List of usage examples for org.apache.commons.httpclient HttpClient HttpClient
public HttpClient()
From source file:com.hw13c.HttpClientPost.java
public static void main(String[] args) { output = new File("out"); input = new File("in"); try {//from w w w . jav a 2 s. c o m // URL urls = new URL("http://www.bbc.com/sport/0/sports-personality/30267315"); // 1. URL urls = new URL("http://abcnews.go.com/US/nypd-officer-indicted-eric-garner-choke-hold-death/story?id=27341079"); URL urls = new URL( "http://www.chron.com/news/us/article/UN-campaign-seeks-64-million-for-Syrian-refugees-5932973.php"); //URL urls = new URL("http://www.bbc.com/news/health-30254697"); FileUtils.copyURLToFile(urls, input); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } // verifyArgs(args); HttpClientPost httpClientPost = new HttpClientPost(); //httpClientPost.input = new File(args[0]); //httpClientPost.output = new File(args[1]); httpClientPost.client = new HttpClient(); httpClientPost.client.getParams().setParameter("http.useragent", "Calais Rest Client"); httpClientPost.run(); try { queryRDFTriples(); } catch (RepositoryException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (RDFParseException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } }
From source file:net.mojodna.searchable.solr.SolrSearcher.java
/** * @param args//from w ww . ja v a 2 s. c o m * @throws Exception */ public static void main(String[] args) throws Exception { SolrSearcher searcher = new SolrSearcher(); searcher.setHttpClient(new HttpClient()); ResultSet results = searcher.search("wisdm"); System.out.println(results.getResults()); }
From source file:com.era7.bioinfo.annotation.AutomaticQualityControl.java
public static void main(String[] args) { if (args.length != 4) { System.out.println("This program expects four parameters: \n" + "1. Gene annotation XML filename \n" + "2. Reference protein set (.fasta)\n" + "3. Output TXT filename\n" + "4. Initial Blast XML results filename (the one used at the very beginning of the semiautomatic annotation process)\n"); } else {/*ww w. jav a2 s . c o m*/ BufferedWriter outBuff = null; try { File inFile = new File(args[0]); File fastaFile = new File(args[1]); File outFile = new File(args[2]); File blastFile = new File(args[3]); //Primero cargo todos los datos del archivo xml del blast BufferedReader buffReader = new BufferedReader(new FileReader(blastFile)); StringBuilder stBuilder = new StringBuilder(); String line = null; while ((line = buffReader.readLine()) != null) { stBuilder.append(line); } buffReader.close(); System.out.println("Creating blastoutput..."); BlastOutput blastOutput = new BlastOutput(stBuilder.toString()); System.out.println("BlastOutput created! :)"); stBuilder.delete(0, stBuilder.length()); HashMap<String, String> blastProteinsMap = new HashMap<String, String>(); ArrayList<Iteration> iterations = blastOutput.getBlastOutputIterations(); for (Iteration iteration : iterations) { blastProteinsMap.put(iteration.getQueryDef().split("\\|")[1].trim(), iteration.toString()); } //freeing some memory blastOutput = null; //------------------------------------------------------------------------ //Initializing writer for output file outBuff = new BufferedWriter(new FileWriter(outFile)); //reading gene annotation xml file..... buffReader = new BufferedReader(new FileReader(inFile)); stBuilder = new StringBuilder(); line = null; while ((line = buffReader.readLine()) != null) { stBuilder.append(line); } buffReader.close(); XMLElement genesXML = new XMLElement(stBuilder.toString()); //freeing some memory I don't need anymore stBuilder.delete(0, stBuilder.length()); //reading file with the reference proteins set ArrayList<String> proteinsReferenceSet = new ArrayList<String>(); buffReader = new BufferedReader(new FileReader(fastaFile)); while ((line = buffReader.readLine()) != null) { if (line.charAt(0) == '>') { proteinsReferenceSet.add(line.split("\\|")[1]); } } buffReader.close(); Element pGenes = genesXML.asJDomElement().getChild(PredictedGenes.TAG_NAME); List<Element> contigs = pGenes.getChildren(ContigXML.TAG_NAME); System.out.println("There are " + contigs.size() + " contigs to be checked... "); outBuff.write("There are " + contigs.size() + " contigs to be checked... \n"); outBuff.write("Proteins reference set: \n"); for (String st : proteinsReferenceSet) { outBuff.write(st + ","); } outBuff.write("\n"); for (Element elem : contigs) { ContigXML contig = new ContigXML(elem); //escribo el id del contig en el que estoy outBuff.write("Checking contig: " + contig.getId() + "\n"); outBuff.flush(); List<XMLElement> geneList = contig.getChildrenWith(PredictedGene.TAG_NAME); System.out.println("geneList.size() = " + geneList.size()); int numeroDeGenesParaAnalizar = geneList.size() / FACTOR; if (numeroDeGenesParaAnalizar == 0) { numeroDeGenesParaAnalizar++; } ArrayList<Integer> indicesUtilizados = new ArrayList<Integer>(); outBuff.write("\nThe contig has " + geneList.size() + " predicted genes, let's analyze: " + numeroDeGenesParaAnalizar + "\n"); for (int j = 0; j < numeroDeGenesParaAnalizar; j++) { int geneIndex; boolean geneIsDismissed = false; do { geneIsDismissed = false; geneIndex = (int) Math.round(Math.floor(Math.random() * geneList.size())); PredictedGene tempGene = new PredictedGene(geneList.get(geneIndex).asJDomElement()); if (tempGene.getStatus().equals(PredictedGene.STATUS_DISMISSED)) { geneIsDismissed = true; } } while (indicesUtilizados.contains(new Integer(geneIndex)) && geneIsDismissed); indicesUtilizados.add(geneIndex); System.out.println("geneIndex = " + geneIndex); //Ahora hay que sacar el gen correspondiente al indice y hacer el control de calidad PredictedGene gene = new PredictedGene(geneList.get(geneIndex).asJDomElement()); outBuff.write("\nAnalyzing gene with id: " + gene.getId() + " , annotation uniprot id: " + gene.getAnnotationUniprotId() + "\n"); outBuff.write("eValue: " + gene.getEvalue() + "\n"); //--------------PETICION POST HTTP BLAST---------------------- PostMethod post = new PostMethod(BLAST_URL); post.addParameter("program", "blastx"); post.addParameter("sequence", gene.getSequence()); post.addParameter("database", "uniprotkb"); post.addParameter("email", "ppareja@era7.com"); post.addParameter("exp", "1e-10"); post.addParameter("stype", "dna"); // execute the POST HttpClient client = new HttpClient(); int status = client.executeMethod(post); System.out.println("status post = " + status); InputStream inStream = post.getResponseBodyAsStream(); String fileName = "jobid.txt"; FileOutputStream outStream = new FileOutputStream(new File(fileName)); byte[] buffer = new byte[1024]; int len; while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //Once the file is created I just have to read one line in order to extract the job id buffReader = new BufferedReader(new FileReader(new File(fileName))); String jobId = buffReader.readLine(); buffReader.close(); System.out.println("jobId = " + jobId); //--------------HTTP CHECK JOB STATUS REQUEST---------------------- GetMethod get = new GetMethod(CHECK_JOB_STATUS_URL + jobId); String jobStatus = ""; do { try { Thread.sleep(1000);//sleep for 1000 ms } catch (InterruptedException ie) { //If this thread was intrrupted by nother thread } status = client.executeMethod(get); //System.out.println("status get = " + status); inStream = get.getResponseBodyAsStream(); fileName = "jobStatus.txt"; outStream = new FileOutputStream(new File(fileName)); while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //Once the file is created I just have to read one line in order to extract the job id buffReader = new BufferedReader(new FileReader(new File(fileName))); jobStatus = buffReader.readLine(); //System.out.println("jobStatus = " + jobStatus); buffReader.close(); } while (!jobStatus.equals(FINISHED_JOB_STATUS)); //Once