreakend.tsx +5 -0
  53. package/src/components/record/AlleleMissing.tsx +5 -0
  54. package/src/components/record/AlleleNucs.tsx +49 -0
  55. package/src/components/record/AlleleSymbolic.tsx +5 -0
  56. package/src/components/record/Alt.tsx +17 -0
  57. package/src/components/record/Chrom.tsx +5 -0
  58. package/src/components/record/Filter.tsx +9 -0
  59. package/src/components/record/Format.tsx +31 -0
  60. package/src/components/record/Id.tsx +9 -0
  61. package/src/components/record/Info.tsx +53 -0
  62. package/src/components/record/Pager.tsx +64 -0
  63. package/src/components/record/Pos.tsx +5 -0
  64. package/src/components/record/Qual.tsx +5 -0
  65. package/src/components/record/RecordDownload.tsx +36 -0
  66. package/src/components/record/Ref.tsx +6 -0
  67. package/src/components/record/field/Field.tsx +20 -0
  68. package/src/components/record/field/FieldMultipleValue.tsx +22 -0
  69. package/src/components/record/field/FieldSingleValue.tsx +35 -0
  70. package/src/components/record/field/FieldValueCharacter.tsx +11 -0
  71. package/src/components/record/field/FieldValueFlag.tsx +11 -0
  72. package/src/components/record/field/FieldValueFloat.tsx +17 -0
  73. package/src/components/record/field/FieldValueInteger.tsx +11 -0
  74. package/src/components/record/field/FieldValueString.tsx +14 -0
  75. package/src/components/record/format/GenotypeField.tsx +63 -0
  76. package/src/components/record/info/ClinVar.tsx +37 -0
  77. package/src/components/record/info/Consequence.tsx +19 -0
  78. package/src/components/record/info/Gene.tsx +11 -0
  79. package/src/components/record/info/GnomAD.tsx +29 -0
  80. package/src/components/record/info/Hgvs.tsx +18 -0
  81. package/src/components/record/info/HpoTerm.tsx +12 -0
  82. package/src/components/record/info/PubMed.tsx +19 -0
  83. package/src/components/tree/DecisionTreeBoolMultiQuery.tsx +21 -0
  84. package/src/components/tree/DecisionTreeBoolQuery.tsx +22 -0
  85. package/src/components/tree/DecisionTreeNode.tsx +64 -0
  86. package/src/components/tree/DecisionTreeNodeBool.tsx +35 -0
  87. package/src/components/tree/DecisionTreeNodeBoolMulti.tsx +32 -0
  88. package/src/components/tree/DecisionTreeNodeCategorical.tsx +32 -0
  89. package/src/components/tree/DecisionTreeNodeExists.tsx +25 -0
  90. package/src/components/tree/DecisionTreeNodeLeaf.tsx +6 -0
  91. package/src/components/tree/DecisionTreeOutcomeNode.tsx +11 -0
  92. package/src/components/tree/DecisionTreePath.tsx +27 -0
  93. package/src/igv.d.ts +4 -1
  94. package/src/index.tsx +40 -0
  95. package/src/mocks/GRCh37/alignment.bam.blob +0 -0
  96. package/src/mocks/GRCh37/decisionTree.json +354 -0
  97. package/src/mocks/GRCh37/fasta/1-10042288-10042788.fasta.gz.blob +0 -0
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  133. package/src/mocks/GRCh37/fasta/Y-2655391-2655891.fasta.gz.blob +0 -0
  134. package/src/mocks/GRCh37/genes.txt.gz.blob +0 -0
  135. package/src/mocks/GRCh37/static.ts +192 -0
  136. package/src/mocks/GRCh37/vcf/family.vcf.blob +104 -0
  137. package/src/mocks/GRCh37/vcf/no_vep.vcf.blob +61 -0
  138. package/src/mocks/GRCh37/vcf/samples_0.vcf.blob +93 -0
  139. package/src/mocks/GRCh37/vcf/samples_1.vcf.blob +93 -0
  140. package/src/mocks/GRCh37/vcf/samples_100.vcf.blob +93 -0
  141. package/src/mocks/GRCh38/alignment.bam.blob +0 -0
