4.0.0 org.phenotips phenotips-parent 1.3-rc-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 AGPL 3.0 https://www.gnu.org/licenses/agpl-3.0.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-1.3-rc-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 1.3-rc-2 1.2 7.1.4 1.7.22 3.11 2.53.1 1.9.13 2.8.6 2.0.15 1.6 1.1 5.5.4 3.0 0.12.3 false 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 3.5 org.apache.commons commons-collections4 4.1 org.apache.commons commons-csv 1.4 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 1.1.9 javax.servlet javax.servlet-api 3.0.1 provided joda-time joda-time 2.9.7 org.json json 20160810 org.xwiki.platform xwiki-platform-repository-server-api ${xwiki.version} org.xwiki.platform xwiki-platform-search-solr-query org.apache.httpcomponents httpcore 4.4.5 org.apache.httpcomponents httpclient 4.5.2 commons-logging commons-logging org.apache.httpcomponents httpasyncclient 4.1.2 commons-logging commons-logging rome rome 1.0 jdom jdom commons-codec commons-codec 1.10 commons-io commons-io 2.5 org.seleniumhq.selenium selenium-api ${selenium.version} org.seleniumhq.selenium selenium-support ${selenium.version} org.codehaus.jackson jackson-core-asl ${jackson.codehaus.version} org.codehaus.jackson jackson-mapper-asl ${jackson.codehaus.version} com.fasterxml.jackson.core jackson-core ${jackson.fasterxml.version} com.fasterxml.jackson.core jackson-databind ${jackson.fasterxml.version} com.fasterxml.jackson.core jackson-annotations ${jackson.fasterxml.version} javax.ws.rs jsr311-api 1.0 org.restlet.jse org.restlet ${restlet.version} org.restlet.jse org.restlet.ext.jackson ${restlet.version} org.restlet.jse org.restlet.ext.jaxrs ${restlet.version} org.restlet.jse org.restlet.lib.org.json junit junit 4.12 test org.mockito mockito-core 1.10.19 test org.hibernate hibernate-core 3.6.9.Final org.jasypt jasypt 1.9.2 org.hsqldb hsqldb 2.3.4 mysql mysql-connector-java 5.1.40 antlr antlr 2.7.6 net.sourceforge.htmlcleaner htmlcleaner 2.18 com.google.guava guava 14.0.1 install org.apache.maven.wagon wagon-webdav-jackrabbit 2.6 org.phenotips phenotips-functional-tests-lifecycle ${testframework.version} org.xwiki.commons xwiki-commons-tool-xar-handlers ${xwiki.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 ${project.version.previous} org/phenotips/vocabulary/VocabularyManager 7012 java.util.List getAvailableVocabularies() New method for getting all the vocabularies; it's esential for a Manager to be able to say what it manages. org/phenotips/vocabulary/Vocabulary 7012 java.lang.String getIdentifier() New methods for better vocabulary identification. org/phenotips/vocabulary/Vocabulary 7012 java.lang.String getName() New methods for better vocabulary identification. org/phenotips/vocabulary/Vocabulary 7012 java.lang.String getWebsite() New methods for better vocabulary identification; helps specify the vocabulary's website org/phenotips/vocabulary/Vocabulary 7012 java.lang.String getCitation() New methods for better vocabulary identification org/phenotips/vocabulary/Vocabulary 7012 java.util.List search(java.lang.String) New search method for a simpler API org/phenotips/vocabulary/VocabularyTerm 7012 * getTranslated*(*) New methods for vocabulary term translations org/phenotips/vocabulary/SolrVocabularyResourceManager 7002 void initialize(java.lang.String) Transformed the class into a singleton org/phenotips/vocabulary/SolrVocabularyResourceManager 7004 org.xwiki.cache.Cache getTermCache() org.xwiki.cache.Cache getTermCache(String) Transformed the class into a singleton org/phenotips/vocabulary/SolrVocabularyResourceManager 7004 org.apache.solr.client.solrj.SolrClient getSolrConnection() org.apache.solr.client.solrj.SolrClient getSolrConnection(String) Transformed the class into a singleton org/phenotips/data/permissions/PermissionsManager 7012 java.util.Collection listAllVisibilityOptions() New methods in support of disabled visibilities. org/phenotips/data/permissions/PermissionsManager 7012 org.phenotips.data.permissions.Visibility getDefaultVisibility() New API method. org/phenotips/data/permissions/Visibility 7012 boolean isDisabled() New methods in support of disabled visibilities. ** 7006 net.sf.json.