source: ccr/trunk/nhin-vista/projects/NHINC/Current/Product/Production/Adapters/General/DocumentRepository/src/gov/hhs/fha/nhinc/repository/util/DocumentLoadUtil.java@ 507

Last change on this file since 507 was 507, checked in by George Lilly, 15 years ago

NHIN gateway and adaptor for use on linux with VistA EHR and RPMS
File size: 17.7 KB
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1package gov.hhs.fha.nhinc.repository.util;
2
3import gov.hhs.fha.nhinc.repository.model.EventCode;
4import gov.hhs.fha.nhinc.repository.service.DocumentService;
5import java.io.File;
6import java.io.FileInputStream;
7import java.io.FileOutputStream;
8import java.io.IOException;
9import java.io.InputStream;
10import java.io.OutputStream;
11import java.text.SimpleDateFormat;
12import java.util.Date;
13import java.util.HashSet;
14import java.util.PropertyResourceBundle;
15import java.util.Set;
16import org.apache.commons.logging.Log;
17import org.apache.commons.logging.LogFactory;
18import org.w3c.dom.Document;
19import org.w3c.dom.Element;
20import org.w3c.dom.NodeList;
21import org.w3c.dom.Node;
22
23/**
24 * Utility to load documents from an XML file into the database.
25 *
26 * @author Neil Webb
27 */
28public class DocumentLoadUtil
29{
30 private static final String DATE_FORMAT_STRING = "yyyyMMddhhmmssZ";
31 private static Log log = LogFactory.getLog(DocumentLoadUtil.class);
32
33 private static void loadData(String absoluteFilePath) throws Exception
34 {
35 // Load file into XML
36 Document doc = XmlUtil.getDocumentFromFile(absoluteFilePath);
37 if (doc == null)
38 {
39 throw new Exception("Could not load document from file for: " + absoluteFilePath);
40 }
41
42 // Traverse the DOM and load documents into database
43 NodeList docNodes = doc.getElementsByTagName("Document");
44 if ((docNodes != null) && (docNodes.getLength() > 0))
45 {
46 for (int i = 0; i < docNodes.getLength(); i++)
47 {
48 Node node = docNodes.item(i);
49 if (node instanceof Element)
50 {
51 storeDocument((Element)node);
52 }
53 }
54 }
55 }
56
57 private static void storeDocument(Element documentElement) throws Exception
58 {
59 if (documentElement == null)
60 {
61 throw new Exception("Document element was null.");
62 }
63 gov.hhs.fha.nhinc.repository.model.Document doc = new gov.hhs.fha.nhinc.repository.model.Document();
64 doc.setDocumentid(getChildElementLongValue(documentElement, "documentId"));
65 doc.setDocumentUniqueId(getChildElementStringValue(documentElement, "documentUniqueId"));
66 doc.setDocumentTitle(getChildElementStringValue(documentElement, "documentTitle"));
67 doc.setAuthorPerson(getChildElementStringValue(documentElement, "authorPerson"));
68 doc.setAuthorInstitution(getChildElementStringValue(documentElement, "authorInstitution"));
69 doc.setAuthorRole(getChildElementStringValue(documentElement, "authorRole"));
70 doc.setAuthorSpecialty(getChildElementStringValue(documentElement, "authorSpecialty"));
71 doc.setAvailablityStatus(getChildElementStringValue(documentElement, "availablityStatus"));
72 doc.setClassCode(getChildElementStringValue(documentElement, "classCode"));
73 doc.setClassCodeScheme(getChildElementStringValue(documentElement, "classCodeScheme"));
74 doc.setClassCodeDisplayName(getChildElementStringValue(documentElement, "classCodeDisplayName"));
75 doc.setConfidentialityCode(getChildElementStringValue(documentElement, "confidentialityCode"));
76 doc.setConfidentialityCodeScheme(getChildElementStringValue(documentElement, "confidentialityCodeScheme"));
77 doc.setConfidentialityCodeDisplayName(getChildElementStringValue(documentElement, "confidentialityCodeDisplayName"));
78 doc.setFormatCode(getChildElementStringValue(documentElement, "formatCode"));
79 doc.setFormatCodeScheme(getChildElementStringValue(documentElement, "formatCodeScheme"));
80 doc.setFormatCodeDisplayName(getChildElementStringValue(documentElement, "formatCodeDisplayName"));