  142. package/src/mocks/GRCh38/decisionTree.json +369 -0
  143. package/src/mocks/GRCh38/fasta/chr1-152548062-152548562.fasta.gz.blob +0 -0
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  177. package/src/mocks/static.ts +1636 -0
  178. package/src/mocks/utils.ts +16 -0
  179. package/src/store/index.tsx +163 -0
  180. package/src/utils/ApiUtils.ts +253 -0
  181. package/src/utils/decisionTreeUtils.ts +14 -0
  182. package/src/utils/field.ts +49 -0
  183. package/src/utils/query.ts +130 -0
  184. package/src/utils/sample.ts +5 -0
  185. package/src/utils/sortUtils.ts +65 -0
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@@ -1,66 +0,0 @@
1
- <template>
2
- <div>
3
- <b-table small responsive="true" borderless :fields="fields" :items="items">
4
- <template v-slot:head()>
5
- {{ '' }}
6
- </template>
7
- <template v-slot:cell(actions)="data">
8
- <InfoButton :info="data.item.metadata.description" />
9
- </template>
10
- <template v-slot:cell(key)="data">
11
- {{ data.item.key }}
12
- </template>
13
- <template v-slot:cell(val)="data">
14
- <RecordInfoDetailsItem :metadata="data.item.metadata" :value="data.item.val" :details="true" />
15
- </template>
16
- </b-table>
17
- </div>
18
- </template>
19
-
20
- <script lang="ts">
21
- import Vue, { PropType } from 'vue';
22
- import { Vcf } from '@molgenis/vip-report-api';
23
- import RecordInfoDetailsItem from '@/components/RecordInfoDetailsItem.vue';
24
- import InfoButton from '@/components/InfoButton.vue';
25
- import { BvTableFieldArray } from 'bootstrap-vue/src/components/table';
26
-
27
- interface Item {
28
- key: string;
29
- val: string | string[] | number | number[] | boolean;
30
- metadata: Vcf.InfoMetadata;
31
- }
32
- export default Vue.extend({
33
- components: { InfoButton, RecordInfoDetailsItem },
34
- props: {
35
- metadata: Array as PropType<Vcf.InfoMetadata[]>,
36
- info: Object as PropType<Vcf.InfoContainer>
37
- },
38
- computed: {
39
- fields(): BvTableFieldArray {
40
- return [
41
- { key: 'actions', label: '', class: ['compact', 'align-middle'] },
42
- { key: 'key', label: 'key' },
43
- { key: 'val', label: 'value' }
44
- ];
45
- },
46
- items(): Item[] {
47
- const items: Item[] = [];
48
- for (const metadata of this.metadata) {
49
- const info = this.info[metadata.id];
50
- if (info !== undefined && info !== null) {
51
- const item = {
52
- key: metadata.id,
53
- val: info as string | string[] | number | number[] | boolean,
54
- metadata: metadata
55
- };
56
- items.push(item);
57
- }
58
- }
59
- items.sort(function (thisItem, thatItem) {
60
- return thisItem.key.localeCompare(thatItem.key);
61
- });
62
- return items;
63
- }
64
- }
65
- });
66
- </script>
@@ -1,32 +0,0 @@
1
- <template>
2
- <div>
3
- <div>
4
- <span v-for="(alleleIndex, index) in data.GT.a" :key="index">
5
- <Allele :allele="alleles[alleleIndex]" :abbreviate="false" />
6
- <span v-if="index < data.GT.a.length - 1">
7
- {{ data.GT.p ? '|' : '/' }}
8
- </span>
9
- </span>
10
- </div>
11
- <RecordInfoDetails
12
- :metadata="metadata"
13
- :info="Object.fromEntries(Object.entries(data).filter(([key]) => key !== 'GT'))"
14
- />
15
- </div>
16
- </template>
17
-
18
- <script lang="ts">
19
- import Vue, { PropType } from 'vue';
20
- import { Vcf } from '@molgenis/vip-report-api';
21
- import RecordInfoDetails from '@/components/RecordInfoDetails.vue';
22
- import Allele from '@/components/Allele.vue';
