private void runApplyRepo(
final ISelectedRepos repos, final RService r, final IProgressMonitor monitor)
throws CoreException {
monitor.subTask("Setting repository configuration...");
try {
if (repos.getBioCMirror() != null) {
final FunctionCall call = r.createFunctionCall("options");
call.addChar("BioC_mirror", repos.getBioCMirror().getURL());
call.evalVoid(monitor);
}
{
final List<RRepo> selectedRepos = (List<RRepo>) repos.getRepos();
final String[] ids = new String[selectedRepos.size()];
final String[] urls = new String[selectedRepos.size()];
for (int i = 0; i < urls.length; i++) {
final RRepo repo = selectedRepos.get(i);
ids[i] = repo.getId();
urls[i] = repo.getURL();
}
final RVector<RCharacterStore> data =
new RVectorImpl<RCharacterStore>(
new RCharacterDataImpl(urls), RObject.CLASSNAME_CHARACTER, ids);
final FunctionCall call = r.createFunctionCall("options");
call.add("repos", data);
call.evalVoid(monitor);
}
} catch (final CoreException e) {
throw new CoreException(
new Status(
IStatus.ERROR,
RCore.PLUGIN_ID,
"An error occurred when setting repository configuration in R.",
e));
}
}
@Override
protected void doSubmitCommandL(
final String[] lines,
final SrcfileData srcfile,
final IRSrcref srcref,
final IProgressMonitor monitor)
throws CoreException {
if ((fCurrentPrompt.meta
& (IRBasicAdapter.META_PROMPT_DEFAULT | IRBasicAdapter.META_PROMPT_SUSPENDED))
== 0) {
super.doSubmitCommandL(lines, srcfile, srcref, monitor);
return;
}
final FunctionCall prepare = createFunctionCall("rj:::.statet.prepareCommand");
prepare.add("lines", fRObjectFactory.createVector(fRObjectFactory.createCharData(lines)));
if (srcfile != null && srcref != null) {
final List<String> attributeNames = new ArrayList<String>();
final List<RObject> attributeValues = new ArrayList<RObject>();
if (srcfile.getName() != null) {
prepare.addChar("filename", srcfile.getName());
}
// if (srcfile.workspacePath != null) {
// attributeNames.add("statet.Path");
// attributeValues.add(fRObjectFactory.createVector(fRObjectFactory.createCharData(
// new String[] { srcfile.workspacePath } )));
// }
if (srcfile.getTimestamp() != 0) {
attributeNames.add("timestamp");
attributeValues.add(
fRObjectFactory.createVector(
fRObjectFactory.createNumData(new double[] {srcfile.getTimestamp()})));
}
final int[] rjSrcref = RDbg.createRJSrcref(srcref);
if (rjSrcref != null) {
attributeNames.add("linesSrcref");
attributeValues.add(fRObjectFactory.createVector(fRObjectFactory.createIntData(rjSrcref)));
}
if (attributeNames.size() > 0) {
prepare.add(
"srcfileAttributes",
fRObjectFactory.createList(
attributeValues.toArray(new RObject[attributeValues.size()]),
attributeNames.toArray(new String[attributeNames.size()])));
}
if (srcref instanceof IRModelSrcref) {
// Move to abstract controller or breakpoint adapter?