81 doc.setPatientId(getChildElementStringValue(documentElement, "patientId"));
82 doc.setStatus(getChildElementStringValue(documentElement, "status"));
83 doc.setComments(getChildElementStringValue(documentElement, "comments"));
84 doc.setFacilityCode(getChildElementStringValue(documentElement, "facilityCode"));
85 doc.setFacilityCodeScheme(getChildElementStringValue(documentElement, "facilityCodeScheme"));
86 doc.setFacilityCodeDisplayName(getChildElementStringValue(documentElement, "facilityCodeDisplayName"));
87 doc.setIntendedRecipientPerson(getChildElementStringValue(documentElement, "intendedRecipientPerson"));
88 doc.setIntendedRecipientOrganization(getChildElementStringValue(documentElement, "intendedRecipientOrganization"));
89 doc.setLanguageCode(getChildElementStringValue(documentElement, "languageCode"));
90 doc.setLegalAuthenticator(getChildElementStringValue(documentElement, "legalAuthenticator"));
91 doc.setMimeType(getChildElementStringValue(documentElement, "mimeType"));
92 doc.setParentDocumentId(getChildElementStringValue(documentElement, "parentDocumentId"));
93 doc.setParentDocumentRelationship(getChildElementStringValue(documentElement, "parentDocumentRelationship"));
94 doc.setPracticeSetting(getChildElementStringValue(documentElement, "practiceSetting"));
95 doc.setPracticeSettingScheme(getChildElementStringValue(documentElement, "practiceSettingScheme"));
96 doc.setPracticeSettingDisplayName(getChildElementStringValue(documentElement, "practiceSettingDisplayName"));
97 doc.setSize(getChildElementIntegerValue(documentElement, "size"));
98 doc.setSourcePatientId(getChildElementStringValue(documentElement, "sourcePatientId"));
99 doc.setPid3(getChildElementStringValue(documentElement, "pid3"));
100 doc.setPid5(getChildElementStringValue(documentElement, "pid5"));
101 doc.setPid8(getChildElementStringValue(documentElement, "pid8"));
102 doc.setPid7(getChildElementStringValue(documentElement, "pid7"));
103 doc.setPid11(getChildElementStringValue(documentElement, "pid11"));
104 doc.setTypeCode(getChildElementStringValue(documentElement, "typeCode"));
105 doc.setTypeCodeScheme(getChildElementStringValue(documentElement, "typeCodeScheme"));
106 doc.setTypeCodeDisplayName(getChildElementStringValue(documentElement, "typeCodeDisplayName"));
107 doc.setDocumentUri(getChildElementStringValue(documentElement, "documentUri"));
108 doc.setRawData(getChildElementByteArray(documentElement, "rawData"));
109
110 // Date fields
111 doc.setCreationTime(parseDate(getChildElementStringValue(documentElement, "creationTime"),DATE_FORMAT_STRING));
112 doc.setServiceStartTime(parseDate(getChildElementStringValue(documentElement, "serviceStartTime"),DATE_FORMAT_STRING));
113 doc.setServiceStopTime(parseDate(getChildElementStringValue(documentElement, "serviceStopTime"),DATE_FORMAT_STRING));
114// doc.setServiceStartTime(parseDate(getChildElementStringValue(documentElement, "serviceStartTime"), "yyyyMMddhhmmss"));
115// doc.setServiceStopTime(parseDate(getChildElementStringValue(documentElement, "serviceStopTime"), "yyyyMMddhhmmss"));
116
117 loadEventCodes(documentElement, doc);
118
119 DocumentService docService = new DocumentService();
120 docService.saveDocument(doc);
121 }
122
123 private static Date parseDate(String value, String dateFormat)
124 {
125 Date parsedDate = null;
126 if ((value != null) && (dateFormat != null))
127 {
128 try
129 {
130 String formatString = prepareDateFormatString(dateFormat, value);
131 SimpleDateFormat dateFormatter = new SimpleDateFormat(formatString);
132 parsedDate = dateFormatter.parse(value);
133 }
134 catch (Throwable t)
135 {
136 log.error("Error parsing date '" + value + "' using format: '" +
137 dateFormat + "': " + t.getMessage(), t);
138 }
139 }
140 return parsedDate;
141 }
142
143 /**
144 * Prepare a date format string based on the length of the date string
145 * to be parsed.
