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GitHub / bridgedb / BridgeDb

The BridgeDb Library source code

JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bridgedb%2FBridgeDb

Stars: 26
Forks: 21
Open Issues: 45

License: apache-2.0
Language: Java
Repo Size: 32.6 MB
Dependencies: 219

Created: over 10 years ago
Updated: about 2 months ago
Last pushed: 28 days ago
Last synced: 28 days ago

Commit Stats

Commits: 2087
Authors: 37
Mean commits per author: 56.41
Development Distribution Score: 0.759
More commit stats: https://commits.ecosyste.ms/hosts/GitHub/repositories/bridgedb/BridgeDb

Topics: bioinformatics, bridgedb, database, hacktoberfest, identifier-mapping, java, mysql-backend, uri

Files

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Dependencies

examples/pom.xml maven

org.bridgedb.webservice:org.bridgedb.webservice.biomart 3.0.16-SNAPSHOT compile
org.bridgedb.webservice:org.bridgedb.webservice.bridgerest 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.bio 3.0.16-SNAPSHOT compile
commons-discovery:commons-discovery 0.4
org.apache.axis:axis 1.4
org.apache.axis:axis-jaxrpc 1.4
wsdl4j:wsdl4j 1.6.2

org.bridgedb/pom.xml maven

org.junit.jupiter:junit-jupiter-api ${junit5.jupiter.version} test
org.junit.jupiter:junit-jupiter-engine ${junit5.jupiter.version} test
org.junit.platform:junit-platform-surefire-provider 1.3.2 test
org.junit.vintage:junit-vintage-engine ${junit5.jupiter.version} test

org.bridgedb.bio/pom.xml maven

org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT compile
org.junit.jupiter:junit-jupiter-api ${junit5.jupiter.version} test
org.junit.jupiter:junit-jupiter-engine ${junit5.jupiter.version} test
org.junit.platform:junit-platform-surefire-provider ${junit-platform-surefire-provider} test
org.junit.vintage:junit-vintage-engine ${junit5.jupiter.version} test

org.bridgedb.file.orthoxml/pom.xml maven

org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.bio 3.0.16-SNAPSHOT compile
org.group.project:orthoxml 0.1.0 system

org.bridgedb.gui/pom.xml maven

com.jgoodies:forms 1.2.1 compile
org.bridgedb:org.bridgedb ${project.version} compile

org.bridgedb.rdb/pom.xml maven

org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.bio 3.0.16-SNAPSHOT compile
mysql:mysql-connector-java ${mysql.version}
org.apache.derby:derby ${derby.version}
org.apache.derby:derbyclient ${derby.version}
org.junit.jupiter:junit-jupiter-api ${junit5.jupiter.version} test
org.junit.jupiter:junit-jupiter-engine ${junit5.jupiter.version} test
org.junit.platform:junit-platform-launcher 1.8.2 test
org.junit.vintage:junit-vintage-engine ${junit5.jupiter.version} test

org.bridgedb.rdb.construct/pom.xml maven

org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.bio 3.0.16-SNAPSHOT compile
mysql:mysql-connector-java ${mysql.version}
org.apache.derby:derby ${derby.version}
org.apache.derby:derbyclient ${derby.version}

org.bridgedb.rdf/pom.xml maven

org.bridgedb:org.bridgedb.bio 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.utils 3.0.16-SNAPSHOT compile
org.eclipse.rdf4j:rdf4j-rio-turtle ${rdf4j.version} compile
org.eclipse.rdf4j:rdf4j-sail-memory ${rdf4j.version} compile
org.eclipse.rdf4j:rdf4j-sail-nativerdf ${rdf4j.version} compile
org.eclipse.rdf4j:rdf4j-repository-sail ${rdf4j.version}
org.eclipse.rdf4j:rdf4j-rio-api ${rdf4j.version}
org.eclipse.rdf4j:rdf4j-rio-n3 ${rdf4j.version}
org.eclipse.rdf4j:rdf4j-rio-rdfxml ${rdf4j.version}
org.eclipse.rdf4j:rdf4j-rio-testsuite ${rdf4j.version}
org.eclipse.rdf4j:rdf4j-rio-trig ${rdf4j.version}
org.eclipse.rdf4j:rdf4j-rio-trix ${rdf4j.version}
org.slf4j:slf4j-api ${slf4j.version}
org.slf4j:slf4j-log4j12 ${slf4j.version}
org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.utils 3.0.16-SNAPSHOT test
org.hamcrest:hamcrest-library ${hamcrest.version} test
org.junit.jupiter:junit-jupiter-api ${junit5.jupiter.version} test
org.junit.jupiter:junit-jupiter-engine ${junit5.jupiter.version} test
org.junit.platform:junit-platform-surefire-provider ${junit-platform-surefire-provider} test
org.junit.vintage:junit-vintage-engine ${junit5.jupiter.version} test