* toJSON(*) org.json.JSONObject Switched from net.sf.json to org.json. org/phenotips/data/Patient 7005 void updateFromJSON(net.sf.json.JSONObject) void updateFromJSON(org.json.JSONObject) Switched from net.sf.json to org.json. org/phenotips/data/* 7005 * * Switched from net.sf.json to org.json. org/phenotips/data/push/** 7006 net.sf.json.JSONObject getLocalPatientJSON(java.lang.String, java.lang.String) org.json.JSONObject Switched from net.sf.json to org.json. org/phenotips/data/receive/** 7006 net.sf.json.JSONObject *(*) org.json.JSONObject Switched from net.sf.json to org.json. org/phenotips/data/push/PushPatientData 7004 org.phenotips.data.push.PushServerSendPatientResponse sendPatient(org.phenotips.data.Patient, java.util.Set, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String) Needed for synchronizing consents org/phenotips/data/push/PushPatientService 7004 org.phenotips.data.push.PushServerSendPatientResponse sendPatient(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String) Needed for synchronizing consents org/phenotips/data/push/PushPatientService 7004 org.phenotips.data.push.PushServerSendPatientResponse sendPatient(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String) Needed for synchronizing consents org/phenotips/data/push/PushServerSendPatientResponse 7012 boolean isActionFailed_MissingConsent() Needed for synchronizing consents org/phenotips/data/push/script/PushPatientScriptService 7004 org.phenotips.data.push.PushServerSendPatientResponse sendPatient(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String) Needed for synchronizing consents org/phenotips/data/push/script/PushPatientScriptService 7004 org.phenotips.data.push.PushServerSendPatientResponse sendPatient(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String) Needed for synchronizing consents org/phenotips/data/PatientRepository 7012 boolean deletePatient(java.lang.String) Delete patient functionality for script services accessibility. org/phenotips/data/PatientDataController 7004 void save(org.phenotips.data.Patient) Needed for save optimization org/phenotips/data/push/PushServerConfigurationResponse 7012 org.json.JSONArray getConsents() Needed for synchronizing consents org/phenotips/data/push/PushServerResponse 7012 boolean isClientDoesNotAcceptServerProtocolVersion() Better push protocol versioning mechanism org/phenotips/data/push/PushServerResponse 7012 boolean isServerDoesNotAcceptClientProtocolVersion() Better push protocol versioning mechanism org/phenotips/data/push/PushServerResponse 7002 boolean isIncorrectProtocolVersion() Better push protocol versioning mechanism org/phenotips/data/shareprotocol/ShareProtocol 6011 POST_PROTOCOL_VERSION Renamed to better reflect its meaning org/phenotips/data/shareprotocol/ShareProtocol 6011 JSON_RESPONSE_PROTOCOL_VERSION Renamed to better reflect its meaning org/phenotips/data/Feature 7012 java.lang.String getPropertyName() New methods for extending pushable data org/phenotips/data/Feature 7012 java.util.List getCategories() New methods for extending pushable data org/phenotips/configuration/RecordSection 7012 boolean isExpandedByDefault() New methods for configuring which sections should be collapsed and expanded in edit mode by default org/phenotips/data/PatientData 7012 boolean containsKey(java.lang.String) Will be used in new controllers org/phenotips/data/permissions/PermissionsManager 7012 java.util.* filterByVisibility(java.util.