List of usage examples for org.dom4j.io SAXReader read
public Document read(InputSource in) throws DocumentException
Reads a Document from the given InputSource using SAX
From source file:bio2rdf.datahub_get_stats_0_1.datahub_get_stats.java
License:Apache License
public void tHttpRequest_1Process(final java.util.Map<String, Object> globalMap) throws TalendException { globalMap.put("tHttpRequest_1_SUBPROCESS_STATE", 0); final boolean execStat = this.execStat; String iterateId = ""; int iterateLoop = 0; String currentComponent = ""; java.util.Map<String, Object> resourceMap = new java.util.HashMap<String, Object>(); try {//from www . jav a2s . c o m String currentMethodName = new java.lang.Exception().getStackTrace()[0].getMethodName(); boolean resumeIt = currentMethodName.equals(resumeEntryMethodName); if (resumeEntryMethodName == null || resumeIt || globalResumeTicket) {// start // the // resume globalResumeTicket = true; row6Struct row6 = new row6Struct(); row7Struct row7 = new row7Struct(); row8Struct row8 = new row8Struct(); row9Struct row9 = new row9Struct(); row10Struct row10 = new row10Struct(); row10Struct row5 = row10; /** * [tBufferOutput_1 begin ] start */ ok_Hash.put("tBufferOutput_1", false); start_Hash.put("tBufferOutput_1", System.currentTimeMillis()); currentComponent = "tBufferOutput_1"; int tos_count_tBufferOutput_1 = 0; /** * [tBufferOutput_1 begin ] stop */ /** * [tLogRow_2 begin ] start */ ok_Hash.put("tLogRow_2", false); start_Hash.put("tLogRow_2", System.currentTimeMillis()); currentComponent = "tLogRow_2"; int tos_count_tLogRow_2 = 0; /** * [tLogRow_2 begin ] stop */ /** * [tFilterRow_1 begin ] start */ ok_Hash.put("tFilterRow_1", false); start_Hash.put("tFilterRow_1", System.currentTimeMillis()); currentComponent = "tFilterRow_1"; int tos_count_tFilterRow_1 = 0; int nb_line_tFilterRow_1 = 0; int nb_line_ok_tFilterRow_1 = 0; int nb_line_reject_tFilterRow_1 = 0; class Operator_tFilterRow_1 { private String sErrorMsg = ""; private boolean bMatchFlag = true; private String sUnionFlag = "&&"; public Operator_tFilterRow_1(String unionFlag) { sUnionFlag = unionFlag; bMatchFlag = "||".equals(unionFlag) ? false : true; } public String getErrorMsg() { if (sErrorMsg != null && sErrorMsg.length() > 1) return sErrorMsg.substring(1); else return null; } public boolean getMatchFlag() { return bMatchFlag; } public void matches(boolean partMatched, String reason) { // no need to care about the next judgement if ("||".equals(sUnionFlag) && bMatchFlag) { return; } if (!partMatched) { sErrorMsg += "|" + reason; } if ("||".equals(sUnionFlag)) bMatchFlag = bMatchFlag || partMatched; else bMatchFlag = bMatchFlag && partMatched; } } /** * [tFilterRow_1 begin ] stop */ /** * [tJavaRow_2 begin ] start */ ok_Hash.put("tJavaRow_2", false); start_Hash.put("tJavaRow_2", System.currentTimeMillis()); currentComponent = "tJavaRow_2"; int tos_count_tJavaRow_2 = 0; int nb_line_tJavaRow_2 = 0; /** * [tJavaRow_2 begin ] stop */ /** * [tExtractRegexFields_1 begin ] start */ ok_Hash.put("tExtractRegexFields_1", false); start_Hash.put("tExtractRegexFields_1", System.currentTimeMillis()); currentComponent = "tExtractRegexFields_1"; int tos_count_tExtractRegexFields_1 = 0; java.util.regex.Pattern pattern_tExtractRegexFields_1 = java.util.regex.Pattern .compile("http:\\/\\/bio2rdf.org\\/(.*)_vocabulary:Resource"); /** * [tExtractRegexFields_1 begin ] stop */ /** * [tExtractJSONFields_1 begin ] start */ ok_Hash.put("tExtractJSONFields_1", false); start_Hash.put("tExtractJSONFields_1", System.currentTimeMillis()); currentComponent = "tExtractJSONFields_1"; int tos_count_tExtractJSONFields_1 = 0; int nb_line_tExtractJSONFields_1 = 0; class ConvertJSONString_tExtractJSONFields_1 { final static int Brace = 0; // { final static int Bracket = 1; // [ private int barceType = -1; private String originalJsonString = ""; private String originalLoopString = ""; private String jsonString4XML = null; private String loopString4XML = null; private String additionRoot = null; public void barceType() { for (int c = 0; c < originalJsonString.length(); ++c) { if (originalJsonString.charAt(c) == '{') { barceType = Brace; break; } else if (originalJsonString.charAt(c) == '[') { barceType = Bracket; break; } } } public void setJsonString(String originalJsonString) { this.originalJsonString = originalJsonString; } public void setLoopString(String originalLoopString) { this.originalLoopString = originalLoopString; } public String getJsonString4XML() { return jsonString4XML; } public String getLoopString4XML() { if (loopString4XML.length() > 1 && loopString4XML.endsWith("/")) { loopString4XML = loopString4XML.substring(0, loopString4XML.length() - 1); } return loopString4XML; } public void setAdditionRoot(String additionRoot) { this.additionRoot = additionRoot; } public String getAdditionRoot() { return additionRoot; } public void generate() { barceType(); jsonString4XML = originalJsonString; loopString4XML = originalLoopString; if (Brace == barceType) { if (isNeedAddRoot(originalJsonString)) { jsonString4XML = "{ \"root\": " + originalJsonString + " }"; loopString4XML = "root" + originalLoopString; setAdditionRoot("root"); } } else if (Bracket == barceType) { jsonString4XML = "{ \"root\" : { \"object\": " + originalJsonString + " } }"; loopString4XML = "root/object" + originalLoopString; setAdditionRoot("object"); } } public boolean isNeedAddRoot(String originalJsonString) { boolean isNeedAddRoot = false; net.sf.json.JSONObject jso = net.sf.json.JSONObject.fromObject(originalJsonString); String jsonKey = ""; Object firstObject = null; if (jso.names().size() == 1) { jsonKey = jso.names().get(0).toString(); firstObject = jso.get(jsonKey); } if (jso.size() > 1 || (firstObject != null && firstObject instanceof net.sf.json.JSONArray && ((net.sf.json.JSONArray) firstObject).size() > 1)) { isNeedAddRoot = true; } return isNeedAddRoot; } } ConvertJSONString_tExtractJSONFields_1 cjs_tExtractJSONFields_1 = new ConvertJSONString_tExtractJSONFields_1(); de.odysseus.staxon.json.JsonXMLConfig config_tExtractJSONFields_1 = new de.odysseus.staxon.json.JsonXMLConfigBuilder() .multiplePI(false).build(); de.odysseus.staxon.json.JsonXMLInputFactory