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;
}
@Override
public void setSelectedRepos(final ISelectedRepos repos) {
List<RRepo> selectedRepos;
{
final Collection<RRepo> selected = repos.getRepos();
selectedRepos = new ArrayList<>(selected.size());
for (final RRepo repo : fAllRepos) {
if (selected.contains(repo)) {
selectedRepos.add(repo);
}
}
}
RRepo selectedCRAN;
{
final RRepo repo = repos.getCRANMirror();
selectedCRAN = (repo != null) ? Util.findRepo(fAllCRAN, repo) : null;
fRequireConfirm &= ~REQUIRE_CRAN;
}
RRepo selectedBioC;
{
final RRepo repo = repos.getBioCMirror();
selectedBioC = (repo != null) ? Util.findRepo(fAllBioC, repo) : null;
fRequireConfirm &= ~REQUIRE_BIOC;
}
final SelectedRepos previousSettings = fSelectedRepos;
final SelectedRepos newSettings =
new SelectedRepos(
selectedRepos, selectedCRAN, previousSettings.getBioCVersion(), selectedBioC);
for (final RRepo repo : fAllRepos) {
if (repo instanceof RVarRepo) {
((RVarRepo) repo).updateURL(newSettings);
}
}
fSelectedRepos = newSettings;
savePrefs(newSettings);
if (!newSettings.equals(previousSettings)) {
fRequireLoad |= (REQUIRE_REPO_PKGS);
final Change event = new Change(fREnv);
event.fRepos = 1;
fireUpdate(event);
}
}
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;
}