23
-
24
- export default Vue.extend({
25
- components: { Allele, RecordInfoDetails },
26
- props: {
27
- metadata: Object as PropType<Vcf.FormatMetadataContainer>,
28
- data: Object as PropType<unknown>,
29
- alleles: Array as PropType<(string | null)[]>
30
- }
31
- });
32
- </script>
@@ -1,605 +0,0 @@
1
- <template>
2
- <div>
3
- <b-row>
4
- <b-col>
5
- <RecordTableControls />
6
- </b-col>
7
- </b-row>
8
- <b-table
9
- id="classifier-table"
10
- class="mt-3"
11
- ref="table"
12
- responsive="true"
13
- hover
14
- small
15
- :items="provider"
16
- :fields="fields"
17
- :show-empty="true"
18
- :busy.sync="isTableBusy"
19
- :sort-by.sync="sortBy"
20
- :sort-desc.sync="sortDesc"
21
- :current-page="page.currentPage"
22
- :per-page="page.perPage"
23
- :empty-text="$t('emptyTableMessage')"
24
- :key="sample ? sample.index : 'no-sample'"
25
- >
26
- <template v-slot:head()="data">
27
- {{ data.label ? $t(data.label) : '' }}
28
- </template>
29
- <template v-slot:cell(actions)="data">
30
- <b-button class="btn-xs" @click="info(data.item, data.index, $event.target)" mr="3">
31
- <b-icon-search />
32
- </b-button>
33
- </template>
34
- <template v-slot:cell(p)="data">
35
- <b-button class="btn-link" variant="link" @click="selectRecord(data.item)">{{
36
- data.item.p | formatNumber(true) | append(data.item.c + ':')
37
- }}</b-button>
38
- </template>
39
- <template v-slot:cell(r)="data">
40
- <Allele :allele="data.item.r" />
41
- </template>
42
- <template v-slot:cell(a)="data">
43
- <span v-for="(alt, index) in data.item.a" :key="index">
44
- <Allele :allele="alt" />
45
- <span v-if="index < data.item.a.length - 1">, </span>
46
- </span>
47
- </template>
48
- <template v-slot:cell(s)="data">
49
- <Genotype
50
- :genotype="data.item.s[sample.index].GT"
51
- :alleles="[data.item.r].concat(data.item.a)"
52
- :readDepth="data.item.s[sample.index].DP"
53
- :allelicDepth="data.item.s[sample.index].AD"
54
- />
55
- </template>
56
- <template v-slot:cell(father)="data">
57
- <Genotype
58
- :genotype="data.item.s[samplePaternal.index].GT"
59
- :alleles="[data.item.r].concat(data.item.a)"
60
- :readDepth="data.item.s[samplePaternal.index].DP"
61
- :allelicDepth="data.item.s[samplePaternal.index].AD"
62
- />
63
- </template>
64
- <template v-slot:cell(mother)="data">
65
- <Genotype
66
- :genotype="data.item.s[sampleMaternal.index].GT"
67
- :alleles="[data.item.r].concat(data.item.a)"
68
- :readDepth="data.item.s[sampleMaternal.index].DP"
69
- :allelicDepth="data.item.s[sampleMaternal.index].AD"
70
- />
71
- </template>
72
- <template v-slot:cell(expand)="data">
73
- <b-button
74
- v-if="data.item.effect.items.length > 1"
75
- class="btn-xs"
76
- @click="data.item.expand = !data.item.expand"
77
- mr="3"
78
- >
79
- <b-icon-chevron-up v-if="data.item.expand" />
80
- <b-icon-chevron-down v-else />
81
- </b-button>
82
- </template>
83
- <template v-slot:cell(effect)="data">
84
- <RecordInfoDetailsItemMultiline
85
- :metadata="data.item.effect.metadata"
86
- :values="data.item.expand ? data.item.effect.items : data.item.effect.items.slice(0, 1)"
87
- />
88
- </template>
89
- <template v-slot:cell(gene)="data">
90
- <RecordInfoDetailsItemMultiline
91
- :metadata="data.item.gene.metadata"
92
- :values="data.item.expand ? data.item.gene.items : data.item.gene.items.slice(0, 1)"
93
- />
94
- </template>
95