I'm here the blast should've already finished //--------------JOB RESULTS HTTP REQUEST---------------------- get = new GetMethod(JOB_RESULT_URL + jobId + "/out"); status = client.executeMethod(get); System.out.println("status get = " + status); inStream = get.getResponseBodyAsStream(); fileName = "jobResults.txt"; outStream = new FileOutputStream(new File(fileName)); while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //--------parsing the blast results file----- TreeSet<GeneEValuePair> featuresBlast = new TreeSet<GeneEValuePair>(); buffReader = new BufferedReader(new FileReader(new File(fileName))); while ((line = buffReader.readLine()) != null) { if (line.length() > 3) { String prefix = line.substring(0, 3); if (prefix.equals("TR:") || prefix.equals("SP:")) { String[] columns = line.split(" "); String id = columns[1]; //System.out.println("id = " + id); String e = ""; String[] arraySt = line.split("\\.\\.\\."); if (arraySt.length > 1) { arraySt = arraySt[1].trim().split(" "); int contador = 0; for (int k = 0; k < arraySt.length && contador <= 2; k++) { String string = arraySt[k]; if (!string.equals("")) { contador++; if (contador == 2) { e = string; } } } } else { //Number before e- String[] arr = arraySt[0].split("e-")[0].split(" "); String numeroAntesE = arr[arr.length - 1]; String numeroDespuesE = arraySt[0].split("e-")[1].split(" ")[0]; e = numeroAntesE + "e-" + numeroDespuesE; } double eValue = Double.parseDouble(e); //System.out.println("eValue = " + eValue); GeneEValuePair g = new GeneEValuePair(id, eValue); featuresBlast.add(g); } } } GeneEValuePair currentGeneEValuePair = new GeneEValuePair(gene.getAnnotationUniprotId(), gene.getEvalue()); System.out.println("currentGeneEValuePair.id = " + currentGeneEValuePair.id); System.out.println("currentGeneEValuePair.eValue = " + currentGeneEValuePair.eValue); boolean blastContainsGene = false; for (GeneEValuePair geneEValuePair : featuresBlast) { if (geneEValuePair.id.equals(currentGeneEValuePair.id)) { blastContainsGene = true; //le pongo la e que tiene en el wu-blast para poder comparar currentGeneEValuePair.eValue = geneEValuePair.eValue; break; } } if (blastContainsGene) { outBuff.write("The protein was found in the WU-BLAST result.. \n"); //Una vez que se que esta en el blast tengo que ver que sea la mejor GeneEValuePair first = featuresBlast.first(); outBuff.write("Protein with best eValue according to the WU-BLAST result: " + first.id + " , " + first.eValue + "\n"); if (first.id.equals(currentGeneEValuePair.id)) { outBuff.write("Proteins with best eValue match up \n"); } else { if (first.eValue == currentGeneEValuePair.eValue) { outBuff.write( "The one with best eValue is not the same protein but has the same eValue \n"); } else if (first.eValue > currentGeneEValuePair.eValue) { outBuff.write( "The one with best eValue is not the same protein but has a worse eValue :) \n"); } else { outBuff.write( "The best protein from BLAST has an eValue smaller than ours, checking if it's part of the reference set...\n"); //System.exit(-1); if (proteinsReferenceSet.contains(first.id)) { //The protein is in the reference set and that shouldn't happen outBuff.write( "The protein was found on the reference set, checking if it belongs to the same contig...\n"); String iterationSt = blastProteinsMap.get(gene.getAnnotationUniprotId()); if (iterationSt != null) { outBuff.write( "The protein was found in the BLAST used at the beginning of the annotation process.\n"); Iteration iteration = new Iteration(iterationSt); ArrayList<Hit> hits = iteration.getIterationHits(); boolean contigFound = false; Hit errorHit = null; for (Hit hit : hits) { if (hit.getHitDef().indexOf(contig.getId()) >= 0) { contigFound = true; errorHit = hit; break; } } if (contigFound) { outBuff.write( "ERROR: A hit from the same contig was find in the Blast file: \n" + errorHit.toString() + "\n"); } else { outBuff.write("There is no hit with the same contig! :)\n"); } } else { outBuff.write( "The protein is NOT in the BLAST used at the beginning of the annotation process.