Skip to content
This repository has been archived by the owner on Mar 13, 2023. It is now read-only.

Commit

Permalink
Merge branch 'release-staging/1.7.0' into release
Browse files Browse the repository at this point in the history
  • Loading branch information
@benknoll-umn
benknoll-umn committed Jul 24, 2017
2 parents 9987d94 + a9d786f commit d9c7e14
Show file tree
Hide file tree
Showing 15 changed files with 1,057 additions and 1,274 deletions.
4 changes: 3 additions & 1 deletion README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,9 @@ The system is being developed by our biomedical NLP/IE program at the University
This is a collaborative project that aims to serve biomedical and clinical researchers, allowing for customization
with different texts.

This project is a collection of GPL-licensed extensions and utilities for the BioMedICUS system.
This project is a collection of GPL-licensed extensions and utilities for the BioMedICUS system.
Any extensions or use of the BioMedICUS project with this extension installed must be compliant with
the GPLv3 license.


Wiki
Expand Down
233 changes: 116 additions & 117 deletions pom.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,128 +16,127 @@
~ along with this program. If not, see <http://www.gnu.org/licenses/>.
-->

<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/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>edu.umn.biomedicus</groupId>
<artifactId>biomedicus-gpl</artifactId>
<packaging>jar</packaging>
<version>1.6.0</version>
<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns="http://maven.apache.org/POM/4.0.0"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>edu.umn.biomedicus</groupId>
<artifactId>biomedicus-gpl</artifactId>
<packaging>jar</packaging>
<version>1.7.0</version>

<name>biomedicus-gpl</name>
<description>BioMedICUS Annotation System - GPL Extensions</description>
<name>biomedicus-gpl</name>
<description>BioMedICUS Annotation System - GPL Extensions</description>

<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<biomedicus.version>1.6.0</biomedicus.version>
</properties>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
</properties>

<dependencies>
<dependency>
<groupId>edu.umn.biomedicus</groupId>
<artifactId>biomedicus-core</artifactId>
<version>${biomedicus.version}</version>
</dependency>
<dependency>
<groupId>edu.umn.biomedicus</groupId>
<artifactId>biomedicus-uima</artifactId>
<version>${biomedicus.version}</version>
</dependency>
<dependency>
<groupId>edu.stanford.nlp</groupId>
<artifactId>stanford-corenlp</artifactId>
<version>3.6.0</version>
</dependency>
<dependency>
<groupId>nz.ac.waikato.cms.weka</groupId>
<artifactId>weka-stable</artifactId>
<version>3.8.0</version>
</dependency>
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
<version>3.0.0</version>
<optional>true</optional>
</dependency>
</dependencies>
<dependencies>
<dependency>
<groupId>edu.umn.biomedicus</groupId>
<artifactId>biomedicus-core</artifactId>
<version>1.7.0</version>
</dependency>
<dependency>
<groupId>edu.umn.biomedicus</groupId>
<artifactId>biomedicus-uima</artifactId>
<version>1.7.0</version>
</dependency>
<dependency>
<groupId>edu.stanford.nlp</groupId>
<artifactId>stanford-corenlp</artifactId>
<version>3.6.0</version>
</dependency>
<dependency>
<groupId>nz.ac.waikato.cms.weka</groupId>
<artifactId>weka-stable</artifactId>
<version>3.8.0</version>
</dependency>
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
<version>3.0.0</version>
<optional>true</optional>
</dependency>
</dependencies>


<build>
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
<includes>
<include>**/*.xml</include>
</includes>
</resource>
<resource>
<directory>src/main/resources</directory>
<filtering>false</filtering>
<excludes>
<exclude>**/*.xml</exclude>
</excludes>
</resource>
</resources>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.5.2</version>
<executions>
<execution>
<id>make-bundles</id>
<goals>
<goal>single</goal>
</goals>
<phase>package</phase>
<configuration>
<descriptors>
<descriptor>src/assembly/descriptor.xml</descriptor>
</descriptors>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
<pluginManagement>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
<includes>
<include>**/*.xml</include>
</includes>
</resource>
<resource>
<directory>src/main/resources</directory>
<filtering>false</filtering>
<excludes>
<exclude>**/*.xml</exclude>
</excludes>
</resource>
</resources>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.5.2</version>
<executions>
<execution>
<id>make-bundles</id>
<goals>
<goal>single</goal>
</goals>
<phase>package</phase>
<configuration>
<descriptors>
<descriptor>src/assembly/descriptor.xml</descriptor>
</descriptors>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
<pluginManagement>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>

