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Merge pull request #72 from jmmut/feature/genotyped-validator
EVA-519 add GenotypedVcfJobParametersValidator and test
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.../uk/ac/ebi/eva/pipeline/parameters/validation/job/GenotypedVcfJobParametersValidator.java
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| /* | ||
| * Copyright 2017 EMBL - European Bioinformatics Institute | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
| package uk.ac.ebi.eva.pipeline.parameters.validation.job; | ||
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| import org.springframework.batch.core.JobParameters; | ||
| import org.springframework.batch.core.JobParametersInvalidException; | ||
| import org.springframework.batch.core.JobParametersValidator; | ||
| import org.springframework.batch.core.job.CompositeJobParametersValidator; | ||
| import org.springframework.batch.core.job.DefaultJobParametersValidator; | ||
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| import uk.ac.ebi.eva.pipeline.parameters.JobParametersNames; | ||
| import uk.ac.ebi.eva.pipeline.parameters.validation.step.AnnotationLoaderStepParametersValidator; | ||
| import uk.ac.ebi.eva.pipeline.parameters.validation.step.FileLoaderStepParametersValidator; | ||
| import uk.ac.ebi.eva.pipeline.parameters.validation.step.PopulationStatisticsGeneratorStepParametersValidator; | ||
| import uk.ac.ebi.eva.pipeline.parameters.validation.step.PopulationStatisticsLoaderStepParametersValidator; | ||
| import uk.ac.ebi.eva.pipeline.parameters.validation.step.VariantLoaderStepParametersValidator; | ||
| import uk.ac.ebi.eva.pipeline.parameters.validation.step.VepAnnotationGeneratorStepParametersValidator; | ||
| import uk.ac.ebi.eva.pipeline.parameters.validation.step.VepInputGeneratorStepParametersValidator; | ||
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| import java.util.ArrayList; | ||
| import java.util.List; | ||
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| /** | ||
| * Validates the job parameters necessary to execute an {@link uk.ac.ebi.eva.pipeline.jobs.GenotypedVcfJob} | ||
| */ | ||
| public class GenotypedVcfJobParametersValidator extends DefaultJobParametersValidator { | ||
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| @Override | ||
| public void validate(JobParameters parameters) throws JobParametersInvalidException { | ||
| compositeJobParametersValidator(parameters).validate(parameters); | ||
| } | ||
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| private CompositeJobParametersValidator compositeJobParametersValidator(JobParameters jobParameters) { | ||
| List<JobParametersValidator> jobParametersValidators = new ArrayList<>(); | ||
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| jobParametersValidators.add(new VariantLoaderStepParametersValidator()); | ||
| jobParametersValidators.add(new FileLoaderStepParametersValidator()); | ||
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| Boolean skipAnnotation = Boolean.valueOf(jobParameters.getString(JobParametersNames.ANNOTATION_SKIP)); | ||
| if (!skipAnnotation) { | ||
| jobParametersValidators.add(new VepInputGeneratorStepParametersValidator()); | ||
| jobParametersValidators.add(new VepAnnotationGeneratorStepParametersValidator()); | ||
| jobParametersValidators.add(new AnnotationLoaderStepParametersValidator()); | ||
| } | ||
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| Boolean skipStats = Boolean.valueOf(jobParameters.getString(JobParametersNames.STATISTICS_SKIP)); | ||
| if (!skipStats) { | ||
| jobParametersValidators.add(new PopulationStatisticsGeneratorStepParametersValidator()); | ||
| jobParametersValidators.add(new PopulationStatisticsLoaderStepParametersValidator()); | ||
| } | ||
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| CompositeJobParametersValidator compositeJobParametersValidator = new CompositeJobParametersValidator(); | ||
| compositeJobParametersValidator.setValidators(jobParametersValidators); | ||
| return compositeJobParametersValidator; | ||
| } | ||
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| } |
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234 changes: 234 additions & 0 deletions
234
