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adding data resolver with tests, renaming package from jacksonlaborat…
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9 changes: 0 additions & 9 deletions
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oan-etl/src/main/java/org/jacksonlaboratory/ontology/GraphLoader.java
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4 changes: 2 additions & 2 deletions
4
...g/jacksonlaboratory/graph/Operations.java → ...in/java/org/jax/oan/graph/Operations.java
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oan-etl/src/main/java/org/jax/oan/ontology/GraphLoader.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| package org.jax.oan.ontology; | ||
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| import org.jax.oan.exception.OntologyAnnotationNetworkException; | ||
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| import java.io.IOException; | ||
| import java.nio.file.Path; | ||
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| public interface GraphLoader { | ||
| void load(Path dataDirectory) throws IOException, OntologyAnnotationNetworkException; | ||
| } |
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oan-etl/src/main/java/org/jax/oan/ontology/HpoDataResolver.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,70 @@ | ||
| package org.jax.oan.ontology; | ||
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| import org.jax.oan.exception.OntologyAnnotationNetworkDataException; | ||
| import org.jax.oan.exception.OntologyAnnotationNetworkException; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
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| import java.nio.file.Files; | ||
| import java.nio.file.Path; | ||
| import java.util.List; | ||
| import java.util.Objects; | ||
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| public class HpoDataResolver { | ||
| private static final Logger LOGGER = LoggerFactory.getLogger(HpoDataResolver.class); | ||
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| private final Path dataDirectory; | ||
| public static HpoDataResolver of(Path dataDirectory) throws OntologyAnnotationNetworkException { | ||
| return new HpoDataResolver(dataDirectory); | ||
| } | ||
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| private HpoDataResolver(Path dataDirectory) throws OntologyAnnotationNetworkException { | ||
| Objects.requireNonNull(dataDirectory, "Data directory must not be null!"); | ||
| this.dataDirectory = dataDirectory; | ||
| validateHpoFiles(); | ||
| } | ||
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| private void validateHpoFiles() throws OntologyAnnotationNetworkException { | ||
| boolean error = false; | ||
| List<Path> requiredFiles = List.of(hpJson(), hgncCompleteSet(), mim2geneMedgen(), phenotypeAnnotations(), | ||
| orpha2Gene(), loinc()); | ||
| for (Path file : requiredFiles) { | ||
| if (!Files.isRegularFile(file)) { | ||
| LOGGER.error("Missing required file `{}` in `{}`.", file.toFile().getName(), dataDirectory.toAbsolutePath()); | ||
| error = true; | ||
| } | ||
| } | ||
| if (error) { | ||
| throw new OntologyAnnotationNetworkDataException("Missing one or more required files in OntologyAnnotationNetwork data directory!"); | ||
| } | ||
| } | ||
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| public Path dataDirectory() { | ||
| return dataDirectory; | ||
| } | ||
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| public Path hpJson(){ | ||
| return dataDirectory.resolve("hp-simple-non-classified.json"); | ||
| } | ||
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| public Path hgncCompleteSet() { | ||
| return dataDirectory.resolve("hgnc_complete_set.txt"); | ||
| } | ||
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| public Path mim2geneMedgen() { | ||
| return dataDirectory.resolve("mim2gene_medgen"); | ||
| } | ||
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| public Path phenotypeAnnotations() { | ||
| return dataDirectory.resolve("phenotype.hpoa"); | ||
| } | ||
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| public Path orpha2Gene(){ | ||
| return dataDirectory.resolve("en_product6.xml"); | ||
| } | ||
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| public Path loinc(){ | ||
| return dataDirectory.resolve("loinc2hpo-annotations-merged.tsv"); | ||
| } | ||
| } |
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4 changes: 2 additions & 2 deletions
4
...cksonlaboratory/graph/OperationsTest.java → ...ava/org/jax/oan/graph/OperationsTest.java
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29
oan-etl/src/test/java/org/jax/oan/ontology/HpoDataResolverTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| package org.jax.oan.ontology; | ||
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| import org.jax.oan.exception.OntologyAnnotationNetworkDataException; | ||
| import org.jax.oan.exception.OntologyAnnotationNetworkException; | ||
| import org.junit.jupiter.api.Test; | ||
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| import java.nio.file.Path; | ||
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| import static org.junit.jupiter.api.Assertions.*; | ||
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| class HpoDataResolverTest { | ||
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| @Test | ||
| void of() throws OntologyAnnotationNetworkException { | ||
| Path dataDirectory = Path.of("src/test/resources"); | ||
| HpoDataResolver dataResolver = HpoDataResolver.of(dataDirectory); | ||
| assertEquals(dataResolver.hpJson(), dataDirectory.resolve("hp-simple-non-classified.json")); | ||
| assertEquals(dataResolver.mim2geneMedgen(), dataDirectory.resolve("mim2gene_medgen")); | ||
| assertEquals(dataResolver.hgncCompleteSet(), dataDirectory.resolve("hgnc_complete_set.txt")); | ||
| assertEquals(dataResolver.phenotypeAnnotations(), dataDirectory.resolve("phenotype.hpoa")); | ||
| assertEquals(dataResolver.loinc(), dataDirectory.resolve("loinc2hpo-annotations-merged.tsv")); | ||
| assertEquals(dataDirectory, dataResolver.dataDirectory()); | ||
| } | ||
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| @Test | ||
| void error() { | ||
| assertThrows(OntologyAnnotationNetworkDataException.class, () -> HpoDataResolver.of(Path.of("src/main/resources"))); | ||
| } | ||
| } |
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