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Add a scigraph based clinical text annotation module.
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Jose
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Joe C
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Jun 12, 2016
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,147 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
|
|
||
| <!-- | ||
| * See the NOTICE file distributed with this work for additional | ||
| * information regarding copyright ownership. | ||
| * | ||
| * This program is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU Affero General Public License as published by | ||
| * the Free Software Foundation, either version 3 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU Affero General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU Affero General Public License | ||
| * 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/maven-v4_0_0.xsd"> | ||
| <modelVersion>4.0.0</modelVersion> | ||
| <parent> | ||
| <groupId>org.phenotips</groupId> | ||
| <artifactId>clinical-text-analysis-extension</artifactId> | ||
| <version>1.3-SNAPSHOT</version> | ||
| </parent> | ||
| <artifactId>clinical-text-analysis-extension-generic-rest</artifactId> | ||
| <name>PhenoTips - Clinical Text Analysis - Generic REST implementation for the Java APIs</name> | ||
| <repositories> | ||
| <repository> | ||
| <id>CRBS</id> | ||
| <name>CRBS Maven Repo</name> | ||
| <url>http://maven.crbs.ucsd.edu/nexus/content/repositories/NIF-snapshot/</url> | ||
| </repository> | ||
| </repositories> | ||
| <dependencies> | ||
| <dependency> | ||
| <groupId>org.xwiki.commons</groupId> | ||
| <artifactId>xwiki-commons-component-api</artifactId> | ||
| <version>${xwiki.version}</version> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.apache.commons</groupId> | ||
| <artifactId>commons-lang3</artifactId> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.xwiki.platform</groupId> | ||
| <artifactId>xwiki-platform-bridge</artifactId> | ||
| <version>${xwiki.version}</version> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.xwiki.platform</groupId> | ||
| <artifactId>xwiki-platform-extension-distribution</artifactId> | ||
| <version>${xwiki.version}</version> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.xwiki.platform</groupId> | ||
| <artifactId>xwiki-platform-model</artifactId> | ||
| <version>${xwiki.version}</version> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.xwiki.platform</groupId> | ||
| <artifactId>xwiki-platform-oldcore</artifactId> | ||
| <version>${xwiki.version}</version> | ||
| <exclusions> | ||
| <exclusion> | ||
| <groupId>commons-validator</groupId> | ||
| <artifactId>commons-validator</artifactId> | ||
| </exclusion> | ||
| </exclusions> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.xwiki.platform</groupId> | ||
| <artifactId>xwiki-platform-query-manager</artifactId> | ||
| <version>${xwiki.version}</version> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.xwiki.commons</groupId> | ||
| <artifactId>xwiki-commons-context</artifactId> | ||
| <version>${xwiki.version}</version> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>${project.groupId}</groupId> | ||
| <artifactId>clinical-text-analysis-extension-api</artifactId> | ||
| <version>${project.version}</version> | ||
| <exclusions> | ||
| <exclusion> | ||
| <groupId>commons-validator</groupId> | ||
| <artifactId>commons-validator</artifactId> | ||
| </exclusion> | ||
| </exclusions> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>${project.groupId}</groupId> | ||
| <artifactId>phenotips-constants</artifactId> | ||
| <version>${phenotips.version}</version> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>${project.groupId}</groupId> | ||
| <artifactId>vocabularies-api</artifactId> | ||
| <version>${phenotips.version}</version> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>net.sf.json-lib</groupId> | ||
| <artifactId>json-lib</artifactId> | ||
| <classifier>jdk15</classifier> | ||
| <version>2.3</version> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.slf4j</groupId> | ||
| <artifactId>slf4j-api</artifactId> | ||
| </dependency> | ||
| <!-- Test dependencies --> | ||
| <dependency> | ||
| <groupId>org.xwiki.commons</groupId> | ||
