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Merge pull request #229 from TheJacksonLaboratory/release_v1.0.3
Release v1.0.3
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| { | ||
| "id": "example-phenopacket", | ||
| "subject": { | ||
| "id": "Sample", | ||
| "timeAtLastEncounter": { | ||
| "age": { | ||
| "iso8601duration": "P2Y" | ||
| } | ||
| } | ||
| }, | ||
| "phenotypicFeatures": [{ | ||
| "type": { | ||
| "id": "HP:0008330", | ||
| "label": "Reduced von Willebrand factor activity" | ||
| } | ||
| }], | ||
| "metaData": { | ||
| "created": "2021-07-13T15:08:53.846Z", | ||
| "createdBy": "ExampleOrg:ExampleCurator", | ||
| "resources": [{ | ||
| "id": "hp", | ||
| "name": "human phenotype ontology", | ||
| "url": "http://purl.obolibrary.org/obo/hp.owl", | ||
| "version": "unknown HPO version", | ||
| "namespacePrefix": "HP", | ||
| "iriPrefix": "http://purl.obolibrary.org/obo/HP_" | ||
| }], | ||
| "phenopacketSchemaVersion": "2.0.0" | ||
| } | ||
| } |
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50 changes: 50 additions & 0 deletions
50
svanna-cli/src/main/java/org/monarchinitiative/svanna/cli/cmd/AnalysisData.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| package org.monarchinitiative.svanna.cli.cmd; | ||
|
|
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| import org.monarchinitiative.phenol.ontology.data.TermId; | ||
|
|
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| import java.nio.file.Path; | ||
| import java.util.List; | ||
| import java.util.Objects; | ||
|
|
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| /** | ||
| * SvAnna requires these inputs for the analysis. | ||
| */ | ||
| class AnalysisData { | ||
|
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| private final List<TermId> phenotypeTerms; | ||
| private final Path vcf; | ||
|
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| AnalysisData(List<TermId> phenotypeTerms, Path vcf) { | ||
| this.phenotypeTerms = phenotypeTerms; | ||
| this.vcf = vcf; | ||
| } | ||
|
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| List<TermId> phenotypeTerms() { | ||
| return phenotypeTerms; | ||
| } | ||
|
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| Path vcf() { | ||
| return vcf; | ||
| } | ||
|
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| @Override | ||
| public boolean equals(Object o) { | ||
| if (this == o) return true; | ||
| if (o == null || getClass() != o.getClass()) return false; | ||
| AnalysisData that = (AnalysisData) o; | ||
| return Objects.equals(phenotypeTerms, that.phenotypeTerms) && Objects.equals(vcf, that.vcf); | ||
| } | ||
|
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| @Override | ||
| public int hashCode() { | ||
| return Objects.hash(phenotypeTerms, vcf); | ||
| } | ||
|
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| @Override | ||
| public String toString() { | ||
| return "AnalysisData{" + | ||
| "phenotypeTerms=" + phenotypeTerms + | ||
| ", vcf=" + vcf + | ||
| '}'; | ||
| } | ||
| } |
28 changes: 28 additions & 0 deletions
28
svanna-cli/src/main/java/org/monarchinitiative/svanna/cli/cmd/AnalysisInputException.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| package org.monarchinitiative.svanna.cli.cmd; | ||
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| import org.monarchinitiative.svanna.core.SvAnnaRuntimeException; | ||
|
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| /** | ||
| * An exception thrown if inputs for the analysis are incomplete or otherwise invalid. | ||
| */ | ||
| class AnalysisInputException extends SvAnnaRuntimeException { | ||
| AnalysisInputException() { | ||
| super(); | ||
| } | ||
|
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| AnalysisInputException(String message) { | ||
| super(message); | ||
| } | ||
|
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| AnalysisInputException(String message, Throwable cause) { | ||
| super(message, cause); | ||
| } | ||
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| AnalysisInputException(Throwable cause) { | ||
| super(cause); | ||
| } | ||
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| AnalysisInputException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) { | ||
| super(message, cause, enableSuppression, writableStackTrace); | ||
| } | ||
| } |
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