void
CfHandler::check()
{
if (_subscriber.nextConfig(0)) {
doConfigure();
}
}
void PropertyConfiguratorImpl::doConfigure(const std::string& initFileName) throw (ConfigureFailure) {
std::ifstream initFile(initFileName.c_str());
if (!initFile) {
throw ConfigureFailure(std::string("File ") + initFileName + " does not exist");
}
doConfigure(initFile);
}
void doDefaultConfigure(struct sqlConnection *conn, struct column *colList)
/* Do configuration starting with defaults. */
{
struct column *col;
for (col=colList; col != NULL; col = col->next)
col->on = col->defaultOn;
cartRemovePrefix(cart, colConfigPrefix);
cartRemove(cart, colOrderVar);
//restoreDefaultOrder(&colList);
doConfigure(conn, colList); //, NULL);
}
Component* ComponentFactory::create(const tnt::Compident& ci,
const tnt::Urlmapper& um, tnt::Comploader& cl)
{
if (theComponent == 0)
{
doConfigure(TntConfig::it());
theComponent = doCreate(ci, um, cl);
}
return theComponent;
}
static void configAllVis(struct sqlConnection *conn, struct column *colList,
boolean how)
/* Respond to hide all button in configuration page. */
{
char varName[64];
struct column *col;
for (col = colList; col != NULL; col = col->next)
{
safef(varName, sizeof(varName), "%s%s.vis", colConfigPrefix, col->name);
cartSetBoolean(cart, varName, how);
}
doConfigure(conn, colList); //, NULL);
}
void doMiddle(struct cart *theCart)
/* Write the middle parts of the HTML page.
* This routine sets up some globals and then
* dispatches to the appropriate page-maker. */
{
cart = theCart;
if (hIsGisaidServer())
{
validateGisaidUser(cart);
}
if (cartVarExists(cart, confVarName))
doConfigure(conn, colList);
else if (cartVarExists(cart, defaultConfName))
doDefaultConfigure(conn, colList);
else if (cartVarExists(cart, hideAllConfName))
doConfigHideAll(conn, colList);
else if (cartVarExists(cart, showAllConfName))
doConfigShowAll(conn, colList);
else if (cartVarExists(cart, getSeqPageVarName))
doGetSeqPage(conn, colList);
else if (cartVarExists(cart, advFilterVarName))
doAdvFilter(conn, colList);
else if (cartVarExists(cart, advFilterClearVarName))
doAdvFilterClear(conn, colList);
else if ((col = advFilterKeyPastePressed(colList)) != NULL)
doAdvFilterKeyPaste(conn, colList, col);
else if ((col = advFilterKeyPastedPressed(colList)) != NULL)
doAdvFilterKeyPasted(conn, colList, col);
else if ((col = advFilterKeyUploadPressed(colList)) != NULL)
doAdvFilterKeyUpload(conn, colList, col);
else if ((col = advFilterKeyClearPressed(colList)) != NULL)
doAdvFilterKeyClear(conn, colList, col);
else
displayData(conn, colList);
cartRemovePrefix(cart, "gisaidTable.do.");
}
void displayData(struct sqlConnection *conn, struct column *colList)
/* Display data in neighborhood of gene. */
{
struct subjInfo *subjList = NULL;
struct column *ordList = colList;
struct column *ord = curOrder(ordList);
if (ord == NULL) /* no columns are visible, go to back to configure page */
{
doConfigure(conn, colList);
return;
}
if (cartVarExists(cart, getTextVarName))
{
subjList = getOrderedList(ord, colList, conn, BIGNUM);
doGetText(conn, colList, subjList);
}
else if (cartVarExists(cart, getSeqVarName))
{
subjList = getOrderedList(ord, colList, conn, BIGNUM);
doGetSeq(conn, subjList, cartString(cart, getSeqHowVarName));
}
else if (cartVarExists(cart, redirectName))
{
subjList = getOrderedList(ord, colList, conn, BIGNUM);
if (subjList)
{
cartRemove(cart, redirectName);
}
else /* if everything has been filtered out, we'll have to go back */
{
hPrintf("No subject(s) found with the filtering conditions specified.<br>");