...ac/ebi/eva/pipeline/parameters/validation/job/GenotypedVcfJobParametersValidatorTest.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,234 @@ | ||
| /* | ||
| * Copyright 2017 EMBL - European Bioinformatics Institute | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
| package uk.ac.ebi.eva.pipeline.parameters.validation.job; | ||
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| import org.junit.Before; | ||
| import org.junit.Rule; | ||
| import org.junit.Test; | ||
| import org.springframework.batch.core.JobParameter; | ||
| import org.springframework.batch.core.JobParameters; | ||
| import org.springframework.batch.core.JobParametersInvalidException; | ||
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| import uk.ac.ebi.eva.pipeline.parameters.JobParametersNames; | ||
| import uk.ac.ebi.eva.test.rules.PipelineTemporaryFolderRule; | ||
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| import java.util.Map; | ||
| import java.util.TreeMap; | ||
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| /** | ||
| * Tests that the arguments necessary to run a {@link uk.ac.ebi.eva.pipeline.jobs.AggregatedVcfJob} are | ||
| * correctly validated | ||
| */ | ||
| public class GenotypedVcfJobParametersValidatorTest { | ||
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| private GenotypedVcfJobParametersValidator validator; | ||
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| @Rule | ||
| public PipelineTemporaryFolderRule temporaryFolder = new PipelineTemporaryFolderRule(); | ||
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| private Map<String, JobParameter> requiredParameters; | ||
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| private Map<String, JobParameter> annotationParameters; | ||
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| private Map<String, JobParameter> statsParameters; | ||
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| private Map<String, JobParameter> optionalParameters; | ||
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| @Before | ||
| public void setUp() throws Exception { | ||
| validator = new GenotypedVcfJobParametersValidator(); | ||
| final String dir = temporaryFolder.getRoot().getCanonicalPath(); | ||
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| requiredParameters = new TreeMap<>(); | ||
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| // variant load step | ||
| requiredParameters.put(JobParametersNames.DB_NAME, new JobParameter("database")); | ||
| requiredParameters.put(JobParametersNames.DB_COLLECTIONS_VARIANTS_NAME, new JobParameter("variants")); | ||
| requiredParameters.put(JobParametersNames.INPUT_STUDY_ID, new JobParameter("inputStudyId")); | ||
| requiredParameters.put(JobParametersNames.INPUT_VCF_ID, new JobParameter("inputVcfId")); | ||
| requiredParameters.put(JobParametersNames.INPUT_VCF_AGGREGATION, new JobParameter("NONE")); | ||
| requiredParameters.put(JobParametersNames.INPUT_VCF, | ||
| new JobParameter(temporaryFolder.newFile().getCanonicalPath())); | ||
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| // file load step | ||
| requiredParameters.put(JobParametersNames.DB_COLLECTIONS_FILES_NAME, new JobParameter("collectionsFilesName")); | ||
| requiredParameters.put(JobParametersNames.INPUT_STUDY_NAME, new JobParameter("inputStudyName")); | ||
| requiredParameters.put(JobParametersNames.INPUT_STUDY_TYPE, new JobParameter("COLLECTION")); | ||
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| // skips | ||
| requiredParameters.put(JobParametersNames.ANNOTATION_SKIP, new JobParameter("false")); | ||
| requiredParameters.put(JobParametersNames.STATISTICS_SKIP, new JobParameter("false")); | ||
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| // annotation | ||
| annotationParameters = new TreeMap<>(); | ||
| annotationParameters.put(JobParametersNames.OUTPUT_DIR_ANNOTATION, new JobParameter(dir)); | ||
| annotationParameters.put(JobParametersNames.APP_VEP_CACHE_SPECIES, new JobParameter("Human")); | ||
| annotationParameters.put(JobParametersNames.APP_VEP_CACHE_VERSION, new JobParameter("100_A")); | ||
| annotationParameters.put(JobParametersNames.APP_VEP_NUMFORKS, new JobParameter("6")); | ||
| annotationParameters.put(JobParametersNames.APP_VEP_CACHE_PATH, | ||
