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arteymixarteymix
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Merge branch 'hotfix-1.1.24'
2 parents 60bf4d4 + 60b915b commit 5b04cc9

35 files changed

Lines changed: 2150 additions & 2118 deletions

‎.editorconfig‎

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[pom.xml]
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indent_style = tab

‎pom.xml‎

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@@ -5,7 +5,7 @@
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<name>baseCode</name>
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<groupId>baseCode</groupId>
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<artifactId>baseCode</artifactId>
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<version>1.1.23</version>
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<version>1.1.24</version>
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<inceptionYear>2003</inceptionYear>
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<description>
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<![CDATA[Data structures, math and statistics tools, and utilities that are often needed across projects.]]>
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</developer>
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</developers>
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<dependencies>
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<!-- Excel utilities (optional) -->
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<dependency>
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<groupId>org.apache.poi</groupId>
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<artifactId>poi</artifactId>
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<version>5.2.5</version>
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<version>5.4.1</version>
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<optional>true</optional>
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</dependency>
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<dependency>
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<groupId>colt</groupId>
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<artifactId>colt</artifactId>
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<dependency>
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<groupId>commons-net</groupId>
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<artifactId>commons-net</artifactId>
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<version>3.10.0</version>
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<version>3.11.1</version>
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</dependency>
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<dependency>
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<groupId>org.apache.commons</groupId>
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-configuration2</artifactId>
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<version>2.8.0</version>
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<version>2.12.0</version>
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<exclusions>
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<exclusion>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-lang3</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-lang3</artifactId>
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<!-- 3.15.0 uses a secure random which is extremely slow, see #1194 in Gemma for details -->
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<version>3.14.0</version>
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</dependency>
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<dependency>
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<groupId>commons-io</groupId>
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<artifactId>commons-io</artifactId>
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<version>2.16.1</version>
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<version>2.18.0</version>
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</dependency>
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-collections4</artifactId>
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<version>4.4</version>
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</dependency>
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<dependency>
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<groupId>commons-codec</groupId>
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<artifactId>commons-codec</artifactId>
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<version>1.18.0</version>
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<scope>runtime</scope>
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</dependency>
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<dependency>
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<groupId>commons-logging</groupId>
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<artifactId>commons-logging</artifactId>
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<version>1.3.5</version>
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<scope>runtime</scope>
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</dependency>
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-csv</artifactId>
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<version>1.14.0</version>
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</dependency>
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<!-- HTTP client -->
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<!-- HTTP client (optional, used for AnnotatorClient) -->
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<dependency>
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<groupId>org.apache.httpcomponents</groupId>
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<artifactId>httpcore</artifactId>
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<version>4.4.16</version>
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<optional>true</optional>
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</dependency>
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<dependency>
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<groupId>org.apache.httpcomponents</groupId>
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<artifactId>httpclient</artifactId>
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<version>4.5.14</version>
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<optional>true</optional>
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<exclusions>
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<exclusion>
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<groupId>commons-logging</groupId>
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<artifactId>commons-logging</artifactId>
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</exclusion>
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<exclusion>
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<groupId>commons-codec</groupId>
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<artifactId>commons-codec</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<!-- R engine -->
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<groupId>com.googlecode.matrix-toolkits-java</groupId>
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<artifactId>mtj</artifactId>
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<version>1.0.4</version>
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<exclusions>
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<exclusion>
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<groupId>com.github.fommil.netlib</groupId>
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<artifactId>core</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>com.github.fommil.netlib</groupId>
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<artifactId>core</artifactId>
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<version>1.1.2</version>
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<scope>runtime</scope>
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</dependency>
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<!-- Logging -->
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<groupId>org.slf4j</groupId>
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<artifactId>slf4j-log4j12</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.slf4j</groupId>
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<artifactId>slf4j-api</artifactId>
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</exclusion>
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<exclusion>
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<groupId>xerces</groupId>
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<artifactId>xercesImpl</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>org.apache.jena</groupId>
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<artifactId>jena-tdb</artifactId>
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<version>1.1.2</version>
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<exclusions>
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<exclusion>
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<groupId>org.slf4j</groupId>
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<artifactId>slf4j-api</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.slf4j</groupId>
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<artifactId>slf4j-log4j12</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.slf4j</groupId>
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<artifactId>jcl-over-slf4j</artifactId>
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</exclusion>
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<exclusion>
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<groupId>log4j</groupId>
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<artifactId>log4j</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-lang3</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.apache.thrift</groupId>
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<artifactId>libthrift</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.apache.httpcomponents</groupId>
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<artifactId>httpclient</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.apache.httpcomponents</groupId>
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<artifactId>httpclient-cache</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-csv</artifactId>
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</exclusion>
