@molgenis/vip-report-template 6.1.1 → 7.0.0

package/.nvmrc

@@ -1 +1 @@
-18.18.2
+engine-strict=true

package/.travis.yml

@@ -1,6 +1,8 @@
 os: linux
-dist: focal
+dist: jammy
 language: node_js
+node_js:
+  - 22
 branches:
   only:
     - main
@@ -11,30 +13,26 @@ cache:
     - "~/.pnpm-store"
 before_install:
   - corepack enable
-  - corepack prepare pnpm@latest-8 --activate
+  - corepack prepare pnpm@latest-9 --activate
   - pnpm config set store-dir ~/.pnpm-store
 install:
   - pnpm install
 script:
   - pnpm run lint
-  - pnpm run test
-before_deploy:
+  - pnpm run coverage
   - pnpm run build
+before_deploy:
   - mv dist/index.html dist/vip-report-template.html
 deploy:
-  - provider: npm
-    api_token:
-      secure: TxQUU8xNTVTqhQ6pYTR+ic7Crv6rPZ7UbRo8HJJOGlFA30Vb/O36kh3Vgwx3fM5oinC1I38pzmHjJ4WVz2qiUZcgNzDHMorQhErbfSWLO8G7XTsVkMkyozPPtgdCCT2Z7FfdTKmY5an+V4ZJlreM83+vlJmUzMoGahZElESBk94QkTnPAqk46whXAf/zToEw7OJsxd2N3uPyPB8+rgg5VMApRBsCegt3KyetiMBIYWX+kJLxXEGK7OnJmxz1SGrYHR87YEDog7awBIhrXNcBWc4Lj55oWEqp3JQlpLnVDhEUCSO8cmQkyIMTYZ3eIKoyrDk9vfAYYbDsRvagFXKTZGvv0ZQv8s7a1lWAadTyvgbmo3cvX/KHfam5pGf2DFEXWIHZgvoIzq8GY6V4sjOEWRG2sAn+jKiNT5jPgG8sG0faP2JVr55WoN4jRthk5ABckyS8PByWrwcLILTeBPuX7DpiKtzUzzRw/qHAGo59+bFyZiKIc5I+S59fnttJ6Vz4jpjsavOzNsgIGUsTs3y1kosNLYoJVcI3RjpgHQuOfzawKb2l22B5wbJ1/1llhrSqYCtEjAhUuruB3bhy+/WiN4ulKp29Ct7/IEN3ctBXdMBm2xCPlsPSTBeXzwJNeWykTnpFx9qykjtSj3CwS8ZDnY3M+/dLhywrI46EGa03YRw=
+  - provider: script
+    script: bash scripts/deploy_npm_registry.sh
     on:
       tags: true
-    edge:
-      branch: v2.0.3-beta.4 # workaround for https://travis-ci.community/t/builds-suddenly-fail-with-error-installing-dpl/14270/3
   - provider: releases
     token:
       secure: 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
     file: dist/vip-report-template.html
     on:
       tags: true
-    edge:
-      branch: v2.0.3-beta.4 # workaround for https://travis-ci.community/t/builds-suddenly-fail-with-error-installing-dpl/14270/3
+    edge: true
 