146 * @param dateFormat Date format string (ex. yyyyMMddhhmmssZ)
147 * @param dateString Date string to be parsed (ex. 19990205)
148 * @return Modified format string based on the date string length (ex. yyyyMMdd)
149 */
150 public static String prepareDateFormatString(String dateFormat, String dateString)
151 {
152 String formatString = dateFormat;
153 if ((dateString != null) && (dateFormat != null) && (dateString.length() > 0) && (dateString.length() < dateFormat.length()))
154 {
155 formatString = dateFormat.substring(0, dateString.length());
156 if(log.isDebugEnabled())
157 {
158 log.debug("New dateFormat: " + dateFormat);
159 }
160 }
161 return formatString;
162 }
163
164 private static void loadEventCodes(Element documentElement, gov.hhs.fha.nhinc.repository.model.Document doc)
165 {
166 if (documentElement != null)
167 {
168 NodeList nodes = documentElement.getElementsByTagName("eventCode");
169 if ((nodes != null) && (nodes.getLength() > 0))
170 {
171 Set<EventCode> eventCodes = new HashSet<EventCode>();
172 for (int i = 0; i < nodes.getLength(); i++)
173 {
174 // eventCode element - load data
175 Node node = nodes.item(i);
176 if (node instanceof Element)
177 {
178 Element eventCodeElement = (Element)node;
179 EventCode eventCode = new EventCode();
180 eventCode.setDocument(doc);
181 eventCode.setEventCodeId(getChildElementLongValue(eventCodeElement, "codeId"));
182 eventCode.setEventCode(getChildElementStringValue(eventCodeElement, "code"));
183 eventCode.setEventCodeScheme(getChildElementStringValue(eventCodeElement, "codeSchema"));
184 eventCode.setEventCodeDisplayName(getChildElementStringValue(eventCodeElement, "codeDisplayName"));
185 eventCodes.add(eventCode);
186 }
187 }
188 doc.setEventCodes(eventCodes);
189 }
190 }
191 }
192
193 private static String getChildElementStringValue(Element element, String childElementName)
194 {
195 String value = null;
196 if ((element != null) && (childElementName != null))
197 {
198 if(log.isDebugEnabled())
199 {
200 log.debug("Extracting child element '" + childElementName + "' from '" + element.getTagName() + "'");
201 }
202 NodeList nodes = element.getElementsByTagName(childElementName);
203 if ((nodes != null) && (nodes.getLength() > 0))
204 {
205 Node node = nodes.item(0);
206 if (node instanceof Element)
207 {
208 Element childElement = (Element)node;
209 value = childElement.getTextContent();
210 }
211 }
212 }
213 return value;
214 }
215
216 private static Long getChildElementLongValue(Element element, String childElementName)
217 {
218 Long value = null;
219 if ((element != null) && (childElementName != null))
220 {
221 if(log.isDebugEnabled())
222 {
223 log.debug("Extracting child element '" + childElementName + "' from '" + element.getTagName() + "'");
224 }
225 NodeList nodes = element.getElementsByTagName(childElementName);
226 if ((nodes != null) && (nodes.getLength() > 0))
227 {
228 Node node = nodes.item(0);
229 if (node instanceof Element)
230 {
231 Element childElement = (Element)node;
232 String strVal = childElement.getTextContent();
233 if (strVal != null)
234 {
235 try
236 {
237 value = Long.parseLong(strVal);
238 }
239 catch (Throwable t)
240 {
241 log.error("Failed to parse long from '" + strVal + "'", t);
242 }
243 }
244 }
245 }
246 }
247 return value;
248 }
249
250 private static Integer getChildElementIntegerValue(Element element, String childElementName)
251 {
252 Integer value = null;
253 if ((element != null) && (childElementName != null))
254 {
255 if(log.isDebugEnabled())
256 {
257 log.debug("Extracting child element '" + childElementName + "' from '" + element.getTagName() + "'");
258 }
259 NodeList nodes = element.getElementsByTagName(childElementName);
260 if ((nodes != null) && (nodes.getLength() > 0))
261 {
262 Node node = nodes.item(0);
263 if (node instanceof Element)
264 {
265 Element childElement = (Element)node;
266 String strVal = childElement.getTextContent();
267 if (strVal != null)
268 {
269 try
270 {
271 value = new Integer(strVal);
272 }
273 catch (Throwable t)
274 {
275 log.error("Failed to parse integer from '" + strVal + "'",t);
276 }
277 }
278 }
279 }
280 }
281 return value;
282 }
283
284 private static byte[] getChildElementByteArray(Element element, String childElementName)
285 {
286 byte[] value = null;
287 if ((element != null) && (childElementName != null))
288 {
289 if(log.isDebugEnabled())
290 {
291 log.debug("Extracting child element '" + childElementName + "' from '" + element.getTagName() + "'");
292 }
293 NodeList nodes = element.getElementsByTagName(childElementName);
294 if ((nodes != null) && (nodes.getLength() > 0))
295 {
296 Node node = nodes.item(0);
297 if (node instanceof Element)
298 {
299 Element childElement = (Element)node;
300 String encStrVal = childElement.getTextContent();
301 if (encStrVal != null)
302 {
303 value = encStrVal.getBytes();
304 }
305 }
306 }
307 }
308 return value;
309 }
310
311 /**
312 * This method copies files from input folder to output folder...
