@molgenis/vip-report-template 7.1.2 → 8.0.0

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 (156) hide show
  1. package/.gitattributes +3 -1
  2. package/.travis.yml +1 -0
  3. package/README.md +13 -0
  4. package/eslint.config.mjs +6 -1
  5. package/package.json +6 -5
  6. package/scripts/validateConfig/README.txt +5 -0
  7. package/scripts/validateConfig/compileValidator.ts +17 -0
  8. package/scripts/validateConfig/createSchema.ts +6 -0
  9. package/scripts/validateConfig/schema.ts +370 -0
  10. package/src/App.tsx +2 -1
  11. package/src/components/DatasetDropdown.tsx +1 -1
  12. package/src/components/GenomeBrowser.tsx +14 -4
  13. package/src/components/RecordsTable.tsx +23 -6
  14. package/src/components/VariantConsequenceContainer.tsx +9 -2
  15. package/src/components/VariantInfoTable.tsx +1 -1
  16. package/src/components/VariantsContainer.tsx +47 -9
  17. package/src/components/VariantsContainerHeader.tsx +1 -8
  18. package/src/components/field/composed/FieldGenotype.tsx +1 -1
  19. package/src/components/field/composed/FieldGenotypeStr.tsx +18 -10
  20. package/src/components/field/composed/FieldGnomAd.tsx +1 -1
  21. package/src/components/field/composed/FieldInheritanceModes.tsx +1 -4
  22. package/src/components/field/composed/FieldVkgl.tsx +1 -1
  23. package/src/components/field/typed/FieldCategorical.tsx +1 -1
  24. package/src/components/field/typed/FieldCharacter.tsx +1 -1
  25. package/src/components/field/typed/FieldFlag.tsx +1 -1
  26. package/src/components/field/typed/FieldFloat.tsx +1 -1
  27. package/src/components/field/typed/FieldInteger.tsx +1 -1
  28. package/src/components/field/typed/FieldString.tsx +1 -1
  29. package/src/components/filter/Filter.tsx +1 -0
  30. package/src/components/filter/composed/FilterAllelicImbalance.tsx +1 -0
  31. package/src/components/filter/composed/FilterComposed.tsx +7 -0
  32. package/src/components/filter/composed/FilterDeNovo.tsx +1 -0
  33. package/src/components/filter/composed/FilterHpo.tsx +1 -0
  34. package/src/components/filter/composed/FilterInheritance.tsx +1 -0
  35. package/src/components/filter/composed/FilterLocus.tsx +17 -3
  36. package/src/components/filter/composed/FilterPick.tsx +30 -0
  37. package/src/components/filter/composed/FilterVipC.tsx +1 -0
  38. package/src/components/filter/composed/FilterVipCS.tsx +1 -0
  39. package/src/components/filter/fixed/FilterFixed.tsx +7 -0
  40. package/src/components/filter/typed/FilterCategorical.tsx +18 -1
  41. package/src/components/filter/typed/FilterFlag.tsx +2 -0
  42. package/src/components/filter/typed/FilterInterval.tsx +29 -1
  43. package/src/components/filter/typed/FilterString.tsx +8 -1
  44. package/src/components/filter/typed/FilterTyped.tsx +1 -0
  45. package/src/components/form/ButtonApply.tsx +6 -2
  46. package/src/mocks/GRCh38/README.txt +15 -0
  47. package/src/mocks/GRCh38/decisionTree.json +201 -0
  48. package/src/mocks/GRCh38/family.ped +6 -0
  49. package/src/mocks/GRCh38/field_metadata.json +36 -11
  50. package/src/mocks/GRCh38/sample1.ped +1 -0
  51. package/src/mocks/GRCh38/static.ts +36 -148
  52. package/src/mocks/GRCh38/str.ped +1 -0
  53. package/src/mocks/GRCh38/vcf/family.db.blob +0 -0
  54. package/src/mocks/GRCh38/vcf/family.vcf +312 -0
