protected String getRallyXML(String apiUrl) throws Exception {
String responseXML = "";
DefaultHttpClient httpClient = new DefaultHttpClient();
Base64 base64 = new Base64();
String encodeString =
new String(base64.encode((rallyApiHttpUsername + ":" + rallyApiHttpPassword).getBytes()));
HttpGet httpGet = new HttpGet(apiUrl);
httpGet.addHeader("Authorization", "Basic " + encodeString);
HttpResponse response = httpClient.execute(httpGet);
HttpEntity entity = response.getEntity();
if (entity != null) {
InputStreamReader reader = new InputStreamReader(entity.getContent());
BufferedReader br = new BufferedReader(reader);
StringBuilder sb = new StringBuilder();
String line = "";
while ((line = br.readLine()) != null) {
sb.append(line);
}
responseXML = sb.toString();
}
log.debug("responseXML=" + responseXML);
return responseXML;
}
public String getEntityString(HttpEntity entity) throws Exception {
StringBuilder sb = new StringBuilder();
if (entity != null) {
InputStreamReader reader = new InputStreamReader(entity.getContent());
BufferedReader br = new BufferedReader(reader);
String line = "";
while ((line = br.readLine()) != null) {
sb.append(line);
}
}
return sb.toString();
}
public String loadStream(InputStream is) {
StringBuilder sb = new StringBuilder();
try {
InputStreamReader reader = new InputStreamReader(is);
BufferedReader br = new BufferedReader(reader);
String line = "";
while ((line = br.readLine()) != null) {
sb.append(line);
}
} catch (Exception e) {
log.error("", e);
}
return sb.toString();
}
public void run() {
try {
PrintWriter pw = null;
if (os != null) pw = new PrintWriter(os);
InputStreamReader isr = new InputStreamReader(is);
BufferedReader br = new BufferedReader(isr);
String line = null;
while ((line = br.readLine()) != null) {
if (pw != null) pw.println(line);
logger.info(type + ">" + line);
}
if (pw != null) pw.flush();
} catch (IOException ioe) {
logger.fatal("IOE: ", ioe);
}
}
private CIJob getJob(ApplicationInfo appInfo) throws PhrescoException {
Gson gson = new Gson();
try {
BufferedReader br = new BufferedReader(new FileReader(getCIJobPath(appInfo)));
CIJob job = gson.fromJson(br, CIJob.class);
br.close();
return job;
} catch (FileNotFoundException e) {
S_LOGGER.debug(e.getLocalizedMessage());
return null;
} catch (com.google.gson.JsonParseException e) {
S_LOGGER.debug("it is already adpted project !!!!! " + e.getLocalizedMessage());
return null;
} catch (IOException e) {
S_LOGGER.debug(e.getLocalizedMessage());
return null;
}
}
public List<CIJob> getJobs(ApplicationInfo appInfo) throws PhrescoException {
S_LOGGER.debug("GetJobs Called!");
try {
boolean adaptedProject = adaptExistingJobs(appInfo);
S_LOGGER.debug("Project adapted for new feature => " + adaptedProject);
Gson gson = new Gson();
BufferedReader br = new BufferedReader(new FileReader(getCIJobPath(appInfo)));
Type type = new TypeToken<List<CIJob>>() {}.getType();
List<CIJob> jobs = gson.fromJson(br, type);
br.close();
return jobs;
} catch (FileNotFoundException e) {
S_LOGGER.debug("FileNotFoundException");
return null;
} catch (IOException e) {
S_LOGGER.debug("IOException");
throw new PhrescoException(e);
}
}
/**
* Builds a SgrScoreCalculator object
*
* @param data - name of file containing sgr data
* @param winSize - size of display window
* @throws IOException - if the file cannot be accessed
*/
public SgrScoreCalculator(String data, int winSize, CurationSet curation) throws IOException {
super(winSize);
BufferedReader br = new BufferedReader(new FileReader(data));
String line;
double minAbsScore = Double.POSITIVE_INFINITY;
Set<String> unmatchedIds = new HashSet<String>();
while ((line = br.readLine()) != null) {
String[] tokens = line.split("\t");
String refId = curation.getRefSequence().getName();
if (!tokens[0].equals(refId)) {
if (!unmatchedIds.contains(tokens[0])) {
logger.warn(
"Score id "
+ tokens[0]
+ " does not match main sequence id "
+ refId
+ ". Skipping score.");
unmatchedIds.add(tokens[0]);
}
continue;
}
Double score = new Double(Double.parseDouble(tokens[2]));
// chuck out scores outside of the given range
int pos = Integer.parseInt(tokens[1]);
if (pos >= curation.getLow() && pos <= curation.getHigh()) {
scoreMap.put(pos, score);
}
if (Math.abs(score) < minAbsScore) {
minAbsScore = Math.abs(score);
}
if (score.doubleValue() < minScore) {
minScore = score;
}
if (score.doubleValue() > maxScore) {
maxScore = score;
}
}
while (minAbsScore * factor < 1) {
factor *= 10;
}
}
public void run() {
try {
PrintWriter writer = null;
if (out != null) {
writer = new PrintWriter(out);
}
BufferedReader br = new BufferedReader(new InputStreamReader(in));
String line = br.readLine();
while (line != null) {
if (writer != null) {
writer.println(line);
}
log4JLevel.log(log, line);
line = br.readLine();
}
if (writer != null) {
writer.flush();
}
} catch (IOException e) {
throw new IoRuntimeException("Exception gobbling stream ", e);
}
}