jsonXMLInputFactory_tExtractJSONFields_1 = new de.odysseus.staxon.json.JsonXMLInputFactory( config_tExtractJSONFields_1); javax.xml.stream.XMLOutputFactory xmlOutputFactory_tExtractJSONFields_1 = javax.xml.stream.XMLOutputFactory .newInstance(); boolean isGetWholeJson_tExtractJSONFields_1 = false; class OriginalJSONString_tExtractJSONFields_1 { } OriginalJSONString_tExtractJSONFields_1 originalJSONString_tExtractJSONFields_1 = new OriginalJSONString_tExtractJSONFields_1(); class XML_API_tExtractJSONFields_1 { public boolean isDefNull(org.dom4j.Node node) throws javax.xml.transform.TransformerException { if (node != null && node instanceof org.dom4j.Element) { org.dom4j.Attribute attri = ((org.dom4j.Element) node).attribute("nil"); if (attri != null && ("true").equals(attri.getText())) { return true; } } return false; } public boolean isMissing(org.dom4j.Node node) throws javax.xml.transform.TransformerException { return node == null ? true : false; } public boolean isEmpty(org.dom4j.Node node) throws javax.xml.transform.TransformerException { if (node != null) { return node.getText().length() == 0; } return false; } } String jsonStr_tExtractJSONFields_1 = ""; String xmlStr_tExtractJSONFields_1 = ""; XML_API_tExtractJSONFields_1 xml_api_tExtractJSONFields_1 = new XML_API_tExtractJSONFields_1(); /** * [tExtractJSONFields_1 begin ] stop */ /** * [tHttpRequest_1 begin ] start */ ok_Hash.put("tHttpRequest_1", false); start_Hash.put("tHttpRequest_1", System.currentTimeMillis()); currentComponent = "tHttpRequest_1"; int tos_count_tHttpRequest_1 = 0; /** * [tHttpRequest_1 begin ] stop */ /** * [tHttpRequest_1 main ] start */ currentComponent = "tHttpRequest_1"; java.net.URL url_tHttpRequest_1 = new java.net.URL("http://" + context.endpoint_namespace + ".bio2rdf.org/sparql?default-graph-uri=&query=PREFIX+void%3A+%3Chttp%3A%2F%2Frdfs.org%2Fns%2Fvoid%23%3E%0D%0APREFIX+ds%3A+%3Chttp%3A%2F%2Fbio2rdf.org%2Fbio2rdf.dataset_vocabulary%3A%3E%0D%0A%0D%0ASELECT+*%0D%0A+%7B+%5B%5D+void%3Asubset+%5B%0D%0A+++++++a+ds%3ADataset-Type-Count%3B%0D%0A+++++++void%3Aclass+%3Flink%3B%0D%0A+++++++void%3AdistinctEntities+%3FdistinctCount%3B%0D%0A+++%5D%0D%0A+++FILTER+regex%28str%28%3Flink%29%2C+%27.*bio2rdf.org%5C%5C%2F.*_vocabulary%3AResource%27%2C+%27i%27%29%0D%0A+%7D&format=application%2Fsparql-results%2Bjson&timeout=0&debug=on"); java.net.HttpURLConnection urlConn_tHttpRequest_1 = (java.net.HttpURLConnection) url_tHttpRequest_1 .openConnection(); urlConn_tHttpRequest_1.setRequestMethod("GET"); urlConn_tHttpRequest_1.setDoOutput(true); urlConn_tHttpRequest_1.setDoInput(true); urlConn_tHttpRequest_1.setUseCaches(false); urlConn_tHttpRequest_1.connect(); byte[] buffer_tHttpRequest_1 = new byte[1024]; int bos_buffer_tHttpRequest_1 = 0; StringBuilder sb_tHttpRequest_1 = new StringBuilder(); if (java.net.HttpURLConnection.HTTP_OK == (urlConn_tHttpRequest_1.getResponseCode())) { java.io.InputStream bis_tHttpRequest_1 = new java.io.BufferedInputStream( urlConn_tHttpRequest_1.getInputStream()); while ((bos_buffer_tHttpRequest_1 = bis_tHttpRequest_1.read(buffer_tHttpRequest_1)) != -1) { sb_tHttpRequest_1.append(new String(buffer_tHttpRequest_1, 0, bos_buffer_tHttpRequest_1)); } bis_tHttpRequest_1.close(); } else { System.err.println(urlConn_tHttpRequest_1.getResponseCode() + " " + urlConn_tHttpRequest_1.getResponseMessage()); } row6.ResponseContent = sb_tHttpRequest_1.toString(); urlConn_tHttpRequest_1.disconnect(); tos_count_tHttpRequest_1++; /** * [tHttpRequest_1 main ] stop */ /** * [tExtractJSONFields_1 main ] start */ currentComponent = "tExtractJSONFields_1"; if (row6.ResponseContent != null) {// C_01 jsonStr_tExtractJSONFields_1 = row6.ResponseContent.toString(); row7 = null; org.dom4j.io.SAXReader reader_tExtractJSONFields_1 = new org.dom4j.io.SAXReader(); org.dom4j.Document doc_tExtractJSONFields_1 = null; java.util.HashMap xmlNameSpaceMap_tExtractJSONFields_1 = new java.util.HashMap<String, String>(); org.dom4j.XPath x_tExtractJSONFields_1 = null; java.util.List<org.dom4j.tree.AbstractNode> nodeList_tExtractJSONFields_1 = null; boolean isStructError_tExtractJSONFields_1 = true; String loopQuery_tExtractJSONFields_1 = "/results/bindings"; String oraginalJsonStr_tExtractJSONFields_1 = jsonStr_tExtractJSONFields_1; cjs_tExtractJSONFields_1.setJsonString(jsonStr_tExtractJSONFields_1); cjs_tExtractJSONFields_1.setLoopString(loopQuery_tExtractJSONFields_1); java.io.ByteArrayInputStream bais_tExtractJSONFields_1 = null; java.io.ByteArrayOutputStream baos_tExtractJSONFields_1 = new java.io.ByteArrayOutputStream(); try { cjs_tExtractJSONFields_1.generate(); jsonStr_tExtractJSONFields_1 = cjs_tExtractJSONFields_1.getJsonString4XML(); loopQuery_tExtractJSONFields_1 = cjs_tExtractJSONFields_1.getLoopString4XML(); bais_tExtractJSONFields_1 = new ByteArrayInputStream( jsonStr_tExtractJSONFields_1.getBytes("UTF-8")); javax.xml.stream.XMLEventReader xmlEventReader_tExtractJSONFields_1 = jsonXMLInputFactory_tExtractJSONFields_1 .createXMLEventReader(bais_tExtractJSONFields_1); javax.xml.stream.XMLEventWriter xmLEventWriter_tExtractJSONFields_1 = xmlOutputFactory_tExtractJSONFields_1 .createXMLEventWriter(baos_tExtractJSONFields_1, "UTF-8"); xmLEventWriter_tExtractJSONFields_1.add(xmlEventReader_tExtractJSONFields_1); // convert json string to xml xmlStr_tExtractJSONFields_1 = baos_tExtractJSONFields_1.toString(); xmLEventWriter_tExtractJSONFields_1.close(); xmlEventReader_tExtractJSONFields_1.close(); doc_tExtractJSONFields_1 = reader_tExtractJSONFields_1 .read(new java.io.StringReader(xmlStr_tExtractJSONFields_1)); x_tExtractJSONFields_1 = doc_tExtractJSONFields_1 .createXPath(loopQuery_tExtractJSONFields_1); x_tExtractJSONFields_1.setNamespaceURIs(xmlNameSpaceMap_tExtractJSONFields_1); nodeList_tExtractJSONFields_1 = (java.util.List<org.dom4j.tree.AbstractNode>) x_tExtractJSONFields_1 .selectNodes(doc_tExtractJSONFields_1); isStructError_tExtractJSONFields_1 = false; } catch (java.lang.Exception ex_tExtractJSONFields_1) { System.err.println(ex_tExtractJSONFields_1.getMessage()); } finally { baos_tExtractJSONFields_1.close(); if (bais_tExtractJSONFields_1 != null) { bais_tExtractJSONFields_1.close(); } } org.dom4j.Node