*, org.phenotips.data.permissions.Visibility) Needed for matching notification org/phenotips/security/authorization/AuthorizationModule 7005 java.lang.Boolean hasAccess(org.xwiki.users.User, org.xwiki.security.authorization.Right, org.xwiki.model.reference.DocumentReference) java.lang.Boolean hasAccess(org.xwiki.users.User, org.xwiki.security.authorization.Right, org.xwiki.model.reference.EntityReference) Made more generic to also be able to deal with spaces org/phenotips/security/authorization/AuthorizationService 7005 boolean hasAccess(org.xwiki.users.User, org.xwiki.security.authorization.Right, org.xwiki.model.reference.DocumentReference) boolean hasAccess(org.xwiki.users.User, org.xwiki.security.authorization.Right, org.xwiki.model.reference.EntityReference) Made more generic to also be able to deal with spaces org/phenotips/data/permissions/script/SecurePatientAccess 8001 Moved the functionality into an internal package, since script services shouldn't have that much application logic org/phenotips/data/rest/Relations 8001 Moved the functionality into a different module org/phenotips/data/rest/DateTimeAdapter 8001 Moved the functionality into a different module org/phenotips/data/rest/PatientsResource 7012 javax.ws.rs.core.Response add(java.lang.String) The method can now add one patient or many patients, renamed from addPatient org/phenotips/data/rest/PatientsResource 7002 javax.ws.rs.core.Response addPatient(java.lang.String) The method can now add one patient or many patients, renamed to add org/phenotips/data/permissions/AccessLevel 7012 org.xwiki.security.authorization.Right getGrantedRight() New API method bringing XWiki Rights into PhenoTips Permissions. org/phenotips/data/permissions/PermissionsManager 7012 void fireRightsUpdateEvent(java.lang.String) New way of notifying listeners that permissions on an entity have changed. org/phenotips/data/push/PushServerResponse 7012 java.lang.String getServerProtocolVersion() Improved handling of older push server protocol versions. **/internal/** **/test/** org/phenotips/data/rest/model/* org.apache.maven.plugins maven-remote-resources-plugin license-resources process org.phenotips:phenotips-license-resources:${buildtools.version} org.jacoco jacoco-maven-plugin 0.7.9 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 1.4.1 org.apache.maven.plugins maven-checkstyle-plugin 2.17 com.puppycrawl.tools checkstyle 6.19 org.phenotips phenotips-checkstyle-configuration ${buildtools.version} true ${checkstyle.skip} checkstyle.xml check com.mycila license-maven-plugin 3.0 ${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 3.0.2 org.apache.maven.plugins maven-remote-resources-plugin 1.5 org.apache.maven.plugins maven-release-plugin 2.5.3 -Pquick deploy forked-path true true false phenotips-@{project.version} org.apache.maven.plugins maven-clean-plugin 3.0.0 org.apache.maven.plugins maven-source-plugin 3.0.1 org.apache.maven.plugins maven-plugin-plugin 3.5 org.apache.maven.plugins maven-install-plugin 2.5.2 org.apache.maven.plugins maven-compiler-plugin 3.6.1 1.7 1.7 org.apache.maven.plugins maven-surefire-plugin 2.19.1 **/*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 3.0.2 ${project.groupId}:${project.artifactId} org.apache.maven.plugins maven-assembly-plugin 3.0.0 org.apache.maven.plugins maven-dependency-plugin 3.0.0 javax.inject:javax.inject org.xwiki.commons:xwiki-commons-stability org.mockito:mockito-core junit:junit org.hamcrest:hamcrest-library javax.servlet:javax.servlet-api org.apache.maven.plugins maven-war-plugin 3.0.0 ${project.groupId}:${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 2.9 org.codehaus.mojo clirr-maven-plugin 2.8 clirr-check check ${clirr.previous.version} ${clirr.skip} org.apache.maven.plugins maven-gpg-plugin 1.6 org.apache.maven.plugins maven-javadoc-plugin 2.10.4 *.internal.* 300m org.phenotips.tools.javadoc.NoteTaglet org.phenotips.tools.javadoc.TodoTaglet org.phenotips.tools.javadoc.FixmeTaglet org.phenotips.tools.javadoc.WarningTaglet ${project.groupId} phenotips-taglets ${buildtools.version} org.apache.maven.plugins maven-site-plugin 3.6 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} org.codehaus.mojo exec-maven-plugin 1.5.0 org.codehaus.mojo build-helper-maven-plugin 1.12 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 windows windows cmd /c start.bat ${it.server.port} ${it.server.stopPort} cmd /c stop.bat ${it.server.stopPort} resources components distribution