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| Original file line number | Diff line number | Diff line change |
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| package org.broad.igv.ga4gh; | ||
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| import com.google.gson.Gson; | ||
| import org.apache.commons.io.IOUtils; | ||
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| import javax.net.ssl.HttpsURLConnection; | ||
| import java.io.BufferedReader; | ||
| import java.io.DataOutputStream; | ||
| import java.io.IOException; | ||
| import java.io.InputStreamReader; | ||
| import java.net.HttpURLConnection; | ||
| import java.net.MalformedURLException; | ||
| import java.net.URL; | ||
| import java.util.HashMap; | ||
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| /** | ||
| * Created by jrobinso on 6/16/14. | ||
| * <p/> | ||
| * Class to full around with the Google Global Alliance API | ||
| * <p/> | ||
| * TEST CASE | ||
| * HG00096 (GBR low coverage) | ||
| * 1:70,231,000-70,232,000 | ||
| * <p/> | ||
| * readset id: CJDmkYn8ChCcnc7i4KaWqmQ | ||
| */ | ||
| public class Ga4gh { | ||
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| // readset id = CJDmkYn8ChCcnc7i4KaWqmQ | ||
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| public static void main(String[] args) throws IOException { | ||
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| //datasets(); | ||
| //readset(); | ||
| //readsetSearch(); | ||
| reads(); | ||
| } | ||
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| public static void datasets() throws IOException { | ||
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| String baseURL = "https://www.googleapis.com/genomics/v1beta/datasets/376902546192?key=AIzaSyC-dujgw4P1QvNd8i_c-I-S_P1uxVZzn0w"; | ||
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| // Create a URLConnection | ||
| java.net.URLConnection connection = new java.net.URL(baseURL).openConnection(); | ||
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| // Read the response | ||
| java.io.BufferedReader br = new java.io.BufferedReader(new java.io.InputStreamReader(connection.getInputStream())); | ||
| java.lang.StringBuffer sb = new java.lang.StringBuffer(); | ||
| java.lang.String str = br.readLine(); | ||
| while (str != null) { | ||
| sb.append(str); | ||
| str = br.readLine(); | ||
| } | ||
| br.close(); | ||
| java.lang.String responseString = sb.toString(); | ||
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| System.out.println(responseString); | ||
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| } | ||
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| public static void readset() throws IOException { | ||
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| String baseURL = "https://www.googleapis.com/genomics/v1beta/readsets/CJDmkYn8ChCcnc7i4KaWqmQ?key=AIzaSyC-dujgw4P1QvNd8i_c-I-S_P1uxVZzn0w"; | ||
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| // Create a URLConnection | ||
| java.net.URLConnection connection = new java.net.URL(baseURL).openConnection(); | ||
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| // Read the response | ||
| java.io.BufferedReader br = new java.io.BufferedReader(new java.io.InputStreamReader(connection.getInputStream())); | ||
| java.lang.StringBuffer sb = new java.lang.StringBuffer(); | ||
| java.lang.String str = br.readLine(); | ||
| while (str != null) { | ||
| sb.append(str); | ||
| str = br.readLine(); | ||
| } | ||
| br.close(); | ||
| java.lang.String responseString = sb.toString(); | ||
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| System.out.println(responseString); | ||
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| } | ||
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| public static void reads() throws IOException { | ||
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| URL baseURL = new URL("https://www.googleapis.com/genomics/v1beta/reads/search?key=AIzaSyC-dujgw4P1QvNd8i_c-I-S_P1uxVZzn0w"); | ||
| String key = "AIzaSyC-dujgw4P1QvNd8i_c-I-S_P1uxVZzn0w"; | ||
| String datasetId = "376902546192"; | ||
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| // JSON content to post | ||
| java.lang.String contentToPost = //"key=" + key + " " + | ||
| "{readsetIds: [\"CJDmkYn8ChCcnc7i4KaWqmQ\"], " + | ||
| "sequenceName: 1, " + | ||
| "sequenceStart: 70231000, " + | ||
| "sequenceEnd: 70232000}"; | ||
| System.out.println(contentToPost); | ||
| byte[] bytes = contentToPost.getBytes(); | ||
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| // Create a URLConnection | ||
| HttpURLConnection connection = (HttpURLConnection) baseURL.openConnection(); | ||
| connection.setUseCaches(false); | ||
| connection.setDoInput(true); | ||
| connection.setDoOutput(true); | ||
| connection.setRequestMethod("POST"); | ||
| //connection.setRequestProperty("Content-Length", "" + bytes.length); | ||
| connection.setRequestProperty("Content-Type", "application/json"); | ||
| connection.setRequestProperty("Cache-Control", "no-cache"); | ||
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| // Post content | ||
| java.io.OutputStream stream = connection.getOutputStream(); | ||
| stream.write(bytes); | ||
| stream.close(); | ||
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| // Read the response | ||
| java.io.BufferedReader br = new java.io.BufferedReader(new java.io.InputStreamReader(connection.getInputStream())); | ||
| java.lang.String str; | ||
| Gson gson = new Gson(); | ||
| while ((str = br.readLine()) != null) { | ||
| // Object obj = gson.fromJson(str, HashMap.class); | ||
| System.out.println(str); | ||
| } | ||
| br.close(); | ||
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| } | ||
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| public static void readsetSearch() throws IOException { | ||
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| URL baseURL = new URL("https://www.googleapis.com/genomics/v1beta/readsets/search?key=AIzaSyC-dujgw4P1QvNd8i_c-I-S_P1uxVZzn0w"); | ||
| String key = "AIzaSyC-dujgw4P1QvNd8i_c-I-S_P1uxVZzn0w"; | ||
| String datasetId = "376902546192"; | ||
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| // JSON content to post | ||
| java.lang.String contentToPost = //"key=" + key + " " + | ||
| "{datasetIds: [" + datasetId + "]}"; | ||
| System.out.println(contentToPost); | ||
| byte[] bytes = contentToPost.getBytes(); | ||
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| // Create a URLConnection | ||
| HttpURLConnection connection = (HttpURLConnection) baseURL.openConnection(); | ||
| connection.setUseCaches(false); | ||
| connection.setDoInput(true); | ||
| connection.setDoOutput(true); | ||
| connection.setRequestMethod("POST"); | ||
| //connection.setRequestProperty("Content-Length", "" + bytes.length); | ||
| connection.setRequestProperty("Content-Type", "application/json"); | ||
| connection.setRequestProperty("Cache-Control", "no-cache"); | ||
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| // Post content | ||
| java.io.OutputStream stream = connection.getOutputStream(); | ||
| stream.write(bytes); | ||
| stream.close(); | ||
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| // Read the response | ||
| java.io.BufferedReader br = new java.io.BufferedReader(new java.io.InputStreamReader(connection.getInputStream())); | ||
| java.lang.String str; | ||
| while ((str = br.readLine()) != null) { | ||
| System.out.println(str); | ||
| } | ||
| br.close(); | ||
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| } | ||
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| } |
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