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Merge pull request #129 from EBISPOT/dev
update stable with plenty of changes from dev
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| name: Build & publish zooma images | ||
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| on: | ||
| push: | ||
| branches: [ "dev", "stable" ] | ||
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| env: | ||
| REGISTRY: ghcr.io | ||
| IMAGE_NAME: ${{ github.repository }} | ||
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| jobs: | ||
| build-and-push-image: | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| contents: read | ||
| packages: write | ||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v2 | ||
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| - name: Log in to the Container registry | ||
| uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9 | ||
| with: | ||
| registry: ${{ env.REGISTRY }} | ||
| username: ${{ github.actor }} | ||
| password: ${{ secrets.GITHUB_TOKEN }} | ||
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| - name: Build and push zooma Docker image | ||
| run: | | ||
| docker build -t ghcr.io/ebispot/zooma:${{ github.sha }} . | ||
| docker tag ghcr.io/ebispot/zooma:${{ github.sha }} ghcr.io/ebispot/zooma:${{ github.ref_name }} | ||
| docker push --all-tags ghcr.io/ebispot/zooma |
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| @@ -0,0 +1,64 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <project xmlns="http://maven.apache.org/POM/4.0.0" | ||
| xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" | ||
| xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> | ||
| <parent> | ||
| <artifactId>zooma2</artifactId> | ||
| <groupId>uk.ac.ebi.fgpt</groupId> | ||
| <version>2.1.11-SNAPSHOT</version> | ||
| </parent> | ||
| <modelVersion>4.0.0</modelVersion> | ||
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| <artifactId>ols-client</artifactId> | ||
| <groupId>uk.ac.ebi.pride.utilities</groupId> | ||
| <version>2.9</version> | ||
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| <properties> | ||
| <maven.compiler.source>1.7</maven.compiler.source> | ||
| <maven.compiler.target>1.7</maven.compiler.target> | ||
| </properties> | ||
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| <dependencies> | ||
| <dependency> | ||
| <groupId>org.slf4j</groupId> | ||
| <artifactId>slf4j-api</artifactId> | ||
| <version>${org.slf4j.version}</version> | ||
| </dependency> | ||
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| <dependency> | ||
| <groupId>org.slf4j</groupId> | ||
| <artifactId>jcl-over-slf4j</artifactId> | ||
| <version>${org.slf4j.version}</version> | ||
| </dependency> | ||
| <!-- TODO - Review Spring Framework dependencies after issue PLIBT-138 is closed --> | ||
| <dependency> | ||
| <groupId>org.springframework</groupId> | ||
| <artifactId>spring-web</artifactId> | ||
| <!-- <version>4.2.5.RELEASE</version>--> | ||
| <version>${org.springframework.version}</version> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.springframework</groupId> | ||
| <artifactId>spring-test</artifactId> | ||
| <!-- <version>4.2.5.RELEASE</version>--> | ||
| <version>${org.springframework.version}</version> | ||
| </dependency> | ||
| <!-- <dependency>--> | ||
| <!-- <groupId>org.springframework</groupId>--> | ||
| <!-- <artifactId>spring-context-support</artifactId>--> | ||
| <!-- <!– <version>4.2.5.RELEASE</version>–>--> | ||
| <!-- <version>${org.springframework.version}</version>--> | ||
| <!-- </dependency>--> | ||
| <dependency> | ||
| <groupId>com.fasterxml.jackson.core</groupId> | ||
| <artifactId>jackson-databind</artifactId> | ||
| <version>2.7.3</version> | ||
| </dependency> | ||
| <!-- <dependency>--> | ||
| <!-- <groupId>org.apache.commons</groupId>--> | ||
| <!-- <artifactId>commons-lang3</artifactId>--> | ||
| <!-- <version>3.4</version>--> | ||
| <!-- </dependency>--> | ||
| </dependencies> | ||
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| </project> |
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ols-client/src/main/java/uk/ac/ebi/pride/utilities/ols/web/service/client/Client.java
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| package uk.ac.ebi.pride.utilities.ols.web.service.client; | ||
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| import org.springframework.web.client.RestClientException; | ||
| import uk.ac.ebi.pride.utilities.ols.web.service.model.Ontology; | ||
| import uk.ac.ebi.pride.utilities.ols.web.service.model.Term; | ||
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| import java.util.List; | ||
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| /** | ||
| * @author Yasset Perez-Riverol ([email protected]) | ||
| * Cration date 01/03/2016 | ||
| */ | ||
| public interface Client { | ||
| /** | ||
| * This function retrieve the list of Ontologies in the OLS. Each ontology contain the summary description | ||
| * about the ontology including name, IDs, etc. | ||
| * @return List of ontologies. | ||
| */ | ||
| // Zooma | ||
| List<Ontology> getOntologies() throws RestClientException; | ||
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| /** | ||
| * This function retrieve all the terms that contains in the name the partialName. | ||
| * @param partialName Substring to lookup in the name term | ||
| * @param ontologyId Ontology term | ||
| * @param reverseKeyOrder sort the hash in a reverse order | ||
| * @return list of terms. | ||
| */ | ||
| // Zooma | ||
| List<Term> getTermsByName(String partialName, String ontologyId, boolean reverseKeyOrder) throws RestClientException; | ||
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| /** | ||
| * Retrieve an specific ontology information for an ID | ||
| * @param ontologyId ontology Identifier | ||
| * @return Ontology result. | ||
| * @throws RestClientException if there are problems connecting to the REST service. | ||
| */ | ||
| // Zooma | ||
| Ontology getOntology(String ontologyId) throws RestClientException; | ||
| } |
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