- <template v-slot:cell(inheritance)="data">
96
- <RecordInfoDetailsItemMultiline
97
- :metadata="data.item.inheritance.metadata"
98
- :values="data.item.expand ? data.item.inheritance.items : data.item.inheritance.items.slice(0, 1)"
99
- />
100
- </template>
101
- <template v-slot:cell(hgvsC)="data">
102
- <RecordInfoDetailsItemMultiline
103
- :metadata="data.item.hgvsC.metadata"
104
- :values="data.item.expand ? data.item.hgvsC.items : data.item.hgvsC.items.slice(0, 1)"
105
- />
106
- </template>
107
- <template v-slot:cell(hgvsP)="data">
108
- <RecordInfoDetailsItemMultiline
109
- :metadata="data.item.hgvsP.metadata"
110
- :values="data.item.expand ? data.item.hgvsP.items : data.item.hgvsP.items.slice(0, 1)"
111
- />
112
- </template>
113
- <template v-slot:cell(gnomAD)="data">
114
- <RecordInfoDetailsItemMultiline
115
- :metadata="data.item.gnomAD.metadata"
116
- :values="data.item.expand ? data.item.gnomAD.items : data.item.gnomAD.items.slice(0, 1)"
117
- />
118
- </template>
119
- <template v-slot:cell(mvl)="data">
120
- <RecordInfoDetailsItemMultiline
121
- :metadata="data.item.mvl.metadata"
122
- :values="data.item.expand ? data.item.mvl.items : data.item.mvl.items.slice(0, 1)"
123
- />
124
- </template>
125
- <template v-slot:cell(vkgl)="data">
126
- <RecordInfoDetailsItemMultiline
127
- :metadata="data.item.vkgl.metadata"
128
- :values="data.item.expand ? data.item.vkgl.items : data.item.vkgl.items.slice(0, 1)"
129
- />
130
- </template>
131
- <template v-slot:cell(clinVar)="data">
132
- <RecordInfoDetailsItemMultiline
133
- :metadata="data.item.clinVar.metadata"
134
- :values="data.item.expand ? data.item.clinVar.items : data.item.clinVar.items.slice(0, 1)"
135
- />
136
- </template>
137
- <template v-slot:cell(pubMed)="data">
138
- <RecordInfoDetailsItemMultiline
139
- :metadata="data.item.pubMed.metadata"
140
- :values="data.item.expand ? data.item.pubMed.items : data.item.pubMed.items.slice(0, 1)"
141
- />
142
- </template>
143
- <template v-slot:cell(capice)="data">
144
- <span v-if="data.item.n !== undefined && data.item.n['CAP'] !== undefined">
145
- <span v-for="(score, index) in data.item.n['CAP']" :key="index">
146
- <span>{{ score.toFixed(4) }}</span>
147
- <span v-if="index < data.item.n['CAP'].length - 1">, </span>
148
- </span>
149
- </span>
150
- </template>
151
- <template v-slot:cell(geneMatch)="data">
152
- <AnnotationControl v-if="data.item.annotation" :annotation="data.item.annotation" type="geneMatch" />
153
- </template>
154
- <template v-slot:cell(class)="data">
155
- <AnnotationControl v-if="data.item.annotation" :annotation="data.item.annotation" type="class" />
156
- </template>
157
- <template v-slot:cell(txt)="data">
158
- <AnnotationControl v-if="data.item.annotation" :annotation="data.item.annotation" type="notes" />
159
- </template>
160
- </b-table>
161
- <b-row>
162
- <b-col offset="3" cols="6">
163
- <b-pagination
164
- v-if="page.totalPages > 1"
165
- v-model="page.currentPage"
166
- :total-rows="page.totalRows"
167
- :per-page="page.perPage"
168
- align="center"
169
- aria-controls="classifier-table"
170
- ></b-pagination>
171
- </b-col>
172
- <b-col cols="3" class="text-right">
173
- <span v-if="page.totalRows > 0"
174
- ><em>{{ page.totalRows }} {{ $t(page.totalRows === 1 ? 'record' : 'records') }}</em></span
175
- >
176
- </b-col>
177
- </b-row>
178