\n"); } } else { //The protein was not found on the reference set so everything's ok outBuff.write( "The protein was not found on the reference, everything's ok :)\n"); } } } } else { outBuff.write("The protein was NOT found on the WU-BLAST !! :( \n"); //System.exit(-1); } } } } catch (Exception ex) { ex.printStackTrace(); } finally { try { //closing outputfile outBuff.close(); } catch (IOException ex) { Logger.getLogger(AutomaticQualityControl.class.getName()).log(Level.SEVERE, null, ex); } } } }
From source file:dk.statsbiblioteket.doms.licensemodule.integrationtest.HttpClientPoster.java
public static String postJSON(String url, String content) throws Exception { HttpClient client = new HttpClient(); client.getParams().setParameter("http.useragent", "Dokumentleveringweb XML client"); BufferedReader br = null;//from w ww . jav a 2 s. c o m //TODO property PostMethod method = new PostMethod(url); method.addRequestHeader("Content-Type", "application/json;charset=UTF-8"); method.setRequestBody(content); // How to do this a non-deprecated way? try { int httpCode = client.executeMethod(method); br = new BufferedReader(new InputStreamReader(method.getResponseBodyAsStream())); String readLine; StringBuilder response = new StringBuilder(); while (((readLine = br.readLine()) != null)) { response.append(readLine); } return response.toString(); } catch (Exception e) { throw e; } finally { method.releaseConnection(); if (br != null) try { br.close(); } catch (Exception fe) { fe.printStackTrace(); } } }
From source file:htmlwordtag.HtmlWordTag.java
public static void main(String[] args) throws RepositoryException, MalformedQueryException, QueryEvaluationException { //get current path String current = System.getProperty("user.dir"); //get html file from internet loadhtml();//from w w w. j a va2s .c o m //make director for output verifyArgs(); //translate html file to rdf HtmlWordTag httpClientPost = new HtmlWordTag(); httpClientPost.input = new File("input"); httpClientPost.output = new File("output"); httpClientPost.client = new HttpClient(); httpClientPost.client.getParams().setParameter("http.useragent", "Calais Rest Client"); httpClientPost.run(); //create main memory repository Repository repo = new SailRepository(new MemoryStore()); repo.initialize(); File file = new File(current + "\\output\\website1.html.xml"); RepositoryConnection con = repo.getConnection(); try { con.add(file, null, RDFFormat.RDFXML); } catch (OpenRDFException e) { // handle exception } catch (java.io.IOException e) { // handle io exception } System.out.println(con.isEmpty()); //query entire repostiory String queryString = "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n" + "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n" + "PREFIX c: <http://s.opencalais.com/1/type/em/e/>\n" + "PREFIX p: <http://s.opencalais.com/1/pred/>\n" + "PREFIX geo: <http://s.opencalais.com/1/type/er/Geo/>\n" + "SELECT distinct ?s ?n\n" + "WHERE {\n" + "{ ?s rdf:type c:Organization.\n" + " ?s p:name ?n.\n}" + " UNION \n" + "{ ?s rdf:type c:Person.\n" + " ?s p:name ?n.\n}" + " UNION \n" + "{ ?s rdf:type geo:City.\n" + " ?s p:name ?n.\n}" + "}"; //System.out.println(queryString); //insert query through sparql repository connection TupleQuery tupleQuery = con.prepareTupleQuery(QueryLanguage.SPARQL, queryString); TupleQueryResult result = tupleQuery.evaluate(); File queryresultdir = new File(current + "\\queryresult"); if (!queryresultdir.exists()) { if (queryresultdir.mkdir()) { System.out.println("Directory is created!"); } else { System.out.println("Failed to create directory!"); } } File queryresult = null; try { // create new file queryresult = new File(current + "\\queryresult\\queryresult1.txt"); // tries to create new