org.bridgedb.sql/pom.xml maven

mysql:mysql-connector-java ${mysql.version} compile
org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.utils 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.utils 3.0.16-SNAPSHOT test
org.hamcrest:hamcrest-core ${hamcrest.version} test
org.hamcrest:hamcrest-library ${hamcrest.version} test
org.junit.jupiter:junit-jupiter-api ${junit5.jupiter.version} test
org.junit.jupiter:junit-jupiter-engine ${junit5.jupiter.version} test
org.junit.platform:junit-platform-surefire-provider ${junit-platform-surefire-provider} test
org.junit.vintage:junit-vintage-engine ${junit5.jupiter.version} test

org.bridgedb.tools.batchmapper/pom.xml maven

org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.bio 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.rdb 3.0.16-SNAPSHOT compile

org.bridgedb.tools.info/pom.xml maven

org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.bio 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.rdb 3.0.16-SNAPSHOT compile

org.bridgedb.tools.qc/pom.xml maven

org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.bio 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.rdb 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.rdb.construct 3.0.16-SNAPSHOT compile
com.google.guava:guava [30.0-jre,)

org.bridgedb.uri.api/pom.xml maven

org.bridgedb:org.bridgedb.utils 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.utils 3.0.16-SNAPSHOT test
org.hamcrest:hamcrest-core ${hamcrest.version} test
org.hamcrest:hamcrest-library ${hamcrest.version} test
org.junit.jupiter:junit-jupiter-api ${junit5.jupiter.version} test
org.junit.jupiter:junit-jupiter-engine ${junit5.jupiter.version} test
org.junit.platform:junit-platform-surefire-provider ${junit-platform-surefire-provider} test
org.junit.vintage:junit-vintage-engine ${junit5.jupiter.version} test

org.bridgedb.uri.loader/pom.xml maven

org.bridgedb:org.bridgedb.uri.sql 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.sql 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.uri.sql 3.0.16-SNAPSHOT test
org.hamcrest:hamcrest-core ${hamcrest.version} test
org.hamcrest:hamcrest-library ${hamcrest.version} test
org.junit.jupiter:junit-jupiter-api ${junit5.jupiter.version} test
org.junit.jupiter:junit-jupiter-engine ${junit5.jupiter.version} test
org.junit.platform:junit-platform-surefire-provider ${junit-platform-surefire-provider} test
org.junit.vintage:junit-vintage-engine ${junit5.jupiter.version} test

org.bridgedb.uri.sql/pom.xml maven

mysql:mysql-connector-java ${mysql.version} compile
org.bridgedb:org.bridgedb.rdf 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.sql 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.uri.api 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.sql 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.utils 3.0.16-SNAPSHOT test
org.hamcrest:hamcrest-core ${hamcrest.version} test
org.hamcrest:hamcrest-library ${hamcrest.version} test
org.junit.jupiter:junit-jupiter-api ${junit5.jupiter.version} test
org.junit.jupiter:junit-jupiter-engine ${junit5.jupiter.version} test
org.junit.platform:junit-platform-surefire-provider ${junit-platform-surefire-provider} test
org.junit.vintage:junit-vintage-engine ${junit5.jupiter.version} test

org.bridgedb.uri.ws.client/pom.xml maven

org.bridgedb:org.bridgedb.uri.api 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.uri.ws.core 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.ws.client 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.uri.api 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.uri.sql 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.uri.ws.core 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.utils 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.ws.core 3.0.16-SNAPSHOT test
org.hamcrest:hamcrest-core ${hamcrest.version} test
org.hamcrest:hamcrest-library ${hamcrest.version} test
org.junit.jupiter:junit-jupiter-api ${junit5.jupiter.version} test
org.junit.jupiter:junit-jupiter-engine ${junit5.jupiter.version} test
org.junit.platform:junit-platform-surefire-provider ${junit-platform-surefire-provider} test
org.junit.vintage:junit-vintage-engine ${junit5.jupiter.version} test

org.bridgedb.uri.ws.core/pom.xml maven

org.bridgedb:org.bridgedb.uri.api 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.ws.core 3.0.16-SNAPSHOT compile
com.sun.jersey:jersey-core ${jersey.version}
org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.sql 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.uri.sql 3.0.16-SNAPSHOT test
org.hamcrest:hamcrest-core ${hamcrest.version} test

org.bridgedb.uri.ws.server/pom.xml maven

com.sun.jersey.contribs:jersey-multipart ${jersey.version} compile
com.sun.jersey:jersey-server ${jersey.version} compile
org.apache.cxf:cxf-rt-frontend-jaxrs ${cxf.version} compile
org.apache.velocity:velocity-engine-core 2.3 compile
org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.sql 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.uri.sql 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.uri.ws.core 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb.ws.core 3.0.16-SNAPSHOT compile
javax.servlet:servlet-api ${servlet.version} provided
org.bridgedb:org.bridgedb.ws.server 3.0.16-SNAPSHOT
org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.sql 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.uri.sql 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.utils 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.ws.server 3.0.16-SNAPSHOT test
org.hamcrest:hamcrest-core ${hamcrest.version} test
org.hamcrest:hamcrest-library ${hamcrest.version} test
org.junit.jupiter:junit-jupiter-api ${junit5.jupiter.version} test
org.junit.jupiter:junit-jupiter-engine ${junit5.jupiter.version} test
org.junit.platform:junit-platform-surefire-provider ${junit-platform-surefire-provider} test
org.junit.vintage:junit-vintage-engine ${junit5.jupiter.version} test