node_tExtractJSONFields_1 = null; String str_tExtractJSONFields_1 = ""; for (int i_tExtractJSONFields_1 = 0; isStructError_tExtractJSONFields_1 || (nodeList_tExtractJSONFields_1 != null && i_tExtractJSONFields_1 < nodeList_tExtractJSONFields_1 .size()); i_tExtractJSONFields_1++) { if (!isStructError_tExtractJSONFields_1) { row7 = null; row7 = new row7Struct(); org.dom4j.tree.AbstractNode temp_tExtractJSONFields_1 = nodeList_tExtractJSONFields_1 .get(i_tExtractJSONFields_1); nb_line_tExtractJSONFields_1++; try { org.dom4j.XPath xTmp0_tExtractJSONFields_1 = temp_tExtractJSONFields_1 .createXPath("link/value"); xTmp0_tExtractJSONFields_1.setNamespaceURIs(xmlNameSpaceMap_tExtractJSONFields_1); Object obj0_tExtractJSONFields_1 = xTmp0_tExtractJSONFields_1 .evaluate(temp_tExtractJSONFields_1); if (obj0_tExtractJSONFields_1 instanceof String || obj0_tExtractJSONFields_1 instanceof Number) { node_tExtractJSONFields_1 = temp_tExtractJSONFields_1; str_tExtractJSONFields_1 = String.valueOf(obj0_tExtractJSONFields_1); } else { node_tExtractJSONFields_1 = xTmp0_tExtractJSONFields_1 .selectSingleNode(temp_tExtractJSONFields_1); str_tExtractJSONFields_1 = xTmp0_tExtractJSONFields_1 .valueOf(temp_tExtractJSONFields_1); } if (xml_api_tExtractJSONFields_1.isDefNull(node_tExtractJSONFields_1)) { row7.link = null; } else if (xml_api_tExtractJSONFields_1.isEmpty(node_tExtractJSONFields_1)) { row7.link = ""; } else if (xml_api_tExtractJSONFields_1.isMissing(node_tExtractJSONFields_1)) { row7.link = null; } else { row7.link = str_tExtractJSONFields_1; } org.dom4j.XPath xTmp1_tExtractJSONFields_1 = temp_tExtractJSONFields_1 .createXPath("distinctCount/value"); xTmp1_tExtractJSONFields_1.setNamespaceURIs(xmlNameSpaceMap_tExtractJSONFields_1); Object obj1_tExtractJSONFields_1 = xTmp1_tExtractJSONFields_1 .evaluate(temp_tExtractJSONFields_1); if (obj1_tExtractJSONFields_1 instanceof String || obj1_tExtractJSONFields_1 instanceof Number) { node_tExtractJSONFields_1 = temp_tExtractJSONFields_1; str_tExtractJSONFields_1 = String.valueOf(obj1_tExtractJSONFields_1); } else { node_tExtractJSONFields_1 = xTmp1_tExtractJSONFields_1 .selectSingleNode(temp_tExtractJSONFields_1); str_tExtractJSONFields_1 = xTmp1_tExtractJSONFields_1 .valueOf(temp_tExtractJSONFields_1); } if (xml_api_tExtractJSONFields_1.isDefNull(node_tExtractJSONFields_1)) { row7.count = null; } else if (xml_api_tExtractJSONFields_1.isEmpty(node_tExtractJSONFields_1)) { row7.count = ""; } else if (xml_api_tExtractJSONFields_1.isMissing(node_tExtractJSONFields_1)) { row7.count = null; } else { row7.count = str_tExtractJSONFields_1; } } catch (java.lang.Exception ex_tExtractJSONFields_1) { System.err.println(ex_tExtractJSONFields_1.getMessage()); row7 = null; } } isStructError_tExtractJSONFields_1 = false; tos_count_tExtractJSONFields_1++; /** * [tExtractJSONFields_1 main ] stop */ // Start of branch "row7" if (row7 != null) { /** * [tExtractRegexFields_1 main ] start */ currentComponent = "tExtractRegexFields_1"; row8 = null; if (row7.link != null) {// C_01 java.util.regex.Matcher matcher_tExtractRegexFields_1 = pattern_tExtractRegexFields_1 .matcher(row7.link); int groupCount_tExtractRegexFields_1 = matcher_tExtractRegexFields_1.groupCount(); while (matcher_tExtractRegexFields_1.find()) { try { row8 = new row8Struct(); row8.count = row7.count; String temp_tExtractRegexFields_1 = null; row8.linkNamespace = groupCount_tExtractRegexFields_1 <= 0 ? "" : matcher_tExtractRegexFields_1.group(1); } catch (java.lang.Exception ex_tExtractRegexFields_1) { throw (ex_tExtractRegexFields_1); } tos_count_tExtractRegexFields_1++; /** * [tExtractRegexFields_1 main ] stop */ // Start of branch "row8" if (row8 != null) { /** * [tJavaRow_2 main ] start */ currentComponent = "tJavaRow_2"; // Code gnr selon le schmas d'entre // et de sortie row9.link = row8.linkNamespace; row9.stat = row8.count; nb_line_tJavaRow_2++; tos_count_tJavaRow_2++; /** * [tJavaRow_2 main ] stop */ /** * [tFilterRow_1 main ] start */ currentComponent = "tFilterRow_1"; row10 = null; Operator_tFilterRow_1 ope_tFilterRow_1 = new Operator_tFilterRow_1("&&"); ope_tFilterRow_1.matches((// code sample : use // row9 to define // the condition. // row9.columnName1.equals("foo") // ||!(row9.columnName2.equals("bar")) // replace the following // expression by your // own filter condition !row9.link.contains(".") && !row9.link.contains(" ") && !row9.link.equals(context.endpoint_namespace)), "advanced condition failed"); if (ope_tFilterRow_1.getMatchFlag()) { if (row10 == null) { row10 = new row10Struct(); } row10.link = row9.link; row10.stat = row9.stat; nb_line_ok_tFilterRow_1++; } else { nb_line_reject_tFilterRow_1++; } nb_line_tFilterRow_1++; tos_count_tFilterRow_1++; /** * [tFilterRow_1 main ] stop */ // Start of branch "row10" if (row10 != null) { /** * [tLogRow_2 main ] start */ currentComponent = "tLogRow_2"; row5 = row10; tos_count_tLogRow_2++; /** * [tLogRow_2 main ] stop */ /** * [tBufferOutput_1 main ] start */ currentComponent = "tBufferOutput_1"; String[] row_tBufferOutput_1 = new String[] { "", "", }; if (row5.link != null) { row_tBufferOutput_1[0] = row5.link; } else { row_tBufferOutput_1[0] = null; } if (row5.stat != null) { row_tBufferOutput_1[1] = row5.stat; } else { row_tBufferOutput_1[1] = null; } globalBuffer.add(row_tBufferOutput_1); tos_count_tBufferOutput_1++; /** * [tBufferOutput_1 main ] stop */ } // End of branch "row10" } // End of branch "row8" // end for } } // C_01 } // End of branch "row7" // end for } } // C_01 /** * [tHttpRequest_1 end ] start */ currentComponent = "tHttpRequest_1"; ok_Hash.put("tHttpRequest_1", true); end_Hash.put("tHttpRequest_1", System.currentTimeMillis()); /** * [tHttpRequest_1 end ] stop */ /** * [tExtractJSONFields_1 end ] start */ currentComponent = "tExtractJSONFields_1"; globalMap.put("tExtractJSONFields_1_NB_LINE", nb_line_tExtractJSONFields_1); ok_Hash.put("tExtractJSONFields_1", true); end_Hash.put("tExtractJSONFields_1", System.currentTimeMillis()); /** * [tExtractJSONFields_1 end ] stop */ /** * [tExtractRegexFields_1 end ] start */ currentComponent = "tExtractRegexFields_1"; ok_Hash.put("tExtractRegexFields_1", true); end_Hash.put("tExtractRegexFields_1", System.currentTimeMillis()); /** * [tExtractRegexFields_1 end ] stop */ /** * [tJavaRow_2 end ] start */ currentComponent = "tJavaRow_2"; globalMap.put("tJavaRow_2_NB_LINE", nb_line_tJavaRow_2); ok_Hash.put("tJavaRow_2", true); end_Hash.put("tJavaRow_2", System.currentTimeMillis()); /** * [tJavaRow_2 end ] stop */ /** * [tFilterRow_1 end ] start */ currentComponent = "tFilterRow_1"; globalMap.put("tFilterRow_1_NB_LINE", nb_line_tFilterRow_1); globalMap.put("tFilterRow_1_NB_LINE_OK", nb_line_ok_tFilterRow_1); globalMap.put("tFilterRow_1_NB_LINE_REJECT", nb_line_reject_tFilterRow_1); ok_Hash.put("tFilterRow_1", true); end_Hash.put("tFilterRow_1", System.currentTimeMillis()); /** * [tFilterRow_1 end ] stop */ /** * [tLogRow_2 end ] start */ currentComponent = "tLogRow_2"; ok_Hash.put("tLogRow_2", true); end_Hash.put("tLogRow_2", System.currentTimeMillis()); /** * [tLogRow_2 end ] stop */ /** * [tBufferOutput_1 end ] start */ currentComponent = "tBufferOutput_1"; ok_Hash.put("tBufferOutput_1", true); end_Hash.put("tBufferOutput_1", System.currentTimeMillis()); /** * [tBufferOutput_1 end ] stop */ } // end the resume } catch (java.lang.Exception e) { TalendException te = new TalendException(e, currentComponent, globalMap); throw te; } catch (java.lang.Error error) { throw error; } finally { try { /** * [tHttpRequest_1 finally ] start */ currentComponent = "tHttpRequest_1"; /** * [tHttpRequest_1 finally ] stop */ /** * [tExtractJSONFields_1 finally ] start */ currentComponent = "tExtractJSONFields_1"; /** * [tExtractJSONFields_1 finally ] stop */ /** * [tExtractRegexFields_1 finally ] start */ currentComponent = "tExtractRegexFields_1"; /** * [tExtractRegexFields_1 finally ] stop */ /** * [tJavaRow_2 finally ] start */ currentComponent = "tJavaRow_2"; /** * [tJavaRow_2 finally ] stop */ /** * [tFilterRow_1 finally ] start */ currentComponent = "tFilterRow_1"; /** * [tFilterRow_1 finally ] stop */ /** * [tLogRow_2 finally ] start */ currentComponent = "tLogRow_2"; /** * [tLogRow_2 finally ] stop */ /** * [tBufferOutput_1 finally ] start */ currentComponent = "tBufferOutput_1"; /** * [tBufferOutput_1 finally ] stop */ } catch (java.lang.Exception e) { // ignore } catch (java.lang.Error error) { // ignore } resourceMap = null; } globalMap.put("tHttpRequest_1_SUBPROCESS_STATE", 1); }
From source file:bio2rdf.upload_all_datasets_0_1.upload_all_datasets.java
License:Apache License
public void tFileList_3Process(final java.util.Map<String, Object> globalMap) throws TalendException { globalMap.put("tFileList_3_SUBPROCESS_STATE", 0); final boolean execStat = this.execStat; String iterateId = ""; int iterateLoop = 0; String currentComponent = ""; java.util.Map<String, Object> resourceMap = new java.util.HashMap<String, Object>(); try {/*from w w w . j a va 2s . co m*/ String currentMethodName = new java.lang.Exception().getStackTrace()[0].getMethodName(); boolean resumeIt = currentMethodName.equals(resumeEntryMethodName); if (resumeEntryMethodName == null || resumeIt || globalResumeTicket) {// start // the // resume globalResumeTicket = true; row6Struct row6 = new row6Struct(); row4Struct row4 = new row4Struct(); row7Struct row7 = new row7Struct(); /** * [tFileList_3 begin ] start */ int NB_ITERATE_tHttpRequest_4 = 0; // for statistics ok_Hash.put("tFileList_3", false); start_Hash.put("tFileList_3", System.currentTimeMillis()); currentComponent = "tFileList_3"; int tos_count_tFileList_3 = 0; String directory_tFileList_3 = context.workspace; final java.util.List<String> maskList_tFileList_3 = new java.util.ArrayList<String>(); final java.util.List<java.util.regex.Pattern> patternList_tFileList_3 = new java.util.ArrayList<java.util.regex.Pattern>(); maskList_tFileList_3.add("datahub_import_*.json"); for (final String filemask_tFileList_3 : maskList_tFileList_3) { String filemask_compile_tFileList_3 = filemask_tFileList_3; filemask_compile_tFileList_3 = org.apache.oro.text.GlobCompiler.globToPerl5( filemask_tFileList_3.toCharArray(), org.apache.oro.text.GlobCompiler.DEFAULT_MASK); java.util.regex.Pattern fileNamePattern_tFileList_3 = java.util.regex.Pattern .compile(filemask_compile_tFileList_3); patternList_tFileList_3.add(fileNamePattern_tFileList_3); } int NB_FILEtFileList_3 = 0; final boolean case_sensitive_tFileList_3 = true; final java.util.List<java.io.File> list_tFileList_3 = new java.util.ArrayList<java.io.File>(); final java.util.List<String> filePath_tFileList_3 = new java.util.ArrayList<String>(); java.io.File file_tFileList_3 = new java.io.File(directory_tFileList_3); file_tFileList_3.listFiles(new java.io.FilenameFilter() { public boolean accept(java.io.File dir, String name) { java.io.File file = new java.io.File(dir, name); if (!file.isDirectory()) { String fileName_tFileList_3 = file.getName(); for (final java.util.regex.Pattern fileNamePattern_tFileList_3 : patternList_tFileList_3) { if (fileNamePattern_tFileList_3.matcher(fileName_tFileList_3).matches()) { if (!filePath_tFileList_3.contains(file.getAbsolutePath())) { list_tFileList_3.add(file); filePath_tFileList_3.add(file.getAbsolutePath()); } } } } return true; } }); java.util.Collections.sort(list_tFileList_3); for (int i_tFileList_3 = 0; i_tFileList_3 < list_tFileList_3.size(); i_tFileList_3++) { java.io.File files_tFileList_3 = list_tFileList_3.get(i_tFileList_3); String fileName_tFileList_3 = files_tFileList_3.getName(); String currentFileName_tFileList_3 = files_tFileList_3.getName(); String currentFilePath_tFileList_3 = files_tFileList_3.getAbsolutePath(); String currentFileDirectory_tFileList_3 = files_tFileList_3.getParent(); String currentFileExtension_tFileList_3 = null; if (files_tFileList_3.getName().contains(".") && files_tFileList_3.isFile()) { currentFileExtension_tFileList_3 = files_tFileList_3.getName() .substring(files_tFileList_3.getName().lastIndexOf(".") + 1); } else { currentFileExtension_tFileList_3 = ""; } NB_FILEtFileList_3++; globalMap.put("tFileList_3_CURRENT_FILE", currentFileName_tFileList_3); globalMap.put("tFileList_3_CURRENT_FILEPATH", currentFilePath_tFileList_3); globalMap.put("tFileList_3_CURRENT_FILEDIRECTORY", currentFileDirectory_tFileList_3); globalMap.put("tFileList_3_CURRENT_FILEEXTENSION", currentFileExtension_tFileList_3); globalMap.put("tFileList_3_NB_FILE", NB_FILEtFileList_3); /** * [tFileList_3 