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Promote changes to BETA Bug Fixes: * Pivotal ID # 176052254: JSON Submission Attributes Validation (#310) * Pivotal ID # 176052264: Inner Folder Mapping (#311) * Pivotal ID # 172671360: Ignore Empty Value Attributes (#314)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| import Dependencies.KotlinLogging | ||
| import Dependencies.KotlinStdLib | ||
| import Dependencies.Log4J | ||
| import TestDependencies.BaseTestCompileDependencies | ||
| import TestDependencies.BaseTestRuntimeDependencies | ||
|
|
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| dependencies { | ||
| api(project(":client:bio-webclient")) | ||
| implementation(KotlinStdLib) | ||
| implementation(Log4J) | ||
| implementation(KotlinLogging) | ||
|
|
||
| BaseTestCompileDependencies.forEach { testImplementation(it) } | ||
| BaseTestRuntimeDependencies.forEach { testImplementation(it) } | ||
| } |
53 changes: 53 additions & 0 deletions
53
...webclient-demo/src/main/kotlin/ac/uk/ebi/biostd/client/demo/SimpleSubmissionDslExample.kt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| package ac.uk.ebi.biostd.client.demo | ||
|
|
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| import ac.uk.ebi.biostd.client.integration.web.SecurityWebClient | ||
| import ebi.ac.uk.dsl.attribute | ||
| import ebi.ac.uk.dsl.file | ||
| import ebi.ac.uk.dsl.link | ||
| import ebi.ac.uk.dsl.section | ||
| import ebi.ac.uk.dsl.submission | ||
| import ebi.ac.uk.model.Attribute | ||
| import ebi.ac.uk.model.extensions.title | ||
| import mu.KotlinLogging | ||
| import java.nio.file.Files | ||
|
|
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| private val logger = KotlinLogging.logger {} | ||
|
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| /** | ||
| * Demonstrate how to submit a simple submission using bio-studies client and kotlin submission dsl. Note that | ||
| * | ||
| * 1. Client Serialization service is used to serialize class representation into json. | ||
| * 2. Files are uploaded into user file directory first. | ||
| */ | ||
| fun main(args: Array<String>) { | ||
| val client = SecurityWebClient | ||
| .create(baseUrl = args[0]) | ||
| .getAuthenticatedClient(args[1], args[2]) | ||
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| val directory = Files.createTempDirectory("submission-files") | ||
| val submissionFile = Files.createTempFile(directory, "sub-file-", ".tmp").toFile() | ||
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| client.uploadFiles(listOf(submissionFile)) | ||
| val response = client.submitSingle(submission { | ||
| title = "my-submission example" | ||
| attribute("Attribute", "Attr Value 1") | ||
| attribute("Another-Attribute", "Another-Attribute Value") | ||
| section("study") { | ||
| attributes = listOf(Attribute("attribute-1", "attributeValue")) | ||
| link("AF069309") { | ||
| attribute("type", "gen") | ||
| } | ||
|
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| file(submissionFile.name) { | ||
| size = 0 | ||
| attribute("Description", "Data File 1") | ||
| } | ||
|
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| section("Author") { | ||
| attribute("Name", "Mr Doctor") | ||
| } | ||
| } | ||
| }) | ||
|
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| logger.info { "successfully created submission ${response.body.accNo}" } | ||
| } |
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19 changes: 19 additions & 0 deletions
19
.../src/main/kotlin/ac/uk/ebi/biostd/json/deserialization/AttributeDetailJsonDeserializer.kt
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| package ac.uk.ebi.biostd.json.deserialization | ||
|
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| import ac.uk.ebi.biostd.json.deserialization.AttributeJsonDeserializerHelper.deserializeNameValue | ||
| import com.fasterxml.jackson.core.JsonParser | ||
| import com.fasterxml.jackson.databind.DeserializationContext | ||
| import com.fasterxml.jackson.databind.JsonNode | ||
| import com.fasterxml.jackson.databind.ObjectMapper | ||
| import com.fasterxml.jackson.databind.deser.std.StdDeserializer | ||
| import ebi.ac.uk.model.AttributeDetail | ||
|
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| internal class AttributeDetailJsonDeserializer : StdDeserializer<AttributeDetail>(AttributeDetail::class.java) { | ||
