Merge pull request #6 from bd2kccd/development

Merge v0.0.1 to Master

pom.xml

@@ -4,7 +4,7 @@
 
     <groupId>edu.pitt.dbmi.ccd</groupId>
     <artifactId>causal-tetrad-rest-client</artifactId>
-    <version>0.0.1-SNAPSHOT</version>
+    <version>0.0.1</version>
     <packaging>jar</packaging>
 
     <name>causal-tetrad-rest-client</name>
@@ -17,6 +17,17 @@
         <maven.compiler.target>1.8</maven.compiler.target>
     </properties>
 
+    <repositories>
+        <repository>
+            <id>ccd-releases</id>
+            <url>https://ccd3.vm.bridges.psc.edu/nexus/content/repositories/releases/</url>
+        </repository>
+        <repository>
+            <id>ccd-snapshots</id>
+            <url>https://ccd3.vm.bridges.psc.edu/nexus/content/repositories/snapshots/</url>
+        </repository>
+    </repositories>
+
     <distributionManagement>
         <repository>
             <id>ccd-releases</id>

src/main/java/edu/pitt/dbmi/ccd/rest/client/RestHttpsClient.java

@@ -16,13 +16,12 @@
 import org.apache.http.ssl.SSLContextBuilder;
 
 /**
- * 
+ *
  * Aug 20, 2016 12:17:02 AM
- * 
+ *
  * @author Chirayu (Kong) Wongchokprasitti, PhD
- * 
+ *
  */
-
 public class RestHttpsClient {
 
     private final String email;
@@ -33,64 +32,57 @@ public class RestHttpsClient {
 
     private final CloseableHttpClient httpClient;
     private final HttpClientContext localContext;
-
-    public RestHttpsClient(String email, String password, String scheme,
-	    String hostname, int port) throws Exception {
-	this.email = email;
-	this.password = password;
-	this.scheme = scheme;
-	this.hostname = hostname;
-	this.port = port;
-	this.httpClient = createHttpClient();
-	this.localContext = establishCustomContext(httpClient);
+
+    public RestHttpsClient(String email, String password, String scheme, String hostname, int port) throws Exception {
+        this.email = email;
+        this.password = password;
+        this.scheme = scheme;
+        this.hostname = hostname;
+        this.port = port;
+        this.httpClient = createHttpClient();
+        this.localContext = establishCustomContext(httpClient);
     }
 
     private CloseableHttpClient createHttpClient() throws Exception {
-	// Trust own CA and all self-signed certs
-	SSLContextBuilder builder = new SSLContextBuilder();
-	builder.loadTrustMaterial(null, new TrustSelfSignedStrategy());
+        // Trust own CA and all self-signed certs
+        SSLContextBuilder builder = new SSLContextBuilder();
+        builder.loadTrustMaterial(null, new TrustSelfSignedStrategy());
 
-	SSLConnectionSocketFactory sslsf = new SSLConnectionSocketFactory(
-		builder.build(),
-		new String[] { "TLSv1.2" },
-		null,
-		SSLConnectionSocketFactory.getDefaultHostnameVerifier());
+        SSLConnectionSocketFactory sslsf = new SSLConnectionSocketFactory(builder.build(), new String[]{"TLSv1.2"},
+                null, SSLConnectionSocketFactory.getDefaultHostnameVerifier());
 
-	CredentialsProvider credsProvider = new BasicCredentialsProvider();
-	credsProvider.setCredentials(new AuthScope(hostname, port),
-		new UsernamePasswordCredentials(email, password));
+        CredentialsProvider credsProvider = new BasicCredentialsProvider();
+        credsProvider.setCredentials(new AuthScope(hostname, port), new UsernamePasswordCredentials(email, password));
 
-	CloseableHttpClient httpClient = HttpClients.custom()
-		.setSSLSocketFactory(sslsf)
-		.setDefaultCredentialsProvider(credsProvider).build();
+        CloseableHttpClient httpClient = HttpClients.custom().setSSLSocketFactory(sslsf)
+                .setDefaultCredentialsProvider(credsProvider).build();
 
-	return httpClient;
+        return httpClient;
     }
 
-    private HttpClientContext establishCustomContext(
-	    CloseableHttpClient httpclient) throws Exception {
-	HttpHost target = new HttpHost(hostname, port, scheme);
-
-	// Create AuthCache instance
-	AuthCache authCache = new BasicAuthCache();
-	// Generate BASIC scheme object and add it to the local
-	// auth cache
-	BasicScheme basicAuth = new BasicScheme();
-	authCache.put(target, basicAuth);
-
-	// Add AuthCache to the execution context
-	HttpClientContext localContext = HttpClientContext.create();
-	localContext.setAuthCache(authCache);
-
-	return localContext;
+    private HttpClientContext establishCustomContext(CloseableHttpClient httpclient) throws Exception {
+        HttpHost target = new HttpHost(hostname, port, scheme);
+
+        // Create AuthCache instance
+        AuthCache authCache = new BasicAuthCache();
+        // Generate BASIC scheme object and add it to the local
+        // auth cache
+        BasicScheme basicAuth = new BasicScheme();
+        authCache.put(target, basicAuth);
+
+        // Add AuthCache to the execution context
+        HttpClientContext localContext = HttpClientContext.create();
+        localContext.setAuthCache(authCache);
+
+        return localContext;
     }
 
     public CloseableHttpClient getHttpClient() {
-	return httpClient;
+        return httpClient;
     }
 
     public HttpClientContext getLocalContext() {
-	return localContext;
+        return localContext;
     }
 
     public static void main(String[] args) throws Exception {

src/main/java/edu/pitt/dbmi/ccd/rest/client/dto/algo/AlgorithmInfo.java

@@ -1,11 +1,11 @@
 package edu.pitt.dbmi.ccd.rest.client.dto.algo;
 
