public String getUrl() {
StringBuilder sb = new StringBuilder();
StringBuilder ori = getOut();
this.setOut(sb);
TreeMap<Integer, cn.bran.japid.template.ActionRunner> parentActionRunners = actionRunners;
actionRunners = new TreeMap<Integer, cn.bran.japid.template.ActionRunner>();
// line 48, japidviews\AdminController\flashPurchaseList.html
p(" "); // line 48, japidviews\AdminController\flashPurchaseList.html
p(
lookup(
"AdminController.flashPurchaseList",
new Object[] {})); // line 49, japidviews\AdminController\flashPurchaseList.html
p(" "); // line 49, japidviews\AdminController\flashPurchaseList.html
this.setOut(ori);
if (actionRunners.size() > 0) {
StringBuilder _sb2 = new StringBuilder();
int segStart = 0;
for (Map.Entry<Integer, cn.bran.japid.template.ActionRunner> _arEntry :
actionRunners.entrySet()) {
int pos = _arEntry.getKey();
_sb2.append(sb.substring(segStart, pos));
segStart = pos;
cn.bran.japid.template.ActionRunner _a_ = _arEntry.getValue();
_sb2.append(_a_.run().getContent().toString());
}
_sb2.append(sb.substring(segStart));
actionRunners = parentActionRunners;
return _sb2.toString();
} else {
actionRunners = parentActionRunners;
return sb.toString();
}
}
public static UUID generateUuidForName(String name) {
TFM_Log.info("Generating spoof UUID for " + name);
name = name.toLowerCase();
try {
final MessageDigest mDigest = MessageDigest.getInstance("SHA1");
byte[] result = mDigest.digest(name.getBytes());
final StringBuilder sb = new StringBuilder();
for (int i = 0; i < result.length; i++) {
sb.append(Integer.toString((result[i] & 0xff) + 0x100, 16).substring(1));
}
return UUID.fromString(
sb.substring(0, 8)
+ "-"
+ sb.substring(8, 12)
+ "-"
+ sb.substring(12, 16)
+ "-"
+ sb.substring(16, 20)
+ "-"
+ sb.substring(20, 32));
} catch (NoSuchAlgorithmException ex) {
TFM_Log.severe(ex);
}
return UUID.randomUUID();
}
/**
* Static method that removes path and filetype from pathname.
*
* @param inString <code>String</code> containing filename with possible extension
*/
static String toStubName(String inString) {
File F = new File(inString);
String name = F.getName(); // strips pathname from filename
StringBuilder buf = new StringBuilder(name);
String stubName;
stubName = null;
int dotIndex = buf.length(); // point to last char
while (dotIndex > 0) {
dotIndex--;
if (buf.charAt(dotIndex) == '.') // look for file type sep
{
break;
}
}
if (dotIndex > 0) {
stubName = buf.substring(0, dotIndex);
}
return stubName;
}
@Override
public String getHeaderField(final String field) {
final List<String> values = headers.get(field);
final StringBuilder sb = new StringBuilder();
for (final String v : values) sb.append(v).append(';');
return sb.substring(0, sb.length() - 1);
}
private String getTag(Document d) {
StringBuilder ab =
new StringBuilder(
d.getValues(DocumentBuilder.FIELD_NAME_IDENTIFIER)[0].replace(
"E:\\I:\\ACM_complete_dataset\\", ""));
return ab.substring(0, ab.indexOf("\\")).toString();
}
private CIJobStatus deleteCI(CIJob job, List<String> builds) throws PhrescoException {
S_LOGGER.debug("Entering Method CIManagerImpl.deleteCI(CIJob job)");
S_LOGGER.debug("Job name " + job.getName());
cli = getCLI(job);
String deleteType = null;
List<String> argList = new ArrayList<String>();
S_LOGGER.debug("job name " + job.getName());
S_LOGGER.debug("Builds " + builds);
if (CollectionUtils.isEmpty(builds)) { // delete job
S_LOGGER.debug("Job deletion started");
S_LOGGER.debug("Command " + FrameworkConstants.CI_JOB_DELETE_COMMAND);
deleteType = DELETE_TYPE_JOB;
argList.add(FrameworkConstants.CI_JOB_DELETE_COMMAND);
argList.add(job.getName());