- <b-modal :id="infoModal.id" size="xl" :title="$t('recordDetails')" no-fade ok-only @hide="resetInfoModal">
179
- <template v-slot:modal-ok>
180
- {{ $t('ok') }}
181
- </template>
182
- <div class="modal-container">
183
- <RecordDetails
184
- v-if="infoModal.record"
185
- :metadata="metadata.records"
186
- :record="infoModal.record"
187
- :sample="sample"
188
- />
189
- </div>
190
- </b-modal>
191
- </div>
192
- </template>
193
-
194
- <script lang="ts">
195
- import { mapActions, mapGetters, mapState } from 'vuex';
196
- import Vue, { PropType } from 'vue';
197
- import { BButton, BTable, BvTableCtxObject, BvTableFieldArray } from 'bootstrap-vue';
198
- import { Api, Vcf } from '@molgenis/vip-report-api';
199
- import { append, formatNumber } from '@/globals/filters';
200
- import RecordDetails from '@/components/RecordDetails.vue';
201
- import Allele from '@/components/Allele.vue';
202
- import Genotype from '@/components/Genotype.vue';
203
- import { getConsequences, getVariant, getInheritanceModesGeneSelector, getPhenotypesSelector } from '@/globals/utils';
204
- import { Consequences } from '@/types/Consequence';
205
- import RecordInfoDetailsItemMultiline from '@/components/RecordInfoDetailsItemMultiline.vue';
206
- import { Annotation } from '@/types/Annotations';
207
- import AnnotationControl from '@/components/annotation/AnnotationControl.vue';
208
- import RecordTableControls from '@/components/RecordTableControls.vue';
209
-
210
- interface Page {
211
- currentPage: number;
212
- perPage: number;
213
- totalRows: number;
214
- totalPages: number;
215
- }
216
-
217
- interface InfoModal {
218
- id: string;
219
- title: string;
220
- record: Vcf.Record | null;
221
- }
222
-
223
- interface Row {
224
- c: string;
225
- p: number;
226
- r: string;
227
- a: (string | null)[];
228
- q: number | null;
229
- f: string[];
230
- s: Vcf.RecordSample[];
231
- effect?: unknown;
232
- gene?: unknown;
233
- inheritance?: unknown;
234
- hgvsC?: unknown;
235
- hgvsP?: unknown;
236
- pubMed?: unknown;
237
- clinVar?: unknown;
238
- gnomAD?: unknown;
239
- mvl?: unknown;
240
- vkgl?: unknown;
241
- expand?: boolean;
242
- annotation?: Annotation;
243
- }
244
-
245
- export default Vue.extend({
246
- components: {
247
- Allele,
248
- AnnotationControl,
249
- Genotype,
250
- RecordDetails,
251
- RecordInfoDetailsItemMultiline,
252
- RecordTableControls
253
- },
254
- props: {
255
- sample: { type: Object as PropType<Api.Sample>, required: false }
256
- },
257
- data: function () {
258
- return {
259
- isTableBusy: false as boolean,
260
- sortBy: null as string | null,
261
- sortDesc: false as boolean,
262
- page: {
263
- currentPage: 1,
264
- perPage: 20
265
- } as Page,
266
- infoModal: {
267
- id: 'info-modal',
268
- title: '',
269
- record: null
270
- } as InfoModal
271
- };
272
- },
273
- computed: {
274
- ...mapGetters([
275
- 'hasConsequences',
276
- 'hasCapice',
277
- 'getAnnotation',
278
- 'isAnnotationEnabled',
279
- 'isRecordsContainPhenotypes',
280
- 'isRecordsContainMvl',
281
- 'isSamplesContainInheritance',
282
- 'isSamplesContainDenovo',
283
- 'isSamplesContainDepth',
284
- 'isRecordsContainIncompletePenetrance',
285
- 'sampleMaternal',
286
- 'samplePaternal'
287
- ]),
288
- ...mapState([
289
- 'metadata',
290
- 'records',
291
- 'annotations',
292
- 'selectedSamplePhenotypes',
293
- 'filterRecordsByPhenotype',
294
