3.0.0 commit

adverse-events/.gitignore

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+HELP.md
+target/
+ginas.ix/
+
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+
+### STS ###
+.apt_generated
+.classpath
+.factorypath
+.project
+.settings
+.springBeans
+.sts4-cache
+
+### IntelliJ IDEA ###
+.idea
+*.iws
+*.iml
+*.ipr
+
+### NetBeans ###
+/nbproject/private/
+/nbbuild/
+/dist/
+/nbdist/
+/.nb-gradle/
+build/
+!**/src/main/**/build/
+!**/src/test/**/build/
+
+### VS Code ###
+.vscode/

adverse-events/.mvn/wrapper/MavenWrapperDownloader.java

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+/*
+ * Copyright 2007-present the original author or authors.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+import java.net.*;
+import java.io.*;
+import java.nio.channels.*;
+import java.util.Properties;
+
+public class MavenWrapperDownloader {
+
+    private static final String WRAPPER_VERSION = "0.5.6";
+    /**
+     * Default URL to download the maven-wrapper.jar from, if no 'downloadUrl' is provided.
+     */
+    private static final String DEFAULT_DOWNLOAD_URL = "https://repo.maven.apache.org/maven2/io/takari/maven-wrapper/"
+            + WRAPPER_VERSION + "/maven-wrapper-" + WRAPPER_VERSION + ".jar";
+
+    /**
+     * Path to the maven-wrapper.properties file, which might contain a downloadUrl property to
+     * use instead of the default one.
+     */
+    private static final String MAVEN_WRAPPER_PROPERTIES_PATH =
+            ".mvn/wrapper/maven-wrapper.properties";
+
+    /**
+     * Path where the maven-wrapper.jar will be saved to.
+     */
+    private static final String MAVEN_WRAPPER_JAR_PATH =
+            ".mvn/wrapper/maven-wrapper.jar";
+
+    /**
+     * Name of the property which should be used to override the default download url for the wrapper.
+     */
+    private static final String PROPERTY_NAME_WRAPPER_URL = "wrapperUrl";
+
+    public static void main(String args[]) {
+        System.out.println("- Downloader started");
+        File baseDirectory = new File(args[0]);
+        System.out.println("- Using base directory: " + baseDirectory.getAbsolutePath());
+
+        // If the maven-wrapper.properties exists, read it and check if it contains a custom
+        // wrapperUrl parameter.
+        File mavenWrapperPropertyFile = new File(baseDirectory, MAVEN_WRAPPER_PROPERTIES_PATH);
+        String url = DEFAULT_DOWNLOAD_URL;
+        if (mavenWrapperPropertyFile.exists()) {
+            FileInputStream mavenWrapperPropertyFileInputStream = null;
+            try {
+                mavenWrapperPropertyFileInputStream = new FileInputStream(mavenWrapperPropertyFile);
+                Properties mavenWrapperProperties = new Properties();
+                mavenWrapperProperties.load(mavenWrapperPropertyFileInputStream);
+                url = mavenWrapperProperties.getProperty(PROPERTY_NAME_WRAPPER_URL, url);
+            } catch (IOException e) {
+                System.out.println("- ERROR loading '" + MAVEN_WRAPPER_PROPERTIES_PATH + "'");
+            } finally {
+                try {
+                    if (mavenWrapperPropertyFileInputStream != null) {
+                        mavenWrapperPropertyFileInputStream.close();
+                    }
+                } catch (IOException e) {
+                    // Ignore ...
+                }
+            }
+        }
+        System.out.println("- Downloading from: " + url);
+
+        File outputFile = new File(baseDirectory.getAbsolutePath(), MAVEN_WRAPPER_JAR_PATH);
+        if (!outputFile.getParentFile().exists()) {
+            if (!outputFile.getParentFile().mkdirs()) {
+                System.out.println(
+                        "- ERROR creating output directory '" + outputFile.getParentFile().getAbsolutePath() + "'");
+            }
+        }
+        System.out.println("- Downloading to: " + outputFile.getAbsolutePath());
+        try {
+            downloadFileFromURL(url, outputFile);
+            System.out.println("Done");
+            System.exit(0);
+        } catch (Throwable e) {
+            System.out.println("- Error downloading");
+            e.printStackTrace();
+            System.exit(1);
+        }
+    }
+
+    private static void downloadFileFromURL(String urlString, File destination) throws Exception {
+        if (System.getenv("MVNW_USERNAME") != null && System.getenv("MVNW_PASSWORD") != null) {
+            String username = System.getenv("MVNW_USERNAME");
+            char[] password = System.getenv("MVNW_PASSWORD").toCharArray();
+            Authenticator.setDefault(new Authenticator() {
+                @Override
+                protected PasswordAuthentication getPasswordAuthentication() {
+                    return new PasswordAuthentication(username, password);
+                }
+            });
+        }
+        URL website = new URL(urlString);
+        ReadableByteChannel rbc;
+        rbc = Channels.newChannel(website.openStream());
+        FileOutputStream fos = new FileOutputStream(destination);
+        fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
+        fos.close();
+        rbc.close();
+    }
+
+}