 /**
- * 
+ *
  * Aug 24, 2016 6:09:21 PM
- * 
+ *
  * @author Chirayu (Kong) Wongchokprasitti, PhD
- * 
+ *
  */
 public class AlgorithmInfo {
 
@@ -18,27 +18,27 @@ public AlgorithmInfo() {
     }
 
     public int getId() {
-	return id;
+        return id;
     }
 
     public void setId(int id) {
-	this.id = id;
+        this.id = id;
     }
 
     public String getName() {
-	return name;
+        return name;
     }
 
     public void setName(String name) {
-	this.name = name;
+        this.name = name;
     }
 
     public String getDescription() {
-	return description;
+        return description;
     }
 
     public void setDescription(String description) {
-	this.description = description;
+        this.description = description;
     }
 
 }

src/main/java/edu/pitt/dbmi/ccd/rest/client/dto/algo/AlgorithmParamRequest.java

@@ -1,63 +1,65 @@
 package edu.pitt.dbmi.ccd.rest.client.dto.algo;
 
+import java.util.List;
 import java.util.Map;
 
 /**
- * 
+ *
  * Aug 25, 2016 2:20:41 PM
- * 
+ *
  * @author Chirayu (Kong) Wongchokprasitti, PhD
- * 
+ *
  */
 public class AlgorithmParamRequest {
 
-	private long datasetFileId;
-
-	private Map<String, Object> dataValidation;
-
-	private Map<String, Object> AlgorithmParameters;
-
-	private Map<String, Object> jvmOptions;
-
-	private Map<String, Object> hpcParameters;
-
-	public long getDatasetFileId() {
-		return datasetFileId;
-	}
-
-	public void setDatasetFileId(long dataFileId) {
-		this.datasetFileId = dataFileId;
-	}
-
-	public Map<String, Object> getDataValidation() {
-		return dataValidation;
-	}
-
-	public void setDataValidation(Map<String, Object> dataValidation) {
-		this.dataValidation = dataValidation;
-	}
-
-	public Map<String, Object> getAlgorithmParameters() {
-		return AlgorithmParameters;
-	}
-
-	public void setAlgorithmParameters(Map<String, Object> algorithmParameters) {
-		AlgorithmParameters = algorithmParameters;
-	}
-
-	public Map<String, Object> getJvmOptions() {
-		return jvmOptions;
-	}
-
-	public void setJvmOptions(Map<String, Object> jvmOptions) {
-		this.jvmOptions = jvmOptions;
-	}
-
-	public Map<String, Object> getHpcParameters() {
-		return hpcParameters;
-	}
-
-	public void setHpcParameters(Map<String, Object> hpcParameters) {
-		this.hpcParameters = hpcParameters;
-	}
+    private long datasetFileId;
+
+    private Map<String, Object> dataValidation;
+
+    private Map<String, Object> AlgorithmParameters;
+
+    private Map<String, Object> jvmOptions;
+
+    private List<HpcParameter> hpcParameters;
+
+    public long getDatasetFileId() {
+        return datasetFileId;
+    }
+
+    public void setDatasetFileId(long dataFileId) {
+        this.datasetFileId = dataFileId;
+    }
+
+    public Map<String, Object> getDataValidation() {
+        return dataValidation;
+    }
+
+    public void setDataValidation(Map<String, Object> dataValidation) {
+        this.dataValidation = dataValidation;
+    }
+
+    public Map<String, Object> getAlgorithmParameters() {
+        return AlgorithmParameters;
+    }
+
+    public void setAlgorithmParameters(Map<String, Object> algorithmParameters) {
+        AlgorithmParameters = algorithmParameters;
+    }
+
+    public Map<String, Object> getJvmOptions() {
+        return jvmOptions;
+    }
+
+    public void setJvmOptions(Map<String, Object> jvmOptions) {
+        this.jvmOptions = jvmOptions;
+    }
+
+    public List<HpcParameter> getHpcParameters() {
+        return hpcParameters;
+    }
+
+    public void setHpcParameters(List<HpcParameter> hpcParameters) {
+        this.hpcParameters = hpcParameters;
+    }
+
 }

src/main/java/edu/pitt/dbmi/ccd/rest/client/dto/algo/HpcParameter.java

@@ -0,0 +1,49 @@
+/*
+ * Copyright (C) 2015 University of Pittsburgh.
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library 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
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301  USA
+ */
+package edu.pitt.dbmi.ccd.rest.client.dto.algo;
+
+/**
+ *
+ * Feb 21, 2017 12:24:39 PM
+ *
+ * @author Chirayu Kong Wongchokprasitti, PhD (chw20@pitt.edu)
+ *
+ */
+public class HpcParameter {
+
+    private String key;
+
+    private String value;
+
+    public String getKey() {
+        return key;
+    }
+
+    public void setKey(String key) {
+        this.key = key;
+    }
+
+    public String getValue() {
+        return value;
+    }
+
+    public void setValue(String value) {
+        this.value = value;
+    }
+}

src/main/java/edu/pitt/dbmi/ccd/rest/client/dto/algo/JobInfo.java

@@ -3,11 +3,11 @@
 import java.util.Date;
 
 /**
- * 
+ *
  * Aug 31, 2016 12:48:31 PM
- * 
+ *
  * @author Chirayu (Kong) Wongchokprasitti, PhD
- * 
+ *
  */
 public class JobInfo {
 
@@ -18,11 +18,11 @@ public class JobInfo {
     private Date addedTime;
 
     private String resultFileName;
-    
+
     private String resultJsonFileName;
 
     private String errorResultFileName;
-    
+
     private int status;
 
     public Long getId() {