- 'filterRecordsByInheritance',
295
- 'filterRecordsByDenovo',
296
- 'filterRecordsByDepth'
297
- ]),
298
- genomeAssembly(): string {
299
- return this.metadata.htsFile.genomeAssembly;
300
- },
301
- fields(): BvTableFieldArray {
302
- // field keys must much report api field ids
303
- const fields = [];
304
- fields.push({ key: 'actions', label: '', class: ['compact', 'align-top'] });
305
- fields.push({ key: 'p', label: 'pos', sortable: true });
306
- fields.push({ key: 'r', label: 'ref' });
307
- fields.push(this.sample ? { key: 's', label: 'sample' } : { key: 'a', label: 'alt' });
308
- if (this.sample && this.samplePaternal !== null) {
309
- fields.push({ key: 'father', label: 'father' });
310
- }
311
- if (this.sample && this.sampleMaternal !== null) {
312
- fields.push({ key: 'mother', label: 'mother' });
313
- }
314
- if (this.hasCapice) {
315
- fields.push({ key: 'capice', label: 'capice', sortable: true });
316
- }
317
- if (this.hasConsequences) {
318
- fields.push({ key: 'expand', label: '', class: ['compact', 'align-top'] });
319
- fields.push({ key: 'effect', label: 'effect' });
320
- fields.push({ key: 'gene', label: 'symbol' });
321
- if (this.isSamplesContainInheritance) {
322
- fields.push({ key: 'inheritance', label: 'inheritance' });
323
- }
324
- fields.push({ key: 'hgvsC', label: 'hgvsc' });
325
- fields.push({ key: 'hgvsP', label: 'hgvsp' });
326
- fields.push({ key: 'gnomAD', label: 'gnomad' });
327
- }
328
- if (this.isRecordsContainMvl) {
329
- fields.push({ key: 'mvl', label: 'mvl' });
330
- }
331
- if (this.hasConsequences) {
332
- fields.push({ key: 'vkgl', label: 'vkgl' });
333
- fields.push({ key: 'clinVar', label: 'clinvar' });
334
- fields.push({ key: 'pubMed', label: 'pubmed' });
335
- }
336
- if (this.isAnnotationEnabled) {
337
- fields.push({ key: 'geneMatch', label: 'geneMatch', class: 'input' });
338
- fields.push({ key: 'class', label: 'class', class: 'input' });
339
- fields.push({ key: 'txt', label: 'txt', class: 'input', thStyle: { minWidth: '20rem' } });
340
- }
341
- return fields;
342
- }
343
- },
344
- methods: {
345
- ...mapActions(['loadRecords', 'selectRecord']),
346
- provider(ctx: BvTableCtxObject): Promise<Row[]> {
347
- const params: Api.Params = {
348
- page: ctx.currentPage - 1,
349
- size: ctx.perPage,
350
- query: this.createQuery(),
351
- sort: this.createSort(ctx)
352
- };
353
-
354
- return this.loadRecords(params).then(() => {
355
- const records = this.records as Api.PagedItems<Vcf.Record>;
356
- this.page.totalRows = records.page.totalElements;
357
- this.page.totalPages = Math.ceil(records.page.totalElements / ctx.perPage);
358
- return records.items.map(this.mapRecordToRow);
359
- });
360
- },
361
- info(record: Vcf.Record, index: number, button: BButton): void {
362
- this.infoModal.title = `Row index: ${index}`;
363
- this.infoModal.record = record;
364
- this.$root.$emit('bv::show::modal', this.infoModal.id, button);
365
- },
366
- resetInfoModal(): void {
367
- this.infoModal.title = '';
368
- this.infoModal.record = null;
369
- },
370
- createQuery(): Api.Query | Api.ComposedQuery | undefined {
371
- const queries: (Api.Query | Api.ComposedQuery)[] = [];
372
- if (this.sample) {
373
- queries.push(this.createSampleQuery());
374
- }
375
- if (this.isRecordsContainPhenotypes && this.hasSamplePhenotypes() && this.filterRecordsByPhenotype) {
376