begin ] stop */ /** * [tFileList_3 main ] start */ currentComponent = "tFileList_3"; tos_count_tFileList_3++; /** * [tFileList_3 main ] stop */ NB_ITERATE_tHttpRequest_4++; iterateLoop++; /** * [tLogRow_4 begin ] start */ ok_Hash.put("tLogRow_4", false); start_Hash.put("tLogRow_4", System.currentTimeMillis()); currentComponent = "tLogRow_4"; int tos_count_tLogRow_4 = 0; // ///////////////////// final String OUTPUT_FIELD_SEPARATOR_tLogRow_4 = "|"; java.io.PrintStream consoleOut_tLogRow_4 = null; StringBuilder strBuffer_tLogRow_4 = null; int nb_line_tLogRow_4 = 0; // ///////////////////// /** * [tLogRow_4 begin ] stop */ /** * [tExtractJSONFields_3 begin ] start */ ok_Hash.put("tExtractJSONFields_3", false); start_Hash.put("tExtractJSONFields_3", System.currentTimeMillis()); currentComponent = "tExtractJSONFields_3"; int tos_count_tExtractJSONFields_3 = 0; int nb_line_tExtractJSONFields_3 = 0; class ConvertJSONString_tExtractJSONFields_3 { final static int Brace = 0; // { final static int Bracket = 1; // [ private int barceType = -1; private String originalJsonString = ""; private String originalLoopString = ""; private String jsonString4XML = null; private String loopString4XML = null; private String additionRoot = null; public void barceType() { for (int c = 0; c < originalJsonString.length(); ++c) { if (originalJsonString.charAt(c) == '{') { barceType = Brace; break; } else if (originalJsonString.charAt(c) == '[') { barceType = Bracket; break; } } } public void setJsonString(String originalJsonString) { this.originalJsonString = originalJsonString; } public void setLoopString(String originalLoopString) { this.originalLoopString = originalLoopString; } public String getJsonString4XML() { return jsonString4XML; } public String getLoopString4XML() { if (loopString4XML.length() > 1 && loopString4XML.endsWith("/")) { loopString4XML = loopString4XML.substring(0, loopString4XML.length() - 1); } return loopString4XML; } public void setAdditionRoot(String additionRoot) { this.additionRoot = additionRoot; } public String getAdditionRoot() { return additionRoot; } public void generate() { barceType(); jsonString4XML = originalJsonString; loopString4XML = originalLoopString; if (Brace == barceType) { if (isNeedAddRoot(originalJsonString)) { jsonString4XML = "{ \"root\": " + originalJsonString + " }"; loopString4XML = "root" + originalLoopString; setAdditionRoot("root"); } } else if (Bracket == barceType) { jsonString4XML = "{ \"root\" : { \"object\": " + originalJsonString + " } }"; loopString4XML = "root/object" + originalLoopString; setAdditionRoot("object"); } } public boolean isNeedAddRoot(String originalJsonString) { boolean isNeedAddRoot = false; net.sf.json.JSONObject jso = net.sf.json.JSONObject.fromObject(originalJsonString); String jsonKey = ""; Object firstObject = null; if (jso.names().size() == 1) { jsonKey = jso.names().get(0).toString(); firstObject = jso.get(jsonKey); } if (jso.size() > 1 || (firstObject != null && firstObject instanceof net.sf.json.JSONArray && ((net.sf.json.JSONArray) firstObject).size() > 1)) { isNeedAddRoot = true; } return isNeedAddRoot; } } ConvertJSONString_tExtractJSONFields_3 cjs_tExtractJSONFields_3 = new ConvertJSONString_tExtractJSONFields_3(); de.odysseus.staxon.json.JsonXMLConfig config_tExtractJSONFields_3 = new de.odysseus.staxon.json.JsonXMLConfigBuilder() .multiplePI(false).build(); de.odysseus.staxon.json.JsonXMLInputFactory jsonXMLInputFactory_tExtractJSONFields_3 = new de.odysseus.staxon.json.JsonXMLInputFactory( config_tExtractJSONFields_3); javax.xml.stream.XMLOutputFactory xmlOutputFactory_tExtractJSONFields_3 = javax.xml.stream.XMLOutputFactory .newInstance(); boolean isGetWholeJson_tExtractJSONFields_3 = false; class OriginalJSONString_tExtractJSONFields_3 { } OriginalJSONString_tExtractJSONFields_3 originalJSONString_tExtractJSONFields_3 = new OriginalJSONString_tExtractJSONFields_3(); class XML_API_tExtractJSONFields_3 { public boolean isDefNull(org.dom4j.Node node) throws javax.xml.transform.TransformerException { if (node != null && node instanceof org.dom4j.Element) { org.dom4j.Attribute attri = ((org.dom4j.Element) node).attribute("nil"); if (attri != null && ("true").equals(attri.getText())) { return true; } } return false; } public boolean isMissing(org.dom4j.Node node) throws javax.xml.transform.TransformerException { return node == null ? true : false; } public boolean isEmpty(org.dom4j.Node node) throws javax.xml.transform.TransformerException { if (node != null) { return node.getText().length() == 0; } return false; } } String jsonStr_tExtractJSONFields_3 = ""; String xmlStr_tExtractJSONFields_3 = ""; XML_API_tExtractJSONFields_3 xml_api_tExtractJSONFields_3 = new XML_API_tExtractJSONFields_3(); /** * [tExtractJSONFields_3 begin ] stop */ /** * [tReplicate_1 begin ] start */ ok_Hash.put("tReplicate_1", false); start_Hash.put("tReplicate_1", System.currentTimeMillis()); currentComponent = "tReplicate_1"; int tos_count_tReplicate_1 = 0; /** * [tReplicate_1 begin ] stop */ /** * [tHttpRequest_4 begin ] start */ ok_Hash.put("tHttpRequest_4", false); start_Hash.put("tHttpRequest_4", System.currentTimeMillis()); currentComponent = "tHttpRequest_4"; int tos_count_tHttpRequest_4 = 0; /** * [tHttpRequest_4 begin ] stop */ /** * [tHttpRequest_4 main ] start */ currentComponent = "tHttpRequest_4"; java.net.URL url_tHttpRequest_4 = new java.net.URL( "http://datahub.io/api/action/package_update"); java.net.HttpURLConnection urlConn_tHttpRequest_4 = (java.net.HttpURLConnection) url_tHttpRequest_4 .openConnection(); urlConn_tHttpRequest_4.setRequestMethod("POST"); urlConn_tHttpRequest_4.setDoOutput(true); urlConn_tHttpRequest_4.setDoInput(true); urlConn_tHttpRequest_4.setUseCaches(false); urlConn_tHttpRequest_4.setRequestProperty("Authorization", context.authorizationKey); urlConn_tHttpRequest_4.connect(); byte[] buffer_tHttpRequest_4 = new byte[1024]; int bos_buffer_tHttpRequest_4 = 0; StringBuilder sb_tHttpRequest_4 = new