package/README.md

@@ -1,9 +1,419 @@
 [![Build Status](https://app.travis-ci.com/molgenis/vip-report-template.svg?branch=main)](https://app.travis-ci.com/molgenis/vip-report-template)
+
 # vip-report-template
-The default report template for the [VIP report generator](https://github.com/molgenis/vip-report). This template is a good default for any .vcf file with support for .vcf files annotated with [VIP](https://github.com/molgenis/vip).   
+
+The default report template for the [VIP report generator](https://github.com/molgenis/vip-report). This template is a
+good default for any .vcf file with support for .vcf files annotated with [VIP](https://github.com/molgenis/vip).
+
 ## Usage
+
 ```bash
 $ pnpm install
 $ pnpm run build # build report template in dist folder
 $ pnpm run dev   # dev server on localhost:3000
 ```
+
+## Config
+
+The config.json file is used to configure which fields, filters and sort options are shown on screen.
+Furthermore, it is used to pass the vip pipeline configuration to the report template.
+There are 3 top level elements:
+
+- vip: used to pass the VIP configuration
+- sample_variants: to configure the sample variants screen
+- variants: to configure the variants screen
+
+Example:
+
+```
+{
+  "vip": {VIP_CONFIG_HERE},
+  "sample_variants": {SAMPLE_VARIANTS_SCREEN_CONFIG_HERE},
+  "variants": {VARIANTS_SCREEN_CONFIG_HERE},
+  "sample_variant": {SAMPLE_VARIANT_SCREEN_CONFIG_HERE},
+  "variant": {VARIANT_SCREEN_CONFIG_HERE},
+  "sample_variant_consequence": {SAMPLE_VARIANT_CONSEQUENCE_SCREEN_CONFIG_HERE},
+  "variant_consequence": {VARIANT_CONSEQUENCE_SCREEN_CONFIG_HERE}
+}
+```
+
+### VIP config
+
+### Configuring screen content
+
+#### Variant types
+
+For the sample variant view multiple "subviews":
+
+- all: which shows all types of variants
+- snv: shows the single nucleotide variants and small indels.
+- sv: shows structural variants
+- str: shows the short tandem repeats.
+  All of these screens can be configured independently, if the configuration for a specific variant type view is
+  missing, the "all" configuration is used for this specific view.
+
+Example:
+
+```
+    "cells": {
+      "all": [FIELDS_CONFIG_HERE],
+      "snv": [FIELDS_CONFIG_HERE],
+      "sv": [FIELDS_CONFIG_HERE],
+```
+
+"str" is missing in this example, the "all" config is used for the str view.
+
+#### Cells
+
+This section specifies which information should be shown in the table with variant information.
+Per cell the following information can/should be specified:
+
+- "type": the type of field, one of:
+    - fixed: the standard columns of an VCF file, excluding the FORMAT and INFO columns,
+      one of: pos,id,ref,alt,qual,filter
+    - info: a VCF INFO field
+    - format: a VCF FORMAT field, currently unsupported
+    - genotype: a VCF FORMAT field in the context of the current sample of the screen.
+    - composed: a custom field based on information from multiple fields, see the "Composed" section.
+- "name": the name of the field in the VCF file
+- "label": optional label, name is used if no label is specified.
+- "description": optional description to be shown in the tooltip for the column on screen.
+
+Example:
+
+```
+        {
+          "type": "info",
+          "name": "myInfoField"
+        },
+        {
+          "type": "composed",
+          "name": "my_composed_fieldname",
+          "label": "My Composed Field Label",
+          "description": "Description explaining that this is just and example field."
+        },
+```
+
+##### Groups
+
+Cells can be grouped to indicate that certain cells belong together, an example of this are the child fields of the VEP
+INFO field.
+
+Example:
+
+```
+        {
+          "type": "info",
+          "name": "myInfoField"
+        },
+        {
+            "type": "group",
+            "fields": [
+              {
+                "type": "info",
+                "name": "CSQ/Consequence",
+              },
+              {
+                "type": "info",
+                "name": "CSQ/SYMBOL"
+              }
+            ]
+        }
+```
+
+##### Composed
+
+The following composed field are available:
+
+| id                 | required                                | optional                                                                                                                                                                                | description                                                                                                                                                                                                                                                                                                 |
+|--------------------|-----------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| clinVar            | `INFO/CSQ/clinVar_CLNSIG`               | `INFO/CSQ/clinVar_CLNID`, `INFO/CSQ/clinVar_CLNREVSTAT`                                                                                                                                 | This field shows the ClinVar values with a tooltip containing the ClinVar star rating.                                                                                                                                                                                                                      |
