@molgenis/vip-report-template 2.7.2 → 3.0.0-beta2

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 (591) 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 +156 -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 +48 -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 +37 -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 +30 -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 +169 -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
  186. package/src/utils/utils.ts +3 -0
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@@ -0,0 +1,1636 @@
1
+ export const samples1 = {
2
+ samples: [
3
+ {
4
+ person: {
5
+ familyId: "FAM001",
6
+ individualId: "SAMPLE1",
7
+ sex: "MALE",
8
+ affectedStatus: "AFFECTED",
9
+ },
10
+ index: 0,
11
+ proband: true,
12
+ },
13
+ ],
14
+ phenotypes: [
15
+ {
16
+ phenotypicFeaturesList: [
17
+ {
18
+ type: {
19
+ id: "HP:0000951",
20
+ label: "HP:0000951",
21
+ },
22
+ },
23
+ ],
24
+ subject: {
25
+ id: "SAMPLE1",
26
+ },
27
+ },
28
+ ],
29
+ };
30
+
31
+ export const samples100 = {
32
+ samples: [
33
+ {
34
+ person: {
35
+ familyId: "MISSING_0",
36
+ individualId: "SAMPLE0",
37
+ paternalId: "0",
38
+ maternalId: "0",
39
+ sex: "UNKNOWN_SEX",
40
+ affectedStatus: "MISSING",
41
+ },
42
+ index: 0,
43
+ proband: true,
44
+ },
45
+ {
46
+ person: {
47
+ familyId: "MISSING_1",
48
+ individualId: "SAMPLE1",
49
+ paternalId: "0",
50
+ maternalId: "0",
51
+ sex: "UNKNOWN_SEX",
52
+ affectedStatus: "MISSING",
53
+ },
54
+ index: 1,
55
+ proband: true,
56
+ },
57
+ {
58
+ person: {
59
+ familyId: "MISSING_2",
60
+ individualId: "SAMPLE2",
61
+ paternalId: "0",
62
+ maternalId: "0",
63
+ sex: "UNKNOWN_SEX",
64
+ affectedStatus: "MISSING",
65
+ },
66
+ index: 2,
67
+ proband: true,
68
+ },
69
+ {
70
+ person: {
71
+ familyId: "MISSING_3",
72
+ individualId: "SAMPLE3",
73
+ paternalId: "0",
74
+ maternalId: "0",
75
+ sex: "UNKNOWN_SEX",
76
+ affectedStatus: "MISSING",
77
+ },
78
+ index: 3,
79
+ proband: true,
80
+ },
81
+ {
82
+ person: {
83
+ familyId: "MISSING_4",
84
+ individualId: "SAMPLE4",
85
+ paternalId: "0",
86
+ maternalId: "0",
87
+ sex: "UNKNOWN_SEX",
88
+ affectedStatus: "MISSING",
89
+ },
90
+ index: 4,
91
+ proband: true,
92
+ },
93
+ {
94
+ person: {
95
+ familyId: "MISSING_5",
96
+ individualId: "SAMPLE5",
97
+ paternalId: "0",
98
+ maternalId: "0",
99
+ sex: "UNKNOWN_SEX",
100
+ affectedStatus: "MISSING",
101
+ },
102
+ index: 5,
103
+ proband: true,
104
+ },
105
+ {
106
+ person: {
107
+ familyId: "MISSING_6",
108
+ individualId: "SAMPLE6",
109
+ paternalId: "0",
110
+ maternalId: "0",
111
+ sex: "UNKNOWN_SEX",
112
+ affectedStatus: "MISSING",
113
+ },
114
+ index: 6,
115
+ proband: true,
116
+ },
117
+ {
118
+ person: {
119
+ familyId: "MISSING_7",
120
+ individualId: "SAMPLE7",
121
+ paternalId: "0",
122
+ maternalId: "0",
123
+ sex: "UNKNOWN_SEX",
124
+ affectedStatus: "MISSING",
125
+ },
126
+ index: 7,
127
+ proband: true,
128
+ },
129
+ {
130
+ person: {
131
+ familyId: "MISSING_8",
132
+ individualId: "SAMPLE8",
133
+ paternalId: "0",
134
+ maternalId: "0",
135
+ sex: "UNKNOWN_SEX",
136
+ affectedStatus: "MISSING",
137
+ },
138
+ index: 8,
139
+ proband: true,
140
+ },
141
+ {
142
+ person: {
143
+ familyId: "MISSING_9",
144
+ individualId: "SAMPLE9",
145
+ paternalId: "0",
146
+ maternalId: "0",
147
+ sex: "UNKNOWN_SEX",
148
+ affectedStatus: "MISSING",
149
+ },
150
+ index: 9,
151
+ proband: true,
152
+ },
153
+ {
154
+ person: {
155
+ familyId: "MISSING_10",
156
+ individualId: "SAMPLE10",
157
+ paternalId: "0",
158
+ maternalId: "0",
159
+ sex: "UNKNOWN_SEX",
160
+ affectedStatus: "MISSING",
161
+ },
162
+ index: 10,
163
+ proband: true,
164
+ },
165
+ {
166
+ person: {
167
+ familyId: "MISSING_11",
168
+ individualId: "SAMPLE11",
169
+ paternalId: "0",
170
+ maternalId: "0",
171
+ sex: "UNKNOWN_SEX",
172
+ affectedStatus: "MISSING",
173
+ },
174
+ index: 11,
175
+ proband: true,
176
+ },
177
+ {
178
+ person: {
179
+ familyId: "MISSING_12",
180
+ individualId: "SAMPLE12",
181
+ paternalId: "0",
182
+ maternalId: "0",
183
+ sex: "UNKNOWN_SEX",
184
+ affectedStatus: "MISSING",
185
+ },
186
+ index: 12,
187
+ proband: true,
188
+ },
189
+ {
190
+ person: {
191
+ familyId: "MISSING_13",
192
+ individualId: "SAMPLE13",
193
+ paternalId: "0",
194
+ maternalId: "0",
195
+ sex: "UNKNOWN_SEX",
196
+ affectedStatus: "MISSING",
197
+ },
198
+ index: 13,
199
+ proband: true,
200
+ },
201
+ {
202
+ person: {
203
+ familyId: "MISSING_14",
204
+ individualId: "SAMPLE14",
205
+ paternalId: "0",
206
+ maternalId: "0",
207
+ sex: "UNKNOWN_SEX",
208
+ affectedStatus: "MISSING",
209
+ },
210
+ index: 14,
211
+ proband: true,
212
+ },
213
+ {
214
+ person: {
215
+ familyId: "MISSING_15",
216
+ individualId: "SAMPLE15",
217
