void doMiddle(struct cart *cart)
/* Write body of web page. */
{
struct trackDb *tdbList = NULL;
char *organism = NULL;
char *db = NULL;
getDbAndGenome(cart, &db, &organism, NULL);
char *chrom = cartUsualString(cart, "c", hDefaultChrom(db));
measureTiming = isNotEmpty(cartOptionalString(cart, "measureTiming"));
// QUESTION: Do We need track list ??? trackHash ??? Can't we just get one track and no children
trackHash = trackHashMakeWithComposites(db,chrom,&tdbList,FALSE);
cartWebStart(cart, db, "Search for " FILE_SEARCH_WHAT " in the %s %s Assembly",
organism, hFreezeFromDb(db));
webIncludeResourceFile("HGStyle.css");
webIncludeResourceFile("jquery-ui.css");
webIncludeResourceFile("ui.dropdownchecklist.css");
jsIncludeFile("jquery.js", NULL);
jsIncludeFile("jquery-ui.js", NULL);
jsIncludeFile("ui.dropdownchecklist.js",NULL);
jsIncludeFile("utils.js",NULL);
// This line is needed to get the multi-selects initialized
jsIncludeFile("ddcl.js",NULL);
printf("<script type='text/javascript'>$(document).ready(function() "
"{ findTracks.updateMdbHelp(0); });</script>\n");
doFileSearch(db,organism,cart,tdbList);
printf("<BR>\n");
webEnd();
}
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();
}
void dispatch()
/* Look at input variables and figure out which page to show. */
{
char *db, *organism;
int maxSize = 4000;
int minPerfect = 15;
int minGood = 15;
char *fPrimer = cartUsualString(cart, "wp_f", "");
char *rPrimer = cartUsualString(cart, "wp_r", "");
boolean flipReverse = cartUsualBoolean(cart, "wp_flipReverse", FALSE);
struct pcrServer *serverList = getServerList();
getDbAndGenome(cart, &db, &organism, oldVars);
/* Get variables. */
maxSize = cartUsualInt(cart, "wp_size", maxSize);
minPerfect = cartUsualInt(cart, "wp_perfect", minPerfect);
minGood = cartUsualInt(cart, "wp_good", minGood);
if (minPerfect < 15)
minPerfect = 15;
if (minGood < minPerfect)
minGood = minPerfect;
/* Decide based on transient variables what page to put up.
* By default put up get primer page. */
if (isNotEmpty(fPrimer) && isNotEmpty(rPrimer) &&
!cartVarExists(cart, "wp_showPage"))
{
struct pcrServer *server = NULL;
struct targetPcrServer *targetServer = NULL;
char *target = cartUsualString(cart, "wp_target", "genome");
if (isEmpty(target) || sameString(target, "genome"))
server = findServer(db, serverList);
else
{
targetServer = getTargetServerList(db, target);
if (targetServer == NULL)
errAbort("Can't find targetPcr server for db=%s, target=%s",
db, target);
}
fPrimer = gfPcrMakePrimer(fPrimer);
rPrimer = gfPcrMakePrimer(rPrimer);
if (doPcr(server, targetServer, fPrimer, rPrimer,
maxSize, minPerfect, minGood, flipReverse))
return;
}
doGetPrimers(db, organism, serverList,
fPrimer, rPrimer, maxSize, minPerfect, minGood, flipReverse);
}
void doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
char *db = NULL;
char *ignored;
struct trackDb *tracks;
struct trackRef *tr;
struct group *group, *groups = NULL;
cart = theCart;
cartWebStart(cart, NULL, "ENCODE Track Data Versions (%s)", db);
getDbAndGenome(cart, &db, &ignored, NULL);
tracks = hTrackDb(db);
