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pom.xml
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<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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.ohdsi</groupId>
<artifactId>WebAPI</artifactId>
<packaging>war</packaging>
<version>2.15.0-SNAPSHOT</version>
<name>WebAPI</name>
<properties>
<build.number>${BUILD_NUMBER}</build.number>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<!-- Spring Boot manages spring.version as well -->
<spring.boot.version>1.5.22.RELEASE</spring.boot.version>
<log4j2.version>2.17.1</log4j2.version>
<flyway.version>4.2.0</flyway.version>
<waffle.version>2.2.1</waffle.version>
<jna.version>5.5.0</jna.version>
<hibernate.version>5.4.2.Final</hibernate.version>
<postgresql.version>42.3.10</postgresql.version>
<bouncycastle.version>1.69</bouncycastle.version>
<shiro.version>1.12.0</shiro.version>
<dom4j.version>2.1.3</dom4j.version>
<hydra.version>0.4.0</hydra.version>
<featureExtraction.version>3.2.0</featureExtraction.version>
<tomcat.embed.version>8.5.87</tomcat.embed.version>
<commons-fileupload.version>1.5</commons-fileupload.version>
<circe.version>1.12.0</circe.version>
<jersey.version>2.14</jersey.version>
<SqlRender.version>1.19.1</SqlRender.version>
<hive-jdbc.version>3.1.2</hive-jdbc.version>
<pac4j.version>4.0.0</pac4j.version>
<jackson.version>2.12.7</jackson.version>
<start-class>org.ohdsi.webapi.WebApi</start-class>
<skipUnitTests>false</skipUnitTests>
<skipITtests>false</skipITtests>
<miredot.phase>package</miredot.phase>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
<!-- Primary DataSource -->
<!-- default sql server - TODO How about making postgres the default (e.g. in line with open source tech)? -alexfranken -->
<datasource.driverClassName>com.microsoft.sqlserver.jdbc.SQLServerDriver</datasource.driverClassName>
<datasource.url>jdbc:sqlserver://serverName;databaseName=databaseName</datasource.url>
<datasource.username>user</datasource.username>
<datasource.password>password</datasource.password>
<!--<datasource.validationQuery>SELECT 1</datasource.validationQuery>-->
<datasource.dialect>sql server</datasource.dialect>
<datasource.ohdsi.schema>dbo</datasource.ohdsi.schema>
<datasource.dialect.source>sql server</datasource.dialect.source>
<!-- DB Change Management / Migration -->
<flyway.datasource.driverClassName>com.microsoft.sqlserver.jdbc.SQLServerDriver</flyway.datasource.driverClassName>
<flyway.datasource.url>jdbc:sqlserver://serverName</flyway.datasource.url>
<flyway.datasource.username>userWithWritePrivs</flyway.datasource.username>
<flyway.datasource.password>password</flyway.datasource.password>
<flyway.locations>classpath:db/migration/sqlserver</flyway.locations>
<!-- Note: Schema name is case-sensitive. -->
<flyway.schemas>${datasource.ohdsi.schema}</flyway.schemas>
<flyway.validateOnMigrate>false</flyway.validateOnMigrate>
<flyway.placeholders.ohdsiSchema>${datasource.ohdsi.schema}</flyway.placeholders.ohdsiSchema>
<!-- CDM properties -->
<source.name>CDM_NAME</source.name>
<cdm.version>5</cdm.version>
<!-- Person properties -->
<person.viewDates>false</person.viewDates>
<!-- Heracles properties -->
<heracles.smallcellcount>5</heracles.smallcellcount>
<!-- Kerberos properties -->
<kerberos.timeout>60</kerberos.timeout>
<kerberos.configPath>/etc/krb5.conf</kerberos.configPath>
<kerberos.kinitPath></kerberos.kinitPath>
<spring.batch.repository.tableprefix>${datasource.ohdsi.schema}.BATCH_</spring.batch.repository.tableprefix>
<spring.batch.repository.isolationLevelForCreate>ISOLATION_READ_COMMITTED</spring.batch.repository.isolationLevelForCreate>
<spring.profiles.active>default</spring.profiles.active>
