void dispatchLocation()
/* When this is called no output has been written at all. We
* look at command variables in cart and figure out if we just
* are going write an HTTP location line, which happens when we
* want to invoke say the genome browser or gene sorter without
* another intermediate page. If we need to do more than that
* then we call hggDoUsualHttp. */
{
struct sqlConnection *conn = NULL;
getDbAndGenome(cart, &database, &genome, oldVars);
setUdcCacheDir();
cartSetString(cart, "db", database); /* Some custom tracks code needs this */
withLabels = cartUsualBoolean(cart, hggLabels, TRUE);
conn = hAllocConn(database);
getGenoGraphs(conn);
/* Handle cases that just want a HTTP Location line: */
if (cartVarExists(cart, hggClickX))
{
clickOnImage(conn);
return;
}
hFreeConn(&conn);
/* For other cases we want to print out some of the usual HTTP
* lines including content-type */
hggDoUsualHttp();
}
int main(int argc, char *argv[])
/* Process command line. */
{
cgiSpoof(&argc, argv);
setUdcCacheDir();
cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
long enteredMainTime = clock1000();
oldVars = hashNew(10);
setUdcCacheDir();
cgiSpoof(&argc, argv);
cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
cgiExitTime("hgHubConnect", enteredMainTime);
return 0;
}
int main(int argc, char *argv[])
{
long enteredMainTime = clock1000();
measureTime(NULL);
setUdcCacheDir();
browserName = hBrowserName();
organization = "UCSC";
/* Push very early error handling - this is just
* for the benefit of the cgiVarExists, which
* somehow can't be moved effectively into doMiddle. */
htmlPushEarlyHandlers();
cgiSpoof(&argc, argv);
char * link = webTimeStampedLinkToResourceOnFirstCall("HGStyle.css",TRUE); // resource file link
if (link) // wrapped in html
htmlSetStyle(link);
oldVars = hashNew(10);
if (cgiVarExists("hgt.redirectTool"))
{
printf("Content-type: text/html\n\n");
cart = cartForSession(hUserCookie(), NULL, NULL);
printf("<html><body>\n");
printf("<form id=\"redirForm\" method=\"POST\" action=\"http://tefor.net/crisporMax/crispor.cgi\">\n");
printf("<input type=\"hidden\" name=\"pos\" value=\"%s\">", cartString(cart, "position"));
printf("<input type=\"hidden\" name=\"org\" value=\"%s\">", cartString(cart, "db"));
printf("<input type=\"hidden\" name=\"pam\" value=\"NGG\">\n");
// a hidden submit button, see
// http://stackoverflow.com/questions/477691/submitting-a-form-by-pressing-enter-without-a-submit-button
printf("<input type=\"submit\" style=\"position: absolute; left: -9999px; width: 1px; height: 1px;\">\n");
printf("</form>\n");
// a little javascript that clicks the submit button
printf("<script>document.getElementById(\"redirForm\").submit();</script>\n");
printf("</body></html>\n");
}
else
cartHtmlShell("UCSC Genome Browser v"CGI_VERSION, doMiddle, hUserCookie(), excludeVars, oldVars);
if (measureTiming)
measureTime("Time to write and close cart");
if (measureTiming)
{
fprintf(stdout, "<span class='timing'>Overall total time: %ld millis<br /></span>\n",
clock1000() - enteredMainTime);
}
cgiExitTime("hgTracks", enteredMainTime);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
long enteredMainTime = clock1000();
cgiSpoof(&argc, argv);
setUdcCacheDir();
htmlSetStyle(htmlStyleUndecoratedLink);
if (argc != 1)
usage();
oldVars = hashNew(10);
cartEmptyShell(cartMain, hUserCookie(), excludeVars, oldVars);
cgiExitTime("hgGene", enteredMainTime);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
long enteredMainTime = clock1000();
oldVars = hashNew(10);
cgiSpoof(&argc, argv);
setUdcCacheDir();
/* org has precedence over db when changeInfo='orgChange' */
cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
cgiExitTime("hgBlat", enteredMainTime);
return 0;
}
int main(int argc, char *argv[])
/* Process CGI / command line. */
{
/* Null terminated list of CGI Variables we don't want to save
* permanently. */
char *excludeVars[] = {SEARCH_TERM, CARTJSON_COMMAND, NULL,};
cgiSpoof(&argc, argv);
setUdcCacheDir();
if (cgiOptionalString(SEARCH_TERM))
// Skip the cart for speedy searches
lookupTerm();
else
{
oldVars = hashNew(10);
cartEmptyShellNoContent(doMiddle, hUserCookie(), excludeVars, oldVars);
}
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 2)
usage();
udcSetCacheTimeout(cacheTime);
// UDC cache dir: first check for hg.conf setting, then override with command line option if given.