groups = groupTracks(db, tracks);
for (group = groups; group != NULL; group = group->next)
{
if (group->tracks == NULL || !startsWith("encode", group->name))
continue;
hTableStart();
puts("<TR>");
puts("<TH align=LEFT colspan=3 BGCOLOR=#536ED3>");
printf("<B> %s</B> ", wrapWhiteFont(group->label));
printf(" ");
puts("</TH>\n");
puts("</TR>");
for (tr = group->tracks; tr != NULL; tr = tr->next)
{
char *version = trackDbSetting(tr->track, "dataVersion");
if (version)
stripString(version, "ENCODE ");
puts("<TR><TD>");
printf(" %s", tr->track->shortLabel);
puts("</TD><TD>");
printf(" %s", version ? version : " ");
puts("</TD><TD>");
printf(" %s", tr->track->longLabel);
puts("</TD></TR>");
}
/*
printf("\t%s\t%s\t%s\n", version,
tr->track->shortLabel, tr->track->longLabel);
*/
hTableEnd();
puts("<BR>");
}
cartWebEnd();
}
void doMiddle(struct cart *theCart)
/* Write header and body of html page. */
{
char *userSeq;
char *db, *organism;
boolean clearUserSeq = cgiBoolean("Clear");
cart = theCart;
dnaUtilOpen();
orgChange = sameOk(cgiOptionalString("changeInfo"),"orgChange");
if (orgChange)
{
cgiVarSet("db", hDefaultDbForGenome(cgiOptionalString("org")));
}
getDbAndGenome(cart, &db, &organism, oldVars);
char *oldDb = cloneString(db);
findClosestServer(&db, &organism);
/* Get sequence - from userSeq variable, or if
* that is empty from a file. */
if (clearUserSeq)
{
cartSetString(cart, "userSeq", "");
cartSetString(cart, "seqFile", "");
}
userSeq = cartUsualString(cart, "userSeq", "");
if (isEmpty(userSeq))
{
userSeq = cartOptionalString(cart, "seqFile");
}
if (isEmpty(userSeq) || orgChange)
{
cartWebStart(theCart, db, "%s BLAT Search", trackHubSkipHubName(organism));
if (differentString(oldDb, db))
printf("<HR><P><EM><B>Note:</B> BLAT search is not available for %s %s; "
"defaulting to %s %s</EM></P><HR>\n",
hGenome(oldDb), hFreezeDate(oldDb), organism, hFreezeDate(db));
askForSeq(organism,db);
cartWebEnd();
}
else
{
blatSeq(skipLeadingSpaces(userSeq), organism);
}
}
void cartMain(struct cart *theCart)
/* We got the persistent/CGI variable cart. Now
* set up the globals and make a web page. */
{
struct sqlConnection *conn = NULL;
cart = theCart;
getDbAndGenome(cart, &database, &genome, oldCart);
/* !!! force database to hiv1 until move to server hiv1 is complete
and the default database of hgcentral on it point to hiv1. */
conn = hAllocConn(database);
curSubjId = cgiOptionalString("hgs_subj");
if (curSubjId == NULL) curSubjId = strdup("");
cartHtmlStart("HIV Vaccine Subject View");
webMain(conn);
hFreeConn(&conn);
cartHtmlEnd();
}
void cartMain(struct cart *theCart)
/* We got the persistent/CGI variable cart. Now
* set up the globals and make a web page. */
{
hgBotDelay();
cart = theCart;
getDbAndGenome(cart, &database, &genome, oldVars);
initGenbankTableNames(database);
getGenomeSettings();
if (cartVarExists(cart, hggDoKgMethod))
doKgMethod();
else if (cartVarExists(cart, hggDoTxInfoDescription))
doTxInfoDescription();
else
{
struct sqlConnection *conn = NULL;
char *geneName = cartUsualString(cart, hggGene, NULL);
if (isEmpty(geneName))
{
// Silly googlebots.