<security.provider>DisabledSecurity</security.provider>
<security.token.expiration>43200</security.token.expiration>
<security.origin>http://localhost</security.origin>
<security.ssl.enabled>false</security.ssl.enabled>
<security.oauth.callback.ui>http://localhost/Atlas/#/welcome</security.oauth.callback.ui>
<security.oauth.callback.api>http://localhost:8080/WebAPI/user/oauth/callback</security.oauth.callback.api>
<!-- Available options for callback urlResolver are: query and path -->
<security.oauth.callback.urlResolver>query</security.oauth.callback.urlResolver>
<security.oauth.google.apiKey></security.oauth.google.apiKey>
<security.oauth.google.apiSecret></security.oauth.google.apiSecret>
<security.oauth.facebook.apiKey></security.oauth.facebook.apiKey>
<security.oauth.facebook.apiSecret></security.oauth.facebook.apiSecret>
<security.oauth.github.apiKey></security.oauth.github.apiKey>
<security.oauth.github.apiSecret></security.oauth.github.apiSecret>
<security.oid.clientId></security.oid.clientId>
<security.oid.apiSecret></security.oid.apiSecret>
<security.oid.url></security.oid.url>
<security.oid.logoutUrl></security.oid.logoutUrl>
<security.oid.extraScopes></security.oid.extraScopes>
<security.oid.customParams>{:}</security.oid.customParams>
<security.oid.redirectUrl>http://localhost/index.html#/welcome/</security.oid.redirectUrl>
<security.kerberos.spn></security.kerberos.spn>
<security.kerberos.keytabPath></security.kerberos.keytabPath>
<security.ldap.dn>cn={0},dc=example,dc=org</security.ldap.dn>
<security.ldap.url>ldap://localhost:389</security.ldap.url>
<security.ldap.baseDn></security.ldap.baseDn>
<security.ldap.system.username></security.ldap.system.username>
<security.ldap.system.password></security.ldap.system.password>
<security.ldap.searchString>(&(objectClass=person)(CN={0}))</security.ldap.searchString>
<security.ldap.userMapping.displaynameAttr>displayName</security.ldap.userMapping.displaynameAttr>
<security.ldap.userMapping.firstnameAttr>givenName</security.ldap.userMapping.firstnameAttr>
<security.ldap.userMapping.middlenameAttr>initials</security.ldap.userMapping.middlenameAttr>
<security.ldap.userMapping.lastnameAttr>sn</security.ldap.userMapping.lastnameAttr>
<security.ldap.userMapping.usernameAttr>cn</security.ldap.userMapping.usernameAttr>
<security.ldap.userImport.usernameAttr>cn</security.ldap.userImport.usernameAttr>
<security.ldap.userImport.loginAttr>uid</security.ldap.userImport.loginAttr>
<security.ldap.searchBase>CN=Users,DC=example,DC=org</security.ldap.searchBase>
<security.ad.url></security.ad.url>
<security.ad.searchBase>CN=Users,DC=example,DC=org</security.ad.searchBase>
<security.ad.principalSuffix>@example.org</security.ad.principalSuffix>
<security.ad.system.username></security.ad.system.username>
<security.ad.system.password></security.ad.system.password>
<security.ad.searchFilter>(&(objectClass=person)(cn=%s))</security.ad.searchFilter>
<security.ad.ignore.partial.result.exception>true</security.ad.ignore.partial.result.exception>
<security.ad.result.count.limit>30000</security.ad.result.count.limit> <!-- 0 means no limit -->
<security.ad.default.import.group>public</security.ad.default.import.group>
<security.ad.searchString>(&(objectClass=person)(userPrincipalName=%s))</security.ad.searchString>
<security.ad.userMapping.displaynameAttr>displayname</security.ad.userMapping.displaynameAttr>
<security.ad.userMapping.firstnameAttr>givenname</security.ad.userMapping.firstnameAttr>
<security.ad.userMapping.middlenameAttr>initials</security.ad.userMapping.middlenameAttr>
<security.ad.userMapping.lastnameAttr>sn</security.ad.userMapping.lastnameAttr>
<security.ad.userMapping.usernameAttr>cn</security.ad.userMapping.usernameAttr>
