diff --git a/.github/workflows/build-biosamples-service.yml b/.github/workflows/build-biosamples-service.yml index 8a69f27..3bcd623 100644 --- a/.github/workflows/build-biosamples-service.yml +++ b/.github/workflows/build-biosamples-service.yml @@ -27,7 +27,10 @@ jobs: - name: Build Docker image uses: docker/build-push-action@v6 with: - context: repository-services + context: repository-services/isajson-biosamples file: repository-services/isajson-biosamples/Dockerfile push: false tags: user/app:latest + build-args: | + GPR_USER=${{ secrets.GPR_USER }} + GPR_TOKEN=${{ secrets.GPR_TOKEN }} diff --git a/repository-services/docker-compose.yml b/repository-services/docker-compose.yml index 20fd10e..aa91220 100644 --- a/repository-services/docker-compose.yml +++ b/repository-services/docker-compose.yml @@ -1,16 +1,22 @@ services: isa_biosamples: build: - context: . - dockerfile: isajson-biosamples/Dockerfile + context: ./isajson-biosamples + dockerfile: Dockerfile + args: + GPR_USER: ${GPR_USER} + GPR_TOKEN: ${GPR_TOKEN} ports: - "8032:8032" restart: unless-stopped isa_sra: build: - context: . - dockerfile: isajson-ena/Dockerfile + context: ./isajson-ena + dockerfile: Dockerfile + args: + GPR_USER: ${GPR_USER} + GPR_TOKEN: ${GPR_TOKEN} ports: - "8042:8042" restart: unless-stopped diff --git a/repository-services/isajson-biosamples/Dockerfile b/repository-services/isajson-biosamples/Dockerfile index 6030e71..b922104 100644 --- a/repository-services/isajson-biosamples/Dockerfile +++ b/repository-services/isajson-biosamples/Dockerfile @@ -1,26 +1,36 @@ -# Builder stage: Use gradle image to compile jar file +# Builder stage FROM gradle:jdk11 AS builder WORKDIR /app +# Copy everything from context (the service folder) COPY . . -WORKDIR /app/receipt -RUN ./gradlew build -RUN ./gradlew publishToMavenLocal +ARG GPR_USER +ARG GPR_TOKEN -WORKDIR /app/isajson-biosamples -RUN ./gradlew build -x test -x spotlessApply --info --stacktrace "-Dorg.gradle.jvmargs=--add-exports jdk.compiler/com.sun.tools.javac.api=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.file=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.parser=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.tree=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.util=ALL-UNNAMED" +# Make gradlew executable +RUN chmod +x gradlew +# Build the JAR +RUN mkdir -p /root/.gradle && \ + echo "gpr.user=${GPR_USER}" >> /root/.gradle/gradle.properties && \ + echo "gpr.token=${GPR_TOKEN}" >> /root/.gradle/gradle.properties && \ + ./gradlew build -x test -x spotlessApply --info --stacktrace \ + "-Dorg.gradle.jvmargs=--add-exports jdk.compiler/com.sun.tools.javac.api=ALL-UNNAMED \ + --add-exports jdk.compiler/com.sun.tools.javac.file=ALL-UNNAMED \ + --add-exports jdk.compiler/com.sun.tools.javac.parser=ALL-UNNAMED \ + --add-exports jdk.compiler/com.sun.tools.javac.tree=ALL-UNNAMED \ + --add-exports jdk.compiler/com.sun.tools.javac.util=ALL-UNNAMED" -# Use a lightweight base image to run the jar file -FROM openjdk:11-jre-slim -WORKDIR /app -ARG JAR_FILE=/app/isajson-biosamples/build/libs/*.jar +# Runtime stage +FROM eclipse-temurin:11-jre-alpine + +WORKDIR /app -# Copy the JAR file from the builder stage -COPY --from=builder ${JAR_FILE} app.jar +# Copy the built JAR +COPY --from=builder /app/build/libs/*.jar app.jar -# Set the entry point for the application ENTRYPOINT ["java", "-jar", "app.jar"] + diff --git a/repository-services/isajson-biosamples/build.gradle b/repository-services/isajson-biosamples/build.gradle index 2d1e5c9..a724527 100644 --- a/repository-services/isajson-biosamples/build.gradle +++ b/repository-services/isajson-biosamples/build.gradle @@ -12,6 +12,13 @@ group = 'com.elixir.biohackaton' version = '0.0.1-SNAPSHOT' repositories { + maven { + url = uri("https://maven.pkg.github.com/elixir-europe/mars-repository-lib") + credentials { + username = project.findProperty("gpr.user") ?: System.getenv("GPR_USER") + password = project.findProperty("gpr.token") ?: System.getenv("GPR_TOKEN") + } + } mavenLocal() mavenCentral() } @@ -27,8 +34,8 @@ dependencies { implementation group: 'org.apache.commons', name: 'commons-collections4', version: '4.1' implementation group: 'org.apache.httpcomponents', name: 'httpclient', version: '4.5' implementation group: 'dom4j', name: 'dom4j', version: '1.6.1' - - implementation group: 'com.elixir.biohackaton', name: 'mars-receipt', version: '0.0.1' + + implementation 'com.elixir.mars:mars-repository:0.0.1' compileOnly group: 'org.projectlombok', name: 'lombok', version: '1.18.24' annotationProcessor 'org.projectlombok:lombok:1.18.24' diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/controller/BioSampleSubmissionController.