int main(int argc, char *argv[])
/* Process command line. */
{
long enteredMainTime = clock1000();
cgiSpoof(&argc, argv);
cartEmptyShell(doMiddle, hUserCookie(), excludeVars, NULL);
cgiExitTime("hgFileSearch", enteredMainTime);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
long enteredMainTime = clock1000();
oldVars = hashNew(10);
cgiSpoof(&argc, argv);
cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
cgiExitTime("hgPcr", enteredMainTime);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
long enteredMainTime = clock1000();
cgiSpoof(&argc, argv);
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[])
{
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();
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 command line. */
{
long enteredMainTime = clock1000();
struct dyString *headText = newDyString(512);
char *destination = cgiUsualString("destination", defaultDestination);
if (strstr(destination, "://"))
errAbort("To stop Open Redirect abuse, only relative URLs are supported. "
"Request for destination=[%s] rejected.\n", destination);
dyStringPrintf(headText,
"<META HTTP-EQUIV=\"REFRESH\" CONTENT=\"0;URL=%s\">"
"<META HTTP-EQUIV=\"Pragma\" CONTENT=\"no-cache\">"
"<META HTTP-EQUIV=\"Expires\" CONTENT=\"-1\">"
,destination);
htmShellWithHead("Reset Cart", headText->string, doMiddle, NULL);
dyStringFree(&headText);
cgiExitTime("cartReset", enteredMainTime);
return 0;
}
int main(int argc, char *argv[])
{
long enteredMainTime = clock1000();
cgiSpoof(&argc, argv);
char *database = cgiOptionalString("db");
char *prefix = cgiOptionalString("prefix");
char *type = cgiOptionalString("type");
char *table = checkParams(database, prefix, type);
puts("Content-Type:text/plain");
puts("\n");
if (sameOk(type, ALT_OR_PATCH))
suggestAltOrPatch(database, prefix);
else
suggestGene(database, table, prefix);
cgiExitTime("hgSuggest", enteredMainTime);
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[])
{
long enteredMainTime = clock1000();
measureTime(NULL);
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");
errAbortSetDoContentType(FALSE);
cart = cartForSession(hUserCookie(), NULL, NULL);
extToolRedirect(cart, cgiString("hgt.redirectTool"));
}
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);
termOpt = cgiOptionalString(CV_TERM);
tagOpt = cgiOptionalString(CV_TAG);
typeOpt = cgiOptionalString(CV_TYPE);
targetOpt = cgiOptionalString(CV_TARGET);
labelOpt = cgiOptionalString(CV_LABEL);
organismOpt = cgiUsualString(ORGANISM, organismOpt);
if (organismOpt != NULL)
{
organismOptLower=cloneString(organismOpt);
strLower(organismOptLower);
}
char *bgColor = cgiOptionalString("bgcolor");
if (bgColor)
htmlSetBgColor(strtol(bgColor, 0, 16));
htmlSetStyle(htmlStyleUndecoratedLink);
htmShell("ENCODE Controlled Vocabulary", doMiddle, "get");
cgiExitTime("hgEncodeVocab", enteredMainTime);
return 0;
}
int main(int argc, char *argv[])
{
long enteredMainTime = clock1000();
char *prefix = cgiOptionalString("prefix");
char *database = cgiOptionalString("db");
int exact = cgiOptionalInt("exact", 0);
struct sqlConnection *conn;
char query[2048];
char **row;
struct sqlResult *sr;
int count = 0;
boolean hasKnownCanonical;
struct dyString *str = newDyString(10000);
char *table;
if(prefix == NULL || database == NULL)
fail("Missing prefix or database parameter");
conn = hAllocConn(database);
table = connGeneSuggestTable(conn);
if(table == NULL)
fail("gene autosuggest is not supported for this assembly");
hasKnownCanonical = sameString(table, "knownCanonical");
puts("Content-Type:text/plain");
puts("\n");
dyStringPrintf(str, "[\n");
if(exact)
{
// NOTE that exact is no longer used by the UI as of v271, but there are still some robots using it so we still support it.
if(hasKnownCanonical)
sqlSafef(query, sizeof(query), "select x.geneSymbol, k.chrom, kg.txStart, kg.txEnd, x.kgID, x.description "
"from knownCanonical k, knownGene kg, kgXref x where k.transcript = x.kgID and k.transcript = kg.name "
"and x.geneSymbol = '%s' order by x.geneSymbol, k.chrom, kg.txEnd - kg.txStart desc", prefix);
else
sqlSafef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd, r.name, description.name "
"from %s r, gbCdnaInfo, description where r.name2 = '%s' and gbCdnaInfo.acc = r.name "
"and gbCdnaInfo.description = description.id order by r.name2, r.chrom, r.txEnd - r.txStart desc", table, prefix);
}
else
{
// We use a LIKE query b/c it uses the geneSymbol index (substr queries do not use indices in mysql).
// Also note that we take advantage of the fact that searches are case-insensitive in mysql.
