/**
* this function update the number of extra input file accorrdingly with the current number of
* files it deletes or adds extra input files
*/
private void _updateUploadFileNumber(int numFiles) throws IllegalActionException {
int currentNumberOfFile = 0;
try {
currentNumberOfFile = _getUploadFileNumber();
} catch (IllegalActionException e) {
throw new IllegalActionException(this, "Unable to load opal paraters:" + e.getMessage());
}
int diff = numFiles - currentNumberOfFile;
if (diff > 0) {
// we have to add diff number of input files
for (int i = 0; i < diff; i++) {
try {
(new FilePortParameter(this, "inputFile" + (currentNumberOfFile + 1 + i) + "Dynamic"))
.setContainer(this);
} catch (NameDuplicationException e) {
throw new IllegalActionException(this, "There is a name duplication: " + e.getMessage());
} // catch
} // for
} else if (diff < 0) {
// we have to delete number of files
for (int i = 0; i < Math.abs(diff); i++) {
String fileName = "inputFile" + (currentNumberOfFile - i) + "Dynamic";
try {
FilePortParameter fileToBeDeleted =
(FilePortParameter) this.getAttribute(fileName, FilePortParameter.class);
fileToBeDeleted.getPort().setContainer(null);
fileToBeDeleted.setContainer(null);
} catch (NameDuplicationException e) {
throw new IllegalActionException(
this, "Unable to delete the input file " + fileName + ": " + e.getMessage());
} // catch
} // for
} // if
// diff == 0 don't do anything
} // _updateUploadFileNumber
/**
* This method instantiates the parameters needed for the submission of a Opal job without
* metadata
*/
private void _createSimpleSubmission(AppMetadata app) throws IllegalActionException {
_emptyParamtersArray();
// TODO delete this _interfaceParameters is useless
log.info("Creating simple submission form. For service URL: " + app.getURL());
try {
(new StringParameter(this, "commandLine")).setContainer(this);
(new StringParameter(this, "cpuNumber")).setContainer(this);
// let's try to get the number of files
int numFiles;
try {
numFiles = Integer.parseInt(numberFiles.stringValue());
} catch (NumberFormatException e) {
throw new IllegalActionException(
this, "The numberFiles parameter is not a valid integer, please correct the value");
}
_updateUploadFileNumber(numFiles);
} catch (NameDuplicationException e) {
log.error("The parameter could not be instantiated. Error message: " + e.getMessage(), e);
}
}
/**
* Description of the Method
*
* @exception IllegalActionException Description of the Exception
*/
private void buildResultTree(EntityLibrary newRoot) throws IllegalActionException {
if (isDebugging) log.debug("buildResultTree()");
// iterate over each treepath in results
for (int i = 0; i < results.size(); i++) {
try {
TreePath currentPath = results.getTreePath(i);
if (isDebugging) log.debug(currentPath);
EntityLibrary treeCurrent = newRoot;
for (int j = 1; j < currentPath.getPathCount(); j++) {
NamedObj pathCurrent = (NamedObj) currentPath.getPathComponent(j);
if (pathCurrent instanceof EntityLibrary) {
List<EntityLibrary> children = treeCurrent.entityList(EntityLibrary.class);
boolean alreadyThere = false;
for (EntityLibrary child : children) {
if (isDebugging) log.debug(child.getName());
if (child.getName().equals(pathCurrent.getName())) {
// this EntityLibrary is already there
treeCurrent = child;
alreadyThere = true;
break;
}
}
if (!alreadyThere) {
// create it
EntityLibrary newEntity = copyEntityLibrary((EntityLibrary) pathCurrent);
setContainer(treeCurrent, newEntity);
treeCurrent = newEntity;
}
} else {
List<NamedObj> children = treeCurrent.entityList(NamedObj.class);
boolean alreadyThere = false;
for (NamedObj child : children) {
if (child.getName().equals(pathCurrent.getName())) {
// this NamedObj is already there
alreadyThere = true;
break;
}
}
if (!alreadyThere) {
// create it
NamedObj newEntity = cloneEntity((NamedObj) pathCurrent);
setContainer(treeCurrent, newEntity);
// Leaf node, all done
break;
}
}
}
} catch (IllegalActionException iae) {
throw new IllegalActionException("cannot build search result tree: " + iae);
} catch (NameDuplicationException nde) {
log.error("EXCEPTION CAUGHT: " + nde.getMessage());
} catch (Exception e) {
log.error("EXCEPTION CAUGHT: " + e.getMessage());
}
} // end for loop
}
/**
* If the argument is true, make the port an output port. If the argument is false, make the port
* not an output port. In addition, if the container is an instance of Refinement, and the
* argument is true, find the corresponding port of the controller and make it an input and not an
* output. This makes it possible for the controller to see the outputs of the refinements. This
* method overrides the base class to make the same change on the mirror ports in the controller
* and state refinments. This method invalidates the schedule and resolved types of the director
* of the container, if there is one. It is write-synchronized on the workspace, and increments
* the version of the workspace.