setUdcCacheDir();
udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
if (trackHubCrawl(argv[1]))
{
return 1;
}
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
long enteredMainTime = clock1000();
uglyTime(NULL);
cgiSpoof(&argc, argv);
setUdcCacheDir();
oldCart = hashNew(0);
if (cgiVarExists(hgpDoDownload)) /* use cgiVars -- do not commit to any cart method yet */
{
struct sqlConnection *conn = sqlConnect(visiDb);
cart = cartAndCookieNoContent(hUserCookie(), excludeVars, oldCart);
doDownload(conn);
cartCheckout(&cart);
}
else
{
cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldCart);
}
cgiExitTime("hgVisiGene", enteredMainTime);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 2 && !optionExists("settings"))
usage();
struct trackHubCheckOptions *checkOptions = NULL;
AllocVar(checkOptions);
checkOptions->specHost = (optionExists("test") ? "genome-test.soe.ucsc.edu" : "genome.ucsc.edu");
checkOptions->specHost = optionVal("specHost", checkOptions->specHost);
checkOptions->printMeta = optionExists("printMeta");
checkOptions->checkFiles = !optionExists("noTracks");
checkOptions->checkSettings = optionExists("checkSettings");
struct trackHubSettingSpec *setting = NULL;
AllocVar(setting);
setting->level = optionVal("level", "all");
if (trackHubSettingLevel(setting) < 0)
{
fprintf(stderr, "ERROR: Unrecognized support level %s\n\n", setting->level);
usage();
}
checkOptions->level = setting->level;
char *version = NULL;
if (optionExists("version"))
version = optionVal("version", NULL);
checkOptions->version = version;
char *extraFile = optionVal("extra", NULL);
if (extraFile != NULL)
addExtras(extraFile, checkOptions);
cacheTime = optionInt("cacheTime", cacheTime);
udcSetCacheTimeout(cacheTime);
// UDC cache dir: first check for hg.conf setting, then override with command line option if given.
setUdcCacheDir();
udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
knetUdcInstall(); // make the htslib library use udc
if (optionExists("settings"))
{
showSettings(checkOptions);
return 0;
}
struct dyString *errors = newDyString(1024);
if (trackHubCheck(argv[1], checkOptions, errors))
{
// uniquify and count errors
struct slName *errs = slNameListFromString(errors->string, '\n');
slUniqify(&errs, slNameCmp, slNameFree);
int errCount = slCount(errs);
printf("Found %d problem%s:\n", errCount, errCount == 1 ? "" : "s");
printf("%s\n", slNameListToString(errs, '\n'));
return 1;
}
return 0;
}
int main(int argc, char *argv[])
{
long enteredMainTime = clock1000();
struct dyString *output = newDyString(10000);
setUdcCacheDir();
cgiSpoof(&argc, argv);
pushWarnHandler(htmlVaBadRequestAbort);
pushAbortHandler(htmlVaBadRequestAbort);
char *database = cgiString("db");
char *cmd = cgiString("cmd");
char *jsonp = cgiOptionalString("jsonp");
if (!hDbExists(database))
errAbort("Invalid database '%s'", database);
if (!strcmp(cmd, "defaultPos"))
{
dyStringPrintf(output, "{\"pos\": \"%s\"}", hDefaultPos(database));
}
else if (!strcmp(cmd, "metaDb"))
{
// Return list of values for given metaDb var
// e.g. http://genome.ucsc.edu/hgApi?db=hg18&cmd=metaDb&var=cell
struct sqlConnection *conn = hAllocConn(database);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
if (metaDbExists)
{
char *var = cgiOptionalString("var");
if (!var)
errAbort("Missing var parameter");
boolean fileSearch = (cgiOptionalInt("fileSearch",0) == 1);
struct slPair *pairs = mdbValLabelSearch(conn, var, MDB_VAL_STD_TRUNCATION, FALSE,
!fileSearch, fileSearch);
struct slPair *pair;
dyStringPrintf(output, "[\n");
for (pair = pairs; pair != NULL; pair = pair->next)
{
if (pair != pairs)
dyStringPrintf(output, ",\n");
dyStringPrintf(output, "['%s','%s']", javaScriptLiteralEncode(mdbPairLabel(pair)),
javaScriptLiteralEncode(mdbPairVal(pair)));
}
dyStringPrintf(output, "\n]\n");
}
else
errAbort("Assembly does not support metaDb");
}
// TODO: move to lib since hgTracks and hgApi share
#define METADATA_VALUE_PREFIX "hgt_mdbVal"
else if (startsWith(METADATA_VALUE_PREFIX, cmd))
{
// Returns metaDb value control: drop down or free text, with or without help link.
