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Pivotal #ID 176479720: Mongo Metadata Query (#328)
* added project and basic submission query support
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commons/commons-test/src/main/kotlin/ebi/ac/uk/db/Versions.kt
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| package ebi.ac.uk.db | ||
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| const val MONGO_VERSION = "mongo:4.0.10" | ||
| const val MYSQL_VERSION = "mysql:5.7.33" |
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36
...sistence-mongo/src/main/kotlin/ac/uk/ebi/biostd/persistence/doc/model/SubmissionDocExt.kt
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| package ac.uk.ebi.biostd.persistence.doc.model | ||
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| import ac.uk.ebi.biostd.persistence.common.model.BasicSubmission | ||
| import ebi.ac.uk.model.SubmissionMethod | ||
| import ebi.ac.uk.model.constants.ProcessingStatus | ||
| import java.time.ZoneOffset | ||
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| fun DocSubmission.asBasicSubmission(): BasicSubmission { | ||
| return BasicSubmission( | ||
| accNo = accNo, | ||
| version = version, | ||
| secretKey = secretKey, | ||
| title = title, | ||
| relPath = relPath, | ||
| released = released, | ||
| creationTime = creationTime.atOffset(ZoneOffset.UTC), | ||
| modificationTime = modificationTime.atOffset(ZoneOffset.UTC), | ||
| releaseTime = releaseTime?.atOffset(ZoneOffset.UTC), | ||
| status = status.toProcessingStatus(), | ||
| method = method.toSubmissionMethod(), | ||
| owner = owner) | ||
| } | ||
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| private fun DocProcessingStatus.toProcessingStatus(): ProcessingStatus = | ||
| when (this) { | ||
| DocProcessingStatus.PROCESSED -> ProcessingStatus.PROCESSED | ||
| DocProcessingStatus.PROCESSING -> ProcessingStatus.PROCESSING | ||
| DocProcessingStatus.REQUESTED -> ProcessingStatus.REQUESTED | ||
| } | ||
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| private fun DocSubmissionMethod.toSubmissionMethod(): SubmissionMethod = | ||
| when (this) { | ||
| DocSubmissionMethod.FILE -> SubmissionMethod.FILE | ||
| DocSubmissionMethod.PAGE_TAB -> SubmissionMethod.PAGE_TAB | ||
| DocSubmissionMethod.UNKNOWN -> SubmissionMethod.UNKNOWN | ||
| } |
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87 changes: 87 additions & 0 deletions
87
...st/kotlin/ac/uk/ebi/biostd/persistence/doc/service/SubmissionMongoMetaQueryServiceTest.kt
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| package ac.uk.ebi.biostd.persistence.doc.service | ||
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| import ac.uk.ebi.biostd.persistence.doc.db.repositories.SubmissionMongoRepository | ||
| import ac.uk.ebi.biostd.persistence.doc.integration.MongoDbReposConfig | ||
| import ac.uk.ebi.biostd.persistence.doc.model.DocAttribute | ||
| import ac.uk.ebi.biostd.persistence.doc.model.DocProcessingStatus.PROCESSED | ||
| import ac.uk.ebi.biostd.persistence.doc.test.doc.testDocSubmission | ||
| import ebi.ac.uk.db.MONGO_VERSION | ||
| import ebi.ac.uk.model.constants.SubFields | ||
| import org.assertj.core.api.Assertions.assertThat | ||
| import org.junit.jupiter.api.Test | ||
| import org.junit.jupiter.api.extension.ExtendWith | ||
| import org.springframework.beans.factory.annotation.Autowired | ||
| import org.springframework.boot.test.context.SpringBootTest | ||
| import org.springframework.test.context.DynamicPropertyRegistry | ||
| import org.springframework.test.context.DynamicPropertySource | ||
| import org.springframework.test.context.junit.jupiter.SpringExtension | ||
| import org.testcontainers.containers.MongoDBContainer | ||
| import org.testcontainers.junit.jupiter.Container | ||
| import org.testcontainers.junit.jupiter.Testcontainers | ||
| import org.testcontainers.utility.DockerImageName | ||
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| @ExtendWith(SpringExtension::class) | ||
| @Testcontainers | ||
| @SpringBootTest(classes = [MongoDbReposConfig::class]) | ||
| internal class SubmissionMongoMetaQueryServiceTest { | ||
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| @Autowired | ||
| lateinit var testInstance: SubmissionMongoMetaQueryService | ||
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| @Autowired | ||
| lateinit var submissionMongoRepository: SubmissionMongoRepository | ||
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| @Test | ||
| fun getBasicProject() { | ||
| submissionMongoRepository.save(testDocSubmission.copy( | ||
| accNo = "accNo1", | ||
| version = 1, | ||
| status = PROCESSED, | ||
| attributes = listOf(DocAttribute(SubFields.ACC_NO_TEMPLATE.value, "template")) | ||
| )) | ||
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| val result = testInstance.getBasicProject("accNo1") | ||
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| assertThat(result.accNo).isEqualTo("accNo1") | ||
| } | ||
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| @Test | ||
| fun findLatestBasicByAccNo() { | ||
| submissionMongoRepository.save(testDocSubmission.copy(accNo = "accNo2", version = 1, status = PROCESSED)) | ||
| submissionMongoRepository.save(testDocSubmission.copy(accNo = "accNo2", version = -2, status = PROCESSED)) | ||
| submissionMongoRepository.save(testDocSubmission.copy(accNo = "accNo2", version = 4, status = PROCESSED)) | ||
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| val lastVersion = testInstance.findLatestBasicByAccNo("accNo2") | ||
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| assertThat(lastVersion).isNotNull() | ||
| assertThat(lastVersion!!.version).isEqualTo(4) | ||
| } | ||
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| @Test | ||
| fun `exists by AccNo when exists`() { | ||
| submissionMongoRepository.save(testDocSubmission.copy(accNo = "accNo3", version = 1, status = PROCESSED)) | ||
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| assertThat(submissionMongoRepository.existsByAccNo("accNo3")).isTrue() | ||
| } | ||
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| @Test | ||
| fun `exist by AccNo when don't exists`() { | ||
| submissionMongoRepository.save(testDocSubmission.copy(accNo = "accNo4", version = 1, status = PROCESSED)) | ||
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| assertThat(submissionMongoRepository.existsByAccNo("accNo5")).isFalse() | ||
| } | ||
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| companion object { | ||
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| @Container | ||
| val mongoContainer: MongoDBContainer = MongoDBContainer(DockerImageName.parse(MONGO_VERSION)) | ||
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| @JvmStatic | ||
| @DynamicPropertySource | ||
| fun propertySource(register: DynamicPropertyRegistry) { | ||
| register.add("spring.data.mongodb.uri") { mongoContainer.getReplicaSetUrl("testDb") } | ||
| register.add("spring.data.mongodb.database") { "testDb" } | ||
| register.add("app.persistence.enableMongo") { "true" } | ||
| } | ||
| } | ||
| } |
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