} else { // delete Build
S_LOGGER.debug("Build deletion started");
deleteType = DELETE_TYPE_BUILD;
argList.add(FrameworkConstants.CI_BUILD_DELETE_COMMAND);
argList.add(job.getName());
StringBuilder result = new StringBuilder();
for (String string : builds) {
result.append(string);
result.append(",");
}
String buildNos = result.substring(0, result.length() - 1);
argList.add(buildNos);
S_LOGGER.debug("Command " + FrameworkConstants.CI_BUILD_DELETE_COMMAND);
S_LOGGER.debug("Build numbers " + buildNos);
}
try {
int status = cli.execute(argList);
String message = deleteType + " deletion started in jenkins";
if (status == FrameworkConstants.JOB_STATUS_NOTOK) {
deleteType = deleteType.substring(0, 1).toLowerCase() + deleteType.substring(1);
message = "Error while deleting " + deleteType + " in jenkins";
}
S_LOGGER.debug("Delete CI Status " + status);
S_LOGGER.debug("Delete CI Message " + message);
return new CIJobStatus(status, message);
} finally {
if (cli != null) {
try {
cli.close();
} catch (IOException e) {
if (debugEnabled) {
S_LOGGER.error(
"Entered into catch block of CIManagerImpl.deleteCI(CIJob job) "
+ e.getLocalizedMessage());
}
} catch (InterruptedException e) {
if (debugEnabled) {
S_LOGGER.error(
"Entered into catch block of CIManagerImpl.deleteCI(CIJob job) "
+ e.getLocalizedMessage());
}
}
}
}
}
/**
* Adds human readable shortcuts to the specified string.
*
* @param str text of tooltip
* @param sc shortcut
* @return tooltip
*/
public static String addShortcut(final String str, final String sc) {
if (sc == null || str == null) return str;
final StringBuilder sb = new StringBuilder();
for (final String s : sc.split(" ")) {
String t = "%".equals(s) ? Prop.MAC ? "meta" : "control" : s;
if (t.length() != 1) t = Toolkit.getProperty("AWT." + t.toLowerCase(Locale.ENGLISH), t);
sb.append('+').append(t);
}
return str + " (" + sb.substring(1) + ')';
}
public void searchTags() {
StringBuilder strTags = new StringBuilder();
for (int i = 0; i < tempStrBuilder.length() - 1; i++) {
i = tempStrBuilder.indexOf("<");
if (i == -1) {
break;
}
strTags.append(tempStrBuilder.substring(i, tempStrBuilder.indexOf(">") + 1));
tempStrBuilder.delete(i, tempStrBuilder.indexOf(">") + 1);
tags.add(strTags.toString());
strTags.delete(0, strTags.length());
}
}
private void expect(StringBuilder src, String expected) throws RequestMessageParsingException {
String actual = src.substring(0, expected.length());
if (!actual.equals(expected)) {
String message = String.format("Expected \"%s\" next in \"%s\".", expected, src.toString());
throw new RequestMessageParsingException(message);
}
src.delete(0, expected.length());
}
private String readUntil(StringBuilder src, String stop) throws RequestMessageParsingException {
int stopIndex = src.indexOf(stop);
if (stopIndex == -1) {
String message = String.format("String \"%s\" not found in \"%s\".", stop, src.toString());
throw new RequestMessageParsingException(message);
}
String res = src.substring(0, stopIndex);
src.delete(0, stopIndex);
return res;
}
@Override
public void processTerminated(ProcessEvent event) {
if (firstUnprocessedIndex < output.length()) {
handleSkippedOutput(output.substring(firstUnprocessedIndex).trim());
}
int exitCode = event.getExitCode();
// 0 is normal, 1 is "errors found" — handled by the messages above
if (exitCode != 0 && exitCode != 1) {
compileContext.addMessage(
ERROR, "Compiler terminated with exit code: " + exitCode, "", -1, -1);
}
}
/**
* Advances to the next sequence in the database file and returns true unless there is no more
* sequences in the file and then false is returned.