| new JobParameter(temporaryFolder.getRoot().getCanonicalPath())); | ||
| annotationParameters.put(JobParametersNames.APP_VEP_PATH, | ||
| new JobParameter(temporaryFolder.newFile().getCanonicalPath())); | ||
| annotationParameters.put(JobParametersNames.INPUT_FASTA, | ||
| new JobParameter(temporaryFolder.newFile().getCanonicalPath())); | ||
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| // statistics | ||
| statsParameters = new TreeMap<>(); | ||
| statsParameters.put(JobParametersNames.OUTPUT_DIR_STATISTICS, new JobParameter(dir)); | ||
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| // optionals | ||
| optionalParameters = new TreeMap<>(); | ||
| optionalParameters.put(JobParametersNames.CONFIG_CHUNK_SIZE, new JobParameter("100")); | ||
| optionalParameters.put(JobParametersNames.CONFIG_RESTARTABILITY_ALLOW, new JobParameter("true")); | ||
| optionalParameters.put(JobParametersNames.STATISTICS_OVERWRITE, new JobParameter("true")); | ||
| } | ||
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| // The next tests show behaviour about the required parameters | ||
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| @Test | ||
| public void allJobParametersAreValid() throws JobParametersInvalidException { | ||
| Map<String, JobParameter> parameters = new TreeMap<>(); | ||
| parameters.putAll(requiredParameters); | ||
| parameters.putAll(optionalParameters); | ||
| parameters.putAll(annotationParameters); | ||
| parameters.putAll(statsParameters); | ||
| validator.validate(new JobParameters(parameters)); | ||
| } | ||
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| @Test | ||
| public void allRequiredJobParametersAreValid() throws JobParametersInvalidException { | ||
| Map<String, JobParameter> parameters = new TreeMap<>(); | ||
| parameters.putAll(requiredParameters); | ||
| parameters.putAll(annotationParameters); | ||
| parameters.putAll(statsParameters); | ||
| validator.validate(new JobParameters(parameters)); | ||
| } | ||
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| @Test(expected = JobParametersInvalidException.class) | ||
| public void dbNameIsRequiredSkippingAnnotationAndStats() throws JobParametersInvalidException { | ||
| Map<String, JobParameter> parameters = new TreeMap<>(); | ||
| parameters.putAll(requiredParameters); | ||
| parameters.putAll(optionalParameters); | ||
| parameters.remove(JobParametersNames.DB_NAME); | ||
| parameters.put(JobParametersNames.ANNOTATION_SKIP, new JobParameter("true")); | ||
| parameters.put(JobParametersNames.STATISTICS_SKIP, new JobParameter("true")); | ||
| validator.validate(new JobParameters(parameters)); | ||
| } | ||
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| @Test(expected = JobParametersInvalidException.class) | ||
| public void dbNameIsRequiredWithoutSkippingAnnotation() throws JobParametersInvalidException { | ||
| Map<String, JobParameter> parameters = new TreeMap<>(); | ||
| parameters.putAll(requiredParameters); | ||
| parameters.putAll(optionalParameters); | ||
| parameters.putAll(annotationParameters); | ||
| parameters.remove(JobParametersNames.DB_NAME); | ||
| parameters.put(JobParametersNames.STATISTICS_SKIP, new JobParameter("true")); | ||
| validator.validate(new JobParameters(parameters)); | ||
| } | ||
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| @Test(expected = JobParametersInvalidException.class) | ||
| public void dbNameIsRequiredWithoutSkippingStats() throws JobParametersInvalidException { | ||
| Map<String, JobParameter> parameters = new TreeMap<>(); | ||
| parameters.putAll(requiredParameters); | ||
| parameters.putAll(optionalParameters); | ||
| parameters.putAll(statsParameters); | ||
| parameters.put(JobParametersNames.ANNOTATION_SKIP, new JobParameter("true")); | ||
| parameters.remove(JobParametersNames.DB_NAME); | ||
| validator.validate(new JobParameters(parameters)); | ||
| } | ||
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| @Test(expected = JobParametersInvalidException.class) | ||
| public void dbNameIsRequiredWithoutSkippingAnnotationAndStats() throws JobParametersInvalidException { | ||
| Map<String, JobParameter> parameters = new TreeMap<>(); | ||
| parameters.putAll(requiredParameters); | ||