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/controller/BioSampleSubmissionController.java index bd9e27b..6806eed 100644 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/controller/BioSampleSubmissionController.java +++ b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/controller/BioSampleSubmissionController.java @@ -16,9 +16,9 @@ import com.elixir.biohackaton.ISAToSRA.biosamples.model.BiosampleAccessionsMap; import com.elixir.biohackaton.ISAToSRA.biosamples.service.BioSamplesSubmitter; import com.elixir.biohackaton.ISAToSRA.biosamples.service.MarsReceiptService; -import com.elixir.biohackaton.ISAToSRA.receipt.MarsReceiptException; -import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.IsaJson; -import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Study; +import com.elixir.mars.repository.MarsReceiptException; +import com.elixir.mars.repository.models.isa.IsaJson; +import com.elixir.mars.repository.models.isa.Study; import com.fasterxml.jackson.annotation.JsonInclude; import com.fasterxml.jackson.databind.ObjectMapper; diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/model/BiosampleAccessionsMap.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/model/BiosampleAccessionsMap.java index 44fcaf9..0fc8f90 100644 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/model/BiosampleAccessionsMap.java +++ b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/model/BiosampleAccessionsMap.java @@ -1,6 +1,6 @@ package com.elixir.biohackaton.ISAToSRA.biosamples.model; -import com.elixir.biohackaton.ISAToSRA.receipt.ReceiptAccessionsMap; +import com.elixir.mars.repository.ReceiptAccessionsMap; public class BiosampleAccessionsMap { public ReceiptAccessionsMap sourceAccessionsMap = new ReceiptAccessionsMap(); diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/BioSamplesSubmitter.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/BioSamplesSubmitter.java index 4872c1f..4fb85bc 100644 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/BioSamplesSubmitter.java +++ b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/BioSamplesSubmitter.java @@ -22,14 +22,14 @@ import com.elixir.biohackaton.ISAToSRA.biosamples.model.BioSample; import com.elixir.biohackaton.ISAToSRA.biosamples.model.BiosampleAccessionsMap; import com.elixir.biohackaton.ISAToSRA.biosamples.model.Relationship; -import com.elixir.biohackaton.ISAToSRA.receipt.MarsReceiptException; -import com.elixir.biohackaton.ISAToSRA.receipt.ReceiptAccessionsMap; -import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Category; -import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Characteristic; -import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Sample; -import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Source; -import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Study; -import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Value; +import com.elixir.mars.repository.MarsReceiptException; +import com.elixir.mars.repository.ReceiptAccessionsMap; +import com.elixir.mars.repository.models.isa.Category; +import com.elixir.mars.repository.models.isa.Characteristic; +import com.elixir.mars.repository.models.isa.Sample; +import com.elixir.mars.repository.models.isa.Source; +import com.elixir.mars.repository.models.isa.Study; +import com.elixir.mars.repository.models.isa.Value; import lombok.extern.slf4j.Slf4j; diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/MarsReceiptService.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/MarsReceiptService.java index 8c9921b..206eed7 100644 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/MarsReceiptService.java +++ b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/MarsReceiptService.java @@ -8,10 +8,10 @@ import org.springframework.web.servlet.HandlerInterceptor; import com.elixir.biohackaton.ISAToSRA.biosamples.model.BiosampleAccessionsMap; -import com.elixir.biohackaton.ISAToSRA.receipt.MarsReceiptProvider; -import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.IsaJson; -import com.elixir.biohackaton.ISAToSRA.receipt.marsmodel.MarsError; -import com.elixir.biohackaton.ISAToSRA.receipt.marsmodel.MarsErrorType; +import com.elixir.mars.repository.MarsReceiptProvider; +import com.elixir.mars.repository.models.isa.IsaJson; +import com.elixir.mars.repository.models.receipt.MarsError; +import com.elixir.mars.repository.models.receipt.MarsErrorType; import com.fasterxml.jackson.annotation.JsonInclude; import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.SerializationFeature; diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Assay.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Assay.java deleted file mode 100644 index b0113a1..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Assay.java +++ /dev/null @@ -1,22 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import com.fasterxml.jackson.annotation.JsonProperty; -import java.util.ArrayList; -import lombok.Data; - -@Data -public class Assay { - @JsonProperty("@id") - public String id; - - public String filename; - public MeasurementType measurementType; - public TechnologyType technologyType; - public String technologyPlatform; - public ArrayList characteristicCategories; - public Materials materials; - public ArrayList processSequence; - public ArrayList dataFiles; - public ArrayList unitCategories; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Category.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Category.java deleted file mode 100644 index f9b7182..