StringBuilder(); java.io.InputStream bisParam_tHttpRequest_4 = new java.io.BufferedInputStream( new java.io.FileInputStream(((String) globalMap.get("tFileList_3_CURRENT_FILEPATH")))); java.io.OutputStream bosParam_tHttpRequest_4 = new java.io.BufferedOutputStream( urlConn_tHttpRequest_4.getOutputStream()); while ((bos_buffer_tHttpRequest_4 = bisParam_tHttpRequest_4 .read(buffer_tHttpRequest_4)) != -1) { bosParam_tHttpRequest_4.write(buffer_tHttpRequest_4, 0, bos_buffer_tHttpRequest_4); } bosParam_tHttpRequest_4.flush(); bosParam_tHttpRequest_4.close(); bisParam_tHttpRequest_4.close(); if (java.net.HttpURLConnection.HTTP_OK == (urlConn_tHttpRequest_4.getResponseCode())) { java.io.InputStream bis_tHttpRequest_4 = new java.io.BufferedInputStream( urlConn_tHttpRequest_4.getInputStream()); while ((bos_buffer_tHttpRequest_4 = bis_tHttpRequest_4.read(buffer_tHttpRequest_4)) != -1) { sb_tHttpRequest_4 .append(new String(buffer_tHttpRequest_4, 0, bos_buffer_tHttpRequest_4)); } bis_tHttpRequest_4.close(); } else { System.err.println(urlConn_tHttpRequest_4.getResponseCode() + " " + urlConn_tHttpRequest_4.getResponseMessage()); } row6.ResponseContent = sb_tHttpRequest_4.toString(); urlConn_tHttpRequest_4.disconnect(); tos_count_tHttpRequest_4++; /** * [tHttpRequest_4 main ] stop */ /** * [tReplicate_1 main ] start */ currentComponent = "tReplicate_1"; row4 = new row4Struct(); row4.ResponseContent = row6.ResponseContent; tos_count_tReplicate_1++; /** * [tReplicate_1 main ] stop */ /** * [tExtractJSONFields_3 main ] start */ currentComponent = "tExtractJSONFields_3"; if (row4.ResponseContent != null) {// C_01 jsonStr_tExtractJSONFields_3 = row4.ResponseContent.toString(); row7 = null; org.dom4j.io.SAXReader reader_tExtractJSONFields_3 = new org.dom4j.io.SAXReader(); org.dom4j.Document doc_tExtractJSONFields_3 = null; java.util.HashMap xmlNameSpaceMap_tExtractJSONFields_3 = new java.util.HashMap<String, String>(); org.dom4j.XPath x_tExtractJSONFields_3 = null; java.util.List<org.dom4j.tree.AbstractNode> nodeList_tExtractJSONFields_3 = null; boolean isStructError_tExtractJSONFields_3 = true; String loopQuery_tExtractJSONFields_3 = "/result"; String oraginalJsonStr_tExtractJSONFields_3 = jsonStr_tExtractJSONFields_3; cjs_tExtractJSONFields_3.setJsonString(jsonStr_tExtractJSONFields_3); cjs_tExtractJSONFields_3.setLoopString(loopQuery_tExtractJSONFields_3); java.io.ByteArrayInputStream bais_tExtractJSONFields_3 = null; java.io.ByteArrayOutputStream baos_tExtractJSONFields_3 = new java.io.ByteArrayOutputStream(); try { cjs_tExtractJSONFields_3.generate(); jsonStr_tExtractJSONFields_3 = cjs_tExtractJSONFields_3.getJsonString4XML(); loopQuery_tExtractJSONFields_3 = cjs_tExtractJSONFields_3.getLoopString4XML(); bais_tExtractJSONFields_3 = new ByteArrayInputStream( jsonStr_tExtractJSONFields_3.getBytes("UTF-8")); javax.xml.stream.XMLEventReader xmlEventReader_tExtractJSONFields_3 = jsonXMLInputFactory_tExtractJSONFields_3 .createXMLEventReader(bais_tExtractJSONFields_3); javax.xml.stream.XMLEventWriter xmLEventWriter_tExtractJSONFields_3 = xmlOutputFactory_tExtractJSONFields_3 .createXMLEventWriter(baos_tExtractJSONFields_3, "UTF-8"); xmLEventWriter_tExtractJSONFields_3.add(xmlEventReader_tExtractJSONFields_3); // convert json string to xml xmlStr_tExtractJSONFields_3 = baos_tExtractJSONFields_3.toString(); xmLEventWriter_tExtractJSONFields_3.close(); xmlEventReader_tExtractJSONFields_3.close(); doc_tExtractJSONFields_3 = reader_tExtractJSONFields_3 .read(new java.io.StringReader(xmlStr_tExtractJSONFields_3)); x_tExtractJSONFields_3 = doc_tExtractJSONFields_3 .createXPath(loopQuery_tExtractJSONFields_3); x_tExtractJSONFields_3.setNamespaceURIs(xmlNameSpaceMap_tExtractJSONFields_3); nodeList_tExtractJSONFields_3 = (java.util.List<org.dom4j.tree.AbstractNode>) x_tExtractJSONFields_3 .selectNodes(doc_tExtractJSONFields_3); isStructError_tExtractJSONFields_3 = false; } catch (java.lang.Exception ex_tExtractJSONFields_3) { System.err.println(ex_tExtractJSONFields_3.getMessage()); } finally { baos_tExtractJSONFields_3.close(); if (bais_tExtractJSONFields_3 != null) { bais_tExtractJSONFields_3.close(); } } org.dom4j.Node node_tExtractJSONFields_3 = null; String str_tExtractJSONFields_3 = ""; for (int i_tExtractJSONFields_3 = 0; isStructError_tExtractJSONFields_3 || (nodeList_tExtractJSONFields_3 != null && i_tExtractJSONFields_3 < nodeList_tExtractJSONFields_3 .size()); i_tExtractJSONFields_3++) { if (!isStructError_tExtractJSONFields_3) { row7 = null; row7 = new row7Struct(); org.dom4j.tree.AbstractNode temp_tExtractJSONFields_3 = nodeList_tExtractJSONFields_3 .get(i_tExtractJSONFields_3); nb_line_tExtractJSONFields_3++; try { org.dom4j.XPath xTmp0_tExtractJSONFields_3 = temp_tExtractJSONFields_3 .createXPath("name"); xTmp0_tExtractJSONFields_3 .setNamespaceURIs(xmlNameSpaceMap_tExtractJSONFields_3); Object obj0_tExtractJSONFields_3 = xTmp0_tExtractJSONFields_3 .evaluate(temp_tExtractJSONFields_3); if (obj0_tExtractJSONFields_3 instanceof String || obj0_tExtractJSONFields_3 instanceof Number) { node_tExtractJSONFields_3 = temp_tExtractJSONFields_3; str_tExtractJSONFields_3 = String.valueOf(obj0_tExtractJSONFields_3); } else { node_tExtractJSONFields_3 = xTmp0_tExtractJSONFields_3 .selectSingleNode(temp_tExtractJSONFields_3); str_tExtractJSONFields_3 = xTmp0_tExtractJSONFields_3 .valueOf(temp_tExtractJSONFields_3); } if (xml_api_tExtractJSONFields_3.isDefNull(node_tExtractJSONFields_3)) { row7.ResponseContent = null; } else if (xml_api_tExtractJSONFields_3.isEmpty(node_tExtractJSONFields_3)) { row7.ResponseContent = ""; } else if (xml_api_tExtractJSONFields_3.isMissing(node_tExtractJSONFields_3)) { row7.ResponseContent = null; } else { row7.ResponseContent = str_tExtractJSONFields_3; } } catch (java.lang.Exception ex_tExtractJSONFields_3) { System.err.println(ex_tExtractJSONFields_3.getMessage()); row7 = null; } } isStructError_tExtractJSONFields_3 = false; tos_count_tExtractJSONFields_3++; /** * [tExtractJSONFields_3 main ] stop */ // Start of branch "row7" if (row7 != null) { /** * [tLogRow_4 main ] start */ currentComponent = "tLogRow_4"; // ///////////////////// strBuffer_tLogRow_4 = new StringBuilder(); if (row7.ResponseContent != null) { // strBuffer_tLogRow_4.append(String.valueOf(row7.ResponseContent)); } // if (globalMap.get("tLogRow_CONSOLE") != null) { consoleOut_tLogRow_4 = (java.io.PrintStream) globalMap.get("tLogRow_CONSOLE"); } else { consoleOut_tLogRow_4 = new java.io.PrintStream( new java.io.BufferedOutputStream(System.out)); globalMap.put("tLogRow_CONSOLE", consoleOut_tLogRow_4); } consoleOut_tLogRow_4.println(strBuffer_tLogRow_4.toString()); consoleOut_tLogRow_4.flush(); nb_line_tLogRow_4++; // //// // //// // ///////////////////// tos_count_tLogRow_4++; /** * [tLogRow_4 main ] stop */ } // End of branch "row7" // end for } } // C_01 /** * [tHttpRequest_4 end ] start */ currentComponent = "tHttpRequest_4"; ok_Hash.put("tHttpRequest_4", true); end_Hash.put("tHttpRequest_4", System.currentTimeMillis()); /** * [tHttpRequest_4 end ] stop */ /** * [tReplicate_1 end ] start */ currentComponent = "tReplicate_1"; ok_Hash.put("tReplicate_1", true); end_Hash.put("tReplicate_1", System.currentTimeMillis()); /** * [tReplicate_1 end ] stop */ /** * [tExtractJSONFields_3 end ] start */ currentComponent = "tExtractJSONFields_3"; globalMap.put("tExtractJSONFields_1_NB_LINE", nb_line_tExtractJSONFields_3); ok_Hash.put("tExtractJSONFields_3", true); end_Hash.put("tExtractJSONFields_3", System.currentTimeMillis()); /** * [tExtractJSONFields_3 end ] stop */ /** * [tLogRow_4 end ] start */ currentComponent = "tLogRow_4"; // //// // //// globalMap.put("tLogRow_4_NB_LINE", nb_line_tLogRow_4); // ///////////////////// ok_Hash.put("tLogRow_4", true); end_Hash.put("tLogRow_4", System.currentTimeMillis()); /** * [tLogRow_4 end ] stop */ /** * [tFileList_3 end ] start */ currentComponent = "tFileList_3"; } globalMap.put("tFileList_3_NB_FILE", NB_FILEtFileList_3); ok_Hash.put("tFileList_3", true); end_Hash.put("tFileList_3", System.currentTimeMillis()); /** * [tFileList_3 end ] stop */ } // end the resume } catch (java.lang.Exception e) { TalendException te = new TalendException(e, currentComponent, globalMap); throw te; } catch (java.lang.Error error) { throw error; } finally { try { /** * [tFileList_3 finally ] start */ currentComponent = "tFileList_3"; /** * [tFileList_3 finally ] stop */ /** * [tHttpRequest_4 finally ] start */ currentComponent = "tHttpRequest_4"; /** * [tHttpRequest_4 finally ] stop */ /** * [tReplicate_1 finally ] start */ currentComponent = "tReplicate_1"; /** * [tReplicate_1 finally ] stop */ /** * [tExtractJSONFields_3 finally ] start */ currentComponent = "tExtractJSONFields_3"; /** * [tExtractJSONFields_3 finally ] stop */ /** * [tLogRow_4 finally ] start */ currentComponent = "tLogRow_4"; /** * [tLogRow_4 finally ] stop */ } catch (java.lang.Exception e) { // ignore } catch (java.lang.Error error) { // ignore } resourceMap = null; } globalMap.put("tFileList_3_SUBPROCESS_STATE", 1); }
From source file:BlastResultXMLsplit.BlastXMLsplit.java
public BlastXMLsplit(String filepath, int seqnumber) throws FileNotFoundException, IOException, ParserConfigurationException { SAXReader reader = new SAXReader(); reader.setValidation(false);//from w w w.j a v a2s . c o m try { System.out.println("Xlmfile reading"); Document document = reader.read(new FileInputStream(filepath));//XMLdocument? System.out.println("Xlmfile read done!"); org.dom4j.DocumentFactory DocumentFactory = new org.dom4j.DocumentFactory(); ArrayList str = new ArrayList();//??? String fileoutpath; org.dom4j.Element rootElm = document.getRootElement();// File f = new File(filepath); int count = 1; List<org.dom4j.Element> blastOutput_iterations = rootElm.element("BlastOutput_iterations").elements();//? org.dom4j.Element BlastOutput_program = rootElm.element("BlastOutput_program"); org.dom4j.Element BlastOutput_version = rootElm.element("BlastOutput_version"); org.dom4j.Element BlastOutput_reference = rootElm.element("BlastOutput_reference"); org.dom4j.Element BlastOutput_db = rootElm.element("BlastOutput_db"); //? BlastOutput_program.getParent().remove(BlastOutput_program); BlastOutput_version.getParent().remove(BlastOutput_version); BlastOutput_reference.getParent().remove(BlastOutput_reference); BlastOutput_db.getParent().remove(BlastOutput_db); // org.dom4j.Element BlastOutput_query_def=rootElm.element("BlastOutput_query-def"); //org.dom4j.Element BBlastOutput_query_len=rootElm.element("BlastOutput_query-len"); org.dom4j.Element BlastOutput_param = rootElm.element("BlastOutput_param"); rootElm.remove(BlastOutput_param); String Iteration_queryIDstr, Iteration_queryDefstr, Iteration_query_len; List<org.dom4j.Element> Iterationlist = null; int size = blastOutput_iterations.size(); System.out.println("Your query seqcount is " + size + "\r\n Start dividing your file"); for (int i = 0; i < size; i = i + seqnumber) { //?? fileoutpath = f.getParent() + System.getProperty("file.separator") + count + ".xml"; count++; System.out.println("The " + count + " is located in " + fileoutpath); FileOutputStream fos = new FileOutputStream(fileoutpath); OutputFormat format = OutputFormat.createPrettyPrint(); XMLWriter writer = new XMLWriter(fos, format); // XMLWriter writer = new XMLWriter(new FileOutputStream(fileoutpath)); //w?? org.dom4j.Element firstelement = blastOutput_iterations.get(i); Iteration_queryIDstr = firstelement.element("Iteration_query-ID").getText(); Iteration_queryDefstr = firstelement.element("Iteration_query-def").getText(); Iteration_query_len = firstelement.element("Iteration_query-len").getText(); //org.dom4j.DocumentFactory DocumentFactory = new org.dom4j.DocumentFactory(); Document document2 = DocumentHelper.createDocument(); ; org.dom4j.Element BlastOutputElement = document2.addElement("BlastOutput"); //doc.setRootElement(BlastOutputElement); //; BlastOutputElement.add(BlastOutput_program); BlastOutputElement.add(BlastOutput_version); BlastOutputElement.add(BlastOutput_reference); BlastOutputElement.add(BlastOutput_db); BlastOutputElement.addElement("BlastOutput_query-ID"); BlastOutputElement.element("BlastOutput_query-ID").setText(Iteration_queryIDstr); BlastOutputElement.addElement("BlastOutput_query-def"); BlastOutputElement.element("BlastOutput_query-def").setText(Iteration_queryDefstr); BlastOutputElement.addElement("BlastOutput_query-len"); BlastOutputElement.element("BlastOutput_query-len").setText(Iteration_query_len); // Element