@molgenis/vip-report-template 7.1.3 → 8.0.1

package/src/components/form/ButtonApply.tsx

@@ -1,8 +1,12 @@
 import { Component } from "solid-js";
 
-export const ButtonApply: Component<{ onClick: () => void }> = (props) => {
+export const ButtonApply: Component<{ onClick: () => void; isEnabled?: () => boolean }> = (props) => {
   return (
-    <button class="button is-small is-info" onClick={() => props.onClick()}>
+    <button
+      class="button is-small is-info"
+      onClick={() => props.onClick()}
+      disabled={props.isEnabled !== undefined && !props.isEnabled()}
+    >
       <span class="icon">
         <i class="fas fa-angle-right" />
       </span>

package/src/mocks/GRCh38/README.txt

@@ -0,0 +1,15 @@
+To create or adapt test data:
+- update the resources in this folder
+- use vip-report to generate a new db
+- Update the htsFile path in the database to remove your local paths. (use e.g. intelliJ or webstorm)
+(run fixPaths.sql on all datasources)
+- postfix db files with ".blob"
+
+Parameters for vip-report:
+-i "/path/to/vcf/family.vcf" -f -pb Patient -pd "/path/to/family.ped" -m "/path/to/field_metadata.json" -tc "/path/to/config_vcf.json" -st "/path/to/sampleTree.json" -dt "/path/to/decisionTree.json" -t "/path/to/template.html" -ph "HP:0000951;HP:0003124"
+-i "/path/to/vcf/samples_0.vcf" -f -m "/path/to/field_metadata.json" -tc "/path/to/config_vcf.json" -st "/path/to/sampleTree.json" -dt "/path/to/decisionTree.json" -t "/path/to/template.html"
+-i "/path/to/vcf/samples_1.vcf" -f -pb SAMPLE0 -pd "/path/to/sample1.ped" -m "/path/to/field_metadata.json" -tc "/path/to/config_vcf.json" -st "/path/to/sampleTree.json" -dt "/path/to/decisionTree.json" -t "/path/to/template.html" -ph "HP:0000951"
+-i "/path/to/vcf/samples_100.vcf" -f -m "/path/to/field_metadata.json" -tc "/path/to/config_vcf.json" -st "/path/to/sampleTree.json" -dt "/path/to/decisionTree.json" -t "/path/to/template.html"
+-i "/path/to/vcf/no_vep.vcf" -f -pb Patient -pd "/path/to/family.ped" -m "/path/to/field_metadata.json" -tc "/path/to/config_vcf.json" -st "/path/to/sampleTree.json" -dt "/path/to/decisionTree.json" -t "/path/to/template.html" -ph "HP:0000951;HP:0003124"
+-i "/path/to/vcf/str.vcf" -f -pb Patient -m "/path/to/field_metadata.json" -tc "/path/to/config_cram.json" -st "/path/to/sampleTree.json" -dt "/path/to/decisionTreeStr.json" -t "/path/to/template.html"
+