*
* @param isOutput True to make the port an output.
* @exception IllegalActionException If changing the port status is not permitted.
*/
public void setOutput(boolean isOutput) throws IllegalActionException {
boolean disableStatus = _mirrorDisable;
// check first that this isn't an input sibling port,
// if it is then it *cannot* be set as an output too
if (_hasSibling && isInput() && !isOutput()) {
if (isOutput) {
throw new InternalErrorException(
"TransitionRefinementPort.setOutput:"
+ " cannot set input sibling port to be an output");
} else {
return;
}
}
try {
_workspace.getWriteAccess();
if (_mirrorDisable || (getContainer() == null)) {
// Have already called the super class.
// This time, process the request.
super.setOutput(isOutput);
// now create a sibling if we
// don't otherwise have one
if (!_hasSibling && isOutput) {
try {
TransitionRefinement container = (TransitionRefinement) getContainer();
TransitionRefinementPort sibling =
new TransitionRefinementPort(container, getName() + "_in");
sibling._hasSibling = true;
sibling._mirrorDisable = true;
// set attributes of sibling
sibling.setInput(true);
sibling.setMultiport(isMultiport());
sibling._mirrorDisable = false;
// link the port relation should already exist
// from this port's creation in newPort()
String relationName = getName() + "Relation";
ModalModel model = (ModalModel) container.getContainer();
Relation relation = model.getRelation(relationName);
if (relation != null) {
sibling.link(relation);
}
_hasSibling = true;
} catch (IllegalActionException ex) {
throw new InternalErrorException(
"TransitionRefinementPort.setOutput: Internal error: " + ex.getMessage());
} catch (NameDuplicationException ex) {
throw new InternalErrorException(
"TransitionRefinementPort.setOutput: Internal error: " + ex.getMessage());
}
}
} else {
_mirrorDisable = true;
boolean success = false;
Nameable container = getContainer();
if (container != null) {
Nameable modal = container.getContainer();
if (modal instanceof ModalModel) {
Port port = ((ModalModel) modal).getPort(getName());
if (port instanceof IOPort) {
((IOPort) port).setOutput(isOutput);
success = true;
}
}
}
if (!success) {
super.setOutput(isOutput);
}
}
} finally {
_mirrorDisable = disableStatus;
_workspace.doneWriting();
}
}
/**
* this function adds all the parameters necessary to have the documentation of the OpalClient
* abviously this documentation is fetch from the remote server
*/
private void _addDocumentation(AppMetadata app) throws IllegalActionException {
// let's get the variable we need
Attribute documentation = this.getAttribute("KeplerDocumentation");
if (documentation == null)
throw new IllegalActionException(
this, "Unable to set the custom documentation (KeplerDocumentation not present).");
Attribute userDoc = documentation.getAttribute("userLevelDocumentation");
if (userDoc == null)
throw new IllegalActionException(
this, "Unable to set the custom documentation (userLevelDocumentation not present).");
// -- we have to delete all the documentation that is already there
// before updating it
List tempList = documentation.attributeList();
Attribute[] paramArray = (Attribute[]) tempList.toArray(new Attribute[tempList.size()]);
for (int i = 0; i < paramArray.length; i++) {
try {
if (paramArray[i].getName().startsWith("prop:")
|| paramArray[i].getName().startsWith("port:output")
|| paramArray[i].getName().startsWith("port:baseUrl"))
// let's remove the parameters
paramArray[i].setContainer(null);
} catch (NameDuplicationException e) {
log.error(
"The parameter could not be deleted from the documentation. Error message: "
+ e.getMessage());