// e.g. http://genome.ucsc.edu/hgApi?db=hg18&cmd=hgt_mdbVal3&var=cell
// TODO: Move guts to lib, so that hgTracks::searchTracks.c and hgApi.c can share
struct sqlConnection *conn = hAllocConn(database);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
if (metaDbExists)
{
char *var = cgiOptionalString("var");
if (!var)
errAbort("Missing var parameter");
int ix = atoi(cmd+strlen(METADATA_VALUE_PREFIX)); // 1 based index
if (ix == 0) //
errAbort("Unsupported 'cmd' parameter");
enum cvSearchable searchBy = cvSearchMethod(var);
char name[128];
safef(name,sizeof name,"%s%i",METADATA_VALUE_PREFIX,ix);
if (searchBy == cvSearchBySingleSelect || searchBy == cvSearchByMultiSelect)
{
boolean fileSearch = (cgiOptionalInt("fileSearch",0) == 1);
struct slPair *pairs = mdbValLabelSearch(conn, var, MDB_VAL_STD_TRUNCATION, FALSE,
!fileSearch, fileSearch);
if (slCount(pairs) > 0)
{
char *dropDownHtml =
cgiMakeSelectDropList((searchBy == cvSearchByMultiSelect),
name, pairs, NULL, ANYLABEL, "mdbVal",
"style='min-width: 200px; font-size: .9em;' "
"onchange='findTracksMdbValChanged(this);'");
if (dropDownHtml)
{
dyStringAppend(output,dropDownHtml);
freeMem(dropDownHtml);
}
slPairFreeList(&pairs);
}
}
else if (searchBy == cvSearchByFreeText)
{
dyStringPrintf(output,"<input type='text' name='%s' value='' class='mdbVal freeText' "
"onchange='findTracksMdbValChanged(this);' style='max-width:310px; "
"width:310px; font-size:.9em;'>", name);
}
else if (searchBy == cvSearchByWildList)
{
dyStringPrintf(output,"<input type='text' name='%s' value='' class='mdbVal wildList' "
"title='enter comma separated list of values' "
"onchange='findTracksMdbValChanged(this);' style='max-width:310px; "
"width:310px; font-size:.9em;'>", name);
}
else if (searchBy == cvSearchByDateRange || searchBy == cvSearchByIntegerRange)
{
// TO BE IMPLEMENTED
}
else
errAbort("Metadata variable not searchable");
dyStringPrintf(output,"<span id='helpLink%i'> </span>",ix);
}
else
errAbort("Assembly does not support metaDb");
}
else if (!strcmp(cmd, "tableMetadata"))
{ // returns an html table with metadata for a given track
char *trackName = cgiOptionalString("track");
boolean showLonglabel = (NULL != cgiOptionalString("showLonglabel"));
boolean showShortLabel = (NULL != cgiOptionalString("showShortLabel"));
if (trackName != NULL)
{
// hTrackDbForTrackAndAncestors avoids overhead of getting whole track list!