package/src/mocks/GRCh38/decisionTree.json

@@ -103,6 +103,84 @@
         "nextNode": "vkgl"
       }
     },
+    "clinVar": {
+      "label": "ClinVar",
+      "description": "ClinVar classification",
+      "type": "BOOL_MULTI",
+      "fields": [
+        "INFO/CSQ/clinVar_CLNSIG"
+      ],
+      "outcomes": [
+        {
+          "description": "Conflict",
+          "queries": [
+            {
+              "field": "INFO/CSQ/clinVar_CLNSIG",
+              "operator": "contains_any",
+              "value": [
+                "Conflicting_classifications_of_pathogenicity"
+              ]
+            }
+          ],
+          "outcomeTrue": {
+            "nextNode": "chrom"
+          }
+        },
+        {
+          "description": "LP/P",
+          "queries": [
+            {
+              "field": "INFO/CSQ/clinVar_CLNSIG",
+              "operator": "contains_any",
+              "value": [
+                "Likely_pathogenic",
+                "Pathogenic"
+              ]
+            }
+          ],
+          "outcomeTrue": {
+            "nextNode": "exit_lp"
+          }
+        },
+        {
+          "description": "VUS",
+          "queries": [
+            {
+              "field": "INFO/CSQ/clinVar_CLNSIG",
+              "operator": "contains_any",
+              "value": [
+                "Uncertain_significance"
+              ]
+            }
+          ],
+          "outcomeTrue": {
+            "nextNode": "chrom"
+          }
+        },
+        {
+          "description": "B/LB",
+          "queries": [
+            {
+              "field": "INFO/CSQ/clinVar_CLNSIG",
+              "operator": "contains_any",
+              "value": [
+                "Likely_benign",
+                "Benign"
+              ]
+            }
+          ],
+          "outcomeTrue": {
+            "nextNode": "exit_lb"
+          }
+        }
+      ],
+      "outcomeDefault": {
+        "nextNode": "chrom"
+      },
+      "outcomeMissing": {
+        "nextNode": "chrom"
+      }
+    },
     "vkgl": {
       "label": "vkgl",
       "type": "CATEGORICAL",
@@ -129,6 +207,124 @@
         "nextNode": "filter"
       }
     },
+    "annotSV": {
+      "label": "AnnotSV",
+      "description": "AnnotSV classification",
+      "type": "CATEGORICAL",
+      "field": "INFO/CSQ/ASV_ACMG_class",
+      "outcomeMap": {
+        "5": {
+          "nextNode": "exit_p"
+        },
+        "4": {
+          "nextNode": "exit_lp"
+        },
+        "3": {
+          "nextNode": "exit_vus"
+        },
+        "2": {
+          "nextNode": "exit_lb"
+        },
+        "1": {
+          "nextNode": "exit_b"
+        }
+      },
+      "outcomeMissing": {
+        "nextNode": "spliceAI"
+      },
+      "outcomeDefault": {
+        "nextNode": "spliceAI"
+      }
+    },
+    "spliceAI": {
+      "label": "SpliceAI",
+      "description": "SpliceAI prediction",
+      "type": "BOOL_MULTI",
+      "fields": [
+        "INFO/CSQ/SpliceAI_pred_DS_AG",
+        "INFO/CSQ/SpliceAI_pred_DS_AL",
+        "INFO/CSQ/SpliceAI_pred_DS_DG",
+        "INFO/CSQ/SpliceAI_pred_DS_DL"
+      ],
+      "outcomes": [
+        {
+          "description": "Delta score (acceptor/donor gain/loss) > 0.42",
+          "operator": "OR",
+          "queries": [
+            {
+              "field": "INFO/CSQ/SpliceAI_pred_DS_AG",
+              "operator": ">",
+              "value": 0.42
+            },
+            {
+              "field": "INFO/CSQ/SpliceAI_pred_DS_AL",
+              "operator": ">",
+              "value": 0.42
+            },
+            {
+              "field": "INFO/CSQ/SpliceAI_pred_DS_DG",
+              "operator": ">",
+              "value": 0.42
+            },
+            {
+              "field": "INFO/CSQ/SpliceAI_pred_DS_DL",
+              "operator": ">",
+              "value": 0.42
+            }
+          ],
+          "outcomeTrue": {
+            "nextNode": "exit_lp"
+          }
+        },
+        {
+          "description": "Delta score (acceptor/donor gain/loss) > 0.13",
+          "operator": "OR",
+          "queries": [
+            {
+              "field": "INFO/CSQ/SpliceAI_pred_DS_AG",
+              "operator": ">",
+              "value": 0.13
+            },
+            {
+              "field": "INFO/CSQ/SpliceAI_pred_DS_AL",
+              "operator": ">",
+              "value": 0.13
+            },
+            {
+              "field": "INFO/CSQ/SpliceAI_pred_DS_DG",
+              "operator": ">",
+              "value": 0.13
+            },
+            {
+              "field": "INFO/CSQ/SpliceAI_pred_DS_DL",
+              "operator": ">",
+              "value": 0.13
+            }
+          ],
+          "outcomeTrue": {
+            "nextNode": "exit_vus"
+          }
+        }
+      ],
+      "outcomeDefault": {
+        "nextNode": "utr5"
+      },
+      "outcomeMissing": {
+        "nextNode": "utr5"
+      }
+    },
+    "utr5": {
+      "label": "5' UTR",
+      "description": "5' UTR",
+      "type": "EXISTS",
+      "field": "INFO/CSQ/five_prime_UTR_variant_consequence",
+      "outcomeTrue": {
+        "nextNode": "exit_vus"
+      },
+      "outcomeFalse": {
+        "nextNode": "capice"
+      }
+    },
     "filter": {
       "label": "filter",
       "type": "BOOL",
@@ -369,6 +565,11 @@
       "type": "LEAF",
       "class": "LB"
     },
+    "exit_lt": {
+      "label": "Likely T",
+      "type": "LEAF",
+      "class": "LT"
+    },
     "exit_vus": {
       "label": "Unknown Significance",
       "type": "LEAF",

package/src/mocks/GRCh38/family.ped

@@ -0,0 +1,6 @@
+FAM001	Patient	Father	MotherHasQuiteALongName	1	2
+FAM001	MotherHasQuiteALongName	0	0	2	1
+FAM001	Father	0	0	1	2
+FAM001	Nephew	0	0	1	1
+FAM001	Sister	Father	MotherHasQuiteALongName	2	1
+FAM002	Unrelated	0	0	1	2