<security.ad.userImport.loginAttr>sAMAccountName</security.ad.userImport.loginAttr>
<security.ad.userImport.usernameAttr>cn</security.ad.userImport.usernameAttr>
<security.cas.loginUrl></security.cas.loginUrl>
<security.cas.callbackUrl></security.cas.callbackUrl>
<security.cas.serverUrl></security.cas.serverUrl>
<security.cas.cassvcs></security.cas.cassvcs>
<security.cas.casticket>casticket</security.cas.casticket>
<security.db.datasource.schema>${datasource.ohdsi.schema}</security.db.datasource.schema>
<security.db.datasource.url>${datasource.url}</security.db.datasource.url>
<security.db.datasource.driverClassName>${datasource.driverClassName}</security.db.datasource.driverClassName>
<security.db.datasource.username>${datasource.username}</security.db.datasource.username>
<security.db.datasource.password>${datasource.password}</security.db.datasource.password>
<security.db.datasource.authenticationQuery>select password from ${security.db.datasource.schema}.users where lower(email) = lower(?)</security.db.datasource.authenticationQuery>
<use.single.connect.datasource.for.testing>true</use.single.connect.datasource.for.testing>
<security.googleIap.cloudProjectId></security.googleIap.cloudProjectId>
<security.googleIap.backendServiceId></security.googleIap.backendServiceId>
<security.google.accessToken.enabled>false</security.google.accessToken.enabled>
<security.cors.enabled>true</security.cors.enabled>
<security.maxLoginAttempts>3</security.maxLoginAttempts>
<security.duration.initial>10</security.duration.initial>
<security.duration.increment>10</security.duration.increment>
<security.saml.enabled>false</security.saml.enabled>
<security.saml.entityId></security.saml.entityId>
<security.saml.idpMetadataLocation></security.saml.idpMetadataLocation>
<security.saml.keyManager.keyStoreFile></security.saml.keyManager.keyStoreFile>
<security.saml.keyManager.storePassword></security.saml.keyManager.storePassword>
<security.saml.keyManager.defaultKey></security.saml.keyManager.defaultKey>
<security.saml.keyManager.passwords.arachnenetwork></security.saml.keyManager.passwords.arachnenetwork>
<security.saml.metadataLocation></security.saml.metadataLocation>
<security.saml.callbackUrl></security.saml.callbackUrl>
<security.saml.sloUrl></security.saml.sloUrl>
<security.saml.maximumAuthenticationLifetime>60</security.saml.maximumAuthenticationLifetime>
<security.auth.windows.enabled>true</security.auth.windows.enabled>
<security.auth.kerberos.enabled>true</security.auth.kerberos.enabled>
<security.auth.openid.enabled>true</security.auth.openid.enabled>
<security.auth.facebook.enabled>true</security.auth.facebook.enabled>
<security.auth.github.enabled>true</security.auth.github.enabled>
<security.auth.google.enabled>true</security.auth.google.enabled>
<security.auth.jdbc.enabled>true</security.auth.jdbc.enabled>
<security.auth.ldap.enabled>true</security.auth.ldap.enabled>
<security.auth.ad.enabled>true</security.auth.ad.enabled>
<security.auth.cas.enabled>true</security.auth.cas.enabled>
<spring.datasource.hikari.connection-test-query>SELECT 1</spring.datasource.hikari.connection-test-query>
<spring.datasource.hikari.connection-test-query-timeout>2000</spring.datasource.hikari.connection-test-query-timeout>
<spring.datasource.hikari.maximum-pool-size>5</spring.datasource.hikari.maximum-pool-size>
<spring.datasource.hikari.minimum-idle>1</spring.datasource.hikari.minimum-idle>
<spring.datasource.hikari.connection-timeout>5000</spring.datasource.hikari.connection-timeout>
<spring.datasource.hikari.register-mbeans>true</spring.datasource.hikari.register-mbeans>
<spring.datasource.hikari.mbean-name>authDataSource</spring.datasource.hikari.mbean-name>