*
* @return false if we are already at the end of the file else true
*/
public boolean gotoNextSequence() {
if (reader == null) {
throw new MprcException(
"FASTA stream not initalized properly. Call beforeFirst() before reading first sequence");
}
// we should have been left after reading a header because that is how we detect
// the end of the next sequence
if (nextHeader == null) {
return false;
}
this.currentHeader = nextHeader;
// read in lines until we reach the next header
final StringBuilder sequenceBuilder = new StringBuilder();
String nextLine = null;
try {
nextLine = this.reader.readLine();
} catch (IOException e) {
LOGGER.warn(e);
}
// if the next line is not a header or an end of line then append it to the sequence
while (isSequence(nextLine)) {
sequenceBuilder.append(cleanupSequence(nextLine));
try {
// read in the next line
nextLine = this.reader.readLine();
} catch (IOException e) {
LOGGER.warn(e);
}
}
while (nextLine != null && !isHeader(nextLine)) {
try {
nextLine = this.reader.readLine();
} catch (IOException e) {
LOGGER.warn(e);
}
}
this.nextHeader = nextLine;
// set the current sequence to the concatenation of all strings
// If the sequence ends with an * signalizing end codon, quietly drop it
if (sequenceBuilder.charAt(sequenceBuilder.length() - 1) == '*') {
currentSequence = sequenceBuilder.substring(0, sequenceBuilder.length() - 1);
} else {
currentSequence = sequenceBuilder.toString();
}
// return true since we will have a next header
return true;
}
public static void putCommaSeparatedStringList(Bundle b, String key, ArrayList<String> list) {
if (list != null) {
StringBuilder builder = new StringBuilder();
for (String string : list) {
builder.append(string);
builder.append(",");
}
String commaSeparated = "";
if (builder.length() > 0) {
commaSeparated = builder.substring(0, builder.length() - 1);
}
b.putString(key, commaSeparated);
}
}
private String trim(String s) {
int minIndent = 1000;
final String[] lines = s.split("\n");
for (final String line : lines) {
int pos = 0;
while (pos < line.length() && line.charAt(pos) <= ' ') {
pos++;
}
if (pos < line.length() && pos < minIndent) {
minIndent = pos;
}
}
final StringBuilder sb = new StringBuilder();
for (final String line : lines) {
sb.append(line.length() >= minIndent ? line.substring(minIndent) : line).append('\n');
}
return s.endsWith("\n") ? sb.toString() : sb.substring(0, sb.length() - 1);
}
/**
* Add multiple new nodes (SpeciesZoneType objects) to a manipulation and then submit. HJR
*
* @param manipSpeciesMap - species being added
* @param fullSpeciesMap - full list; for predator/prey info
* @param timestep
* @param isFirstManipulation
* @param networkOrManipulationId
* @return manipulation ID (String)
* @throws SimulationException
*/
public String addMultipleSpeciesType(
HashMap<Integer, SpeciesZoneType> manipSpeciesMap,
HashMap<Integer, SpeciesZoneType> fullSpeciesMap,
int timestep,
boolean isFirstManipulation,
String networkOrManipulationId) {
// job.setNode_Config("5,
// [5],2000,1.000,1,K=9431.818,0,
// [14],1751,20.000,1,X=0.273,0,
// [31],1415,0.008,1,X=1.000,0,
// [42],240,0.205,1,X=0.437,0,
// [70],2494,13.000,1,X=0.155,0");
// In addMultipleSpeciesType: node [70], biomass 2494, K = -1, R = -1.0000, X = 0.1233
// In addMultipleSpeciesType: node [5], biomass 2000, K = 10000, R = 1.0000, X = 0.5000
// In addMultipleSpeciesType: node [42], biomass 240, K = -1, R = -1.0000, X = 0.3478