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Category.java +++ /dev/null @@ -1,11 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import com.fasterxml.jackson.annotation.JsonProperty; -import lombok.Data; - -@Data -public class Category { - @JsonProperty("@id") - public String id; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Characteristic.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Characteristic.java deleted file mode 100644 index 85c36f2..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Characteristic.java +++ /dev/null @@ -1,11 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import lombok.Data; - -@Data -public class Characteristic { - public Category category; - public Value value; - public Unit unit; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/CharacteristicCategory.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/CharacteristicCategory.java deleted file mode 100644 index 938aae7..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/CharacteristicCategory.java +++ /dev/null @@ -1,13 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import com.fasterxml.jackson.annotation.JsonProperty; -import lombok.Data; - -@Data -public class CharacteristicCategory { - @JsonProperty("@id") - public String id; - - public CharacteristicType characteristicType; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/CharacteristicType.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/CharacteristicType.java deleted file mode 100644 index b43c01d..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/CharacteristicType.java +++ /dev/null @@ -1,11 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import lombok.Data; - -@Data -public class CharacteristicType { - public String annotationValue; - public String termAccession; - public String termSource; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Comment.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Comment.java deleted file mode 100644 index 53c6176..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Comment.java +++ /dev/null @@ -1,14 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import com.fasterxml.jackson.annotation.JsonProperty; -import lombok.Data; - -@Data -public class Comment { - public String name; - public Object value; - - @JsonProperty("@id") - public String id; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Component.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Component.java deleted file mode 100644 index 6d98ca1..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Component.java +++ /dev/null @@ -1,10 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import lombok.Data; - -@Data -public class Component { - public String componentName; - public ComponentType componentType; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/ComponentType.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/ComponentType.java deleted file mode 100644 index 197e32a..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/ComponentType.java +++ /dev/null @@ -1,11 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import lombok.Data; - -@Data -public class ComponentType { - public String annotationValue; - public String termSource; - public String termAccession; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/DataFile.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/DataFile.java deleted file mode 100644 index 4efa3a1..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/DataFile.java +++ /dev/null @@ -1,16 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import com.fasterxml.jackson.annotation.JsonProperty; -import java.util.ArrayList; -import lombok.Data; - -@Data -public class DataFile { - @JsonProperty("@id") - public String id; - - public String name; - public String type; - public ArrayList comments; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/DerivesFrom.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/DerivesFrom.java deleted file mode 100644 index 6cbe363..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/DerivesFrom.java +++ /dev/null @@ -1,11 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import com.fasterxml.jackson.annotation.JsonProperty; -import lombok.Data; - -@Data -public class DerivesFrom { - @JsonProperty("@id") - public String id; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/ExecutesProtocol.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/ExecutesProtocol.java deleted file mode 100644 index 261d7d5..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/ExecutesProtocol.java +++ /dev/null @@ -1,11 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import com.fasterxml.jackson.annotation.JsonProperty; -import lombok.Data; - -@Data -public class ExecutesProtocol { - @JsonProperty("@id") - public String id; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/FactorValue.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/FactorValue.java deleted file mode 100644 index 152477d..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/FactorValue.java +++ /dev/null @@ -1,11 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import lombok.Data; - -@Data -public class FactorValue { - public Category category; - public Value value; - public Unit unit; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Input.