private void checkMirrors(final Change event) {
if ((fRequireLoad & (REQUIRE_CRAN | REQUIRE_BIOC)) != 0) {
return;
}
SelectedRepos selected = fSelectedRepos;
fAllCRAN = ConstArrayList.concat(fCustomCRAN, fRCRAN);
RRepo selectedCRAN = selected.getCRANMirror();
if (selected.getCRANMirror() != null) {
selectedCRAN = Util.findRepo(fAllCRAN, selectedCRAN);
} else if (fFirstTime && fSelectedCRANInR != null) {
selectedCRAN = Util.getRepoByURL(fAllCRAN, fSelectedCRANInR);
}
if (selectedCRAN == null) {
fRequireConfirm |= REQUIRE_CRAN;
selectedCRAN = PreferencesUtil.getInstancePrefs().getPreferenceValue(LAST_CRAN_PREF);
if (selectedCRAN != null) {
selectedCRAN = Util.findRepo(fAllCRAN, selectedCRAN);
}
if (!fCustomCRAN.isEmpty()
&& (selectedCRAN == null || !selectedCRAN.getId().startsWith(RRepo.CUSTOM_PREFIX))) {
selectedCRAN = fCustomCRAN.get(0);
}
if (fFirstTime && selectedCRAN == null) {
selectedCRAN = fRCRANByCountry;
}
}
RRepo selectedBioC = selected.getBioCMirror();
fAllBioC = ConstArrayList.concat(fCustomBioC, fRBioC);
if (selectedBioC != null) {
selectedBioC = Util.findRepo(fAllBioC, selectedBioC);
} else if (fFirstTime && fSelectedBioCInR != null) {
selectedBioC = RPkgUtil.getRepoByURL(fAllBioC, fSelectedBioCInR);
}
if (selectedBioC == null) {
fRequireConfirm |= REQUIRE_BIOC;
selectedBioC = PreferencesUtil.getInstancePrefs().getPreferenceValue(LAST_BIOC_PREF);
if (!fCustomBioC.isEmpty()
&& (selectedBioC == null || !selectedBioC.getId().startsWith(RRepo.CUSTOM_PREFIX))) {
selectedBioC = fCustomBioC.get(0);
}
if (fFirstTime && selectedBioC == null) {
selectedBioC = Util.getRepoByURL(fAllBioC, "http://www.bioconductor.org"); // $NON-NLS-1$
}
}
selected = new SelectedRepos(selected.getRepos(), selectedCRAN, fBioCVersion, selectedBioC);
if ((fRequireLoad & (REQUIRE_REPOS)) == 0) {
for (final RRepo repo : fAllRepos) {
if (repo instanceof RVarRepo) {
((RVarRepo) repo).updateURL(selected);
}
}
}
fSelectedRepos = selected;
event.fPkgs = 1;
}
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));
}
}
private void checkRepos(final Change event) {
if ((fRequireLoad & (REQUIRE_CRAN | REQUIRE_BIOC | REQUIRE_REPOS)) != 0) {
return;
}
SelectedRepos selected = fSelectedRepos;
fAllRepos = new ArrayList<>(fCustomRepos.size() + fAddRepos.size() + fRRepos.size());
fAllRepos.addAll(fCustomRepos);
fAllRepos.addAll(fAddRepos);
for (final RRepo repo : fAllRepos) {
if (repo instanceof RVarRepo) {
((RVarRepo) repo).updateURL(selected);
}
}
for (final RRepo repo : fRRepos) {
if (repo instanceof RVarRepo) {
((RVarRepo) repo).updateURL(selected);
}
}
for (final RRepo repo : fRRepos) {
if (!repo.getId().isEmpty()) {
if (RPkgUtil.getRepoById(fAllRepos, repo.getId()) == null) {
fAllRepos.add(repo);
}
} else {
if (Util.getRepoByURL(fAllRepos, repo) == null) {
fAllRepos.add(
RVarRepo.create(RRepo.R_PREFIX + repo.getURL(), repo.getName(), repo.getURL(), null));
}
}
}
{
final Collection<RRepo> selectedRepos = selected.getRepos();
final Collection<RRepo> previous =
(fFirstTime && selectedRepos.isEmpty()) ? fSelectedReposInR : selectedRepos;
final List<RRepo> repos = new ArrayList<>(previous.size());
for (RRepo repo : previous) {
repo = Util.findRepo(fAllRepos, repo);