- queries.push(this.createSamplePhenotypesQuery());
377
- }
378
- if (this.isSamplesContainInheritance && this.filterRecordsByInheritance) {
379
- queries.push(this.createSampleInheritanceQuery());
380
- }
381
- if (this.isSamplesContainDenovo && this.filterRecordsByDenovo) {
382
- queries.push(this.createSampleDenovoQuery());
383
- }
384
- if (this.isSamplesContainDepth && this.filterRecordsByDepth) {
385
- queries.push(this.createSampleReadDepthQuery());
386
- }
387
-
388
- // todo: translate ctx filter param to query
389
-
390
- let query: Api.Query | Api.ComposedQuery | undefined;
391
- if (queries.length === 0) {
392
- query = undefined;
393
- } else if (queries.length === 1) {
394
- query = queries[0];
395
- } else {
396
- query = {
397
- operator: 'and',
398
- args: queries
399
- };
400
- }
401
- return query;
402
- },
403
- createSampleQuery(): Api.Query {
404
- return {
405
- selector: ['s', this.sample.index, 'GT', 't'],
406
- operator: 'in',
407
- args: ['het', 'hom_a', 'part']
408
- };
409
- },
410
- createSampleInheritanceQuery(): Api.ComposedQuery {
411
- return {
412
- operator: 'or',
413
- args: [
414
- {
415
- selector: ['s', this.sample.index, 'VIM'],
416
- operator: '==',
417
- args: 1
418
- },
419
- {
420
- operator: 'and',
421
- args: [
422
- {
423
- selector: getInheritanceModesGeneSelector(this.metadata.records),
424
- operator: '!any_has_any',
425
- args: ['AD', 'AR', 'XLR', 'XLD', 'XL']
426
- },
427
- {
428
- selector: ['s', this.sample.index, 'VI'],
429
- operator: 'has_any',
430
- args: ['AD', 'AR', 'XLR', 'XLD', 'XL']
431
- }
432
- ]
433
- }
434
- ]
435
- };
436
- },
437
- createSampleDenovoQuery(): Api.Query {
438
- return {
439
- selector: ['s', this.sample.index, 'VID'],
440
- operator: '==',
441
- args: 1
442
- };
443
- },
444
- createSampleReadDepthQuery(): Api.Query {
445
- return {
446
- selector: ['s', this.sample.index, 'DP'],
447
- operator: '>=',
448
- args: 20
449
- };
450
- },
451
- hasSamplePhenotypes(): boolean {
452
- return this.selectedSamplePhenotypes !== null && this.selectedSamplePhenotypes.page.totalElements > 0;
453
- },
454
- createSamplePhenotypesQuery(): Api.Query {
455
- const phenotypeIds = (this.selectedSamplePhenotypes.items as Api.Phenotype[])
456
- .flatMap((phenotype) => phenotype.phenotypicFeaturesList)
457
- .map((phenotypicFeature) => phenotypicFeature.type.id);
458
- return {
459
- selector: getPhenotypesSelector(this.metadata.records),
460
- operator: 'any_has_any',
461
- args: [...new Set(phenotypeIds)]
462
- };
463
- },
464
- createSort(ctx: BvTableCtxObject): Api.SortOrder | undefined {
465
- let sort: Api.SortOrder | undefined;
466
- if (ctx.sortBy) {
467
- switch (ctx.sortBy) {
468
- case 'capice':
469
- sort = {
470
- property: ['n', 'CAP'],
471
- compare: ctx.sortDesc
472
- ? (a, b) => {
473
- if (a === null) {
474
- return b === null ? 0 : 1;
475
- } else if (b === null) {
476
- return -1;
477
- } else {
478
- return Math.max(...(b as number[])) - Math.max(...(a as number[]));
479
- }
480
- }
481
- : (a, b) => {
482
- if (a === null) {
483
- return b === null ? 0 : -1;
484
- } else if (b === null) {
485
- return 1;
486
- } else {
487
- return Math.max(...(a as number[])) - Math.max(...(b as number[]));
488
- }
489
- }
490
- };
491
- break;
492
- case 'p':
493
- // workaround for https://github.com/molgenis/vip-report-template/issues/73