org.bridgedb.utils/pom.xml maven

org.apache.logging.log4j:log4j-1.2-api ${log4j.version} compile
org.apache.logging.log4j:log4j-core ${log4j.version} compile
org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT compile
org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT test
org.junit.jupiter:junit-jupiter-api ${junit5.jupiter.version} test
org.junit.jupiter:junit-jupiter-engine ${junit5.jupiter.version} test
org.junit.platform:junit-platform-surefire-provider ${junit-platform-surefire-provider} test
org.junit.vintage:junit-vintage-engine ${junit5.jupiter.version} test

org.bridgedb.webservice.biomart/pom.xml maven

org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT compile
org.junit.jupiter:junit-jupiter-api ${junit5.jupiter.version} test
org.junit.jupiter:junit-jupiter-engine ${junit5.jupiter.version} test
org.junit.platform:junit-platform-surefire-provider ${junit-platform-surefire-provider} test
org.junit.vintage:junit-vintage-engine ${junit5.jupiter.version} test

org.bridgedb.webservice.bridgerest/pom.xml maven

org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT compile

org.bridgedb.ws.client/pom.xml maven

org.bridgedb:org.bridgedb.ws.core 3.0.16-SNAPSHOT compile
com.sun.jersey:jersey-client ${jersey.version}
com.sun.jersey:jersey-core ${jersey.version}
org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.utils 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.ws.core 3.0.16-SNAPSHOT test
org.hamcrest:hamcrest-core ${hamcrest.version} test
org.junit.jupiter:junit-jupiter-api ${junit5.jupiter.version} test
org.junit.jupiter:junit-jupiter-engine ${junit5.jupiter.version} test
org.junit.platform:junit-platform-surefire-provider ${junit-platform-surefire-provider} test
org.junit.vintage:junit-vintage-engine ${junit5.jupiter.version} test

org.bridgedb.ws.core/pom.xml maven

org.bridgedb:org.bridgedb.utils 3.0.16-SNAPSHOT compile
com.sun.jersey:jersey-core ${jersey.version}
javax.xml.bind:jaxb-api 2.2.11
org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.sql 3.0.16-SNAPSHOT test
org.hamcrest:hamcrest-core ${hamcrest.version} test
org.junit.jupiter:junit-jupiter-api ${junit5.jupiter.version} test
org.junit.jupiter:junit-jupiter-engine ${junit5.jupiter.version} test
org.junit.platform:junit-platform-surefire-provider 1.2.0 test
org.junit.vintage:junit-vintage-engine ${junit5.jupiter.version} test

org.bridgedb.ws.server/pom.xml maven

org.bridgedb:org.bridgedb.sql 3.0.16-SNAPSHOT compile
javax.servlet:servlet-api ${servlet.version} provided
com.sun.jersey:jersey-client ${jersey.version}
com.sun.jersey:jersey-core ${jersey.version}
org.apache.cxf:cxf-rt-frontend-jaxrs ${cxf.version}
org.bridgedb:org.bridgedb.ws.core 3.0.16-SNAPSHOT
org.bridgedb:org.bridgedb 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.bio 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.utils 3.0.16-SNAPSHOT test
org.bridgedb:org.bridgedb.ws.core 3.0.16-SNAPSHOT test
org.hamcrest:hamcrest-core ${hamcrest.version} test
org.hamcrest:hamcrest-library ${hamcrest.version} test
org.junit.jupiter:junit-jupiter-api ${junit5.jupiter.version} test
org.junit.jupiter:junit-jupiter-engine ${junit5.jupiter.version} test
org.junit.platform:junit-platform-surefire-provider ${junit-platform-surefire-provider} test
org.junit.vintage:junit-vintage-engine ${junit5.jupiter.version} test

taverna-bridgedb/bridgedb-activity/pom.xml maven

org.bridgedb.webservice:org.bridgedb.webservice.bridgerest 1.1.1-SNAPSHOT compile
org.bridgedb:org.bridgedb 1.1.1-SNAPSHOT compile
org.bridgedb:org.bridgedb.bio 1.1.1-SNAPSHOT compile
net.sf.taverna.t2.core:workflowmodel-api ${t2.core.version}
net.sf.taverna.t2.activities:activity-test-utils ${t2.activities.version} test

taverna-bridgedb/bridgedb-activity-ui/pom.xml maven

${project.groupId}:bridgedb-activity ${project.version}
net.sf.taverna.t2.ui-api:activity-palette-api ${t2.ui.api.version}
net.sf.taverna.t2.ui-api:contextual-views-api ${t2.ui.api.version}
net.sf.taverna.t2.ui-api:menu-api ${t2.ui.api.version}
net.sf.taverna.t2.taverna-workbench:workbench-dev ${t2.workbench.version} test

taverna-bridgedb/pom.xml maven

junit:junit 4.13.1 test

.github/workflows/build.yml actions

actions/checkout v2 composite
actions/setup-java v1 composite