+| gene               | `INFO/CSQ/SYMBOL`                       | `INFO/CSQ/Gene`, `INFO/CSQ/IncompletePenetrance`, `INFO/CSQ/SYMBOL_SOURCE`                                                                                                              | The gene name with a link to https://genenames.org and an indication if the gene is associated with incomplete penetrance.                                                                                                                                                                                  |
+| genotype           | `FORMAT/GT`, `sample` exists            | `FORMAT/REPCN`, `FORMAT/VIAB`, `INFO/SVTYPE`, `INFO/RU`, `INFO/RUMATCH`, `INFO/DisplayRU`                                                                                               | Shows the genotype based on the variant type. For SNV/SV: rendering the REF and ALT nucleotides (rendered with colors per nucleotide) for the alleles rather than the allele numbers. For STR: Shows the genotype as the called repeat unit in combination with the number of repeat units seen per allele. |
+| genotype_maternal  | `FORMAT/GT`, `sample.maternalId` exists | `FORMAT/REPCN`, `FORMAT/VIAB`, `INFO/SVTYPE`, `INFO/RU`, `INFO/RUMATCH`, `INFO/DisplayRU`                                                                                               | Same as `genotype`, but for the maternal sample                                                                                                                                                                                                                                                             |
+| genotype_paternal  | `FORMAT/GT`, `sample.paternalId` exists | `FORMAT/REPCN`, `FORMAT/VIAB`, `INFO/SVTYPE`, `INFO/RU`, `INFO/RUMATCH`, `INFO/DisplayRU`                                                                                               | Same as `genotype`, but for the paternal sample                                                                                                                                                                                                                                                             |
+| gnomAdAf           | `INFO/CSQ/gnomAD_AF`                    | `INFO/CSQ/gnomAD_COV`, `INFO/CSQ/gnomAD_QC`, `INFO/CSQ/ALLELE_NUM`                                                                                                                      | Shows the GnomAD allele frequency with a link to https://gnomad.broadinstitute.org, and an indicator to warn for low quality.                                                                                                                                                                               |
+| hpo                | `INFO/CSQ/HPO`                          | `INFO/CSQ/GADO_PD`                                                                                                                                                                      | Shows the associated HPO terms with a link to https://hpo.jax.org, the column also shows an indicator if the gene received a high or low confidence GADO score.                                                                                                                                             |
+| inheritancePattern | `INFO/CSQ/InheritanceModesGene`         | `FORMAT/VIC`                                                                                                                                                                            | Shows the inheritance patterns of the gene, an indicator is show if the gene is associated with the AR pattern and there is a possible compound AR pattern for the sample.                                                                                                                                  |
+| locus              | `CHROM`, `POS`                          |                                                                                                                                                                                         | show chromosome:position with a link to the report variant detail view.                                                                                                                                                                                                                                     |
+| vipC               | `INFO/CSQ/VIPC`                         | `INFO/CSQ/VIPP`                                                                                                                                                                         | shows the VIP classification with a link to the consequence details view, and the VIP classification path as tooltip.                                                                                                                                                                                       |