// Unfortunately, knownCanonical sometimes has multiple entries for a given gene (e.g. 2 TTn's in mm9 knownCanonical;
// 3 POU5F1's in hg19); we return all of them (#5962).
if(hasKnownCanonical)
sqlSafef(query, sizeof(query), "select x.geneSymbol, k.chrom, kg.txStart, kg.txEnd, x.kgID, x.description "
"from knownCanonical k, knownGene kg, kgXref x where k.transcript = x.kgID and k.transcript = kg.name "
"and x.geneSymbol LIKE '%s%%' order by x.geneSymbol, k.chrom, kg.txStart", prefix);
else
sqlSafef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd, r.name, description.name "
"from %s r, gbCdnaInfo, description where r.name2 LIKE '%s%%' and gbCdnaInfo.acc = r.name "
"and gbCdnaInfo.description = description.id order by r.name2, r.chrom, r.txStart", table, prefix);
}
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
// ignore funny chroms (e.g. _hap chroms. See redmine #4257.
if(!strchr(row[1], '_'))
{
count++;
dyStringPrintf(str, "%s{\"value\": \"%s (%s)\", \"id\": \"%s:%d-%s\", \"internalId\": \"%s\"}", count == 1 ? "" : ",\n",
row[0], javaScriptLiteralEncode(row[5]), row[1], atoi(row[2])+1, row[3], javaScriptLiteralEncode(row[4]));
}
}
dyStringPrintf(str, "\n]\n");
puts(dyStringContents(str));
cgiExitTime("hgSuggest", enteredMainTime);
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;
}
int main(int argc, char *argv[])
{
long enteredMainTime = clock1000();
cgiSpoof(&argc, argv);
char *prefix = cgiOptionalString("prefix");
char *database = cgiOptionalString("db");
initGenbankTableNames(database);
int exact = cgiOptionalInt("exact", 0);
struct sqlConnection *conn;
char query[2048];
char **row;
struct sqlResult *sr;
int count = 0;
boolean hasKnownCanonical;
struct dyString *str = newDyString(10000);
char *table;
pushAbortHandler(htmlVaBadRequestAbort);
if(prefix == NULL || database == NULL)
errAbort("%s", "Missing prefix and/or db CGI parameter");
conn = hAllocConn(database);
table = connGeneSuggestTable(conn);
if(table == NULL)
errAbort("gene autosuggest is not supported for db '%s'", database);
popAbortHandler();
hasKnownCanonical = sameString(table, "knownCanonical");
puts("Content-Type:text/plain");
puts("\n");
dyStringPrintf(str, "[\n");
if(exact)
{
// NOTE that exact is no longer used by the UI as of v271, but there are still some robots using it so we still support it.
if(hasKnownCanonical)
sqlSafef(query, sizeof(query), "select x.geneSymbol, k.chrom, kg.txStart, kg.txEnd, x.kgID, x.description "
"from knownCanonical k, knownGene kg, kgXref x where k.transcript = x.kgID and k.transcript = kg.name "
"and x.geneSymbol = '%s' order by x.geneSymbol, k.chrom, kg.txEnd - kg.txStart desc", prefix);
else
sqlSafef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd, r.name, d.name "
"from %s r, %s g, %s d where r.name2 = '%s' and g.acc = r.name "
"and g.description = d.id order by r.name2, r.chrom, r.txEnd - r.txStart desc", table, gbCdnaInfoTable, descriptionTable, prefix);
}
else
{
// We use a LIKE query b/c it uses the geneSymbol index (substr queries do not use indices in mysql).
// Also note that we take advantage of the fact that searches are case-insensitive in mysql.
// Unfortunately, knownCanonical sometimes has multiple entries for a given gene (e.g. 2 TTn's in mm9 knownCanonical;
// 3 POU5F1's in hg19); we return all of them (#5962).
if(hasKnownCanonical)
sqlSafef(query, sizeof(query), "select x.geneSymbol, k.chrom, kg.txStart, kg.txEnd, x.kgID, x.description "
"from knownCanonical k, knownGene kg, kgXref x where k.transcript = x.kgID and k.transcript = kg.name "
"and x.geneSymbol LIKE '%s%%' order by x.geneSymbol, k.chrom, kg.txStart", prefix);
else
sqlSafef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd, r.name, d.name "
"from %s r, %s g, %s d where r.name2 LIKE '%s%%' and g.acc = r.name "
"and g.description = d.id order by r.name2, r.chrom, r.txStart", table, gbCdnaInfoTable, descriptionTable, prefix);
}
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
// ignore funny chroms (e.g. _hap chroms. See redmine #4257.
if(!strchr(row[1], '_'))
{
// We have some very long descriptions, e.g. 4277 chars for hg38 CLOCK, so truncate:
const int maxDesc = 120;
char *description = row[5];
if (strlen(description) > maxDesc + 4)
strcpy(description + maxDesc, "...");
count++;
dyStringPrintf(str, "%s{\"value\": \"%s (%s)\", "
"\"id\": \"%s:%d-%s\", "
"\"geneSymbol\": \"%s\", "
"\"internalId\": \"%s\"}",
count == 1 ? "" : ",\n", row[0], jsonStringEscape(description),
row[1], atoi(row[2])+1, row[3],
jsonStringEscape(row[0]),
jsonStringEscape(row[4]));
}
}
dyStringPrintf(str, "\n]\n");
puts(dyStringContents(str));
cgiExitTime("hgSuggest", enteredMainTime);
return 0;
}