<organization>
<name>University of Minnesota Institute for Health Informatics NLP/IE Program</name>
<url>http://www.bmhi.umn.edu/ihi/research/nlpie/index.htm</url>
</organization>
<developers>
<developer>
<name>Ben Knoll</name>
<email>benknoll@umn.edu</email>
<organization>NLP/IE Group at the University of Minnesota Institute for Health Informatics
</organization>
<organizationUrl>http://www.bmhi.umn.edu/ihi/research/nlpie/index.htm</organizationUrl>
</developer>
</developers>
<licenses>
<license>
<name>GNU General Public License, Version 3.0 (GPLv3)</name>
<url>https://www.gnu.org/licenses/gpl-3.0.en.html</url>
<distribution>repo</distribution>
</license>
</licenses>
<scm>
<url>https://github.com/NLPIE/BioMedICUS</url>
<connection>scm:git:https://github.com/NLPIE/BioMedICUS.git</connection>
<developerConnection>scm:git:https://github.com/NLPIE/BioMedICUS.git</developerConnection>
</scm>
<organization>
<name>University of Minnesota Institute for Health Informatics NLP/IE Program</name>
<url>http://www.bmhi.umn.edu/ihi/research/nlpie/index.htm</url>
</organization>
<developers>
<developer>
<name>Ben Knoll</name>
<email>benknoll@umn.edu</email>
<organization>NLP/IE Group at the University of Minnesota Institute for Health Informatics
</organization>
<organizationUrl>http://www.bmhi.umn.edu/ihi/research/nlpie/index.htm</organizationUrl>
</developer>
</developers>
<licenses>
<license>
<name>GNU General Public License, Version 3.0 (GPLv3)</name>
<url>https://www.gnu.org/licenses/gpl-3.0.en.html</url>
<distribution>repo</distribution>
</license>
</licenses>
<scm>
<url>https://github.com/NLPIE/BioMedICUS</url>
<connection>scm:git:https://github.com/NLPIE/BioMedICUS.git</connection>
<developerConnection>scm:git:https://github.com/NLPIE/BioMedICUS.git</developerConnection>
</scm>

</project>
110 changes: 55 additions & 55 deletions src/assembly/descriptor.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,59 +15,59 @@
~ along with this program. If not, see <http://www.gnu.org/licenses/>.
-->

<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
<id>release</id>
<formats>
<format>zip</format>
</formats>
<includeBaseDirectory>false</includeBaseDirectory>
<dependencySets>
<dependencySet>
<useProjectArtifact>true</useProjectArtifact>
<useTransitiveDependencies>true</useTransitiveDependencies>
<outputDirectory>lib</outputDirectory>
<unpack>false</unpack>
</dependencySet>
</dependencySets>
<fileSets>
<fileSet>
<directoryMode>0755</directoryMode>
<fileMode>0755</fileMode>
<directory>src/main/bin</directory>
<outputDirectory>bin</outputDirectory>
<includes>
<include>**/*</include>
</includes>
</fileSet>
<fileSet>
<directory>src/main/config</directory>
<outputDirectory>config</outputDirectory>
<includes>
<include>**/*</include>
</includes>
</fileSet>
<fileSet>
<directory>src/main/desc</directory>
<outputDirectory>desc</outputDirectory>
<includes>
<include>**/*</include>
</includes>
</fileSet>
<fileSet>
<directory>src/main/top</directory>
<outputDirectory>/</outputDirectory>
<includes>
<include>**/*</include>
</includes>
</fileSet>
<fileSet>
<directory>.</directory>
<includes>
<include>LICENSE.txt</include>
<include>README.md</include>
</includes>
</fileSet>
</fileSets>
<assembly xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2"
xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
<id>release</id>
<formats>
<format>zip</format>
</formats>
<includeBaseDirectory>false</includeBaseDirectory>
<dependencySets>
<dependencySet>
<useProjectArtifact>true</useProjectArtifact>
<useTransitiveDependencies>true</useTransitiveDependencies>
<outputDirectory>lib</outputDirectory>
<unpack>false</unpack>
</dependencySet>
</dependencySets>
<fileSets>
<fileSet>
<directoryMode>0755</directoryMode>
<fileMode>0755</fileMode>
<directory>src/main/bin</directory>
<outputDirectory>bin</outputDirectory>
<includes>
<include>**/*</include>
</includes>
</fileSet>
<fileSet>
<directory>src/main/config</directory>
<outputDirectory>config</outputDirectory>
<includes>
<include>**/*</include>
</includes>
</fileSet>
<fileSet>
<directory>src/main/desc</directory>
<outputDirectory>desc</outputDirectory>
<includes>
<include>**/*</include>
</includes>
</fileSet>
<fileSet>
<directory>src/main/top</directory>
<outputDirectory>/</outputDirectory>
<includes>
<include>**/*</include>
</includes>
</fileSet>
<fileSet>
<directory>.</directory>
<includes>
<include>LICENSE.txt</include>
<include>README.md</include>
</includes>
</fileSet>
</fileSets>
</assembly>
Loading

0 comments on commit d9c7e14

Please sign in to comment.