hUserAbort("Error: the hgg_gene parameter is missing from the cart and the CGI params.");
}
/* if kgProtMap2 table exists, this means we are doing KG III */
if (hTableExists(database, "kgProtMap2")) kgVersion = KG_III;
conn = hAllocConn(database);
curGeneId = findGeneId(conn, geneName);
getGenePosition(conn);
curGenePred = getCurGenePred(conn);
curGeneName = getGeneName(curGeneId, conn);
spConn = hAllocConn(UNIPROT_DB_NAME);
swissProtAcc = getSwissProtAcc(conn, spConn, curGeneId);
if (isRgdGene(conn)) swissProtAcc=getRgdGeneUniProtAcc(curGeneId, conn);
/* Check command variables, and do the ones that
* don't want to put up the hot link bar etc. */
if (cartVarExists(cart, hggDoGetMrnaSeq))
doGetMrnaSeq(conn, curGeneId, curGeneName);
else if (cartVarExists(cart, hggDoWikiTrack))
doWikiTrack(conn);
else if (cartVarExists(cart, hggDoGetProteinSeq))
doGetProteinSeq(conn, curGeneId, curGeneName);
else if (cartVarExists(cart, hggDoRnaFoldDisplay))
doRnaFoldDisplay(conn, curGeneId, curGeneName);
else if (cartVarExists(cart, hggDoOtherProteinSeq))
doOtherProteinSeq(conn, curGeneName);
else if (cartVarExists(cart, hggDoOtherProteinAli))
doOtherProteinAli(conn, curGeneId, curGeneName);
else
{
/* Default case - start fancy web page. */
measureTiming = isNotEmpty(cartOptionalString(cart, "measureTiming"));
struct trackDb *tdb = hTrackDbForTrack(database, genomeSetting("knownGene"));
isGencode = trackDbSettingOn(tdb, "isGencode");
isGencode2 = trackDbSettingOn(tdb, "isGencode2");
cartWebStart(cart, database, "%s Gene %s (%s) Description and Page Index",
genome, curGeneName, isGencode2 ? curGeneId : curAlignId);
webMain(conn, tdb);
cartWebEnd();
}
hFreeConn(&spConn);
hFreeConn(&conn);
}
cartRemovePrefix(cart, hggDoPrefix);
}
void blatSeq(char *userSeq, char *organism)
/* Blat sequence user pasted in. */
{
FILE *f;
struct dnaSeq *seqList = NULL, *seq;
struct tempName pslTn, faTn;
int maxSingleSize, maxTotalSize, maxSeqCount;
int minSingleSize = minMatchShown;
char *genome, *db;
char *type = cgiString("type");
char *seqLetters = cloneString(userSeq);
struct serverTable *serve;
int conn;
int oneSize, totalSize = 0, seqCount = 0;
boolean isTx = FALSE;
boolean isTxTx = FALSE;
boolean txTxBoth = FALSE;
struct gfOutput *gvo;
boolean qIsProt = FALSE;
enum gfType qType, tType;
struct hash *tFileCache = gfFileCacheNew();
boolean feelingLucky = cgiBoolean("Lucky");
getDbAndGenome(cart, &db, &genome, oldVars);
if(!feelingLucky)
cartWebStart(cart, db, "%s BLAT Results", trackHubSkipHubName(organism));
/* Load user sequence and figure out if it is DNA or protein. */
if (sameWord(type, "DNA"))
{
seqList = faSeqListFromMemText(seqLetters, TRUE);
uToT(seqList);
isTx = FALSE;
}
else if (sameWord(type, "translated RNA") || sameWord(type, "translated DNA"))