+| vipCS              | `FORMAT/VIPC_S`, `sample` exists        | `FORMAT/VIPP_S`                                                                                                                                                                         | shows the VIP classification with a link to the consequence details view, and the VIP classification path as tooltip.                                                                                                                                                                                       |
+| vkgl               | `INFO/CSQ/VKGL_CL`                      | `INFO/CSQ/VKGL_AMC`, `INFO/CSQ/VKGL_ERASMUS`, `INFO/CSQ/VKGL_LUMC`, `INFO/CSQ/VKGL_NKI`, `INFO/CSQ/VKGL_RADBOUD_MUMC`, `INFO/CSQ/VKGL_UMCG`, `INFO/CSQ/VKGL_UMCU`, `INFO/CSQ/VKGL_VUMC` | shows the VKGL classification(s), if data for specific labs is available this is shown in the tooltip.                                                                                                                                                                                                      |
+
+A composed field will be used in the report if the requirements are met, otherwise it will be ignored.
+
+#### Filters
+
+##### Composed
+
+The following composed filters are available:
+
+| id               | required                                                                                           | optional | description                                                                                                                                                                 |
+|------------------|----------------------------------------------------------------------------------------------------|----------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| allelicImbalance | `FORMAT/GT`, `FORMAT/VIAB`, `sample` exists                                                        |          | Filter to select variants that are/are not showing allelic imbalance.                                                                                                       |
+| deNovo           | `FORMAT/VID`, `sample` exists                                                                      |          | Filter to select only variants that are/are not DeNovo                                                                                                                      |
+| hpo              | `INFO/CSQ/HPO`, `sample` exists, `sample.phenotypes` > 0                                           |          | Filter to select variants that match certain HPO terms                                                                                                                      |
+| inheritanceMatch | `FORMAT/VIM`, `sample` exists                                                                      |          | Filter to select variants for which the suitable inheritance patterns for the sample contain the selected pattern.                                                          |
+| locus            | `CHROM`, `POS`                                                                                     |          | Filter to select variants based on their chromosome optionally within a certain position range on this  chromosome.                                                         |
+| vipC             | `INFO/CSQ/VIPC`, parameter `vcf.filter.consequences=true`, `vcf.filter.classes` > 0                |          | Filter on the VIP classification value stored in INFO/CSQ/VIPC, but only includes categories defined in the VIP configuration parameter `vcf.filter.classes`                |
+| vipCS            | `FORMAT/VIPC_S`, `sample` exists, `sample.proband=true`, parameter `vcf.filter.sample_classes` > 0 |          | Filter on the VIP sample classification value stored in FORMAT/VIPC_S, but only includes categories defined in the VIP configuration parameter `vcf.filter_samples.classes` |
+
+#### Sorts
+
+Via this section available sort options and the default sort of the different views can be configured.
+Currently only INFO fields with single numerical values can be used for sorting.
+
+Multiple sort fields can be specified for a single sort option to create a secondary, tertiary, etc. sort.
+
+Example:
+
+```
+{
+  "sorts": {
+    "all": [
+      {
+        "selected": true,
+        "orders": [
+          {
+            "direction": "desc",
+            "field": {
+              "type": "info",
+              "name": "MySortField"
+            }
+          }
+        ]
+      },
+      {
+        "selected": false,
+        "orders": [
+          {
+            "direction": "asc",
+            "field": {
+              "type": "info",
+              "name": "MySortOtherField"
+            }
+          }
+        ]
+      }
+    ],
+    "str": [
+      {
+        "selected": true,