file in the system if (queryresult.exists()) { if (queryresult.delete()) { System.out.println("file queryresult1.txt is already exist."); System.out.println("file queryresult1.txt has been delete."); if (queryresult.createNewFile()) { System.out.println("create queryresult1.txt success"); } else { System.out.println("fail to create queryresult1.txt"); } } else { System.out.println("fail to delete queryresult1.txt."); } } else { if (queryresult.createNewFile()) { System.out.println("create queryresult1.txt success"); } else { System.out.println("fail to create queryresult1.txt"); } } } catch (Exception e) { e.printStackTrace(); } try { PrintWriter outputStream = null; try { outputStream = new PrintWriter(new FileOutputStream(current + "\\queryresult\\queryresult1.txt")); } catch (FileNotFoundException e) { System.out.println("Error to find file queryresult1.txt"); System.exit(0); } //go through all triple in sparql repository while (result.hasNext()) { // iterate over the result BindingSet bindingSet = result.next(); Value valueOfS = bindingSet.getValue("s"); Value valueOfN = bindingSet.getValue("n"); System.out.println(valueOfS + " " + valueOfN); outputStream.println(valueOfS + " " + valueOfN); } outputStream.close(); } finally { result.close(); } //create main memory repository Repository repo2 = new SailRepository(new MemoryStore()); repo2.initialize(); File file2 = new File(current + "\\output\\website2.html.xml"); RepositoryConnection con2 = repo2.getConnection(); try { con2.add(file2, null, RDFFormat.RDFXML); } catch (OpenRDFException e) { // handle exception } catch (java.io.IOException e) { // handle io exception } System.out.println(con2.isEmpty()); //query entire repostiory String queryString2 = "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n" + "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n" + "PREFIX c: <http://s.opencalais.com/1/type/em/e/>\n" + "PREFIX p: <http://s.opencalais.com/1/pred/>\n" + "PREFIX geo: <http://s.opencalais.com/1/type/er/Geo/>\n" + "SELECT distinct ?s ?n\n" + "WHERE {\n" + "{ ?s rdf:type c:Organization.\n" + " ?s p:name ?n.\n}" + " UNION \n" + "{ ?s rdf:type c:Person.\n" + " ?s p:name ?n.\n}" + " UNION \n" + "{ ?s rdf:type geo:City.\n" + " ?s p:name ?n.\n}" + "}"; //System.out.println(queryString2); //insert query through sparql repository connection TupleQuery tupleQuery2 = con2.prepareTupleQuery(QueryLanguage.SPARQL, queryString2); TupleQueryResult result2 = tupleQuery2.evaluate(); File queryresult2 = null; try { // create new file queryresult2 = new File(current + "\\queryresult\\queryresult2.txt"); // tries to create new file in the system if (queryresult2.exists()) { if (queryresult2.delete()) { System.out.println("file queryresult2.txt is already exist."); System.out.println("file queryresult2.txt has been delete."); if (queryresult2.createNewFile()) { System.out.println("create queryresult2.txt success"); } else { System.out.println("fail to create queryresult2.txt"); } } else { System.out.println("fail to delete queryresult2.txt."); } } else { if (queryresult2.createNewFile()) { System.out.println("create queryresult2.txt success"); } else { System.out.println("fail to create queryresult2.txt"); } } } catch (Exception e) { e.printStackTrace(); } try { PrintWriter outputStream2 = null; try { outputStream2 = new PrintWriter(new FileOutputStream(current + "\\queryresult\\queryresult2.txt")); } catch (FileNotFoundException e) { System.out.println("Error to find file queryresult2.txt"); System.exit(0); } //go through all triple in sparql repository while (result2.hasNext()) { // iterate over the result BindingSet bindingSet = result2.next(); Value valueOfS = bindingSet.getValue("s"); Value valueOfN = bindingSet.getValue("n"); System.out.println(valueOfS + " " + valueOfN); outputStream2.println(valueOfS + " " + valueOfN); } outputStream2.close(); } finally { result2.close(); } }