| override fun deserialize(jp: JsonParser, ctxt: DeserializationContext): AttributeDetail { | ||
| val mapper = jp.codec as ObjectMapper | ||
| val node: JsonNode = mapper.readTree(jp) | ||
| val (name, value) = deserializeNameValue(node) | ||
|
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| return AttributeDetail(name, value) | ||
| } | ||
| } |
10 changes: 2 additions & 8 deletions
10
...zation/src/main/kotlin/ac/uk/ebi/biostd/json/deserialization/AttributeJsonDeserializer.kt
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18 changes: 18 additions & 0 deletions
18
.../src/main/kotlin/ac/uk/ebi/biostd/json/deserialization/AttributeJsonDeserializerHelper.kt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| package ac.uk.ebi.biostd.json.deserialization | ||
|
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| import ac.uk.ebi.biostd.common.NAME | ||
| import ac.uk.ebi.biostd.common.VALUE | ||
| import ac.uk.ebi.biostd.json.exception.NoAttributeValueException | ||
| import com.fasterxml.jackson.databind.JsonNode | ||
| import com.fasterxml.jackson.databind.node.TextNode | ||
| import uk.ac.ebi.serialization.extensions.getNode | ||
|
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| internal object AttributeJsonDeserializerHelper { | ||
| fun deserializeNameValue(node: JsonNode): Pair<String, String> { | ||
| val name = node.getNode<TextNode>(NAME).textValue() | ||
| val value = node.getNode<TextNode>(VALUE).textValue() | ||
| require(value.isNotBlank()) { throw NoAttributeValueException(name) } | ||
|
|
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| return name to value | ||
| } | ||
| } |
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51 changes: 51 additions & 0 deletions
51
.../src/test/kotlin/ac/uk/ebi/biostd/json/deserialization/AttributeDetailDeserializerTest.kt
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,51 @@ | ||
| package ac.uk.ebi.biostd.json.deserialization | ||
|
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| import ac.uk.ebi.biostd.json.JsonSerializer | ||
| import ac.uk.ebi.biostd.json.exception.NoAttributeValueException | ||
| import ebi.ac.uk.model.AttributeDetail | ||
| import org.assertj.core.api.Assertions.assertThat | ||
| import org.junit.jupiter.api.Test | ||
| import org.junit.jupiter.api.assertThrows | ||
| import uk.ac.ebi.serialization.extensions.deserialize | ||
|
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| class AttributeDetailDeserializerTest { | ||
| private val testInstance = JsonSerializer.mapper | ||
|
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| @Test | ||
| fun `deserialize attribute detail`() { | ||
| val result = testInstance.deserialize<AttributeDetail>("""{ | ||
| |"name": "attr name", | ||
| |"value": "attr value" | ||
| |}""".trimMargin()) | ||
|
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| assertThat(result.name).isEqualTo("attr name") | ||
| assertThat(result.value).isEqualTo("attr value") | ||
| } | ||
|
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| @Test | ||
| fun `deserialize empty`() { | ||
| val exception = assertThrows<IllegalStateException> { testInstance.deserialize<AttributeDetail>("{}") } | ||
| assertThat(exception.message).isEqualTo("Expecting to find property with 'name' in node '{}'") | ||
| } | ||
|
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| @Test | ||
| fun `deserialize with no value property`() { | ||
| val exception = assertThrows<IllegalStateException> { testInstance.deserialize<AttributeDetail>("""{ | ||
| |"name": "attr name" | ||
| |}""".trimMargin()) | ||
| } | ||
|
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| assertThat(exception.message).isEqualTo( | ||
| "Expecting to find property with 'value' in node '{\"name\":\"attr name\"}'") | ||
| } | ||
|
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| @Test | ||
| fun `deserialize no value`() { | ||
| val exception = assertThrows<NoAttributeValueException> { testInstance.deserialize<AttributeDetail>("""{ | ||
| |"name": "attr name", | ||
| |"value": "" | ||
| |}""".trimMargin()) } | ||
|
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| assertThat(exception.message).isEqualTo("The value for the attribute 'attr name' can't be empty") | ||
| } | ||
| } |
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