<!-- If defaultGlobalReadPermissions is set to true (default), then all users can see every artifact. -->
<!-- If it is set to false, WebAPI will filter out the artifacts that a user does not explicitly have -->
<!-- read permissions to -->
<security.defaultGlobalReadPermissions>true</security.defaultGlobalReadPermissions>
<!-- EMBEDDED SERVER CONFIGURATION (ServerProperties) -->
<server.port>8080</server.port>
<server.ssl.key-store></server.ssl.key-store>
<server.ssl.key-store-password></server.ssl.key-store-password>
<server.ssl.key-password></server.ssl.key-password>
<server.servlet.context-path>/WebAPI</server.servlet.context-path>
<arachne.version>1.17.4</arachne.version>
<jersey-media-multipart.version>2.25.1</jersey-media-multipart.version>
<execution.invalidation.period>600000</execution.invalidation.period>
<execution.invalidation.maxage.hours>12</execution.invalidation.maxage.hours>
<execution.status.period>10000</execution.status.period>
<executionengine.url>https://localhost:8888/api/v1/analyze</executionengine.url>
<executionengine.token>Basic YWRtaW5Ab2R5c3NldXNpbmMuY29tOnBhc3N3b3Jk</executionengine.token>
<executionengine.resultExclusions></executionengine.resultExclusions>
<executionengine.updateStatusCallback>http://localhost:8080/WebAPI/executionservice/callbacks/submission/{id}/status/update/{password}</executionengine.updateStatusCallback>
<executionengine.resultCallback>http://localhost:8080/WebAPI/executionservice/callbacks/submission/{id}/result/{password}</executionengine.resultCallback>
<analysis.result.zipVolumeSizeMb>100</analysis.result.zipVolumeSizeMb>
<!-- PASSWORD ENCRYPTION -->
<jasypt.encryptor.enabled>false</jasypt.encryptor.enabled>
<jasypt.encryptor.password></jasypt.encryptor.password>
<jasypt.encryptor.algorithm>PBEWithMD5AndDES</jasypt.encryptor.algorithm>
<!-- ORGANIZATION SETTINGS -->
<organization.name>OHDSI</organization.name>
<!-- JdbcTemplate -->
<jdbc.suppressInvalidApiException>true</jdbc.suppressInvalidApiException>
<!-- Logging -->
<spring.jpa.show-sql>false</spring.jpa.show-sql>
<spring.jpa.properties.hibernate.generate_statistics>false</spring.jpa.properties.hibernate.generate_statistics>
<spring.jpa.properties.hibernate.jdbc.batch_size>200</spring.jpa.properties.hibernate.jdbc.batch_size>
<spring.jpa.properties.hibernate.order_inserts>true</spring.jpa.properties.hibernate.order_inserts>
<logging.level.root>info</logging.level.root>
<logging.level.org.ohdsi>info</logging.level.org.ohdsi>
<logging.level.org.springframework.orm>info</logging.level.org.springframework.orm>
<logging.level.org.springframework.jdbc>info</logging.level.org.springframework.jdbc>
<logging.level.org.springframework.web>info</logging.level.org.springframework.web>
<logging.level.org.hibernate>info</logging.level.org.hibernate>
<logging.level.org.apache.shiro>warn</logging.level.org.apache.shiro>
<!-- Spring Cache properties -->
<spring.cache.type>jcache</spring.cache.type>
<!-- Spring Batch -->
<spring.batch.taskExecutor.corePoolSize>10</spring.batch.taskExecutor.corePoolSize>
<spring.batch.taskExecutor.maxPoolSize>20</spring.batch.taskExecutor.maxPoolSize>
<spring.batch.taskExecutor.queueCapacity>2147483647</spring.batch.taskExecutor.queueCapacity>
<spring.batch.taskExecutor.threadGroupName></spring.batch.taskExecutor.threadGroupName>
<spring.batch.taskExecutor.threadNamePrefix></spring.batch.taskExecutor.threadNamePrefix>
<!-- Sensitive Info settings -->
<sensitiveinfo.admin.role>admin</sensitiveinfo.admin.role>
<sensitiveinfo.moderator.role>Moderator</sensitiveinfo.moderator.role>
<!-- Use "-" for files without extension, "*" for all files, extension must not include a leading dot. Use comma to separate values.