  55. package/src/mocks/GRCh38/vcf/fixPaths.sql +7 -0
  56. package/src/mocks/GRCh38/vcf/no_vep.db.blob +0 -0
  57. package/src/mocks/GRCh38/vcf/{no_vep.vcf.blob → no_vep.vcf} +1 -1
  58. package/src/mocks/GRCh38/vcf/samples_0.db.blob +0 -0
  59. package/src/mocks/GRCh38/vcf/samples_1.db.blob +0 -0
  60. package/src/mocks/GRCh38/vcf/samples_100.db.blob +0 -0
  61. package/src/mocks/GRCh38/vcf/{samples_100.vcf.blob → samples_100.vcf} +6 -6
  62. package/src/mocks/GRCh38/vcf/str.db.blob +0 -0
  63. package/src/mocks/GRCh38/vcf/{str.vcf.blob → str.vcf} +17 -17
  64. package/src/mocks/MockApiClient.ts +60 -226
  65. package/src/mocks/config_cram.json +4 -0
  66. package/src/mocks/config_default_values.json +722 -0
  67. package/src/mocks/config_vcf.json +15 -1
  68. package/src/mocks/sql-wasm.wasm.blob +0 -0
  69. package/src/types/config.d.ts +9 -5
  70. package/src/types/configCells.d.ts +1 -0
  71. package/src/types/configFilter.d.ts +1 -0
  72. package/src/types/configFilterComposed.d.ts +3 -0
  73. package/src/utils/api.ts +21 -49
  74. package/src/utils/config/configCellsComposed.ts +1 -1
  75. package/src/utils/config/configCellsField.ts +2 -0
  76. package/src/utils/config/configFiltersComposed.ts +7 -0
  77. package/src/utils/config/configFiltersField.ts +3 -2
  78. package/src/utils/config/configFiltersFixed.ts +7 -0
  79. package/src/utils/config/configValidator.precompiled.ts +83402 -0
  80. package/src/utils/config/configValidator.ts +3 -368
  81. package/src/utils/csq.ts +5 -10
  82. package/src/utils/decisionTree.ts +8 -9
  83. package/src/utils/query/query.ts +3 -2
  84. package/src/utils/query/queryFilter.ts +2 -3
  85. package/src/utils/query/queryFilterComposed.ts +12 -12
  86. package/src/utils/query/queryFilterField.ts +14 -7
  87. package/src/utils/query/queryFilterFixed.ts +5 -5
  88. package/src/utils/query/querySample.ts +15 -4
  89. package/src/utils/query/selector.ts +5 -20
  90. package/src/utils/query/sort.ts +4 -4
  91. package/src/utils/vcf.ts +20 -11
  92. package/src/views/Help.tsx +2 -2
  93. package/src/views/SampleVariant.tsx +4 -1
  94. package/src/views/Samples.tsx +10 -3
  95. package/src/views/data/data.tsx +2 -2
  96. package/tests/utils/config/configFiltersComposed.test.ts +2 -0
  97. package/tests/utils/config/configFiltersField.test.ts +4 -2
  98. package/tests/utils/config/configFiltersFixed.test.ts +23 -6
  99. package/tests/utils/query/query.test.ts +34 -6
  100. package/tests/utils/query/queryFilter.test.ts +4 -31
  101. package/tests/utils/query/queryFilterComposed.test.ts +13 -13
  102. package/tests/utils/query/queryFilterField.test.ts +5 -5
  103. package/tests/utils/query/queryFilterFixed.test.ts +5 -5
  104. package/tests/utils/query/querySample.test.ts +50 -10
  105. package/tests/utils/query/sort.test.ts +1 -1
  106. package/tests/utils/vcf.test.ts +1 -0
  107. package/vite.config.mts +2 -1
  108. package/src/mocks/GRCh37/alignment.cram.blob +0 -0
  109. package/src/mocks/GRCh37/alignment.cram.crai.blob +0 -0
  110. package/src/mocks/GRCh37/decisionTree.json +0 -355
  111. package/src/mocks/GRCh37/fasta/1-10042288-10042788.fasta.gz.blob +0 -0
  112. package/src/mocks/GRCh37/fasta/1-152520538-152521038.fasta.gz.blob +0 -0
  113. package/src/mocks/GRCh37/fasta/1-16375333-16375833.fasta.gz.blob +0 -0