| <artifactId>xwiki-commons-tool-test-component</artifactId> | ||
| <version>${xwiki.version}</version> | ||
| <scope>test</scope> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>javax.servlet</groupId> | ||
| <artifactId>javax.servlet-api</artifactId> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.mockito</groupId> | ||
| <artifactId>mockito-all</artifactId> | ||
| <version>1.10.8</version> | ||
| </dependency> | ||
|
|
||
| <!-- Scigraph dependencies --> | ||
| <dependency> | ||
| <groupId>com.fasterxml.jackson.dataformat</groupId> | ||
| <artifactId>jackson-dataformat-yaml</artifactId> | ||
| <!-- TODO: What's the best way to get the proper version? --> | ||
| <version>2.5.4</version> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.apache.httpcomponents</groupId> | ||
| <artifactId>fluent-hc</artifactId> | ||
| <version>4.4.1</version> | ||
| </dependency> | ||
| </dependencies> | ||
| <properties> | ||
| <coverage.instructionRatio>0.16</coverage.instructionRatio> | ||
| </properties> | ||
| </project> |
93 changes: 93 additions & 0 deletions
93
generic-rest/src/main/java/org/phenotips/textanalysis/internal/AnnotationAPI.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,93 @@ | ||
| /* | ||
| * See the NOTICE file distributed with this work for additional | ||
| * information regarding copyright ownership. | ||
| * | ||
| * This program is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU Affero General Public License as published by | ||
| * the Free Software Foundation, either version 3 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU Affero General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU Affero General Public License | ||
| * along with this program. If not, see http://www.gnu.org/licenses/ | ||
| */ | ||
| package org.phenotips.textanalysis.internal; | ||
|
|
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| import org.xwiki.component.annotation.Role; | ||
|
|
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| import java.io.InputStream; | ||
| import java.util.Map; | ||
|
|
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| /** | ||
| * Interacts with an annotation REST API endpoint, with methods as defined in {@link GenericRESTAnnotationService}. | ||
| * | ||
| * @version $Id$ | ||
| */ | ||
| @Role | ||
| public interface AnnotationAPI | ||
| { | ||
| /** | ||
| * Execute a post request to the method given, taking content to be the json body of the request. | ||
| * @param method the method | ||
| * @param content the content, to be interpreted as containing a json object | ||
| * @return the response | ||
| * @throws ServiceException if there's an error accessing the method | ||
| */ | ||
| InputStream postJson(String method, InputStream content) throws ServiceException; | ||
|
|
||
| /** | ||
| * Post the form given to the method given. | ||
| * @param method the method | ||
| * @param params the form parameters | ||
| * @return the response | ||
| * @throws ServiceException if there's an error accessing the method | ||
| */ | ||
| InputStream postForm(String method, Map<String, String> params) throws ServiceException; | ||
|
|
||
| /** | ||
| * Send an empty post to the method given. | ||
| * @param method the method | ||
| * @return the response | ||
| * @throws ServiceException if there's an error accessing the method | ||
| */ | ||
| InputStream postEmpty(String method) throws ServiceException; | ||
|
|
||
| /** | ||
| * Send an empty get to the method given. | ||
| * @param method the method | ||
| * @return the response | ||
| * @throws ServiceException if there's an error accessing the method | ||
| */ | ||
| InputStream getEmpty(String method) throws ServiceException; | ||
|
|
||
| /** | ||
| * An exception returned by SciGraph. | ||
| * | ||
| * @version $Id$ | ||
| */ | ||
| class ServiceException extends Exception | ||
| { | ||
| /** | ||
| * CTOR. | ||
| * @param message the message | ||
| */ | ||
| public ServiceException(String message) | ||
| { | ||
| super(message); | ||
| } | ||
|
|
||
| /** | ||
| * CTOR with cause. | ||
| * @param message the message | ||
| * @param cause the cause. | ||
| */ | ||
| public ServiceException(String message, Exception cause) | ||
| { | ||
| super(message, cause); | ||
| } | ||
| } | ||
| } |
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