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Input.java deleted file mode 100644 index 2fdb146..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Input.java +++ /dev/null @@ -1,11 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import com.fasterxml.jackson.annotation.JsonProperty; -import lombok.Data; - -@Data -public class Input { - @JsonProperty("@id") - public String id; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Investigation.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Investigation.java deleted file mode 100644 index e334464..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Investigation.java +++ /dev/null @@ -1,20 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import java.util.ArrayList; -import lombok.Data; - -@Data -public class Investigation { - public String identifier; - public String title; - public String description; - public String submissionDate; - public String publicReleaseDate; - public ArrayList ontologySourceReferences; - public String filename; - public ArrayList comments; - public ArrayList publications; - public ArrayList people; - public ArrayList studies; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/IsaJson.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/IsaJson.java deleted file mode 100644 index 7bdc27d..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/IsaJson.java +++ /dev/null @@ -1,9 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import lombok.Data; - -@Data -public class IsaJson { - public Investigation investigation; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Materials.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Materials.java deleted file mode 100644 index 81dfcf9..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Materials.java +++ /dev/null @@ -1,12 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import java.util.ArrayList; -import lombok.Data; - -@Data -public class Materials { - public ArrayList sources; - public ArrayList samples; - public ArrayList otherMaterials; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/MeasurementType.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/MeasurementType.java deleted file mode 100644 index 2fa6de4..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/MeasurementType.java +++ /dev/null @@ -1,11 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import lombok.Data; - -@Data -public class MeasurementType { - public String annotationValue; - public String termSource; - public String termAccession; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/NextProcess.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/NextProcess.java deleted file mode 100644 index 6de9eeb..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/NextProcess.java +++ /dev/null @@ -1,11 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import com.fasterxml.jackson.annotation.JsonProperty; -import lombok.Data; - -@Data -public class NextProcess { - @JsonProperty("@id") - public String id; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/OtherMaterial.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/OtherMaterial.java deleted file mode 100644 index e214bd0..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/OtherMaterial.java +++ /dev/null @@ -1,17 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import com.fasterxml.jackson.annotation.JsonProperty; -import java.util.ArrayList; -import lombok.Data; - -@Data -public class OtherMaterial { - @JsonProperty("@id") - public String id; // other_material-333 - - public String name; - public String type; // = library name - public ArrayList characteristics; // -> get characteristics - public ArrayList derivesFrom; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Output.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Output.java deleted file mode 100644 index 4314309..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Output.java +++ /dev/null @@ -1,11 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import com.fasterxml.jackson.annotation.JsonProperty; -import lombok.Data; - -@Data -public class Output { - @JsonProperty("@id") - public String id; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Parameter.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Parameter.java deleted file mode 100644 index fc565da..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Parameter.java +++ /dev/null @@ -1,13 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import com.fasterxml.jackson.annotation.JsonProperty; -import lombok.Data; - -@Data -public class Parameter { - @JsonProperty("@id") - public String id; - - public ParameterName parameterName; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/ParameterName.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/ParameterName.java deleted file mode 100644 index f7acb42..