{
seqList = faSeqListFromMemText(seqLetters, TRUE);
uToT(seqList);
isTx = TRUE;
isTxTx = TRUE;
txTxBoth = sameWord(type, "translated DNA");
}
else if (sameWord(type, "protein"))
{
seqList = faSeqListFromMemText(seqLetters, FALSE);
isTx = TRUE;
qIsProt = TRUE;
}
else
{
seqList = faSeqListFromMemTextRaw(seqLetters);
isTx = !seqIsDna(seqList);
if (!isTx)
{
for (seq = seqList; seq != NULL; seq = seq->next)
{
seq->size = dnaFilteredSize(seq->dna);
dnaFilter(seq->dna, seq->dna);
toLowerN(seq->dna, seq->size);
subChar(seq->dna, 'u', 't');
}
}
else
{
for (seq = seqList; seq != NULL; seq = seq->next)
{
seq->size = aaFilteredSize(seq->dna);
aaFilter(seq->dna, seq->dna);
toUpperN(seq->dna, seq->size);
}
qIsProt = TRUE;
}
}
if (seqList != NULL && seqList->name[0] == 0)
{
freeMem(seqList->name);
seqList->name = cloneString("YourSeq");
}
trimUniq(seqList);
/* If feeling lucky only do the first on. */
if(feelingLucky && seqList != NULL)
{
seqList->next = NULL;
}
/* Figure out size allowed. */
maxSingleSize = (isTx ? 10000 : 75000);
maxTotalSize = maxSingleSize * 2.5;
#ifdef LOWELAB
maxSeqCount = 200;
#else
maxSeqCount = 25;
#endif
/* Create temporary file to store sequence. */
trashDirFile(&faTn, "hgSs", "hgSs", ".fa");
faWriteAll(faTn.forCgi, seqList);
/* Create a temporary .psl file with the alignments against genome. */
trashDirFile(&pslTn, "hgSs", "hgSs", ".pslx");
f = mustOpen(pslTn.forCgi, "w");
gvo = gfOutputPsl(0, qIsProt, FALSE, f, FALSE, TRUE);
serve = findServer(db, isTx);
/* Write header for extended (possibly protein) psl file. */
if (isTx)
{
if (isTxTx)
{
qType = gftDnaX;
tType = gftDnaX;
}
else
{
qType = gftProt;
tType = gftDnaX;
}
}
else
{
qType = gftDna;
tType = gftDna;
}
pslxWriteHead(f, qType, tType);
if (qType == gftProt)
{
minSingleSize = 14;
}
else if (qType == gftDnaX)
{
minSingleSize = 36;
}
/* Loop through each sequence. */
for (seq = seqList; seq != NULL; seq = seq->next)
{
printf(" "); fflush(stdout); /* prevent apache cgi timeout by outputting something */
oneSize = realSeqSize(seq, !isTx);
if ((seqCount&1) == 0) // Call bot delay every 2nd time starting with first time
hgBotDelay();
if (++seqCount > maxSeqCount)
{
warn("More than 25 input sequences, stopping at %s.",
seq->name);
break;
}
if (oneSize > maxSingleSize)
{
warn("Sequence %s is %d letters long (max is %d), skipping",
seq->name, oneSize, maxSingleSize);
continue;
}
if (oneSize < minSingleSize)
{
warn("Warning: Sequence %s is only %d letters long (%d is the recommended minimum)",
seq->name, oneSize, minSingleSize);
// we could use "continue;" here to actually enforce skipping,
// but let's give the short sequence a chance, it might work.
// minimum possible length = tileSize+stepSize, so mpl=16 for dna stepSize=5, mpl=10 for protein.