| parameters.putAll(optionalParameters); | ||
| parameters.putAll(annotationParameters); | ||
| parameters.putAll(statsParameters); | ||
| parameters.remove(JobParametersNames.DB_NAME); | ||
| validator.validate(new JobParameters(parameters)); | ||
| } | ||
|
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| // The next tests show what happens when not all the annotation parameters are present | ||
|
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| @Test | ||
| public void annotationParametersAreNotRequiredIfAnnotationIsSkipped() throws JobParametersInvalidException { | ||
| Map<String, JobParameter> parameters = new TreeMap<>(); | ||
| parameters.putAll(requiredParameters); | ||
| parameters.putAll(optionalParameters); | ||
| parameters.putAll(statsParameters); | ||
| parameters.put(JobParametersNames.ANNOTATION_SKIP, new JobParameter("true")); | ||
| validator.validate(new JobParameters(parameters)); | ||
| } | ||
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| @Test(expected = JobParametersInvalidException.class) | ||
| public void annotationParametersAreRequiredIfAnnotationIsNotSkipped() throws JobParametersInvalidException { | ||
| Map<String, JobParameter> parameters = new TreeMap<>(); | ||
| parameters.putAll(requiredParameters); | ||
| parameters.putAll(optionalParameters); | ||
| parameters.putAll(statsParameters); | ||
| validator.validate(new JobParameters(parameters)); | ||
| } | ||
|
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| /** | ||
| * The parameter APP_VEP_CACHE_SPECIES is chosen as one belonging to the annotation parameters. We don't check | ||
| * for every annotation parameter, because in AnnotationLoaderStepParametersValidatorTest, | ||
| * VepAnnotationGeneratorStepParametersValidatorTest and VepInputGeneratorStepParametersValidatorTest, it is already | ||
| * checked that every missing required parameter makes the validation fail. | ||
| */ | ||
| @Test(expected = JobParametersInvalidException.class) | ||
| public void appVepCacheSpeciesIsRequiredIfAnnotationIsNotSkipped() throws JobParametersInvalidException { | ||
| Map<String, JobParameter> parameters = new TreeMap<>(); | ||
| parameters.putAll(requiredParameters); | ||
| parameters.putAll(optionalParameters); | ||
| parameters.putAll(annotationParameters); | ||
| parameters.putAll(statsParameters); | ||
| parameters.remove(JobParametersNames.APP_VEP_CACHE_SPECIES); | ||
| validator.validate(new JobParameters(parameters)); | ||
| } | ||
|
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| // The next tests show what happens when not all the stats parameters are present | ||
|
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| @Test | ||
| public void statsParametersAreNotRequiredIfStatsIsSkipped() throws JobParametersInvalidException { | ||
| Map<String, JobParameter> parameters = new TreeMap<>(); | ||
| parameters.putAll(requiredParameters); | ||
| parameters.putAll(optionalParameters); | ||
| parameters.putAll(annotationParameters); | ||
| parameters.put(JobParametersNames.STATISTICS_SKIP, new JobParameter("true")); | ||
| validator.validate(new JobParameters(parameters)); | ||
| } | ||
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| @Test(expected = JobParametersInvalidException.class) | ||
| public void statsParametersAreRequiredIfStatsIsNotSkipped() throws JobParametersInvalidException { | ||
| Map<String, JobParameter> parameters = new TreeMap<>(); | ||
| parameters.putAll(requiredParameters); | ||
| parameters.putAll(optionalParameters); | ||
| parameters.putAll(annotationParameters); | ||
| validator.validate(new JobParameters(parameters)); | ||
| } | ||
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| @Test(expected = JobParametersInvalidException.class) | ||
| public void outputDirStatistitcsIsRequiredIfStatsIsNotSkipped() throws JobParametersInvalidException { | ||
| Map<String, JobParameter> parameters = new TreeMap<>(); | ||
| parameters.putAll(requiredParameters); | ||
| parameters.putAll(optionalParameters); | ||
| parameters.putAll(annotationParameters); | ||
| parameters.putAll(statsParameters); | ||
| parameters.remove(JobParametersNames.OUTPUT_DIR_STATISTICS); | ||
| validator.validate(new JobParameters(parameters)); | ||
| } | ||
| } |