use new java client to query chebi URIs that replace old python script

Author: Richard Boyce

linkedSPLs/LinkedSPLs-update/mappings/PT-UNII-ChEBI-mapping/ChEBIJavaClient/bin/chebi/service/GetChEBIbyNames.class

@@ -0,0 +1,2 @@
+input=data/FDA/FDAPreferredSubstanceToUNII.txt
+output=mappings/PT-UNII-ChEBI-mapping/UNIIToChEBI.txt

linkedSPLs/LinkedSPLs-update/mappings/PT-UNII-ChEBI-mapping/ChEBIJavaClient/jar/ChEBIJavaClient.jar

@@ -0,0 +1,174 @@
+package chebi.service;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStreamWriter;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+import uk.ac.ebi.chebi.webapps.chebiWS.client.ChebiWebServiceClient;
+import uk.ac.ebi.chebi.webapps.chebiWS.model.ChebiWebServiceFault_Exception;
+import uk.ac.ebi.chebi.webapps.chebiWS.model.*;
+
+public class GetChEBIbyNames {
+
+	private static String absPath = System.getProperty("user.dir");
+
+	public static void main(String[] args) {
+
+		GetChEBIbyNames chebi = new GetChEBIbyNames();
+
+		String configFilePath = absPath + "/mappings/PT-UNII-ChEBI-mapping/ChEBIJavaClient/mappings/config.properties";
+
+		try {
+
+			HashMap<String, String> properties = chebi.readConfigs(configFilePath);
+			String inputPath = absPath +"/"+ properties.get("input");
+			String outputPath = absPath +"/"+ properties.get("output");
+
+			List<String> drugL = readDrugListFile(inputPath);
+			Map<String, String> mappingD = getMappingsD(drugL);
+			printToFile(mappingD, outputPath);
+
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+
+	}
+
+	public static Map<String, String> getMappingsD(List<String> drugL) {
+		Map<String, String> mappingD = new HashMap<String, String>();
+
+		for (String drug : drugL) {
+			if (!drug.isEmpty()) {
+				System.out.println(drug);
+				String chebiURI = getChEBIByName(drug);
+				if (!chebiURI.isEmpty())
+				    mappingD.put(drug.trim(), ("http://purl.obolibrary.org/obo/"+chebiURI.replace(":","_")));
+			}
+		}
+
+		return mappingD;
+	}
+
+	public HashMap<String, String> readConfigs(String propFilePath) throws IOException {
+
+		try {
+			HashMap<String, String> result = new HashMap<String, String>();
+
+			File file = new File(propFilePath);
+			FileInputStream fileInput = new FileInputStream(file);
+			Properties properties = new Properties();
+			properties.load(fileInput);
+			fileInput.close();
+
+			String input = properties.getProperty("input");
+			String output = properties.getProperty("output");
+
+			if (!input.isEmpty() && !output.isEmpty()) {
+
+				result.put("input", input);
+				result.put("output", output);
+
+				return result;
+			} else {
+				System.out.println("Property no found - input: " + input + " | output: " + output);
+
+			}
+
+		} catch (Exception e) {
+			System.out.println("Exception: " + e);
+		}
+		return null;
+
+	}
+
+	public static String getChEBIByName(String drugname) {
+
+		String chebi = "";
+
+		try {
+
+			ChebiWebServiceClient client = new ChebiWebServiceClient();
+			LiteEntityList entities = client.getLiteEntity(drugname, SearchCategory.ALL, 50, StarsCategory.ALL);
+			List<LiteEntity> resultList = entities.getListElement();
+
+			for (LiteEntity liteEntity : resultList) {
+				if (drugname.toLowerCase().equals(liteEntity.getChebiAsciiName().toLowerCase())) {
+					chebi = liteEntity.getChebiId();
+				}
+			}
+
+		} catch (ChebiWebServiceFault_Exception e) {
+			System.err.println(e.getMessage());
+		}
+		return chebi;
+	}
+
+	public static List<String> readDrugListFile(String filePath) {
+
+		List<String> drugL = new ArrayList<String>();
+
+		BufferedReader br;
+		try {
+			br = new BufferedReader(new FileReader(filePath));
+
+			while (true) {
+
+				String line = br.readLine();
+
+				if (line == null) {
+					break;
+				}
+
+				if (!line.isEmpty())
+					drugL.add(line.trim());
+			}
+			br.close();
+
+		} catch (Exception e) {
+			e.printStackTrace();
+		}
+		return drugL;
+	}
+
+	// write string into file of specified format
+	public static void printToFile(Map<String, String> mappingD, String outputPath) {
+		File file = new File(outputPath);
+
+		try {
+
+			if (!file.exists()) {
+				file.createNewFile();
+			}
+
+			FileOutputStream fos = new FileOutputStream(file);
+
+			Iterator it = mappingD.entrySet().iterator();
+
+			FileWriter fw = new FileWriter(file);
+			BufferedWriter bw = new BufferedWriter(fw);
+
+			while (it.hasNext()) {
+				Map.Entry pair = (Map.Entry) it.next();
+				bw.write(pair.getKey() + "\t" + pair.getValue() + "\n");
+			}
+			bw.close();
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+	}
+
+}