+        "orders": [
+          {
+            "direction": "desc",
+            "field": {
+              "type": "info",
+              "name": "MySortPrimarySortField"
+            }
+          },
+          {
+            "direction": "asc",
+            "field": {
+              "type": "info",
+              "name": "MySortSecondarySortField"
+            }
+          }
+        ]
+      },
+      {
+        "selected": false,
+        "orders": [
+          {
+            "direction": "asc",
+            "field": {
+              "type": "info",
+              "name": "MySortOtherField"
+            }
+          }
+        ]
+      }
+    ]
+  }
+}
+```
+
+#### Records per page
+
+Via this section available records per page options and the default can be configured.
+
+Example:
+
+```
+"recordsPerPage": {
+      "str": [
+        {
+          "number": 10
+        },
+        {
+          "number": 20,
+          "selected": true
+        },
+        {
+          "number": 50
+        },
+        {
+          "number": 100
+        }
+      ]
+    }
+```
+
+### Wildcards
+
+Regular expressions like can be used to include multiple fields at once in you config.
+
+Examples:
+Include all INFO fields
+
+```
+        {
+          "type": "info",
+          "name": ".*"
+        }
+```
+
+Include all nested CSQ child fields
+
+```
+        {
+          "type": "info",
+          "name": "CSQ/.*"
+        }
+```
+
+Include all CSQ child fields starting with a "G" and a name of 4 characters long ending with an "e" (Gene)
+
+```
+        {
+          "type": "info",
+          "name": "CSQ/G..e"
+        }
+```
+
+## Metadata
+
+In the metadata json file additional field metadata can be specified in addition or as replacement of the field
+definition in the VCF file
+This is particularly useful for nested fields like VEP, and to specify the categories of a categorical field.
+
+Example:
+
+```
+{
+  "format": {
+     "MyFormatfield": {
+        "label": "My Format field",
+        "description": "This describes my Format field",
+        "numberType": "NUMBER",
+        "numberCount": 1,
+        "type": "INTEGER"
+    },
+    "MyCategoricalFormatField": {
+      "label": "My Categorical Format Field",
+      "description": "This is a format categorical field.",
+      "numberType": "NUMBER",
+      "numberCount": 1,
+      "type": "CATEGORICAL",
+      "categories": {
+        "1": {
+          "label": "Value1",
+          "description": "This is value 1"
+        },
+        "2": {
+          "label": "Value2",
+          "description": "This is value 2"
+        }
+      }
+    }
+  },
+  "info": {
+    "CSQ": {
+      "nestedFields": {
+        "MyNestedfield": {
+          "label": "My nested field",
+          "description": "This describes my nested field",
+          "numberType": "NUMBER",
+          "numberCount": 1,
+          "type": "INTEGER"
+        },
+        "MyCategoricalNestedField": {
+          "label": "My Categorical Nested Field",
+          "description": "This is a nested categorical field.",
+          "numberType": "NUMBER",
+          "numberCount": 1,
+          "type": "CATEGORICAL",
+          "categories": {
+            "1": {
+              "label": "Value1",
+              "description": "This is value 1"
+            },
+            "2": {
+              "label": "Value2",
+              "description": "This is value 2"
+            }
+          }
+        }
+      }
+    },
+    "MyInfofield": {
+      "label": "My INFO field",
+      "description": "This describes my INFO field",
+      "numberType": "NUMBER",
+      "numberCount": 1,
+      "type": "INTEGER"
+    },
+    "MyCategoricalField": {
+      "label": "My Categorical Field",
+      "description": "This is a categorical field.",
+      "numberType": "NUMBER",
+      "numberCount": 1,
+      "type": "CATEGORICAL",
+      "categories": {
+        "1": {
+          "label": "Value1",
+          "description": "This is value 1"
+        },
+        "2": {
+          "label": "Value2",
+          "description": "This is value 2"
+        }
+      }
+    }
+  }
+}
+```
+
+### Null values
+
+In the metadata json file "null" values can be specified for categorical fields, these values should contain a label and
+optionally a description.
+The label value is rendered in filters and used to display the file in tables and views if it is empty, the description
+is used in tooltips.
+In cases where the categorical field is of a type that can have multiple values, an array containing the null value is
+returned if the field is empty.
+
+### Example
+
+```
+"MyCategoricalField": {
+  "label": "My Categorical Field",
+  "description": "This is a categorical field.",
+  "numberType": "NUMBER",
+  "numberCount": 1,
+  "type": "CATEGORICAL",
+  "categories": {
+    "1": {
+      "label": "Value1",
+      "description": "This is value 1"
+    },
+    "2": {
+      "label": "Value2",
+      "description": "This is value 2"
+    }
+  },
+  "nullValue": {
+    "label": "EmptyValue"
+  }
+}
+```