In case of "*" other values will be ignored -->
<sensitiveinfo.analysis.extensions>txt</sensitiveinfo.analysis.extensions>
<!-- Cache Config -->
<cdm.result.cache.warming.enable>true</cdm.result.cache.warming.enable>
<cdm.cache.achilles.warming.enable>false</cdm.cache.achilles.warming.enable>
<!-- Enable or disable warming cdm cache by cron -->
<cdm.cache.cron.warming.enable>false</cdm.cache.cron.warming.enable>
<!-- cron expression to warm cdm cache -->
<!-- cron expression format (asterisk means 'every' - '*' in seconds means 'every second') -->
<!-- default value is '0 0 2 * * *' which means "at 2am every day" -->
<!-- ┌───────second (0-59)-->
<!-- │ ┌────── minute (0-59)-->
<!-- │ │ ┌────── hour (0-23)-->
<!-- │ │ │ ┌────── day of the month (1-31)-->
<!-- │ │ │ │ ┌────── month (1-12) -->
<!-- │ │ │ │ │ ┌────── day of the week (0-7)-->
<!-- * * * * * *-->
<cdm.cache.cron.expression>0 0 2 * * *</cdm.cache.cron.expression>
<cache.generation.invalidAfterDays>30</cache.generation.invalidAfterDays>
<cache.generation.cleanupInterval>3600000</cache.generation.cleanupInterval>
<cache.generation.useAsync>false</cache.generation.useAsync>
<!-- Number of spring jobs that will be used for caching -->
<cache.jobs.count>3</cache.jobs.count>
<!-- Achilles cache -->
<cache.achilles.usePersonCount>true</cache.achilles.usePersonCount>
<cache.webapi.enabled>true</cache.webapi.enabled>
<!-- Build info -->
<buildinfo.atlas.milestone.id>47</buildinfo.atlas.milestone.id>
<buildinfo.webapi.milestone.id>49</buildinfo.webapi.milestone.id>
<buildinfo.atlas.release.tag>*</buildinfo.atlas.release.tag>
<buildinfo.webapi.release.tag>*</buildinfo.webapi.release.tag>
<gis.enabled>false</gis.enabled>
<!-- I18n -->
<i18n.enabled>true</i18n.enabled>
<i18n.defaultLocale>en</i18n.defaultLocale>
<!-- Tags -->
<tag.enabled>true</tag.enabled>
<!-- Period between refreshes of materialized view with statistics -->
<!-- 10 minutes by default -->
<tag.refreshStat.period>600000</tag.refreshStat.period>
<!-- Versioning -->
<versioning.maxAttempt>10</versioning.maxAttempt>
<audit.trail.enabled>false</audit.trail.enabled>
<audit.trail.log.file>/tmp/atlas/audit/audit.log</audit.trail.log.file>
<audit.trail.log.file.pattern>/tmp/atlas/audit/audit-%d{yyyy-MM-dd}-%i.log</audit.trail.log.file.pattern>
<audit.trail.log.extraFile>/tmp/atlas/audit/audit-extra.log</audit.trail.log.extraFile>
<!-- Shiny -->
<shiny.enabled>false</shiny.enabled>
</properties>
<build>
<finalName>WebAPI</finalName>
<sourceDirectory>${basedir}/src/main/java</sourceDirectory>
<testSourceDirectory>${basedir}/src/test/java</testSourceDirectory>
<outputDirectory>${basedir}/target/classes</outputDirectory>
<testOutputDirectory>${basedir}/target/test-classes</testOutputDirectory>
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
<includes>
<include>**/*.properties</include>
<include>log4j.xml</include>
</includes>
</resource>
<resource>
<directory>src/main/resources</directory>
<filtering>false</filtering>
<includes>
<include>**/*.*</include>
</includes>
<excludes>
<exclude>**/*.properties</exclude>
<exclude>log4j.xml</exclude>
</excludes>
</resource>
</resources>
<testResources>
<testResource>
<directory>src/test/resources</directory>
<filtering>true</filtering>
<includes>
<include>**/*.properties</include>
</includes>
</testResource>
<testResource>
<directory>src/test/resources</directory>
<filtering>false</filtering>
<includes>
<include>**/*.*</include>
</includes>
<excludes>
<exclude>**/*.properties</exclude>
</excludes>
</testResource>
</testResources>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.5.0</version>
</plugin>
<plugin>
<groupId>pl.project13.maven</groupId>
<artifactId>git-commit-id-plugin</artifactId>
<version>4.0.0</version>
<executions>
<execution>
<phase>validate</phase>
<goals>
<goal>revision</goal>
</goals>
</execution>
</executions>
<configuration>
<generateGitPropertiesFile>false</generateGitPropertiesFile>
<failOnNoGitDirectory>false</failOnNoGitDirectory>
<!-- only include properties to speed up plugin -->
<!-- ref: https://github.com/git-commit-id/git-commit-id-maven-plugin/issues/462 -->
<includeOnlyProperties>
<includeOnlyProperty>git.branch</includeOnlyProperty>
<includeOnlyProperty>git.commit.id.abbrev</includeOnlyProperty>
</includeOnlyProperties>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.gmaven</groupId>
