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henrietteharmsehenrietteharmse
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Merge pull request #136 from EBISPOT/dev
Survey banner and docker fix
2 parents 667e74f + 0c81b3a commit e9af33b

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‎.gitattributes

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*.tar.gz filter=lfs diff=lfs merge=lfs -text

‎.github/workflows/docker.yml

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@@ -3,6 +3,9 @@ name: Build & publish zooma images
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on:
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push:
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branches: [ "dev", "stable" ]
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pull_request:
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branches:
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- dev
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env:
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REGISTRY: ghcr.io
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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with:
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lfs: true
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- name: Pull Git LFS files
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run: git lfs pull
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- name: Log in to the Container registry
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uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
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- name: Build and push zooma Docker image
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run: |
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docker build -t ghcr.io/ebispot/zooma:${{ github.sha }} .
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docker tag ghcr.io/ebispot/zooma:${{ github.sha }} ghcr.io/ebispot/zooma:${{ github.ref_name }}
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if [[ "${{ github.event_name }}" == "pull_request" ]]; then
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TAG="PR-${{ github.event.pull_request.number }}"
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else
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TAG="${{ github.ref_name }}"
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fi
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docker tag ghcr.io/ebispot/zooma:${{ github.sha }} ghcr.io/ebispot/zooma:${TAG}
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docker push --all-tags ghcr.io/ebispot/zooma

‎Dockerfile

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@@ -6,16 +6,22 @@ ENV ZOOMA_OPTS="-Xms1g -Xmx4g"
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RUN mkdir /opt/zooma_github /opt/zooma
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RUN apt-get update && apt-get install -y nano maven
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COPY . /opt/zooma_github/
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RUN rm -rf /root/.m2/
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RUN tar -xvzf /opt/zooma_github/ols-client/lib/m2directory.tar.gz -C /root/
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ENV OJDBC6="https://www.oracle.com/webapps/redirect/signon?nexturl=https://download.oracle.com/otn/utilities_drivers/jdbc/11204/ojdbc6.jar"
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RUN wget $OJDBC6 -O /lib/ojdbc6.jar \
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&& mvn install:install-file -DgroupId=com.oracle -DartifactId=ojdbc6 -Dpackaging=jar -Dversion=11.2.0.4 -Dfile=/lib/ojdbc6.jar \
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&& test /root/.m2/repository/com/oracle/ojdbc6/11.2.0.4/ojdbc6-11.2.0.4.jar
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RUN mvn install:install-file -DcreateChecksum=true -Dpackaging=jar -Dfile=/opt/zooma_github/zooma-lodestar/lib/jena-core-2.12.0.jar -DgroupId=org.apache.jena -DartifactId=jena-core -Dversion=2.12.0
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RUN mvn install:install-file -DcreateChecksum=true -Dpackaging=jar -Dfile=/opt/zooma_github/zooma-lodestar/lib/jena-arq-2.12.0.jar -DgroupId=org.apache.jena -DartifactId=jena-arq -Dversion=2.12.0
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RUN mvn install:install-file -DcreateChecksum=true -Dpackaging=jar -Dfile=/opt/zooma_github/zooma-lodestar/lib/lode-core-api-1.3.jar -DgroupId=ebi-lode -DartifactId=lode-core-api -Dversion=1.3
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RUN mvn install:install-file -DcreateChecksum=true -Dpackaging=jar -Dfile=/opt/zooma_github/zooma-lodestar/lib/lode-virtuoso-impl-1.3.jar -DgroupId=ebi-lode -DartifactId=lode-virtuoso-impl -Dversion=1.3
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RUN mvn install:install-file -DcreateChecksum=true -Dpackaging=jar -Dfile=/opt/zooma_github/zooma-ui/lib/jackson-mapper-asl-1.5.3.jar -DgroupId=org.codehaus.jackson -DartifactId=jackson-mapper-asl -Dversion=1.5.3
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RUN mvn install:install-file -DcreateChecksum=true -Dpackaging=jar -Dfile=/opt/zooma_github/zooma-ui/lib/jackson-core-asl-1.5.3.jar -DgroupId=org.codehaus.jackson -DartifactId=jackson-core-asl -Dversion=1.5.3
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RUN cd /opt/zooma_github && mvn clean package
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RUN mkdir /opt/tmp && unzip /opt/zooma_github/zooma-builder-app/target/zooma-builder.zip -d /opt/tmp
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RUN cp /opt/zooma_github/zooma-ui/target/zooma.war /usr/local/tomcat/webapps/