if (qIsProt && oneSize < 1) // protein does not tolerate oneSize==0
continue;
}
totalSize += oneSize;
if (totalSize > maxTotalSize)
{
warn("Sequence %s would take us over the %d letter limit, stopping here.",
seq->name, maxTotalSize);
break;
}
conn = gfConnect(serve->host, serve->port);
if (isTx)
{
gvo->reportTargetStrand = TRUE;
if (isTxTx)
{
gfAlignTransTrans(&conn, serve->nibDir, seq, FALSE, 5,
tFileCache, gvo, !txTxBoth);
if (txTxBoth)
{
reverseComplement(seq->dna, seq->size);
conn = gfConnect(serve->host, serve->port);
gfAlignTransTrans(&conn, serve->nibDir, seq, TRUE, 5,
tFileCache, gvo, FALSE);
}
}
else
{
gfAlignTrans(&conn, serve->nibDir, seq, 5, tFileCache, gvo);
}
}
else
{
gfAlignStrand(&conn, serve->nibDir, seq, FALSE, minMatchShown, tFileCache, gvo);
reverseComplement(seq->dna, seq->size);
conn = gfConnect(serve->host, serve->port);
gfAlignStrand(&conn, serve->nibDir, seq, TRUE, minMatchShown, tFileCache, gvo);
}
gfOutputQuery(gvo, f);
}
carefulClose(&f);
showAliPlaces(pslTn.forCgi, faTn.forCgi, serve->db, qType, tType,
organism, feelingLucky);
if(!feelingLucky)
cartWebEnd();
gfFileCacheFree(&tFileCache);
}
static void webStartWrapperDetailedInternal(struct cart *theCart,
char *db, char *headerText, char *textOutBuf,
boolean withHttpHeader, boolean withLogo, boolean skipSectionHeader,
boolean withHtmlHeader)
/* output a CGI and HTML header with the given title in printf format */
{
char uiState[256];
char *scriptName = cgiScriptName();
boolean isEncode = FALSE;
if (theCart)
{
char *theGenome = NULL;
char *genomeEnc = NULL;
getDbAndGenome(theCart, &db, &theGenome, NULL);
genomeEnc = cgiEncode(theGenome);
safef(uiState, sizeof(uiState), "?%s=%s&%s=%s&%s=%u",
orgCgiName, genomeEnc,
dbCgiName, db,
cartSessionVarName(), cartSessionId(theCart));
}
else
{
uiState[0] = 0;
uiState[1] = 0;
}
if (db == NULL)
db = hDefaultDb();
boolean dbIsFound = hDbExists(db);
boolean haveBlat = FALSE;
if (dbIsFound)
haveBlat = hIsBlatIndexedDatabase(db);
if (scriptName == NULL)
scriptName = cloneString("");
/* don't output two headers */
if(webHeadAlreadyOutputed)
return;
if (sameString(cgiUsualString("action",""),"encodeReleaseLog") ||
rStringIn("EncodeDataVersions", scriptName))
isEncode = TRUE;
/* Preamble. */
dnaUtilOpen();
if (withHttpHeader)
puts("Content-type:text/html\n");
if (withHtmlHeader)
{
char *newString, *ptr1, *ptr2;
char *browserVersion;
if (btIE == cgiClientBrowser(&browserVersion, NULL, NULL) && *browserVersion < '8')
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 3.2//EN\">");
else
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" "
"\"http://www.w3.org/TR/html4/loose.dtd\">");
// Strict would be nice since it fixes atleast one IE problem (use of :hover CSS pseudoclass)
puts(
"<HTML>" "\n"
"<HEAD>" "\n"
);
printf("\t%s\n", headerText);
printf("\t<META HTTP-EQUIV=\"Content-Type\" CONTENT=\"text/html;CHARSET=iso-8859-1\">" "\n"
"\t<META http-equiv=\"Content-Script-Type\" content=\"text/javascript\">" "\n"
"\t<META HTTP-EQUIV=\"Pragma\" CONTENT=\"no-cache\">" "\n"
"\t<META HTTP-EQUIV=\"Expires\" CONTENT=\"-1\">" "\n"
"\t<TITLE>"
);
/* we need to take any HTML formatting out of the titlebar string */