<artifactId>gmaven-plugin</artifactId>
<version>1.5</version>
<executions>
<execution>
<id>add-git-branch-info</id>
<phase>generate-resources</phase>
<goals>
<goal>execute</goal>
</goals>
<configuration>
<source>
if (project.properties.getProperty("git.branch") == null) project.properties.setProperty("git.branch", "*");
if (project.properties.getProperty("git.commit.id.abbrev") == null) project.properties.setProperty("git.commit.id.abbrev", "*");
</source>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<version>${spring.boot.version}</version>
<!-- executable-war via 'java -jar WebAPI-exec.war' currently fails with Jersey FileNotFound exception. TODO -->
<configuration>
<!-- Since we filter properties files via Maven, do not add resources. -->
<addResources>false</addResources>
<mainClass>org.ohdsi.webapi.WebApi</mainClass>
<additionalProperties>
<git.branch>${git.branch}</git.branch>
<git.commit.id>${git.commit.id.abbrev}</git.commit.id>
<atlas.milestone.id>${buildinfo.atlas.milestone.id}</atlas.milestone.id>
<webapi.milestone.id>${buildinfo.webapi.milestone.id}</webapi.milestone.id>
<atlas.release.tag>${buildinfo.atlas.release.tag}</atlas.release.tag>
<webapi.release.tag>${buildinfo.webapi.release.tag}</webapi.release.tag>
</additionalProperties>
</configuration>
<executions>
<execution>
<goals>
<goal>build-info</goal>
<goal>repackage</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.22.2</version>
<configuration>
<skipTests>${skipUnitTests}</skipTests>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.10.1</version>
<inherited>true</inherited>
<configuration>
<compilerArgs>
<!-- Prevents recompilation due to missing package-info.class, see MCOMPILER-205 -->
<arg>-Xpkginfo:always</arg>
</compilerArgs>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>3.3.1</version>
<configuration>
<failOnMissingWebXml>false</failOnMissingWebXml>
<attachClasses>true</attachClasses>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>2.22.2</version>
<configuration>
<skipITs>${skipITtests}</skipITs>
</configuration>
<executions>
<execution>
<phase>test</phase>
<goals>
<goal>integration-test</goal>
</goals>
<configuration>
<includes>
<include>**/*IT.java</include>
</includes>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>com.qmino</groupId>
<artifactId>miredot-plugin</artifactId>
<version>2.4.0</version>
<executions>
<execution>
<phase>${miredot.phase}</phase>
<goals>
<goal>restdoc</goal>
</goals>
</execution>
</executions>
<configuration>
<licence>cHJvamVjdHxvcmcub2hkc2kuV2ViQVBJfDIwMzAtMDEtMDF8ZmFsc2V8LTEjTUN3Q0ZDOEFFWEdzU0lISUJiMzBBWC9WazlGcmdPME1BaFI4MVM5bkViQUpXN0tiWE9zR1NpRFlPam5zaXc9PQ==</licence>
<restModel>
<httpStatusCodes>
<httpStatusCode>
<httpCode>200</httpCode>
<document>always</document>
<defaultMessage>The service call has completed successfully.</defaultMessage>
</httpStatusCode>
<httpStatusCode>
<httpCode>401</httpCode>
<document>Authorization Exception</document>
<defaultMessage>The user is not authorized to use this service.</defaultMessage>
</httpStatusCode>
<httpStatusCode>
<httpCode>412</httpCode>
<document>put,post</document>
<defaultMessage>Invalid JSON/XML input.</defaultMessage>
</httpStatusCode>
<httpStatusCode>
<httpCode>500</httpCode>
<document>always</document>
<defaultMessage>The service call has not succeeded.</defaultMessage>
</httpStatusCode>
</httpStatusCodes>
</restModel>
<output>
<html>
<intro>api.html</intro>
</html>
</output>
</configuration>
</plugin>
</plugins>
</build>
<repositories>
<repository>
<id>ohdsi</id>
<name>repo.ohdsi.org</name>
<url>https://repo.ohdsi.org/nexus/content/groups/public</url>
</repository>
</repositories>
<pluginRepositories>
<pluginRepository>
<id>central</id>
<url>https://repo.maven.apache.org/maven2</url>
</pluginRepository>
<pluginRepository>
<id>ohdsi</id>
<name>repo.ohdsi.org</name>
<url>https://repo.ohdsi.org/nexus/content/groups/public</url>
</pluginRepository>
</pluginRepositories>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
<version>${log4j2.version}</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
<version>${log4j2.version}</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-web</artifactId>
<version>${log4j2.version}</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<version>${log4j2.version}</version>
</dependency>
<dependency>
<!-- Import dependency management from Spring Boot -->