313 * @param source
314 * @param dest
315 * @throws java.io.IOException
316 */
317 private static void copyFile(File source, File dest) throws IOException {
318 if (!dest.exists()) {
319 dest.createNewFile();
320 }
321 InputStream in = null;
322 OutputStream out = null;
323 try {
324 in = new FileInputStream(source);
325 out = new FileOutputStream(dest);
326 byte[] buf = new byte[1024];
327 int len;
328 while ((len = in.read(buf)) > 0) {
329 out.write(buf, 0, len);
330 }
331 } finally {
332 in.close();
333 out.close();
334 source.deleteOnExit();
335 }
336 }
337
338 /**
339 * Method reads bunch of files kept under a folder and move them to different folder after processing..
340 */
341 public static void readFiles() {
342 String propFileName = "filespath";
343 PropertyResourceBundle prop = (PropertyResourceBundle) PropertyResourceBundle.getBundle(propFileName);
344 String inFilePath = prop.getString("inFilePath");
345 String outFilePath = prop.getString("outFilePath");
346 log.info("In Put File Path -> " + inFilePath);
347 log.info("Out Put File Path -> " + outFilePath);
348 File inputfolder = new File(inFilePath);
349 File files[] = inputfolder.listFiles();
350 if (files.length != 0) {
351 String inFileName = "";
352 File destFile = null;
353 String absolutePath = "";
354 for (File inFile : files) {
355 if (inFile.isFile()) {
356 try {
357 absolutePath = inFile.getAbsolutePath();
358 try {
359 log.info("absolutePath" + absolutePath);
360 loadData(absolutePath);
361 } catch (Throwable t) {
362 log.debug("Failed to load documents: " + t.getMessage());
363 t.printStackTrace();
364 }
365 Thread.sleep(500);
366 } catch (InterruptedException ex) {
367 log.error(ex.getMessage());
368 }
369 inFileName = inFile.getName();
370 destFile = new File(outFilePath, inFileName);
371 try {
372 copyFile(inFile, destFile);
373 //inFile.delete();
374 } catch (IOException ex) {
375 log.error(ex.getMessage());
376 }
377 }
378 }
379 } else {
380 log.info("Input files Not found under the specific directory, Please verify filespath.properties and run again");
381 }
382 }
383
384 /**
385 * Entry point for the document load utility. The absolute path to the
386 * source file is expected as the only parameter.
387 *
388 * @param args Absolute path to source file as only parameter.
389 */
390 public static void main(String[] args)
391 {
392 log.debug("Begin DocumentLoad");
393 try {
394 if (args.length == 0) {
395 readFiles();
396 }
397 if (args.length == 1) {
398 loadData(args[0]);
399 }
400 if (args.length > 1) {
401 throw new Exception("Only one argument of the absolute path to a " +
402 "source file is expected or bunch files expected using a propery file, review ReadMe.tx before uploading");
403 }
404
405 } catch (Throwable t) {
406 log.debug("Failed to load documents: " + t.getMessage());
407 t.printStackTrace();
408 }
409 log.debug("End DocumentLoad");
410 System.exit(0);
411 }
412}
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