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/ParameterName.java +++ /dev/null @@ -1,13 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import com.fasterxml.jackson.annotation.JsonIgnoreProperties; -import lombok.Data; - -@Data -@JsonIgnoreProperties(ignoreUnknown = true) -public class ParameterName { - public String annotationValue; - public String termAccession; - public String termSource; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/ParameterValue.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/ParameterValue.java deleted file mode 100644 index 069ecb7..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/ParameterValue.java +++ /dev/null @@ -1,11 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import lombok.Data; - -@Data -public class ParameterValue { - public Category category; - public Value value; - public Unit unit; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Person.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Person.java deleted file mode 100644 index 7b27624..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Person.java +++ /dev/null @@ -1,23 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import com.fasterxml.jackson.annotation.JsonProperty; -import java.util.ArrayList; -import lombok.Data; - -@Data -public class Person { - @JsonProperty("@id") - public String id; - - public String lastName; - public String firstName; - public String midInitials; - public String email; - public String phone; - public String fax; - public String address; - public String affiliation; - public ArrayList roles; - public ArrayList comments; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/PreviousProcess.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/PreviousProcess.java deleted file mode 100644 index 51e18ce..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/PreviousProcess.java +++ /dev/null @@ -1,11 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import com.fasterxml.jackson.annotation.JsonProperty; -import lombok.Data; - -@Data -public class PreviousProcess { - @JsonProperty("@id") - public String id; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/ProcessSequence.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/ProcessSequence.java deleted file mode 100644 index fcd232e..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/ProcessSequence.java +++ /dev/null @@ -1,24 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import com.fasterxml.jackson.annotation.JsonIgnoreProperties; -import com.fasterxml.jackson.annotation.JsonProperty; -import java.util.ArrayList; -import lombok.Data; - -@Data -@JsonIgnoreProperties(ignoreUnknown = true) -public class ProcessSequence { - @JsonProperty("@id") - public String id; - - public String name; - public ExecutesProtocol executesProtocol; - public ArrayList parameterValues; - public String performer; - public String date; - public PreviousProcess previousProcess; - public NextProcess nextProcess; - public ArrayList inputs; - public ArrayList outputs; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Protocol.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Protocol.java deleted file mode 100644 index 9dd923d..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Protocol.java +++ /dev/null @@ -1,20 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import com.fasterxml.jackson.annotation.JsonProperty; -import java.util.ArrayList; -import lombok.Data; - -@Data -public class Protocol { - @JsonProperty("@id") - public String id; - - public String name; - public ProtocolType protocolType; - public String description; - public String uri; - public String version; - public ArrayList parameters; - public ArrayList components; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/ProtocolType.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/ProtocolType.java deleted file mode 100644 index b167c2f..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/ProtocolType.java +++ /dev/null @@ -1,11 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import lombok.Data; - -@Data -public class ProtocolType { - public String annotationValue; - public String termAccession; - public String termSource; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Role.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Role.java deleted file mode 100644 index 742e6e1..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Role.java +++ /dev/null @@ -1,11 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import lombok.Data; - -@Data -public class Role { - public String termAccession; - public String termSource; - public String annotationValue; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Sample.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Sample.java deleted file mode 100644 index 0b3cb03..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Sample.java +++ /dev/null @@ -1,17 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import com.fasterxml.jackson.annotation.JsonProperty; -import java.util.ArrayList; -import lombok.Data; - -@Data -public class Sample { - @JsonProperty("@id") - public String id; - - public String name; - public ArrayList derivesFrom; - public ArrayList characteristics; - public ArrayList factorValues; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Source.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Source.java deleted file mode 100644 index a6e58a6..