final IRModelSrcref modelSrcref = (IRModelSrcref) srcref;
final List<IRLangSourceElement> elements = modelSrcref.getElements();
if (elements.size() > 0) {
final List<String> elementIds = new ArrayList<String>(elements.size());
final List<RObject> elementIndexes = new ArrayList<RObject>(elements.size());
for (final IRLangSourceElement element : elements) {
if (TAG_ELEMENT_FILTER.include(element)) {
final FDef fdef = (FDef) element.getAdapter(FDef.class);
if (fdef != null) {
final String elementId = RDbg.getElementId(element);
final RAstNode cont = fdef.getContChild();
final int[] path =
RAst.computeRExpressionIndex(cont, RAst.getRRootNode(cont, modelSrcref));
if (elementId != null && path != null) {
final int[] fullPath = new int[path.length + 1];
fullPath[0] = 1;
System.arraycopy(path, 0, fullPath, 1, path.length);
elementIds.add(elementId);
elementIndexes.add(
fRObjectFactory.createVector(fRObjectFactory.createIntData(fullPath)));
}
}
}
}
if (elementIds.size() > 0) {
prepare.add(
"elementIds",
fRObjectFactory.createList(
elementIndexes.toArray(new RObject[elementIndexes.size()]),
elementIds.toArray(new String[elementIds.size()])));
}
}
}
}
prepare.evalVoid(monitor);
final boolean addToHistory = (fCurrentPrompt.meta & IRBasicAdapter.META_HISTORY_DONTADD) == 0;
fCurrentInput = lines[0];
doBeforeSubmitL();
for (int i = 1; i < lines.length; i++) {
setCurrentPromptL(fContinuePromptText, addToHistory);
fCurrentInput = lines[i];
doBeforeSubmitL();
}
fCurrentInput = "rj:::.statet.evalCommand()";
doSubmitL(monitor);
}
@Override
public void doSubmitFileCommandToConsole(
final String[] lines,
final SrcfileData srcfile,
final ISourceUnit su,
final IProgressMonitor monitor)
throws CoreException {
if (srcfile != null
&& su instanceof IRWorkspaceSourceUnit
&& su.getModelTypeId() == RModel.TYPE_ID) {
try {
final IRModelInfo modelInfo =
(IRModelInfo) su.getModelInfo(RModel.TYPE_ID, IRModelManager.MODEL_FILE, monitor);
if (modelInfo != null) {
final IRLangSourceElement fileElement = modelInfo.getSourceElement();
final RAstNode rootNode = (RAstNode) fileElement.getAdapter(IAstNode.class);
final List<? extends IRLangSourceElement> elements =
modelInfo.getSourceElement().getSourceChildren(TAG_ELEMENT_FILTER);
final List<String> elementIds = new ArrayList<String>(elements.size());
final List<RObject> elementIndexes = new ArrayList<RObject>(elements.size());
for (final IRLangSourceElement element : elements) {
final FDef fdef = (FDef) element.getAdapter(FDef.class);
if (fdef != null) {
final String elementId = RDbg.getElementId(element);
final RAstNode cont = fdef.getContChild();
final int[] path = RAst.computeRExpressionIndex(cont, rootNode);
if (elementId != null && path != null) {
elementIds.add(elementId);
elementIndexes.add(
fRObjectFactory.createVector(fRObjectFactory.createIntData(path)));
}
}
}
final FunctionCall prepare =
createFunctionCall("rj:::.statet.prepareSource"); // $NON-NLS-1$
prepare.add(
fRObjectFactory.createList(
new RObject[] {
fRObjectFactory.createVector(
fRObjectFactory.createCharData(new String[] {srcfile.getPath()})),
fRObjectFactory.createVector(
fRObjectFactory.createNumData(new double[] {srcfile.getTimestamp()})),
fRObjectFactory.createVector(
fRObjectFactory.createIntData(new int[] {rootNode.getChildCount()})),
fRObjectFactory.createList(
elementIndexes.toArray(new RObject[elementIndexes.size()]),
elementIds.toArray(new String[elementIds.size()])),
},
new String[] {
"path", "timestamp", "exprsLength", "elementIds"
})); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
prepare.evalVoid(monitor);
}
} catch (final CoreException e) {
RConsoleCorePlugin.log(
new Status(
IStatus.ERROR,
RConsoleCorePlugin.PLUGIN_ID,
-1,
NLS.bind(
"An error occurred when preparing element tagging for file ''{0}''.",
srcfile.getPath()),
e));
}
}
super.doSubmitFileCommandToConsole(lines, srcfile, su, monitor);
}