4.0.0 org.phenotips phenotips-parent 1.1.2 pom 3.0 PhenoTips - Parent POM PhenoTips is a software tool providing an easy-to-use Web interface and standardized database back-end for collecting clinical symptoms and physical findings observed in patients with genetic disorders. http://phenotips.org/ 2011 LGPL 2.1 http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html repo scm:git:git://github.com/phenotips/phenotips.git scm:git:git@github.com:phenotips/phenotips.git https://github.com/phenotips/phenotips.git/tree/master/ phenotips-1.1.2 University of Toronto, Computational Biology Lab http://compbio.cs.toronto.edu/ nexus.phenotips.org dav:https://nexus.phenotips.org/nexus/content/sites/site/${project.groupId}/${project.artifactId}/${project.version} nexus.phenotips.org Maven2 Remote Repository for Releases https://nexus.phenotips.org/nexus/content/repositories/releases nexus.phenotips.org Maven2 Development Repository for Snapshots https://nexus.phenotips.org/nexus/content/repositories/snapshots phenotips-releases PhenoTips Releases repository https://nexus.phenotips.org/nexus/content/repositories/releases/ true fail false fail phenotips-snapshots PhenoTips Snapshots repository https://nexus.phenotips.org/nexus/content/repositories/snapshots/ false fail true fail phenotips-externals PhenoTips external repositories mirror https://nexus.phenotips.org/nexus/content/groups/public/ true false phenotips-externals PhenoTips external repositories mirror https://nexus.phenotips.org/nexus/content/groups/public/ true false phenotips-external-snapshots PhenoTips external snapshot repositories mirror https://nexus.phenotips.org/nexus/content/groups/public-snapshots/ false true UTF-8 1.1.2 5.4.7 1.7.10 1.0 1.0-milestone-3 4.10.4 false false false 1.00 PhenoTips.Skin .* .* ${project.build.directory}/package/ 8080 8079 sh start.sh ${it.server.port} ${it.server.stopPort} sh stop.sh ${it.server.stopPort} http://localhost org.apache.commons commons-lang3 3.3.2 org.slf4j slf4j-api ${slf4j.version} org.slf4j jcl-over-slf4j ${slf4j.version} org.slf4j log4j-over-slf4j ${slf4j.version} ch.qos.logback logback-classic 1.1.2 javax.servlet servlet-api 2.5 provided net.sf.json-lib json-lib jdk15 2.4 commons-logging commons-logging com.google.guava guava 13.0.1 org.apache.httpcomponents httpcore-nio 4.4 org.apache.httpcomponents httpcore 4.4 org.apache.httpcomponents httpclient 4.3.5 commons-logging commons-logging org.apache.httpcomponents httpmime 4.3.5 org.apache.httpcomponents httpasyncclient 4.0.2 commons-logging commons-logging rome rome 1.0 jdom jdom commons-codec commons-codec 1.10 commons-io commons-io 2.4 xalan xalan 2.7.2 install org.apache.maven.wagon wagon-webdav-jackrabbit 2.6 org.phenotips phenotips-functional-tests-lifecycle ${testframework.version} maven-compiler-plugin -Xlint:all true true org.apache.maven.plugins maven-checkstyle-plugin com.mycila license-maven-plugin org.codehaus.mojo clirr-maven-plugin 7009 **/hpoa/annotation/PrettyPrint PrettyPrint() 7002 **/obo2solr/Main void failWithMessage(java.lang.String) 8001 **/hpoa/utils/maps/*MapOperator 7012 **/data/permissions/Visibility int getPermissiveness() 7012 **/measurements/MeasurementsChartConfiguration java.lang.String getChartSource() 7012 **/ontology/OntologyTerm net.sf.json.JSON toJson() 7012 **/ontology/OntologyService java.util.Set termSuggest(java.lang.String, java.lang.Integer, java.lang.String, java.lang.String) 7012 **/measurements/MeasurementsChartConfiguration java.net.URL getChartSourceLink() 8001 **/measurements/MeasurementsScriptService org/phenotips/diagnosis/DiagnosisService 7004 java.util.List getDiagnosis(java.util.List, int) The API should accept both ontology terms and non-standard features. org/phenotips/diagnosis/script/DiagnosisScriptService 7004 java.util.List get(java.util.List, int) The script service passes both ontology terms and non-standard features to the API. **/internal/** **/test/** **/phenotips/hpoa/PhenotypeMappingScriptService **/phenotips/measurements/MeasurementHandler org.apache.maven.plugins