  114. package/src/mocks/GRCh37/fasta/1-16376162-16376662.fasta.gz.blob +0 -0
  115. package/src/mocks/GRCh37/fasta/1-17348965-17349469.fasta.gz.blob +0 -0
  116. package/src/mocks/GRCh37/fasta/1-17348969-17349469.fasta.gz.blob +0 -0
  117. package/src/mocks/GRCh37/fasta/1-17354844-17355344.fasta.gz.blob +0 -0
  118. package/src/mocks/GRCh37/fasta/10-126091249-126091749.fasta.gz.blob +0 -0
  119. package/src/mocks/GRCh37/fasta/11-134013975-134014475.fasta.gz.blob +0 -0
  120. package/src/mocks/GRCh37/fasta/13-77569878-77570378.fasta.gz.blob +0 -0
  121. package/src/mocks/GRCh37/fasta/14-105167610-105168110.fasta.gz.blob +0 -0
  122. package/src/mocks/GRCh37/fasta/14-89307588-89308088.fasta.gz.blob +0 -0
  123. package/src/mocks/GRCh37/fasta/14-89309945-89310445.fasta.gz.blob +0 -0
  124. package/src/mocks/GRCh37/fasta/14-89336157-89336657.fasta.gz.blob +0 -0
  125. package/src/mocks/GRCh37/fasta/17-29555814-29556314.fasta.gz.blob +0 -0
  126. package/src/mocks/GRCh37/fasta/17-29585172-29585672.fasta.gz.blob +0 -0
  127. package/src/mocks/GRCh37/fasta/17-29663629-29664129.fasta.gz.blob +0 -0
  128. package/src/mocks/GRCh37/fasta/17-29675976-29676476.fasta.gz.blob +0 -0
  129. package/src/mocks/GRCh37/fasta/17-29683733-29684233.fasta.gz.blob +0 -0
  130. package/src/mocks/GRCh37/fasta/19-11215896-11216396.fasta.gz.blob +0 -0
  131. package/src/mocks/GRCh37/fasta/19-11223801-11224301.fasta.gz.blob +0 -0
  132. package/src/mocks/GRCh37/fasta/19-17449149-17449649.fasta.gz.blob +0 -0
  133. package/src/mocks/GRCh37/fasta/19-17451747-17452247.fasta.gz.blob +0 -0
  134. package/src/mocks/GRCh37/fasta/2-47635417-47635917.fasta.gz.blob +0 -0
  135. package/src/mocks/GRCh37/fasta/20-62326742-62327242.fasta.gz.blob +0 -0
  136. package/src/mocks/GRCh37/fasta/22-50627343-50627843.fasta.gz.blob +0 -0
  137. package/src/mocks/GRCh37/fasta/22-50721296-50721796.fasta.gz.blob +0 -0
  138. package/src/mocks/GRCh37/fasta/4-106320044-106320544.fasta.gz.blob +0 -0
  139. package/src/mocks/GRCh37/fasta/7-42017061-42017561.fasta.gz.blob +0 -0
  140. package/src/mocks/GRCh37/fasta/7-42064707-42065207.fasta.gz.blob +0 -0
  141. package/src/mocks/GRCh37/fasta/8-145140250-145140750.fasta.gz.blob +0 -0
  142. package/src/mocks/GRCh37/fasta/8-61764893-61765393.fasta.gz.blob +0 -0
  143. package/src/mocks/GRCh37/fasta/9-107546383-107546883.fasta.gz.blob +0 -0
  144. package/src/mocks/GRCh37/fasta/9-107584614-107585114.fasta.gz.blob +0 -0
  145. package/src/mocks/GRCh37/fasta/MT-15076-15576.fasta.gz.blob +0 -0
  146. package/src/mocks/GRCh37/fasta/X-48932771-48933271.fasta.gz.blob +0 -0
  147. package/src/mocks/GRCh37/fasta/Y-2655391-2655891.fasta.gz.blob +0 -0
  148. package/src/mocks/GRCh37/field_metadata.json +0 -794
  149. package/src/mocks/GRCh37/genes.gff.gz.blob +0 -0
  150. package/src/mocks/GRCh37/sampleTree.json +0 -143
  151. package/src/mocks/GRCh37/static.ts +0 -189
  152. package/src/mocks/GRCh37/vcf/family.vcf.blob +0 -134
  153. package/src/mocks/GRCh38/vcf/family.vcf.blob +0 -272
  154. package/src/mocks/static.ts +0 -1636
  155. /package/src/mocks/GRCh38/vcf/{samples_0.vcf.blob → samples_0.vcf} +0 -0
  156. /package/src/mocks/GRCh38/vcf/{samples_1.vcf.blob → samples_1.vcf} +0 -0

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