package/src/mocks/GRCh38/field_metadata.json

@@ -86,12 +86,39 @@
     "VIPC_S": {
       "label": "VIP sample classification",
       "numberType": "OTHER",
-      "type": "STRING",
+      "type": "CATEGORICAL",
       "separator": ","
     }
   },
   "info": {
+    "n_object0": {
+      "nestedAttributes" : {
+        "separator": "|"
+      },
+      "nestedFields": {
+        "n_array1": {
+          "label": "Array",
+          "description": "Test array",
+          "numberType": "OTHER",
+          "separator": "&",
+          "type": "INTEGER",
+          "index": 2
+        },
+        "n_string1": {
+          "label": "String",
+          "description": "Test string",
+          "numberType": "NUMBER",
+          "numberCount": 1,
+          "type": "STRING",
+          "index": 0
+        }
+      }
+    },
     "CSQ": {
+      "nestedAttributes" : {
+        "prefix": "Consequence annotations from Ensembl VEP. Format: ",
+        "separator": "|"
+      },
       "nestedFields": {
         "ALLELE_NUM": {
           "label": "Allele Nr.",
@@ -495,7 +522,7 @@
           "description": "Human Phenotype Ontology (HPO) terms describing phenotypic abnormalities, see https://hpo.jax.org/ and https://doi.org/10.1093/nar/gkad1005",
           "numberType": "OTHER",
           "separator": "&",
-          "type": "STRING"
+          "type": "CATEGORICAL"
         },
         "IMPACT": {
           "label": "Impact",
@@ -599,7 +626,7 @@
           "description": "Boolean indicating if this is the VEP picked transcript.",
           "numberType": "NUMBER",
           "numberCount": 1,
-          "type": "INTEGER"
+          "type": "FLAG"
         },
         "PolyPhen": {
           "label": "PolyPhen",
@@ -685,14 +712,6 @@
           "numberCount": 1,
           "type": "STRING"
         },
-        "VIPC": {
-          "label": "VIP classification",
-          "description": "Variant consequence classification predicted by the Variant Interpretation Pipeline (VIP), see https://vip.molgeniscloud.org/ and https://doi.org/10.1101/2024.04.11.24305656",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "STRING",
-          "required": true
-        },
         "VIPP": {
           "label": "VIP path",
           "description": "VIP decision tree path",
@@ -802,6 +821,12 @@
       "numberType": "NUMBER",
       "numberCount": 1,
       "type": "STRING"
+    },
+    "VIPC_S": {
+      "label": "VIP sample classification",
+      "numberType": "OTHER",
+      "type": "CATEGORICAL",
+      "separator": ","
     }
   }
 }

package/src/mocks/GRCh38/sample1.ped

@@ -0,0 +1 @@
+FAM001	SAMPLE0	0	0	1	2

package/src/mocks/GRCh38/static.ts

@@ -32,25 +32,48 @@ import fastaUrl_chrM_15075_15575 from "./fasta/chrM-15075-15575.fasta.gz.blob";
 import fastaUrl_chrX_49075112_49075612 from "./fasta/chrX-49075112-49075612.fasta.gz.blob";
 import fastaUrl_chrY_2787350_2787850 from "./fasta/chrY-2787350-2787850.fasta.gz.blob";
 import genesUrl from "./genes.gff.gz.blob";
-import vcfUrlFamily from "./vcf/family.vcf.blob";
-import vcfUrlNoVep from "./vcf/no_vep.vcf.blob";
-import vcfUrlSamples0 from "./vcf/samples_0.vcf.blob";
-import vcfUrlSamples1 from "./vcf/samples_1.vcf.blob";
-import vcfUrlSamples100 from "./vcf/samples_100.vcf.blob";
-import vcfUrlStr from "./vcf/str.vcf.blob";
-/* eslint-enable */
-import decisionTreeJson from "./decisionTree.json";
-import decisionTreeStrJson from "./decisionTreeStr.json";
-import sampleTreeJson from "./sampleTree.json";
-import vcfMetaJson from "./field_metadata.json";
+import databaseFamily from "./vcf/family.db.blob";
+import databaseSamples0 from "./vcf/samples_0.db.blob";
+import databaseNoVep from "./vcf/no_vep.db.blob";
+import databaseSamples1 from "./vcf/samples_1.db.blob";
+import databaseSamples100 from "./vcf/samples_100.db.blob";
+import databaseStr from "./vcf/str.db.blob";
+import sqlWasm from "../sql-wasm.wasm.blob";
+
 import { fetchAsBytes } from "../utils";
-import { DecisionTree } from "@molgenis/vip-report-api";
-import { SupplementaryMetadata } from "@molgenis/vip-report-vcf";
 
 export async function fetchCram() {
   return await fetchAsBytes(cramUrl as string);
 }
 