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-dependencies</artifactId>
<version>${spring.boot.version}</version>
<type>pom</type>
<scope>import</scope>
</dependency>
<dependency>
<groupId>com.amazon.redshift</groupId>
<artifactId>redshift-jdbc42-no-awssdk</artifactId>
<version>1.2.10.1009</version>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>${jackson.version}</version>
<exclusions>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
</exclusion>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
<version>${jackson.version}</version>
</dependency>
<!-- <dependency> <groupId>org.springframework.boot</groupId> <artifactId>spring-boot-starter-actuator</artifactId>
<version>${spring.boot.version}</version> </dependency> -->
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter</artifactId>
<exclusions>
<exclusion>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-logging</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- It is overriding a transitive dependency from the dependency above -->
<!-- After migrating to Spring Boot 2.x we should get rid of it -->
<dependency>
<groupId>org.yaml</groupId>
<artifactId>snakeyaml</artifactId>
<version>2.0</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
<exclusions>
<exclusion>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-validator</artifactId>
</exclusion>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-log4j2</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-tomcat</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-batch</artifactId>
</dependency>
<!-- We are intentionally overriding the Tomcat version from Spring Boot 1.5.22.RELEASE -->
<!-- and assuming tomcat-jdbc.jar will be in the Tomcat installation folder (\apache-tomcat-8.5.xxx\lib). -->
<!-- WebAPI.war.original should not contain overridden libraries -->
<dependency>
<groupId>org.apache.tomcat.embed</groupId>
<artifactId>tomcat-embed-el</artifactId>
<version>${tomcat.embed.version}</version>
</dependency>
<!-- It is overriding a transitive dependency from the dependency above -->
<!-- After migrating to Spring Boot 2.x we should get rid of it -->
<dependency>
<groupId>com.thoughtworks.xstream</groupId>
<artifactId>xstream</artifactId>
<version>1.4.19</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-jdbc</artifactId>
</dependency>
<dependency>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-jdbc</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-juli</artifactId>
<version>${tomcat.embed.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-jersey</artifactId>
<exclusions>
<exclusion>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-validator</artifactId>
</exclusion>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</exclusion>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
</exclusion>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-jpa</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-cache</artifactId>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>${hibernate.version}</version>
<exclusions>
<exclusion>
<groupId>org.dom4j</groupId>
<artifactId>dom4j</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-validator</artifactId>
<version>5.4.2.Final</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
<version>${hibernate.version}</version>
<exclusions>
<exclusion>
<groupId>org.dom4j</groupId>
<artifactId>dom4j</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<version>3.1.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>javax.cache</groupId>
<artifactId>cache-api</artifactId>
<version>1.1.1</version>
</dependency> <dependency>
<groupId>org.ohdsi.sql</groupId>
<artifactId>SqlRender</artifactId>
<version>${SqlRender.version}</version>
</dependency>
<dependency>
<groupId>commons-dbutils</groupId>
<artifactId>commons-dbutils</artifactId>
<version>1.6</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.7</version>
</dependency>
<dependency>
<groupId>com.sun.xml.security</groupId>
<artifactId>xml-security-impl</artifactId>
<version>1.0</version>
</dependency>
<!-- It is overriding a transitive dependency from the dependency above -->
<!-- After migrating to Spring Boot 2.x we should get rid of it -->
<!-- It is currently inefficient as com.nimbusds:nimbus-jose-jwt has hard bounds [1.3.1,2.3] -->
<dependency>
<groupId>net.minidev</groupId>
<artifactId>json-smart</artifactId>