throw new IllegalActionException(
this,
"Error resetting the ducumentation, there is a duplicated name: " + e.getMessage());
}
}
// After deleting we can finally set the documentation
String stringDoc = _docHead;
// let's set the general documentaion
if (app.getUsage() != null) stringDoc += "<p>" + app.getUsage() + "</p>";
if (app.getInfo() != null) {
String[] infos = app.getInfo();
for (int i = 0; i < infos.length; i++) stringDoc += "<pre>" + forXML(infos[i]) + "</pre>";
} // if
log.debug("the stringDoc is: " + stringDoc);
((ConfigurableAttribute) userDoc).setExpression(stringDoc);
// -- let's set the documentation for the various properties --
// some properties are always there... hence also the documentation
// should be always there
try {
((ConfigurableAttribute) userDoc).value();
ConfigurableAttribute parameterDoc = new ConfigurableAttribute(documentation, "port:output");
parameterDoc.setExpression(
"It returns a list of Strings, containing the URL of the output files");
parameterDoc = new ConfigurableAttribute(documentation, "port:baseUrl");
parameterDoc.setExpression(
"The base URL containing the working directory of the running jobs");
parameterDoc = new ConfigurableAttribute(documentation, "prop:serviceURL");
parameterDoc.setExpression("The URL of the Opal service that you want to execute");
parameterDoc = new ConfigurableAttribute(documentation, "prop:numberOfExtraInputFiles");
parameterDoc.setExpression(
"The number of extra input files that are needed to execture the application");
// parameterDoc = new ConfigurableAttribute(documentation,
// "prop:methods");
// parameterDoc.setExpression("Not implemented yet.");
} catch (NameDuplicationException e) {
log.error("The parameter could not be instantiated. Error message: " + e.getMessage());
throw new IllegalActionException(
this, "Error building the ducumentation, there is a duplicated name: " + e.getMessage());
} catch (IOException e) {
log.error("There is an error while setting the general documentation: " + e.getMessage());
}
// we have to list the documentation for every parameters
if (app.isArgMetadataEnable()) {
Group[] group = app.getGroups();
try {
if (group != null) {
for (int i = 0; i < group.length; i++) {
// first the parameters
ArgParam[] argParams = group[i].getArgParams();
if (argParams != null) {
for (int paramCount = 0; paramCount < argParams.length; paramCount++) {
ConfigurableAttribute parameterDoc =
new ConfigurableAttribute(
documentation, "prop:" + argParams[paramCount].getId());
parameterDoc.setExpression(forXML(argParams[paramCount].getTextDesc()));
} // for argParam
} // argParams
// and then the flags
ArgFlag[] argFlags = group[i].getArgFlags();
if (argFlags != null) {
for (int paramCount = 0; paramCount < argFlags.length; paramCount++) {
ConfigurableAttribute parameterDoc =
new ConfigurableAttribute(
documentation, "prop:" + argFlags[paramCount].getId());
parameterDoc.setExpression(forXML(argFlags[paramCount].getTextDesc()));
log.info(
"The parameter "
+ argFlags[paramCount].getId()
+ " has the following doc: "
+ parameterDoc.value());
parameterDoc.validate();
}
} // argFlags
}
} // group
} catch (NameDuplicationException e) {
log.error("The parameter could not be instantiated. Error message: " + e.getMessage());
throw new IllegalActionException(
this,
"Error building the ducumentation, there is a duplicated name: " + e.getMessage());
} catch (IOException e) {
log.error(
"There is an error while setting the documentation of an element with messge: "
+ e.getMessage());
}
} // if we have metadata
else {
// if we don't have metadata we document the standard parameters