adverse-events/.mvn/wrapper/maven-wrapper.properties

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+distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.8.1/apache-maven-3.8.1-bin.zip
+wrapperUrl=https://repo.maven.apache.org/maven2/io/takari/maven-wrapper/0.5.6/maven-wrapper-0.5.6.jar

adverse-events/README.md

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+# GSRS 3 Adverse Event Microservice
+
+This microservice is an entity service for storing, retrieving, searching and mapping Adverse Event to substances.
+
+## Core Dependency Repos
+
+- https://github.com/ncats/gsrs-spring-starter
+- https://github.com/ncats/gsrs-spring-module-substances
+- https://github.com/ncats/gsrs-spring-module-adverse-events
+
+The three dependencies are Spring-boot "starters." This `gsrs-main-deployment/adverse-events` service includes these starter libraries to actually create an executable runnable deployment.    
+
+## Build Instructions
+
+This entity microservice can be built into a war file for deployment in a J2EE web container. The simplest way to do this is:
+
+```
+./mvnw clean package -DskipTests
+```
+
+To include the tests, remove `-DskipTests` from the command. 
+
+This will create a file `target/adverse-events.war` 
+
+## Running and Debugging
+
+You can run the microservice locally for testing and debugging by running the following command, optionally skipping tests:
+
+```
+./mvnw clean spring-boot:run -DskipTests
+```
+
+## Configuration
+
+Configuration will be affected by the default configurations included in the core dependencies. These will be supplemented by configuration in [./src/main/resources/application.conf](./src/main/resources/application.conf).  
+
+Examine this file.  It contains example properties, but you may need to change several properties to run locally as an embedded instance during debugging and development, or to deploy for production
+
+For local embedded Tomcat deployment, each microservice needs its own port. Here we use port 8086 but it could be another port unique port number not used by any other microservice.   
+
+```
+## Local embedded Tomcat Instance
+# Where indexes and other file resources are kept.
+ix.home="./ginas.ix"
+# Should be the port the gateway runs on.
+application.host= "http://localhost:8081"
+# The port your microservice runs on
+server.port=8086
+``` 
+
+In production, you may be running the GSRS as a single Tomcat instance.  If so, the `application.host` will use the same port as your gateway port. Also, your `ix.home` folder needs to be unique to the adverse events microservice.  For example, `ix.home="/path/to/tomcat/webapps/gsrs_adverse_events.ix"`
+
+```
+## Production Single Tomcat Instance
+# Where indexes and other file resources are kept.
+ix.home="/path/to/tomcat/webapps/gsrs_clinical-trials.ix
+# Should be the port the gateway runs on.
+application.host= "http://localhost:8080"
+# Not needed, so comment out.
+# server.port=8080
+``` 
+
+
+
+Configuration can be modifed before or after building or running the deployed microservice.  The main thing to note is that this configuration will be copied during packaging to a location in the war file, and the war file will be unzipped when placed in the Tomcat `webapps` folder.  Since different configurations are needed for development and production, one approach to take is to have an alternative copy of `application.conf` in a secure location on the server. This can then copied to the deployed location on the production server before run time.  Once tomcat unzips your war file, you will find the configuration here:    