<version>2.4.9</version>
</dependency>
<dependency>
<groupId>net.minidev</groupId>
<artifactId>asm</artifactId>
<version>1.0.2</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.12.0</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
<version>1.10.0</version>
</dependency>
<dependency>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-core</artifactId>
<version>${flyway.version}</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>4.5.13</version>
</dependency>
<dependency>
<groupId>org.springframework.batch</groupId>
<artifactId>spring-batch-admin-manager</artifactId>
<version>2.0.0.M1</version>
<exclusions>
<exclusion>
<artifactId>freemarker</artifactId>
<groupId>org.freemarker</groupId>
</exclusion>
<exclusion>
<artifactId>commons-dbcp</artifactId>
<groupId>commons-dbcp</groupId>
</exclusion>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</exclusion>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
</exclusion>
<exclusion>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- overriding commons-fileupload version from the plug-in above -->
<dependency>
<groupId>commons-fileupload</groupId>
<artifactId>commons-fileupload</artifactId>
<version>${commons-fileupload.version}</version>
</dependency>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>${postgresql.version}</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>com.microsoft.sqlserver</groupId>
<artifactId>mssql-jdbc</artifactId>
<version>10.2.1.jre8</version>
</dependency>
<dependency>
<groupId>com.microsoft.azure</groupId>
<artifactId>msal4j</artifactId>
<version>1.9.0</version>
</dependency>
<dependency>
<groupId>com.opencsv</groupId>
<artifactId>opencsv</artifactId>
<version>3.7</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>org.eclipse.collections</groupId>
<artifactId>eclipse-collections-api</artifactId>
<version>8.0.0</version>
</dependency>
<dependency>
<groupId>org.eclipse.collections</groupId>
<artifactId>eclipse-collections</artifactId>
<version>8.0.0</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-collections4</artifactId>
<version>4.1</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>org.apache.shiro</groupId>
<artifactId>shiro-core</artifactId>
<version>${shiro.version}</version>
</dependency>
<dependency>
<groupId>org.apache.shiro</groupId>
<artifactId>shiro-web</artifactId>
<version>${shiro.version}</version>
</dependency>
<dependency>
<groupId>org.apache.shiro</groupId>
<artifactId>shiro-spring</artifactId>
<version>${shiro.version}</version>
</dependency>
<dependency>
<groupId>com.github.waffle</groupId>
<artifactId>waffle-shiro</artifactId>
<version>2.2.1</version>
</dependency>
<dependency>
<groupId>com.github.waffle</groupId>
<artifactId>waffle-jna</artifactId>
<version>${waffle.version}</version>
<exclusions>
<exclusion>
<groupId>net.java.dev.jna</groupId>
<artifactId>jna</artifactId>
</exclusion>
<exclusion>
<groupId>net.java.dev.jna</groupId>
<artifactId>jna-platform</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>net.java.dev.jna</groupId>
<artifactId>jna</artifactId>
<version>${jna.version}</version>
</dependency>
<dependency>
<groupId>net.java.dev.jna</groupId>
<artifactId>jna-platform</artifactId>
<version>${jna.version}</version>
</dependency>
<dependency>
<groupId>io.jsonwebtoken</groupId>
<artifactId>jjwt</artifactId>
<version>0.9.1</version>
<exclusions>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>io.buji</groupId>
<artifactId>buji-pac4j</artifactId>
<version>5.0.1</version>
</dependency>
<dependency>
<groupId>org.pac4j</groupId>
<artifactId>pac4j-oauth</artifactId>
<version>${pac4j.version}</version>
<exclusions>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.pac4j</groupId>
<artifactId>pac4j-oidc</artifactId>
<version>${pac4j.version}</version>
<exclusions>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.pac4j</groupId>
<artifactId>pac4j-http</artifactId>
<version>${pac4j.version}</version>
<exclusions>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.pac4j</groupId>
<artifactId>pac4j-saml-opensamlv3</artifactId>
<version>${pac4j.version}</version>
</dependency>
<dependency>
<groupId>org.ohdsi</groupId>
<artifactId>circe</artifactId>
<version>${circe.version}</version>
<exclusions>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</exclusion>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>