// In addMultipleSpeciesType: node [31], biomass 1415, K = -1, R = -1.0000, X = 0.7953
// In addMultipleSpeciesType: node [14], biomass 1752, K = -1, R = -1.0000, X = 0.0010
StringBuilder builder = new StringBuilder();
builder.append(fullSpeciesMap.size()).append(",");
for (SpeciesZoneType species : fullSpeciesMap.values()) {
System.out.printf(
"In addMultipleSpeciesType: node [%d], " + "biomass %d, K = %d, R = %6.4f, X = %6.4f\n",
species.getNodeIndex(),
+(int) species.getCurrentBiomass(),
(int) species.getParamK(),
species.getParamR(),
species.getParamX());
builder.append("[").append(species.getNodeIndex()).append("]").append(",");
builder.append((int) species.getCurrentBiomass()).append(",");
builder.append(roundToThreeDigits(species.getPerSpeciesBiomass())).append(",");
String systemParam = this.setSystemParameters(species, fullSpeciesMap, timestep);
builder.append(systemParam);
System.out.println(builder);
}
String node_config = builder.substring(0, builder.length() - 1);
// call processsim job here
return node_config;
}
/**
* Extract the XML message and construct validated Message object based on the terminator string
* (either "</request>" or "</response>"). Returns null if communication is interrupted in any
* way.
*/
static Message extractMessage(BufferedReader in, String terminator) {
try {
String line = in.readLine();
if (line == null) {
return null;
}
StringBuilder buf = new StringBuilder(line);
while (!buf.substring(buf.length() - terminator.length(), buf.length()).equals(terminator)) {
line = in.readLine();
if (line == null) {
return null;
}
buf.append(line);
}
return new Message(buf.toString());
} catch (IOException ioe) {
return null;
}
}
public static String getOperationsList() {
StringBuilder sb = new StringBuilder();
for (String s : getPropertyFile().stringPropertyNames()) sb.append("'").append(s).append("', ");
if (sb.length() < 3) return "";
return sb.substring(0, sb.length() - 2);
}
/**
* returns null on eof. throws exception or returns parsed object.
*
* @return
* @throws java.io.IOException
*/
public DynMap readNext() throws TrendrrException {
StringBuilder json = new StringBuilder("{");
try {
long numRead = 0;
int openBrackets = 1;
boolean isQuote = false;
boolean isEscape = false;
// read until the first open bracket
int current = this.reader.read();
while (current != '{' && current != -1) {
numRead++;
if (numRead > this.maxBufferedChars) {
throw new TrendrrParseException(
"Read "
+ this.maxBufferedChars
+ " chars without a valid json dict. Beginning with: "
+ json.substring(0, 256));
}
current = this.reader.read();
}
do {
current = this.reader.read();
if (current == -1) {
return null;
}
char c = (char) current;
json.append(c);
if (!isQuote) {
if (c == '{') {
openBrackets++;
} else if (c == '}') {
openBrackets--;
}
}
if (c == '"' && !isEscape) {
isQuote = !isQuote;
}
if (isQuote && !isEscape && c == '\\') {
isEscape = true;
} else {
isEscape = false;
}
numRead++;
if (numRead > this.maxBufferedChars) {
throw new TrendrrParseException(
"Read "
+ this.maxBufferedChars
+ " chars without a valid json dict. Beginning with: "
+ json.substring(0, 256));
}
} while (openBrackets != 0);
DynMap dm = DynMapFactory.instanceFromJSON(json.toString());
if (dm == null) {
throw new TrendrrParseException("unable to parse json string");
}
return dm;
} catch (IOException x) {
throw new TrendrrIOException(x);
}
}