struct trackDb *tdb = hTrackDbForTrackAndAncestors(database, trackName);
if (tdb != NULL)
{
char * html = metadataAsHtmlTable(database,tdb,showLonglabel,showShortLabel);
if (html)
{
dyStringAppend(output,html);
freeMem(html);
}
else
dyStringPrintf(output,"No metadata found for track %s.",trackName);
}
else
dyStringPrintf(output,"Track %s not found",trackName);
}
else
dyStringAppend(output,"No track variable found");
}
else if (sameString(cmd, "codonToPos") || sameString(cmd, "exonToPos"))
{
char query[256];
struct sqlResult *sr;
char **row;
struct genePred *gp;
char *name = cgiString("name");
char *table = cgiString("table");
int num = cgiInt("num");
struct sqlConnection *conn = hAllocConn(database);
sqlSafef(query, sizeof(query), "select name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds from %s where name = '%s'", table, name);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
gp = genePredLoad(row);
boolean found;
int start, end;
if (sameString(cmd, "codonToPos"))
found = codonToPos(gp, num, &start, &end);
else
found = exonToPos(gp, num, &start, &end);
if (found)
dyStringPrintf(output, "{\"pos\": \"%s:%d-%d\"}", gp->chrom, start + 1, end);
else
dyStringPrintf(output, "{\"error\": \"%d is an invalid %s for this gene\"}", num, sameString(cmd, "codonToPos") ? "codon" : "exon");
}
else
dyStringPrintf(output, "{\"error\": \"Couldn't find item: %s\"}", name);
sqlFreeResult(&sr);
hFreeConn(&conn);
}
else
{
warn("unknown cmd: %s",cmd);
errAbort("Unsupported 'cmd' parameter");
}
apiOut(dyStringContents(output), jsonp);
cgiExitTime("hgApi", enteredMainTime);
return 0;
}
void refreshNamedSessionCustomTracks(char *centralDbName)
/* refreshNamedSessionCustomTracks -- cron robot for keeping alive custom
* tracks that are referenced by saved sessions. */
{
struct sqlConnection *conn = hConnectCentral();
struct slPair *updateList = NULL, *update;
char *actualDbName = sqlGetDatabase(conn);
int liveCount=0, expiredCount=0;
setUdcCacheDir(); /* programs that use udc must call this to initialize cache dir location */
if (!sameString(centralDbName, actualDbName))
errAbort("Central database specified in hg.conf file is %s but %s "
"was specified on the command line.",
actualDbName, centralDbName);
else
verbose(2, "Got connection to %s\n", centralDbName);
long long threshold = 0;
int atime = optionInt("atime", 0);
if (atime > 0)
{
time_t now = time(NULL);
threshold = now - ((long long)atime * 24 * 60 * 60);
}
if (sqlTableExists(conn, savedSessionTable))
{
struct sessionInfo *sessionList = NULL, *si;
struct sqlResult *sr = NULL;
char **row = NULL;
char query[512];
safef(query, sizeof(query),
"select userName,sessionName,UNIX_TIMESTAMP(lastUse),contents from %s "
"order by userName,sessionName", savedSessionTable);
sr = sqlGetResult(conn, query);
// Slurp results into memory instead of processing row by row,
// reducing the chance of lost connection.
while ((row = sqlNextRow(sr)) != NULL)
{
if (atime > 0)
{
long long lastUse = atoll(row[2]);
if (lastUse < threshold)
{
verbose(2, "User %s session %s is older than %d days, skipping.\n",
row[0], row[1], atime);
continue;
}
}
AllocVar(si);
safecpy(si->userName, sizeof(si->userName), row[0]);
safecpy(si->sessionName, sizeof(si->sessionName), row[1]);
si->contents = cloneString(row[3]);
slAddHead(&sessionList, si);
}
sqlFreeResult(&sr);
for (si = sessionList; si != NULL; si = si->next)
{
char *updateIfAny = scanSettingsForCT(si->userName, si->sessionName, si->contents,
&liveCount, &expiredCount);
if (updateIfAny)
{
AllocVar(update);
update->name = updateIfAny;
slAddHead(&updateList, update);
}
}
}
/* Now that we're done reading from savedSessionTable, we can modify it: */
if (optionExists("hardcore"))
{
for (update = updateList; update != NULL; update = update->next)
sqlUpdate(conn, update->name);
}
hDisconnectCentral(&conn);
verbose(1, "Found %d live and %d expired custom tracks in %s.\n",
liveCount, expiredCount, centralDbName);
}