hPrintf("Click <a href=\"gisaidTable?gisaidTable.do.advFilter=filter+%c28now+on%c29\">here</a> to return to Select Subjects.<br>", '%', '%');
}
}
else
{
subjList = getOrderedList(ord, colList, conn, displayCount);
doMainDisplay(conn, colList, subjList);
}
}
void GlobalConfiguration::configure(const Configuration::Ptr& configuration)
{
_configuration = configuration;
logging.device = _configuration->get("logging.device", "None");
logging.separator = " " + _configuration->get("logging.separator", "|") + " ";
logging.escape_newline = _configuration->get("logging.escape_newline", false);
debug.global_level = _configuration->get("debug.global_level", 0);
if(_configuration->hasProperty("debug.level")) {
StringVector properties;
_configuration->getProperties("debug.level", properties);
for(auto& property : properties) {
debug.level.insert(std::make_pair(property, _configuration->get<int32_t>("debug.level." + property)));
}
}
doConfigure(_configuration);
}
bool CrossRefPlugin::resolve (Document &doc)
{
/*
* Prompt for username and password if needed
*/
if (_global_prefs->getCrossRefUsername ().empty ()) {
Glib::ustring message =
String::ucompose (
"<b><big>%1</big></b>\n\n%2\n",
_("CrossRef credentials not found"),
_("To use the CrossRef service, a free account is needed. "
"Login information may be set in Preferences, or the CrossRef plugin "
"may be disabled.")
);
Gtk::MessageDialog dialog(message, true, Gtk::MESSAGE_WARNING,
Gtk::BUTTONS_NONE, true);
dialog.add_button (Gtk::Stock::CANCEL, 0);
dialog.add_button (_("_Preferences"), 1);
dialog.add_button (_("_Disable CrossRef"), 2);
do {
int response = dialog.run ();
if (response == 1) {
// Preferences
doConfigure ();
if (!_global_prefs->getCrossRefUsername ().empty ())
break;
// if they didn't give us one then we loop around
// else we go ahead
} else if (response == 2) {
// Disable
_global_prefs->disablePlugin (this);
return false;
} else {
// Cancel
return false;
}
} while (1);
}
Glib::ustring messagetext =
String::ucompose (
"<b><big>%1</big></b>\n\n%2\n",
_("Downloading metadata"),
String::ucompose (
_("Contacting crossref.org to retrieve metadata for '%1'"),
doc.getField("doi"))
);
Glib::ustring const username = _global_prefs->getCrossRefUsername ();
Glib::ustring const password = _global_prefs->getCrossRefPassword ();
Glib::ustring const url =
Glib::ustring("http://www.crossref.org/openurl/?pid=")
+ username
+ (password.empty() ? "" : ":")
+ password
+ Glib::ustring("&id=doi:")
+ Gnome::Vfs::escape_string(doc.getField("doi"))
+ Glib::ustring ("&noredirect=true");
DEBUG ("CrossRefPlugin::resolve: using url '%1'", url);
// FIXME: even if we don't get any metadata,
// an exceptionless download+parse is considered
// a success.
// Nobody notices as long as crossref is the last resort
bool success = true;
try {
Glib::ustring &xml = Transfer::readRemoteFile (
_("Downloading Metadata"), messagetext, url);
DEBUG (xml);
// XXX
// Test for "Missing WWW-Authenticate header" for bad username/password
// Test for "No DOI found" for bad DOI
CrossRefParser parser (doc.getBibData());
Glib::Markup::ParseContext context (parser);
try {
context.parse (xml);
context.end_parse ();
} catch (Glib::MarkupError const ex) {
DEBUG ("Markuperror while parsing:\n'''%1\n'''", xml);
//Utility::exceptionDialog (&ex, _("Parsing CrossRef XML. The DOI could be invalid, or not known to crossref.org"));
success = false;
}
} catch (Transfer::Exception ex) {
//Utility::exceptionDialog (&ex, _("Downloading metadata"));
success = false;
}
DEBUG ("resolve returning %1", success);
return success;
}