if (repo != null) {
repos.add(repo);
}
}
selected =
new SelectedRepos(
repos, selected.getCRANMirror(), selected.getBioCVersion(), selected.getBioCMirror());
fSelectedRepos = selected;
}
fRequireLoad |= REQUIRE_REPO_PKGS;
event.fRepos = 1;
}
private ISelectedRepos runLoadRepos(final RService r, final IProgressMonitor monitor)
throws CoreException {
try {
String bioCVersion;
{
final RObject data =
r.evalData("as.character(tools:::.BioC_version_associated_with_R_version)", monitor);
bioCVersion = RDataUtil.checkSingleCharValue(data);
}
final boolean loadRMirrors = ((fRequireLoad & (REQUIRE_CRAN | REQUIRE_BIOC)) != 0);
final boolean loadRRepos = ((fRequireLoad & (REQUIRE_REPOS)) != 0);
List<RRepo> rCRAN = null;
List<RRepo> rBioC = null;
String selectedCRAN = null;
RRepo rCRANByCountry = null;
String selectedBioC = null;
if (loadRMirrors) {
monitor.subTask("Fetching available mirrors...");
final String region = Locale.getDefault().getCountry().toLowerCase();
{
final RObject data =
r.evalData(
"getCRANmirrors()[c('Name', 'URL', 'CountryCode')]", monitor); // $NON-NLS-1$
final RDataFrame df = RDataUtil.checkRDataFrame(data);
final RCharacterStore names =
RDataUtil.checkRCharVector(df.get("Name")).getData(); // $NON-NLS-1$
final RCharacterStore urls =
RDataUtil.checkRCharVector(df.get("URL")).getData(); // $NON-NLS-1$
final RCharacterStore regions =
RDataUtil.checkRCharVector(df.get("CountryCode")).getData(); // $NON-NLS-1$
final int l = RDataUtil.checkIntLength(names);
rCRAN = new ArrayList<>(l);
for (int i = 0; i < l; i++) {
final String url = Util.checkURL(urls.getChar(i));
if (!url.isEmpty()) {
final RRepo repo = new RRepo(RRepo.R_PREFIX + url, names.getChar(i), url, null);
rCRAN.add(repo);
if (rCRANByCountry == null
&& !region.isEmpty()
&& region.equals(regions.getChar(i))) {
rCRANByCountry = repo;
}
}
}
}
{
final String[][] fix =
new String[][] {
{"Seattle (USA)", "http://www.bioconductor.org"},
{"Bethesda (USA)", "http://watson.nci.nih.gov/bioc_mirror"},
{"Dortmund (Germany)", "http://bioconductor.statistik.tu-dortmund.de"},
{"Bergen (Norway)", "http://bioconductor.uib.no"},
{"Cambridge (UK)", "http://mirrors.ebi.ac.uk/bioconductor"}
};
rBioC = new ArrayList<>(fix.length);
for (int i = 0; i < fix.length; i++) {
final String url = Util.checkURL(fix[i][1]);
if (!url.isEmpty()) {
rBioC.add(new RRepo(RRepo.R_PREFIX + url, fix[i][0], url, null));
}
}
}
}
List<RRepo> rrepos = null;
List<RRepo> selected = null;
if (loadRRepos) {
monitor.subTask("Fetching available repositories...");
{
final RObject data = r.evalData("options('repos')[[1L]]", monitor); // $NON-NLS-1$
if (data.getRObjectType() != RObject.TYPE_NULL) {
final RCharacterStore urls = RDataUtil.checkRCharVector(data).getData();
final RStore ids = ((RVector<?>) data).getNames();
final int l = RDataUtil.checkIntLength(urls);
selected = new ArrayList<>(l);
for (int i = 0; i < l; i++) {
final String id = (ids != null) ? ids.getChar(i) : null;
final String url = urls.getChar(i);
final RRepo repo = Util.createRepoFromR(id, null, url);
if (repo != null) {
selected.add(repo);
}
}
} else {
selected = new ArrayList<>(4);
}
}
final RObject data =
r.evalData(
"local({"
+ //$NON-NLS-1$