try {
ConfigurableAttribute parameterDoc =
new ConfigurableAttribute(documentation, "prop:commandLine");
parameterDoc.setExpression(
"Insert the command line you want to execute (without the application name)");
parameterDoc = new ConfigurableAttribute(documentation, "prop:cpuNumber");
parameterDoc.setExpression("If it is a parallel application insert the CPU number");
parameterDoc = new ConfigurableAttribute(documentation, "prop:inputFile");
parameterDoc.setExpression("Select an input file");
} catch (NameDuplicationException e) {
log.error("The parameter could not be instantiated. Error message: " + e.getMessage());
throw new IllegalActionException(
this,
"Error building the ducumentation, there is a duplicated name: " + e.getMessage());
}
}
} // _addDocumentation
/**
* this function instantiate all the parameter necessary to display an advanced submission form
* for the current selected opal service
*/
private void _createSubmission(AppMetadata app) throws IllegalActionException {
_emptyParamtersArray();
log.info("Creating complex submission form. For service URL: " + app.getURL());
try {
Group[] group = app.getGroups();
ArrayList tempParam = new ArrayList();
if (group != null) {
for (int i = 0; i < group.length; i++) {
// first the parameters
ArgParam[] argParams = group[i].getArgParams();
if (argParams != null) {
for (int paramCount = 0; paramCount < argParams.length; paramCount++) {
if (argParams[paramCount].getType().equals("FILE")
&& argParams[paramCount].getIoType().equals("INPUT")) {
// This is an input file box
FilePortParameter param =
new FilePortParameter(this, argParams[paramCount].getId());
if (argParams[paramCount].getSelectedValue() != null)
// setting the default value
param.setExpression(argParams[paramCount].getSelectedValue());
tempParam.add(param);
} else if (argParams[paramCount].getValues() != null) {
String[] choices = argParams[paramCount].getValues();
// this is a multiple choices
StringParameter param = new StringParameter(this, argParams[paramCount].getId());
for (int z = 0; z < choices.length; z++) param.addChoice(choices[z]);
if (argParams[paramCount].getSelectedValue() != null)
// setting the default value
param.setExpression(argParams[paramCount].getSelectedValue());
tempParam.add(param);
} else {
// this is a string
StringParameter param = new StringParameter(this, argParams[paramCount].getId());
if (argParams[paramCount].getSelectedValue() != null)
// setting the default value
param.setExpression(argParams[paramCount].getSelectedValue());
tempParam.add(param);
} // else
} // for argParam
} // argParams
// and then the flags
ArgFlag[] argFlags = group[i].getArgFlags();
if (argFlags != null) {
for (int paramCount = 0; paramCount < argFlags.length; paramCount++) {
Parameter check = null;
if (argFlags[paramCount].isSelected())
check = new Parameter(this, argFlags[paramCount].getId(), BooleanToken.TRUE);
else check = new Parameter(this, argFlags[paramCount].getId(), BooleanToken.FALSE);
check.setTypeEquals(BaseType.BOOLEAN);
tempParam.add(check);
}
} // argFlags
}
} // group
// set the numberFiles to 0
StringParameter param = (StringParameter) this.getAttribute("numberFiles");
if (param != null) param.setToken(new StringToken("0"));
// not needed anymore delete the tempParam
// _interfaceParameters = (Parameter []) tempParam.toArray(new
// Parameter[tempParam.size()]);
} catch (NameDuplicationException e) {
log.error("The parameter could not be instantiated. Error message: " + e.getMessage());
throw new IllegalActionException(
this, "The complex submission form could not be initialized: " + e.getMessage());
}
return;
}