+
+```
+path/to/webapps/adverse-events/WEB-INF/classes/application.conf
+```
+
+Overwrite this file with your production version of your configuration.
+
+## Configure the Gateway
+
+The gateway needs to know how to route traffic to and from the microservice.  As above, there are different configuration patterns depending on how the GSRS is deployed. 
+
+For the local embedded context, these properties should be added to other routes in the gateway `src/main/resources/application.yml`  Here we use port 8086 as we configured this `server.port` in `adverse-events/src/java/main/resources/application.conf`
+
+```
+zuul:
+  routes:
+
+    ...
+  
+    #############################
+    #START adverse-events section
+    #############################
+    adverseeventpt_core:
+       path: /api/v1/adverseeventpt/**
+       url: http://localhost:8086/api/v1/adverseeventpt
+       serviceId: adverseeventpt_core
+    adverseeventpt_core_alt:
+       path: /api/v1/adverseeventpt(**)/**
+       url: http://localhost:8086/api/v1/adverseeventpt
+       serviceId: adverseeventpt_core
+    adverseeventdme_core:
+       path: /api/v1/adverseeventdme/**
+       url: http://localhost:8086/api/v1/adverseeventdme
+       serviceId: adverseeventdme_core
+    adverseeventdme_core_alt:
+       path: /api/v1/adverseeventdme(**)/**
+       url: http://localhost:8086/api/v1/adverseeventdme
+       serviceId: adverseeventdme_core
+    adverseeventcvm_core:
+       path: /api/v1/adverseeventcvm/**
+       url: http://localhost:8086/api/v1/adverseeventcvm
+       serviceId: adverseeventcvm_core
+    adverseeventcvm_core_alt:
+       path: /api/v1/adverseeventcvm(**)/**
+       url: http://localhost:8086/api/v1/adverseeventcvm
+       serviceId: adverseeventcvm_core
+    #############################
+    #END adverse-events section
+    #############################
+    
+    ```
+
+For a single Tomcat instance approach, these properties below should be included with other routes.  In this case we use port 8080 because that is the port Tomcat is running on.    
+
+```
+zuul:
+  routes:
+    ...
+
+    adverseeventpt_core:
+       path: /api/v1/adverseeventpt/**
+       url: http://localhost:8080/adverse-events/api/v1/adverseeventpt
+       serviceId: adverseeventpt_core
+    adverseeventpt_core_alt:
+       path: /api/v1/adverseeventpt(**)/**
+       url: http://localhost:8080/adverse-events/api/v1/adverseeventpt
+       serviceId: adverseeventpt_core
+    adverseeventdme_core:
+       path: /api/v1/adverseeventdme/**
+       url: http://localhost:8080/adverse-events/api/v1/adverseeventdme
+       serviceId: adverseeventdme_core
+    adverseeventdme_core_alt:
+       path: /api/v1/adverseeventdme(**)/**
+       url: http://localhost:8080/adverse-events/api/v1/adverseeventdme
+       serviceId: adverseeventdme_core
+    adverseeventcvm_core:
+       path: /api/v1/adverseeventcvm/**
+       url: http://localhost:8080/adverse-events/api/v1/adverseeventcvm
+       serviceId: adverseeventcvm_core      
+    adverseeventcvm_core_alt:
+       path: /api/v1/adverseeventcvm(**)/**
+       url: http://localhost:8080/adverse-events/api/v1/adverseeventcvm
+       serviceId: adverseeventcvm_core
+
+```
+
+
+

adverse-events/build.sh

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+#!/bin/bash
+./mvnw clean -U package -DskipTests