newString = cloneString(textOutBuf);
for(ptr1=newString, ptr2=textOutBuf; *ptr2 ; ptr2++)
{
if (*ptr2 == '<')
{
for(; *ptr2 && (*ptr2 != '>'); ptr2++)
;
}
else
*ptr1++ = *ptr2;
}
*ptr1 = 0;
htmlTextOut(newString);
printf(" </TITLE>\n ");
webIncludeResourceFile("HGStyle.css");
if (extraStyle != NULL)
puts(extraStyle);
printf("</HEAD>\n");
printBodyTag(stdout);
htmlWarnBoxSetup(stdout);// Sets up a warning box which can be filled with errors as they occur
puts(commonCssStyles());
}
puts(
"<A NAME=\"TOP\"></A>" "\n"
"" "\n"
"<TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0 WIDTH=\"100%\">" "\n");
if (withLogo)
{
puts("<TR><TH COLSPAN=1 ALIGN=\"left\">");
if (isEncode)
{
puts("<A HREF=\"http://www.genome.gov/10005107\" TARGET=\"_BLANK\">"
"<IMG SRC=\"../images/ENCODE_scaleup_logo.png\" height=50 ALT=\"ENCODE Project at NHGRI\">"
"</A>");
puts("<IMG SRC=\"../images/encodeDcc.jpg\" ALT=\"ENCODE Project at UCSC\">");
}
else
{
puts("<IMG SRC=\"../images/title.jpg\">");
}
puts("</TH></TR>" "\n"
"" "\n" );
}
/* Put up the hot links bar. */
char *menuStr = menuBar(theCart);
if(menuStr)
{
puts(menuStr);
}
if (endsWith(scriptName, "hgGateway") && geoMirrorEnabled())
{
// Show an opt-out alert if user is on a host to which user has been automatically redirected (just once, right after they have been redirected)
char *source = cgiOptionalString("source");
char *redirect = cgiOptionalString("redirect");
if (source != NULL && redirect != NULL && sameString(redirect, "auto"))
{
char *domain = cgiServerName();
char *port = cgiServerPort();
// We don't bother maintaining stuff in request URI, because it may contain items like hgsid and other host specific values
int newUriSize = 2048;
char *newUri = needMem(newUriSize);
safef(newUri, newUriSize, "http%s://%s:%s/cgi-bin/hgGateway?redirect=manual&source=%s",
cgiServerHttpsIsOn() ? "s" : "", source, port, domain);
printf("<TR><TD COLSPAN=3 id='redirectTd' onclick=\"javascript:document.getElementById('redirectTd').innerHTML='';\">"
"<div style=\"margin: 10px 25%%; border-style:solid; border-width:thin; border-color:#97D897;\">"
"<h3 style=\"background-color: #97D897; text-align: left; margin-top:0px; margin-bottom:0px;\">"
" You've been redirected to your nearest mirror - %s"
"<idiv style=\"float:right;\">[x]</idiv>"
"</h3> "
"<ul style=\"margin:5px;\">"
"<li>Take me back to <a href=\"%s\">%s</a>"
"<idiv style=\"float:right;\"><a href=\"../goldenPath/help/genomeEuro.html\">What is this?</a></idiv>"
"</li>"
"</ul>"
"</div>"
"</TD></TR>\n"
, domain, newUri, source );
}
}
if(!skipSectionHeader)
/* this HTML must be in calling code if skipSectionHeader is TRUE */
{
puts( // TODO: Replace nested tables with CSS (difficulty is that tables are closed elsewhere)
"<!-- +++++++++++++++++++++ CONTENT TABLES +++++++++++++++++++ -->" "\n"
"<TR><TD COLSPAN=3>\n"
"<div id=firstSection>"
" <!--outer table is for border purposes-->\n"
" <TABLE WIDTH='100%' BGCOLOR='#" HG_COL_BORDER "' BORDER='0' CELLSPACING='0' "
"CELLPADDING='1'><TR><TD>\n"
" <TABLE BGCOLOR='#" HG_COL_INSIDE "' WIDTH='100%' BORDER='0' CELLSPACING='0' "
"CELLPADDING='0'><TR><TD>\n"
" <div class='subheadingBar'><div class='windowSize' id='sectTtl'>"
);