package/eslint.config.mjs

@@ -0,0 +1,11 @@
+import pluginJs from "@eslint/js";
+// workaround: import .js because of https://github.com/solidjs-community/eslint-plugin-solid/issues/118
+import solid from "eslint-plugin-solid/configs/typescript";
+import tseslint from "typescript-eslint";
+
+export default [
+  { files: ["**/*.{js,mjs,cjs,ts,tsx}"] },
+  pluginJs.configs.recommended,
+  solid,
+  ...tseslint.configs.recommended,
+];

package/package.json

@@ -1,47 +1,38 @@
 {
   "name": "@molgenis/vip-report-template",
-  "version": "6.1.1",
+  "version": "7.0.0",
   "description": "Report Template for Variant Call Format (VCF) Report Generator",
-  "scripts": {
-    "build": "vite build",
-    "build-dev": "vite build --mode dev",
-    "coverage": "vitest run --coverage",
-    "dev": "vite",
-    "format": "prettier --write src/**/*.{tsx,ts}",
-    "lint": "eslint src/**/*.{tsx,ts}",
-    "prepare": "husky",
-    "test": "vitest run",
-    "test:watch": "vitest"
-  },
   "license": "LGPL-3.0",
   "devDependencies": {
-    "@molgenis/vite-plugin-inline": "^1.0.24",
-    "@typescript-eslint/eslint-plugin": "^7.12.0",
-    "@typescript-eslint/parser": "^7.12.0",
-    "@vitest/coverage-v8": "^1.6.0",
-    "bulma": "^1.0.1",
-    "eslint": "^8.57.0",
+    "@molgenis/vite-plugin-inline": "^1.0.27",
+    "@types/async-lock": "^1.4.2",
+    "@types/node": "^22.9.3",
+    "@vitest/coverage-v8": "^2.1.5",
+    "async-lock": "^1.4.1",
+    "bulma": "^1.0.2",
+    "eslint": "^9.15.0",
     "eslint-config-prettier": "^9.1.0",
-    "eslint-plugin-prettier": "^5.1.3",
-    "eslint-plugin-solid": "^0.14.0",
-    "husky": "^9.0.11",
-    "jsdom": "^24.1.0",
-    "prettier": "^3.3.1",
-    "sass": "^1.77.4",
-    "typescript": "^5.4.5",
-    "vite": "^5.2.12",
+    "eslint-plugin-solid": "^0.14.4",
+    "husky": "^9.1.7",
+    "jsdom": "^25.0.1",
+    "prettier": "^3.3.3",
+    "sass": "^1.81.0",
+    "typescript": "^5.6.3",
+    "typescript-eslint": "^8.15.0",
+    "vite": "^5.4.11",
     "vite-plugin-solid": "^2.10.2",
-    "vitest": "^1.6.0"
+    "vitest": "^2.1.5"
   },
   "dependencies": {
-    "@fortawesome/fontawesome-svg-core": "^6.5.2",
-    "@fortawesome/free-solid-svg-icons": "^6.5.2",
-    "@molgenis/vip-report-api": "^5.0.4",
-    "@molgenis/vip-report-vcf": "^2.0.2",
-    "@solidjs/router": "^0.13.5",
+    "@fortawesome/fontawesome-svg-core": "^6.7.1",
+    "@fortawesome/free-solid-svg-icons": "^6.7.1",
+    "@molgenis/vip-report-api": "^6.2.1",
+    "@molgenis/vip-report-vcf": "^3.0.8",
+    "@solidjs/router": "^0.15.1",
+    "ajv": "^8.17.1",
     "base64-js": "^1.5.1",
-    "igv": "^2.15.11",
-    "solid-js": "^1.8.17"
+    "igv": "^3.1.0",
+    "solid-js": "^1.9.3"
   },
   "lint-staged": {
     "src/**/*.{tsx,ts}": [
@@ -59,5 +50,19 @@
   "repository": {
     "type": "git",
     "url": "git+https://github.com/molgenis/vip-report-template.git"
+  },
+  "engines": {
+    "node": "22",
+    "pnpm": "9"
+  },
+  "scripts": {
+    "build": "vite build",
+    "build-dev": "vite build --mode dev",
+    "coverage": "vitest run --coverage",
+    "dev": "vite",
+    "format": "prettier --write src/**/*.{json,tsx,ts}",
+    "lint": "eslint src/**/*.{json,tsx,ts}",
+    "test": "vitest run",
+    "test:watch": "vitest"
   }
-}
+}

package/scripts/deploy_npm_registry.sh

@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+pnpm config set registry "https://registry.npmjs.org"
+pnpm config set //registry.npmjs.org/:_authToken "${NPM_TOKEN}"
+# workaround: packageManager is added to package.json after git checkout resulting in 'Unclean working tree' error
+pnpm publish --no-git-checks .