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Validate Variation object embedded in the the Phenopacket Schema #133

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merged 5 commits into from
Nov 12, 2022
Merged

Validate Variation object embedded in the the Phenopacket Schema #133

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466f335
Relax validation of VRS-like `Variation` struct.
ielis Nov 8, 2022
c988c3b
Replace `vrs.json` with `Variation` adapter.
ielis Nov 9, 2022
c686ba0
Rework CNV syntax in `Retinoblastoma` example.
ielis Nov 9, 2022
3cc7161
Update wording in the `README.md` of the JSON schema folder.
ielis Nov 9, 2022
26ce086
Absence of a required field in `VariationDescriptor` leads to a valid…
ielis Nov 9, 2022
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498 changes: 498 additions & 0 deletions phenopacket-tools-cli/src/examples/phenopackets/retinoblastoma.json
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34 changes: 26 additions & 8 deletions ...ools-cli/src/main/java/org/phenopackets/phenopackettools/cli/examples/Retinoblastoma.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
package org.phenopackets.phenopackettools.cli.examples;

import org.ga4gh.vrs.v1.*;
import org.ga4gh.vrs.v1.Number;
import org.phenopackets.phenopackettools.builder.PhenopacketBuilder;
import org.phenopackets.phenopackettools.builder.builders.*;
import org.phenopackets.phenopackettools.builder.constants.Laterality;
Expand Down Expand Up @@ -71,10 +73,10 @@ Interpretation interpretation() {
* @return Genomic interpretation related to a somatic missense mutation in the RB1 gene.
*/
GenomicInterpretation somaticRb1Missense() {
AlleleBuilder abuilder = AlleleBuilder.builder();
abuilder.sequenceId("refseq:NC_000013.11");
abuilder.interbaseStartEnd( 48367511, 48367512);
abuilder.altAllele("T");
AlleleBuilder abuilder = AlleleBuilder.builder()
.sequenceId("refseq:NC_000013.11")
.interbaseStartEnd( 48367511, 48367512)
.altAllele("T");
VariationDescriptorBuilder vbuilder = VariationDescriptorBuilder.builder("rs121913300")
.variation(abuilder.buildVariation())
.genomic()
Expand All @@ -100,15 +102,31 @@ GenomicInterpretation somaticRb1Missense() {


GenomicInterpretation germlineRb1Deletion() {
CopyNumberBuilder abuilder = CopyNumberBuilder.builder();
CopyNumber cnv = CopyNumber.newBuilder()
.setDerivedSequenceExpression(DerivedSequenceExpression.newBuilder()
.setLocation(SequenceLocation.newBuilder()
.setSequenceId("refseq:NC_000013.14")
.setSequenceInterval(SequenceInterval.newBuilder()
.setStartNumber(Number.newBuilder().
setValue(25981249)
.build())
.setEndNumber(Number.newBuilder()
.setValue(61706822)
.build())
.build())
.build())
.build())
.setNumber(Number.newBuilder().setValue(1).build())
.build();
//abuilder.copyNumberId("ga4gh:VCN.AFfJws1M4Lg8w1O3XknmHYc9TU2hHYpp");
// original coordinates in paper were given as 13q12.13q21.2(26,555,387–62,280,955 for hg19
//chr13 25981249 61706822 -- lifted over to hg38
Variation variation = Variation.newBuilder()
.setCopyNumber(cnv)
.build();

abuilder.alleleLocation("refseq:NC_000013.14",25981249, 61706822);//VRS uses inter-residue coordinates
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abuilder.oneCopy();
VariationDescriptorBuilder vbuilder = VariationDescriptorBuilder.builder();
vbuilder.variation(abuilder.buildVariation());
vbuilder.variation(variation);
vbuilder.mosaicism(40.0);
VariantInterpretationBuilder vibuilder = VariantInterpretationBuilder.builder(vbuilder);
vibuilder.pathogenic();
Expand Down
25 changes: 25 additions & 0 deletions ...main/resources/org/phenopackets/phenopackettools/validator/jsonschema/README.md
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Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
# README

This folder contains JSON schemas for validating top-level Phenopacket Schema elements and the `Variation` element
embedded in the Phenopacket Schema.

## VRSATILE notes

The datatype of the `VcfRecord.pos` field in `vrsatile.proto` is:
```
uint64 pos = 3;
```

Since Protobuf's `JSONFormat` serializes `uint64` fields into a JSON `string` instead of a JSON `number`,
the JSON schema element for validation of the `VcfRecord.pos` field is:

```
"type": "string",
"pattern": "^[1-9][0-9]*$"
```

instead of a more straightforward:

```
"type": "integer"
```
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