494
- sort = undefined;
495
- break;
496
- default:
497
- sort = { property: ctx.sortBy, compare: ctx.sortDesc ? 'desc' : 'asc' };
498
- break;
499
- }
500
- } else {
501
- sort = undefined;
502
- }
503
- return sort;
504
- },
505
- mapRecordToRow(record: Vcf.Record) {
506
- const row: Row = { ...record };
507
- if (this.hasConsequences) {
508
- const consequences: Consequences = getConsequences(record, this.metadata.records);
509
- row.effect = {
510
- metadata: consequences.metadata.effect,
511
- items: consequences.items.map((consequence) => consequence.effect)
512
- };
513
- row.gene = {
514
- metadata: {
515
- id: 'GeneObject',
516
- type: 'Other',
517
- number: { type: 'NUMBER', count: 1 },
518
- description: 'GeneObject'
519
- },
520
- items: consequences.items.map((consequence) =>
521
- consequence.symbol !== null
522
- ? {
523
- symbol: consequence.symbol,
524
- incompletePenetrance: consequence.incompletePenetrance
525
- }
526
- : null
527
- )
528
- };
529
- if (this.isSamplesContainInheritance) {
530
- row.inheritance = {
531
- metadata: consequences.metadata.inheritance,
532
- items: consequences.items.map((consequence) => consequence.inheritance)
533
- };
534
- }
535
- row.hgvsC = {
536
- metadata: consequences.metadata.hgvsC,
537
- items: consequences.items.map((consequence) => consequence.hgvsC)
538
- };
539
- row.hgvsP = {
540
- metadata: consequences.metadata.hgvsP,
541
- items: consequences.items.map((consequence) => consequence.hgvsP)
542
- };
543
- row.gnomAD = {
544
- metadata: consequences.metadata.gnomAD,
545
- items: consequences.items.map((consequence) =>
546
- consequence.gnomAD !== null
547
- ? {
548
- variant: getVariant(record, consequence),
549
- gnomAD: consequence.gnomAD
550
- }
551
- : null
552
- )
553
- };
554
- row.mvl = {
555
- metadata: consequences.metadata.mvl,
556
- items: consequences.items.map((consequence) => consequence.mvl)
557
- };
558
- row.vkgl = {
559
- metadata: consequences.metadata.vkgl,
560
- items: consequences.items.map((consequence) => consequence.vkgl)
561
- };
562
- row.clinVar = {
563
- metadata: consequences.metadata.clinVar,
564
- items: consequences.items.map((consequence) => consequence.clinVar)
565
- };
566
- row.pubMed = {
567
- metadata: consequences.metadata.pubMed,
568
- items: consequences.items.map((consequence) => consequence.pubMed)
569
- };
570
- row.expand = false;
571
- }
572
- if (this.isAnnotationEnabled) {
573
- row.annotation = this.getAnnotation(record);
574
- }
575
- return row;
576
- }
577
- },
578
- filters: { append, formatNumber },
579
- watch: {
580
- sample() {
581
- this.page.currentPage = 1;
582
- (this.$refs.table as BTable).refresh();
583
- },
584
- '$store.state.annotations': function () {
585
- (this.$refs.table as BTable).refresh();
586
- },
587
- '$store.state.filterRecordsByPhenotype'() {
588
- this.page.currentPage = 1;
589
- (this.$refs.table as BTable).refresh();
590
- },
591
- '$store.state.filterRecordsByInheritance'() {
592
- this.page.currentPage = 1;
593
- (this.$refs.table as BTable).refresh();
594
- },
595
- '$store.state.filterRecordsByDenovo'() {
596
- this.page.currentPage = 1;
597
- (this.$refs.table as BTable).refresh();
598
- },
599
- '$store.state.filterRecordsByDepth'() {
600
- this.page.currentPage = 1;
601
- (this.$refs.table as BTable).refresh();
602
- }
603
- }
604
- });
605
- </script>