From source file:com.leosys.core.utils.SendMessage.java
public static String postMessage(String phoneNo, String sendText) throws IOException { HttpClient client = new HttpClient(); PostMethod post = new PostMethod("http://sms.webchinese.cn/web_api/"); post.addRequestHeader("Content-Type", "application/x-www-form-urlencoded;charset=gbk");// ? NameValuePair[] data = { new NameValuePair("Uid", "fanyy"), // ?? new NameValuePair("Key", "694de3e5ca9f7015eaef"), // ??, new NameValuePair("smsMob", phoneNo), // ?? new NameValuePair("smsText", sendText + "??") };// post.setRequestBody(data);//from w w w.ja v a 2 s . c o m client.executeMethod(post); Header[] headers = post.getResponseHeaders(); int statusCode = post.getStatusCode(); System.out.println("statusCode:" + statusCode); for (Header h : headers) { System.out.println(h.toString()); } String result = new String(post.getResponseBodyAsString().getBytes("gbk")); System.out.println(result); post.releaseConnection(); return result; }
From source file:de.mpg.imeji.presentation.util.UrlHelper.java
public static boolean isValidURI(URI uri) { try {// ww w . jav a2s . c o m HttpClient client = new HttpClient(); GetMethod method = new GetMethod(uri.toString()); client.executeMethod(method); return true; } catch (Exception e) { BeanHelper.error(((SessionBean) BeanHelper.getSessionBean(SessionBean.class)).getMessage("error") + " (Non valid URL): " + e); } return false; }
From source file:de.mpg.imeji.presentation.util.SearchAndExportHelper.java
public static String getCitation(Publication publication) { URI uri = publication.getUri(); URI searchAndExportUri = URI.create("http://" + uri.getHost() + "/search/SearchAndExport"); String itemId = null;/* w w w . j a v a 2 s. co m*/ if (uri.getQuery() != null && uri.getQuery().contains("itemId=")) { itemId = uri.getQuery().split("itemId=")[1]; } else if (uri.getPath() != null && uri.getPath().contains("/item/")) { itemId = uri.getPath().split("/item/")[1]; } if (UrlHelper.isValidURI(searchAndExportUri)) { try { HttpClient client = new HttpClient(); String exportUri = searchAndExportUri.toString() + "?cqlQuery=" + URLEncoder.encode( "escidoc.objid=" + itemId + " or escidoc.property.version.objid=" + itemId, "ISO-8859-1") + "&exportFormat=" + publication.getExportFormat() + "&outputFormat=html_linked"; GetMethod method = new GetMethod(exportUri); client.executeMethod(method); return method.getResponseBodyAsString(); } catch (Exception e) { return null; } } return null; }
From source file:com.oneapm.base.tools.UrlPostMethod.java
public static void urlPostMethod(String url, String json) { HttpClient httpClient = new HttpClient(); PostMethod method = new PostMethod(url); try {/*from w w w .ja v a2s.com*/ if (json != null && !json.trim().equals("")) { RequestEntity requestEntity = new StringRequestEntity(json, "application/x-www-form-urlencoded", "utf-8"); method.setRequestEntity(requestEntity); } long startTime = System.currentTimeMillis(); int x = httpClient.executeMethod(method); long elapsedTime = System.currentTimeMillis(); System.out.println(x + ":" + (elapsedTime - startTime)); } catch (IOException e) { e.printStackTrace(); } finally { method.releaseConnection(); } }
From source file:com.renlg.util.NetAssist.java
public static String delegateGet(String url) { StringBuffer response = new StringBuffer(); HttpClient client = new HttpClient(); HttpMethod method = null;/* w ww.j a v a2 s .com*/ try { method = new GetMethod(url); client.executeMethod(method); if (method.getStatusCode() == HttpStatus.SC_OK) { BufferedReader reader = new BufferedReader( new InputStreamReader(method.getResponseBodyAsStream(), "utf8")); String line; while ((line = reader.readLine()) != null) { response.append(line); } reader.close(); } } catch (Exception e) { log.error("HTTP Get" + url + "??", e); } finally { if (method != null) method.releaseConnection(); } return response.toString(); }