maven-remote-resources-plugin license-resources process org.phenotips:phenotips-license-resources:${buildtools.version} org.jacoco jacoco-maven-plugin 0.7.2.201409121644 jacoco-prepare prepare-agent jacoco-check check INSTRUCTION ${coverage.instructionRatio} org.apache.maven.plugins maven-enforcer-plugin org.xwiki.commons xwiki-commons-tool-enforcer-dependencies ${xwiki.version} enforce-plugins enforce Best Practice is to always define plugin versions! false false false enforce-commons-lang3 enforce false Best practice is to use Commons Lang 3.x commons-lang:commons-lang enforce-no-legacy-dependencies enforce true Don't depend on a XWiki Legacy module! .*xwiki.*:.*-legacy-.* ${enforcer.skip} org.apache.maven.plugins maven-enforcer-plugin 1.3.1 org.apache.maven.plugins maven-checkstyle-plugin 2.13 org.phenotips phenotips-checkstyle-configuration ${buildtools.version} true ${checkstyle.skip} checkstyle.xml check com.mycila license-maven-plugin 2.6 ${license.skip}

license.txt

true license-xml-definition.xml license-script-definition.xml license-batch-definition.xml SLASHSTAR_STYLE SLASHSTAR_STYLE src/**/*.java src/**/*.xml src/**/*.bat src/**/*.sh pom.xml **/components.txt **/component-overrides.txt **/it/**/goals.txt **/goal.txt **/P0*.xml **/F0*.xml false org.phenotips phenotips-license-verification-resources ${buildtools.version} check org.apache.maven.plugins maven-resources-plugin 2.7 org.apache.maven.plugins maven-remote-resources-plugin 1.5 org.apache.maven.plugins maven-release-plugin 2.5.1 -Pquick deploy forked-path true true false phenotips-@{project.version} org.apache.maven.plugins maven-clean-plugin 2.6.1 org.apache.maven.plugins maven-source-plugin 2.4 org.apache.maven.plugins maven-plugin-plugin 3.4 org.apache.maven.plugins maven-install-plugin 2.5.2 org.apache.maven.plugins maven-compiler-plugin 3.2 1.7 1.7 org.apache.maven.plugins maven-surefire-plugin 2.18.1 **/*Test.class classesAndMethods 2 pattern ${it.pattern} patternMethod ${it.patternMethod} xwiki.test.baseURL ${it.server.baseURL} xwiki.test.skipStart ${it.skipStart} xwikiPort ${it.server.port} xwikiStopPort ${it.server.stopPort} xwikiExecutionDirectory ${it.server.directory} screenshotDirectory ${basedir}/target/screenshots xwikiExecutionStartCommand ${it.server.startCommand} xwikiExecutionStopCommand ${it.server.stopCommand} xwikiWebappName phenotips xwikiWebappPath org.apache.maven.plugins maven-jar-plugin 2.5 ${project.groupId}:${project.artifactId} org.apache.maven.plugins maven-assembly-plugin 2.5.3 org.apache.maven.plugins maven-dependency-plugin 2.9 org.apache.maven.plugins maven-war-plugin 2.6 ${project.groupId}:${project.artifactId} org.apache.maven.plugins maven-deploy-plugin 2.8.2 org.apache.maven.wagon wagon-webdav-jackrabbit 2.6 org.apache.maven.plugins maven-project-info-reports-plugin 2.8 org.codehaus.mojo clirr-maven-plugin 2.6.1 clirr-check check ${clirr.previous.version} ${clirr.skip} org.apache.maven.plugins maven-gpg-plugin 1.6 org.apache.maven.plugins maven-javadoc-plugin 2.10.1 *.internal.* 300m org.apache.maven.plugins maven-site-plugin 3.4 org.apache.maven.wagon wagon-webdav-jackrabbit 2.6 org.apache.maven.plugins maven-project-info-reports-plugin 2.7 false summary index dependencies dependency-convergence mailing-list issue-tracking scm org.apache.maven.plugins maven-javadoc-plugin 2.9.1 *.internal.* 300m javadoc org.xwiki.commons xwiki-commons-tool-xar-plugin ${xwiki.version} org.phenotips phenotips-packager-maven-plugin ${testframework.version} quick true true true true true true true release performRelease true org.apache.maven.plugins maven-source-plugin attach-sources jar org.apache.maven.plugins maven-javadoc-plugin attach-javadocs jar org.apache.maven.plugins maven-gpg-plugin sign-artifacts verify sign true mac false mac mac os x org.codehaus.mojo exec-maven-plugin 1.3.2 org.codehaus.mojo build-helper-maven-plugin 1.9.1 windows windows cmd /c start.bat ${it.server.port} ${it.server.stopPort} cmd /c stop.bat ${it.server.stopPort} resources components distribution