+export async function fetchDatabaseFamily() {
+  return await fetchAsBytes(databaseFamily as string);
+}
+
+export async function fetchSqlWasm() {
+  return await fetchAsBytes(sqlWasm as string);
+}
+
+export async function fetchDatabaseSamples0() {
+  return await fetchAsBytes(databaseSamples0 as string);
+}
+
+export async function fetchDatabaseNoVep() {
+  return await fetchAsBytes(databaseNoVep as string);
+}
+
+export async function fetchDatabaseSamples1() {
+  return await fetchAsBytes(databaseSamples1 as string);
+}
+
+export async function fetchDatabaseSamples100() {
+  return await fetchAsBytes(databaseSamples100 as string);
+}
+
+export async function fetchDatabaseStr() {
+  return await fetchAsBytes(databaseStr as string);
+}
+
 export async function fetchCrai() {
   return await fetchAsBytes(craiUrl as string);
 }
@@ -63,10 +86,6 @@ export async function fetchStrCrai() {
   return await fetchAsBytes(strCraiUrl as string);
 }
 
-export const decisionTree: DecisionTree = decisionTreeJson as unknown as DecisionTree;
-export const decisionTreeStr: DecisionTree = decisionTreeStrJson as unknown as DecisionTree;
-export const sampleTree: DecisionTree = sampleTreeJson as unknown as DecisionTree;
-
 export async function fetchFastaGz() {
   return {
     "chr1:9982230-9982730": await fetchAsBytes(fastaUrl_chr1_9982230_9982730 as string),
@@ -102,134 +121,3 @@ export async function fetchFastaGz() {
 export async function fetchGenesGz() {
   return await fetchAsBytes(genesUrl as string);
 }
-
-export const vcfMeta = vcfMetaJson as unknown as SupplementaryMetadata;
-
-export async function fetchVcfFamily() {
-  return await fetchAsBytes(vcfUrlFamily as string);
-}
-
-export async function fetchVcfNoVep() {
-  return await fetchAsBytes(vcfUrlNoVep as string);
-}
-
-export async function fetchVcfSamples0() {
-  return await fetchAsBytes(vcfUrlSamples0 as string);
-}
-
-export async function fetchVcfSamples1() {
-  return await fetchAsBytes(vcfUrlSamples1 as string);
-}
-
-export async function fetchVcfSamples100() {
-  return await fetchAsBytes(vcfUrlSamples100 as string);
-}
-
-export async function fetchVcfStr() {
-  return await fetchAsBytes(vcfUrlStr as string);
-}
-
-export const samplesStr = {
-  samples: [
-    {
-      person: {
-        familyId: "FAM001",
-        individualId: "Patient",
-        sex: "FEMALE",
-        affectedStatus: "AFFECTED",
-      },
-      index: 0,
-      proband: true,
-    },
-  ],
-  phenotypes: [],
-};
-
-export const samplesFamily = {
-  samples: [
-    {
-      person: {
-        familyId: "FAM001",
-        individualId: "Patient",
-        paternalId: "Father",
-        maternalId: "MotherHasQuiteALongName",
-        sex: "MALE",
-        affectedStatus: "AFFECTED",
-      },
-      index: 3,
-      proband: true,
-      filter_classes: ["U1", "U2"],
-    },
-    {
-      person: {
-        familyId: "FAM001",
-        individualId: "MotherHasQuiteALongName",
-        paternalId: "0",
-        maternalId: "0",
-        sex: "FEMALE",
-        affectedStatus: "UNAFFECTED",
-      },
-      index: 1,
-      proband: false,
-    },
-    {
-      person: {
-        familyId: "FAM001",
-        individualId: "Father",
-        paternalId: "0",
-        maternalId: "0",
-        sex: "MALE",
-        affectedStatus: "AFFECTED",
-      },
-      index: 0,
-      proband: false,
-    },
-  ],
-  phenotypes: [
-    {
-      phenotypicFeaturesList: [
-        {
-          type: {
-            id: "HP:0000951",
-            label: "HP:0000951",
-          },
-        },
-        {
-          type: {
-            id: "HP:0003124",
-            label: "HP:0003124",
-          },
-        },
-      ],
-      subject: {
-        id: "Patient",
-      },
-    },
-    {
-      phenotypicFeaturesList: [
-        {
-          type: {
-            id: "HP:0000951",
-            label: "HP:0000951",
-          },
-        },
-      ],
-      subject: {
-        id: "MotherHasQuiteALongName",
-      },
-    },
-    {
-      phenotypicFeaturesList: [
-        {
-          type: {
-            id: "HP:0000951",
-            label: "HP:0000951",
-          },
-        },
-      ],
-      subject: {
-        id: "Father",
-      },
-    },
-  ],
-};

package/src/mocks/GRCh38/str.ped

@@ -0,0 +1 @@
+FAM001	Patient	0	0	2	2