‎README.md

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@@ -7,7 +7,7 @@ ZOOMA is an application for discovering optimal ontology mappings, developed by
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## Deploying with Docker
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The preferred method of deployment for ZOOMA is using Docker. If you would like to deploy **the entire OntoTools stack** (OLS, OxO, and ZOOMA), check out the [OntoTools Docker Config](https://github.com/EBISPOT/ontotools-docker-config) repository. If you would like to deploy **ZOOMA only**, read on.
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The preferred method of deployment for ZOOMA is using Docker. If you would like to deploy **the entire OntoTools stack** (OLS, OxO, and ZOOMA), check out the [OntoTools Docker Config](https://github.com/EBISPOT/ontotools-docker-config) repository. If you would like to deploy **ZOOMA only**, read on
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First, create the necessary volumes:
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‎ols-client/lib/m2directory.tar.gz

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version https://git-lfs.github.com/spec/v1
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oid sha256:5ead688d4717b109b0f0314b6126481244915bd7378184d2b6a4a80c8c1d87bc
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size 540467695

‎zooma-ui/src/main/frontend/src/pages/Home.tsx

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return (
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<main>
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<Row>
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<h3>Query</h3>
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<Column small={12} medium={12}>
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<p>Use the text box to find possible ontology mappings for free text terms in the ZOOMA repository of curated annotation knowledge. You can add one term (e.g. 'Homo sapiens') per line. If you also have a type for your term (e.g. 'organism'), put this after the term, separated by a tab.
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If you are new to ZOOMA, take a look at our getting started guide.</p>
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</Column>
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<Column small={12} medium={12}>
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<Row>
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<Row>
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<div className="mt-4">
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<div style={{
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backgroundColor: '#b2dce8',
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padding: '12px 24px',
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borderRadius: '8px',
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marginBottom: '16px',
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textAlign: 'justify',
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overflowX: 'auto'
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}}>
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<p>
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Do data resources managed by EMBL-EBI and our collaborators make a difference to your
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work? <br/><br/>
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Please take 10 minutes to fill in our annual user survey, and help us make the case for
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why sustaining open data resources is critical for life sciences research.<br/><br/>
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Survey link: <a href="https://www.surveymonkey.com/r/HJKYKTT?channel=[webpage]"
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target="_blank">https://www.surveymonkey.com/r/HJKYKTT?channel=[webpage]</a>
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</p>
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</div>
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</div>
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</Row>
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<Row>
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<h3>Query</h3>
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<Column small={12} medium={12}>
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<Row className="align-right">
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<a onClick={this.onClickShowExamples}>
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Show me some examples...
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</a>
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<p>Use the text box to find possible ontology mappings for free text terms in the ZOOMA
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repository of curated annotation knowledge. You can add one term (e.g. 'Homo sapiens') per
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line. If you also have a type for your term (e.g. 'organism'), put this after the term,
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separated by a tab.
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If you are new to ZOOMA, take a look at our getting started guide.</p>
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</Column>
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<Column small={12} medium={12}>
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<Row>
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<Column small={12} medium={12}>
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<Row className="align-right">
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<a onClick={this.onClickShowExamples}>
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Show me some examples...
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</a>
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</Row>
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</Column>
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</Row>
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<Row>
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<textarea style={{minHeight: '300px'}} value={this.state.query}
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onChange={this.onEditQuery}></textarea>
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</Row>
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</Column>
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</Row>
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<Row>
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<textarea style={{minHeight: '300px'}} value={this.state.query} onChange={this.onEditQuery}></textarea>
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</Row>
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</Column>
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</Row>
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<Row>
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<h3>Datasources</h3>
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<Column small={12} medium={12}>
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<p>ZOOMA maps text to ontology terms based on curated mappings from selected datasources (more preferred), and by searching ontologies directly (less preferred). Here, you can select which curated datasources to use, optionally ranked in order of preference. You can also select which ontologies to search directly.</p>
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</Column>
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<Column small={12} medium={12}>
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{
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this.state.datasources &&
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this.state.datasourceConfig &&
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<Datasources datasources={this.state.datasources} datasourceConfig={this.state.datasourceConfig} onConfigChanged={this.onDatasourceConfigChanged} />
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}
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</Column>
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</Row>
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<br/>
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</Row>
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<Row>
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<h3>Datasources</h3>
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<Column small={12} medium={12}>
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<p>ZOOMA maps text to ontology terms based on curated mappings from selected datasources (more
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preferred), and by searching ontologies directly (less preferred). Here, you can select
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which curated datasources to use, optionally ranked in order of preference. You can also
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select which ontologies to search directly.</p>
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</Column>
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<Column small={12} medium={12}>
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{
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this.state.datasources &&
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this.state.datasourceConfig &&
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<Datasources datasources={this.state.datasources}
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datasourceConfig={this.state.datasourceConfig}
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onConfigChanged={this.onDatasourceConfigChanged}/>
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}
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</Column>
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</Row>
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<br/>
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<Row className="align-center">
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<button className="button large"
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disabled={this.state.searching}

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