+ paternalId: "0",
218
+ maternalId: "0",
219
+ sex: "UNKNOWN_SEX",
220
+ affectedStatus: "MISSING",
221
+ },
222
+ index: 15,
223
+ proband: true,
224
+ },
225
+ {
226
+ person: {
227
+ familyId: "MISSING_16",
228
+ individualId: "SAMPLE16",
229
+ paternalId: "0",
230
+ maternalId: "0",
231
+ sex: "UNKNOWN_SEX",
232
+ affectedStatus: "MISSING",
233
+ },
234
+ index: 16,
235
+ proband: true,
236
+ },
237
+ {
238
+ person: {
239
+ familyId: "MISSING_17",
240
+ individualId: "SAMPLE17",
241
+ paternalId: "0",
242
+ maternalId: "0",
243
+ sex: "UNKNOWN_SEX",
244
+ affectedStatus: "MISSING",
245
+ },
246
+ index: 17,
247
+ proband: true,
248
+ },
249
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1542
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1543
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1544
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1546
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1547
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1548
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1550
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1551
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1552
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1554
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1555
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1556
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1558
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1560
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1562
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1564
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1566
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1567
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1568
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1570
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1572
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1574
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1575
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1576
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1578
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1579
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1580
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1582
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1584
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1586
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1588
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1592
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1594
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1595
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1596
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1598
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1600
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1602
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1603
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1604
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1606
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1607
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1608
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1610
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1611
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1612
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1613
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1614
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1615
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1616
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1617
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1618
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1619
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1620
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1621
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1622
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1623
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1624
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1625
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1626
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1627
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1628
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1629
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1630
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1631
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1632
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1633
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1634
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1635
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1636
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