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Source.java +++ /dev/null @@ -1,15 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import com.fasterxml.jackson.annotation.JsonProperty; -import java.util.ArrayList; -import lombok.Data; - -@Data -public class Source { - @JsonProperty("@id") - public String id; - - public String name; - public ArrayList characteristics; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Study.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Study.java deleted file mode 100644 index 0d2e856..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Study.java +++ /dev/null @@ -1,26 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import java.util.ArrayList; -import lombok.Data; - -@Data -public class Study { - public String identifier; - public String title; - public String description; - public String submissionDate; - public String publicReleaseDate; - public String filename; - public ArrayList comments; - public ArrayList publications; - public ArrayList people; - public ArrayList studyDesignDescriptors; - public ArrayList characteristicCategories; - public Materials materials; - public ArrayList protocols; - public ArrayList processSequence; - public ArrayList assays; - public ArrayList factors; - public ArrayList unitCategories; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/TechnologyType.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/TechnologyType.java deleted file mode 100644 index 599ea79..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/TechnologyType.java +++ /dev/null @@ -1,11 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import lombok.Data; - -@Data -public class TechnologyType { - public String annotationValue; - public String termSource; - public String termAccession; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Unit.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Unit.java deleted file mode 100644 index 9f4629b..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Unit.java +++ /dev/null @@ -1,12 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import java.util.ArrayList; -import lombok.Data; - -@Data -public class Unit { - public String termSource; - public String termAccession; - public ArrayList comments; -} diff --git a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Value.java b/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Value.java deleted file mode 100644 index 46639f9..0000000 --- a/repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/model/Value.java +++ /dev/null @@ -1,11 +0,0 @@ -/** Elixir BioHackathon 2022 */ -package com.elixir.biohackaton.ISAToSRA.model; - -import lombok.Data; - -@Data -public class Value { - public String annotationValue; - public String termSource; - public String termAccession; -} diff --git a/repository-services/isajson-biosamples/src/test/java/com/elixir/biohackaton/ISAToSRA/BiosampleReceiptToMarsTest.java b/repository-services/isajson-biosamples/src/test/java/com/elixir/biohackaton/ISAToSRA/BiosampleReceiptToMarsTest.java index 20987bd..e16b4fb 100644 --- a/repository-services/isajson-biosamples/src/test/java/com/elixir/biohackaton/ISAToSRA/BiosampleReceiptToMarsTest.java +++ b/repository-services/isajson-biosamples/src/test/java/com/elixir/biohackaton/ISAToSRA/BiosampleReceiptToMarsTest.java @@ -11,8 +11,8 @@ import com.elixir.biohackaton.ISAToSRA.biosamples.model.BiosampleAccessionsMap; import com.elixir.biohackaton.ISAToSRA.biosamples.service.BioSamplesSubmitter; import com.elixir.biohackaton.ISAToSRA.biosamples.service.MarsReceiptService; -import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.IsaJson; -import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Study; +import com.elixir.mars.repository.models.isa.IsaJson; +import com.elixir.mars.repository.models.isa.Study; import com.fasterxml.jackson.annotation.JsonInclude; import com.fasterxml.jackson.databind.ObjectMapper; diff --git a/repository-services/isajson-ena/Dockerfile b/repository-services/isajson-ena/Dockerfile index 29cdeca..30b16f6 100644 --- a/repository-services/isajson-ena/Dockerfile +++ b/repository-services/isajson-ena/Dockerfile @@ -23,7 +23,7 @@ RUN mkdir -p /root/.gradle && \ --add-exports jdk.compiler/com.sun.tools.javac.util=ALL-UNNAMED" -# Runtime stage +# Runtime stage FROM eclipse-temurin:11-jre-alpine WORKDIR /app diff --git a/repository-services/isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/service/WebinProjectXmlCreator.java b/repository-services/isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/service/WebinProjectXmlCreator.java index 3e81167..4b0b1d8 100644 --- a/repository-services/isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/service/WebinProjectXmlCreator.java +++ b/repository-services/isajson-ena/src/main/java/com/elixir/biohackaton/ISAToSRA/sra/service/WebinProjectXmlCreator.java @@ -1,7 +1,7 @@ /** Elixir BioHackathon 2022 */ package com.elixir.biohackaton.ISAToSRA.sra.service; -import com.elixir.mars.repository.models.isa.*; +import com.elixir.mars.repository.models.isa.Investigation; import org.dom4j.Element; import org.springframework.stereotype.Service;