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<exclusion>
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<artifactId>jsonld-java</artifactId>
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<groupId>com.github.jsonld-java</groupId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>org.jfree</groupId>
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<artifactId>jfreechart</artifactId>
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<version>1.5.4</version>
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<version>1.5.5</version>
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</dependency>
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<!-- xml-apis is dependent on jena -->
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<dependency>
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<artifactId>xercesImpl</artifactId>
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<version>2.12.2</version>
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</dependency>
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<dependency>
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<groupId>com.opencsv</groupId>
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<artifactId>opencsv</artifactId>
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<version>5.9</version>
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<exclusions>
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<exclusion>
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<groupId>commons-beanutils</groupId>
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<artifactId>commons-beanutils</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<!-- Development tools -->
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<dependency>
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<dependency>
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<groupId>commons-beanutils</groupId>
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<artifactId>commons-beanutils</artifactId>
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<version>1.9.4</version>
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<version>1.10.1</version>
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<scope>test</scope>
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<exclusions>
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<exclusion>
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<groupId>commons-logging</groupId>
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<artifactId>commons-logging</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>junit</groupId>
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<dependency>
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<groupId>org.mockito</groupId>
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<artifactId>mockito-core</artifactId>
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<version>4.11.0</version>
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<version>5.15.2</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.assertj</groupId>
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<artifactId>assertj-core</artifactId>
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<version>3.25.3</version>
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<version>3.27.3</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-api</artifactId>
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<version>2.23.1</version>
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<version>2.24.3</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-core</artifactId>
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<version>2.23.1</version>
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<version>2.24.3</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-slf4j-impl</artifactId>
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<version>2.23.1</version>
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<version>2.24.3</version>
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<scope>test</scope>
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</dependency>
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</dependencies>
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<requireMavenVersion>
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<version>[3.0.5,)</version>
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</requireMavenVersion>
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<requireJavaVersion>
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<version>[1.8,)</version>
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</requireJavaVersion>
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<dependencyConvergence/>
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</rules>
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</configuration>
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</execution>
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<repository>
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<id>pavlab</id>
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<name>PavLab</name>
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<url>scpexe://frink.msl.ubc.ca/space/maven2</url>
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<url>scpexe://${pavlab.server}${pavlab.repoDir}</url>
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</repository>
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<site>
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<id>pavlab</id>
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<name>PavLab</name>
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<url>scpexe://frink.msl.ubc.ca/space/web/maven-sites/${project.groupId}/${project.artifactId}-${project.version}</url>
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<url>scpexe://${pavlab.server}${pavlab.siteDir}/${project.groupId}/${project.artifactId}-${project.version}</url>
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</site>
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</distributionManagement>
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<pluginRepositories>
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<repository>
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<id>pavlab</id>
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<name>PavLab</name>
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<url>file:///space/maven2</url>
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<url>file://${pavlab.repoDir}}</url>
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</repository>
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<site>
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<id>pavlab</id>
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<name>PavLab</name>
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<url>file:///space/web/maven-sites/${project.groupId}/${project.artifactId}-${project.version}</url>
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<url>file://${pavlab.siteDir}/${project.groupId}/${project.artifactId}-${project.version}</url>
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</site>
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</distributionManagement>
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</profile>
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<profile>
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<id>depcheck</id>
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<build>
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<plugins>
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<plugin>
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<groupId>org.codehaus.mojo</groupId>
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<artifactId>versions-maven-plugin</artifactId>
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<version>2.17.1</version>
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<configuration>
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<allowMajorUpdates>false</allowMajorUpdates>
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<ignoredVersions>.*-a.*,.*-b.*,.*-M.*</ignoredVersions>
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</configuration>
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</plugin>
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</plugins>
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</build>
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</profile>
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<profile>
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<id>java9</id>
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<activation>
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<jdk>(9,</jdk>
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</activation>
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<properties>
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<maven.compiler.release>8</maven.compiler.release>
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</properties>
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</profile>
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</profiles>
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<properties>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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<maven.compiler.source>8</maven.compiler.source>
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<maven.compiler.target>8</maven.compiler.target>
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<pavlab.server>frink.pavlab.msl.ubc.ca</pavlab.server>
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<pavlab.repoDir>/space/maven2</pavlab.repoDir>
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<pavlab.siteDir>/space/web/maven-sites</pavlab.siteDir>
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<lucene.version>3.6.2</lucene.version>
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</properties>
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</project>

‎src/basecode.properties‎

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load.humanPhenotypeOntology=false
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load.obiOntology=false
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load.seqOntology=false
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load.medicOntology=false
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load.nifstdOntology=false
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load.experimentalFactorOntology=false
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load.uberonOntology=false

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