"p <- file.path(Sys.getenv('HOME'), '.R', 'repositories')\n"
+ //$NON-NLS-1$
"if (!file.exists(p)) p <- file.path(R.home('etc'), 'repositories')\n"
+ //$NON-NLS-1$
"r <- utils::read.delim(p, header = TRUE, comment.char = '#', colClasses = c(rep.int('character', 3L), rep.int('logical', 4L)))\n"
+ //$NON-NLS-1$
"r[c(names(r)[1L], 'URL', 'default')]\n"
+ //$NON-NLS-1$
"})",
monitor); //$NON-NLS-1$
final RDataFrame df = RDataUtil.checkRDataFrame(data);
final RStore ids = df.getRowNames();
final RCharacterStore labels = RDataUtil.checkRCharVector(df.get(0)).getData();
final RCharacterStore urls =
RDataUtil.checkRCharVector(df.get("URL")).getData(); // $NON-NLS-1$
final RLogicalStore isDefault =
(selected.isEmpty())
? RDataUtil.checkRLogiVector(df.get("default")).getData()
: null; //$NON-NLS-1$
{
final int l = RDataUtil.checkIntLength(labels);
rrepos = new ArrayList<>(l + 4);
for (int i = 0; i < l; i++) {
final String id = (ids != null) ? ids.getChar(i) : null;
final String url = urls.getChar(i);
final RRepo repo = Util.createRepoFromR(id, labels.getChar(i), url);
if (repo != null) {
rrepos.add(repo);
if (isDefault != null && isDefault.getLogi(i)) {
selected.add(repo);
}
}
}
}
for (int i = 0; i < selected.size(); i++) {
final RRepo repo = selected.get(i);
RRepo rrepo = null;
if (!repo.getURL().isEmpty()) {
rrepo = RPkgUtil.getRepoByURL(rrepos, repo.getURL());
}
if (rrepo != null) {
selected.set(i, rrepo);
continue;
}
if (!repo.getId().isEmpty()) {
final int j = rrepos.indexOf(repo); // by id
if (j >= 0) {
rrepo = rrepos.get(j);
if (!RVarRepo.hasVars(rrepo.getURL())) {
rrepo.setURL(repo.getURL());
}
selected.set(i, rrepo);
continue;
}
}
repo.setName(RRepo.hintName(repo));
continue;
}
}
if (loadRMirrors) {
if (loadRRepos) {
final RRepo repo = RPkgUtil.getRepoById(rrepos, RRepo.CRAN_ID);
if (repo != null && !repo.getURL().isEmpty() && !RVarRepo.hasVars(repo.getURL())) {
selectedCRAN = repo.getURL();
}
} else {
final RObject data = r.evalData("options('repos')[[1L]]['CRAN']", monitor); // $NON-NLS-1$
if (data.getRObjectType() != RObject.TYPE_NULL) {
final String url = Util.checkURL(RDataUtil.checkSingleChar(data));
if (!url.isEmpty() && !RVarRepo.hasVars(url)) {
selectedCRAN = url;
}
}
}
{
final RObject data = r.evalData("options('BioC_mirror')[[1L]]", monitor); // $NON-NLS-1$
if (data.getRObjectType() != RObject.TYPE_NULL) {
selectedBioC = RDataUtil.checkSingleChar(data);
}
}
}
getWriteLock().lock();
try {
fBioCVersion = bioCVersion;
if (loadRMirrors) {
fRequireLoad &= ~(REQUIRE_CRAN | REQUIRE_BIOC);
fRCRAN = rCRAN;
fRCRANByCountry = rCRANByCountry;
fSelectedCRANInR = selectedCRAN;
fRBioC = rBioC;
fSelectedBioCInR = selectedBioC;
fMirrorsStamp = fRTaskEvent.fStamp;
checkMirrors(fRTaskEvent);
}
if (loadRRepos) {
fRequireLoad &= ~(REQUIRE_REPOS);
fRRepos = rrepos;
fSelectedReposInR = selected;
checkRepos(fRTaskEvent);
}
fFirstTime = false;
if (getReposStatus(fSelectedRepos, fSelectedRepos, fRequireConfirm).isOK()) {
return fSelectedRepos;
}
return null;
} finally {
getWriteLock().unlock();
}
} catch (final Exception e) {
throw new CoreException(
new Status(
IStatus.ERROR,
RCore.PLUGIN_ID,
0,
"An error occurred when loading data for package manager.",
e));
}
}