BlastOutput_param_new=DocumentFactory.createElement("BlastOutput_param"); // for (Iterator it = BlastOutput_param.elementIterator(); it.hasNext();) { // Element tempele=(Element) it.next(); // tempele.getParent().remove(tempele); // BlastOutput_param_new.add(tempele); // } BlastOutputElement.add(BlastOutput_param); //BlastOutputElement.add(BlastOutput_param); if (i + seqnumber < blastOutput_iterations.size()) { Iterationlist = blastOutput_iterations.subList(i, i + seqnumber); } else { Iterationlist = blastOutput_iterations.subList(i, blastOutput_iterations.size() - 1); } //System.out.println(Iterationlist.size()); //?query resetIterationlist(Iterationlist); //?BlastOutput_iterations Element BlastOutput_iterations = DocumentFactory.createElement("BlastOutput_iterations"); //BlastOutputElement.addAttribute("BlastOutput_iterations"); //org.dom4j.Element BlastOutput_iterations = new org.dom4j.Element("BlastOutput_iterations"); for (int j = 0; j < Iterationlist.size(); j++) { Iterationlist.get(j).getParent().remove(Iterationlist.get(j)); //System.out.println(j); BlastOutput_iterations.add(Iterationlist.get(j)); } BlastOutputElement.add(BlastOutput_iterations); // writer.write(document2); writer.close(); BlastOutput_program.getParent().remove(BlastOutput_program); BlastOutput_version.getParent().remove(BlastOutput_version); BlastOutput_reference.getParent().remove(BlastOutput_reference); BlastOutput_db.getParent().remove(BlastOutput_db); BlastOutput_param.getParent().remove(BlastOutput_param); } } catch (DocumentException ex) { Logger.getLogger(BlastXMLsplit.class.getName()).log(Level.SEVERE, null, ex); } }
From source file:boxConnection.SerStreamingServer.java
License:Open Source License
public void record(Socket socket) throws IOException, DocumentException { // BufferedReader input = new BufferedReader(new InputStreamReader(socket.getInputStream())); // String line; // while ((line=input.readLine())!=null) { // System.out.println(line); // }/* w w w .j a v a2s .c om*/ //Pretty print the document to System.out // OutputFormat format = OutputFormat.createPrettyPrint(); // XMLWriter writer = new XMLWriter( System.out, format ); // writer.write( document ); byte[] message = new byte[10000]; int messageLength = 0; messageLength = socket.getInputStream().read(message); // Umlaute filtern for (int i = 0; i < messageLength; i++) { if (message[i] > 0x7e || (message[i] < 0x20 && message[i] != '\t' && message[i] != '\n' && message[i] != '\r')) { message[i] = (byte) ' '; } } SAXReader reader = new SAXReader(); ByteArrayInputStream in = new ByteArrayInputStream(message, 0, messageLength); Document document = reader.read(in); BORecordArgs recordArgs = SerXMLConverter.parseRecordDocument(document); if (recordArgs.getCommand().equals("stop")) { ControlMain.getControl().getView().getTabProgramm().getControl().stopRecord(); Logger.getLogger("SerStreamingServer").info("From DBox: Stop record"); } if (recordArgs.getCommand().equals("record")) { recordArgs.checkTitle(); ControlMain.getControl().getView().getTabProgramm().getControl().startRecord(recordArgs); Logger.getLogger("SerStreamingServer").info("From DBox: Start record"); } server.close(); //server restart this.run(); }
From source file:br.com.atus.util.CEPWebService.java
public Document getDocumento(URL url) throws DocumentException { SAXReader reader = new SAXReader(); Document document = reader.read(url); return document; }
From source file:br.com.cgcop.utilitarios.CEPWebService.java
private Document getDocumento(URL url) throws DocumentException { SAXReader reader = new SAXReader(); Document document = reader.read(url); return document; }
From source file:br.com.sistemapetshop.util.WebServiceCep.java
/** * Carrega o Documento xml a partir do CEP enviado. * * @param cep nmero do cep./*from w ww . jav a 2 s . com*/ * @return {@link Document} xml WebService do site Republic Virtual * @throws DocumentException Quando h problema na formao do documento * XML. * @throws MalformedURLException Quando a h problema no link url. */ private static Document getDocument(String cep) throws DocumentException, MalformedURLException { URL url = new URL(String.format(URL_STRING, cep)); SAXReader reader = new SAXReader(); Document document = reader.read(url); return document; }
From source file:br.com.ufra.cep.service.CepWebService.java
public Document getDocumento(URL url) throws DocumentException { SAXReader reader = new SAXReader(); Document document = reader.read(url); return document; }
From source file:ca.coder2000.recipes.RecipeFile.java
License:Mozilla Public License
/** * Creates a new instance of RecipeFile/* w w w . j a v a2 s .c o m*/ * @param file the file we want this class to load and manage. */ public RecipeFile(File file) { SAXReader reader = new SAXReader(true); reader.setValidation(true); try { reader.setFeature("http://xml.org/sax/features/validation", true); reader.setFeature("http://apache.org/xml/features/validation/schema", true); reader.setProperty("http://apache.org/xml/properties/schema/external-noNamespaceSchemaLocation", "schemas/recipe.xsd"); reader.setErrorHandler(new RecipeErrorHandler()); doc = reader.read(file); checkVersion(); } catch (DocumentException de) { JOptionPane.showMessageDialog(null, de.getMessage(), java.util.ResourceBundle.getBundle("recipe").getString("Error_Parsing_Recipe"), JOptionPane.ERROR_MESSAGE); } catch (SAXException sxe) { JOptionPane.showMessageDialog(null, sxe.getMessage(), java.util.ResourceBundle.getBundle("recipe").getString("Error_Parsing_Recipe"), JOptionPane.ERROR_MESSAGE); } catch (Exception e) { JOptionPane.showMessageDialog(null, e.getMessage(), java.util.ResourceBundle.getBundle("recipe").getString("Error_Parsing_Recipe"), JOptionPane.ERROR_MESSAGE); } }
From source file:ca.upei.roblib.fedora.servletfilter.DrupalAuthModule.java
License:Apache License
protected Document getParsedConfig(InputStream stream) throws DocumentException, IOException { SAXReader reader = new SAXReader(); Document document = reader.read(stream); return document; }