htmlTextOut(textOutBuf);
puts(" </div></div>\n"
" <TABLE BGCOLOR='#" HG_COL_INSIDE "' WIDTH='100%' CELLPADDING=0>"
"<TR><TH HEIGHT=10></TH></TR>\n"
" <TR><TD WIDTH=10> </TD><TD>\n\n"
);
};
webPushErrHandlers();
/* set the flag */
webHeadAlreadyOutputed = TRUE;
} /* static void webStartWrapperDetailedInternal() */
int main(int argc, char *argv[])
/* Process command line. */
{
pushCarefulMemHandler(100000000);
cgiSpoof(&argc, argv);
htmlSetStyle(htmlStyleUndecoratedLink);
htmlSetBgColor(HG_CL_OUTSIDE);
oldCart = hashNew(10);
cart = cartAndCookie(hUserCookie(), excludeVars, oldCart);
getDbAndGenome(cart, &database, &genome, oldCart);
//hSetDb(database);
conn = hAllocConn(database);
database = strdup("h1n1");
/* Get sortOn. Revert to default by subject Id. */
orderOn = cartUsualString(cart, orderVarName, "+subjId");
displayCountString = cartUsualString(cart, countVarName, "50");
if (sameString(displayCountString, "all"))
displayCount = BIGNUM;
else
displayCount = atoi(displayCountString);
colList = getColumns(conn);
if (cgiVarExists("submit_filter"))
{
struct dyString *head = dyStringNew(1024);
boolean redir = cgiVarExists(redirectName);
struct subjInfo *subjList = NULL;
struct column *ordList = colList;
struct column *ord = curOrder(ordList);
subjList = getOrderedList(ord, colList, conn, BIGNUM);
saveSubjList(subjList);
if ((!subjList || redir))
{
if (subjList && redir)
{
dyStringPrintf(head,
"<META HTTP-EQUIV=\"REFRESH\" CONTENT=\"0;URL=/cgi-bin/%s\">"
"<META HTTP-EQUIV=\"Pragma\" CONTENT=\"no-cache\">"
"<META HTTP-EQUIV=\"Expires\" CONTENT=\"-1\">"
, cgiString(redirectName));
cartRemove(cart, redirectName);
}
htmStartWithHead(stdout, head->string, "GISAID Table View");
if (!subjList) /* 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+%%28now+on%%29\">here</a> "
"to return to Select Subjects.<br>");
}
cartCheckout(&cart);
htmlEnd();
hFreeConn(&conn);
return 0;
}
}
htmStart(stdout, "GISAID Table View");
cartWarnCatcher(doMiddle, cart, htmlVaWarn);
cartCheckout(&cart);
htmlEnd();
hFreeConn(&conn);
return 0;
}
void doMiddle(struct cart *theCart)
/* Set up pretty web display. */
{
struct sqlConnection *conn, *conn2;
struct sqlConnection *connCentral = hConnectCentral();
char query[256], query2[256];
struct sqlResult *sr, *sr2;
char **row, **row2;
char buf[128];
char *answer;
char *database;
char *genome, *genomeDesc;
char *kgID, *chrom, *txStart, *txEnd;
int iCnt = 1;
cart = theCart;
cartWebStart(theCart, database, "UCSC Known Genes List \n");
getDbAndGenome(cart, &database, &genome, oldVars);
if (!hTableExistsDb(database, "knownGene"))
{
printf("<br>Database %s currently does not have UCSC Known Genes.", database);
cartWebEnd();
return;
}
sprintf(query, "select description from dbDb where name = '%s'", database);
genomeDesc = strdup(sqlQuickQuery(connCentral, query, buf, sizeof(buf)));
hDisconnectCentral(&connCentral);
printf("<H2>%s Genome (%s Assembly)</H2>\n", genome, genomeDesc);
conn = hAllocConn(database);
conn2= hAllocConn(database);
sprintf(query2,"select kgID from %s.kgXref order by geneSymbol;",
database);
/* use the following for quck testing */
/*sprintf(query2,"select kgID, geneSymbol, description, spID, refseq from %s.kgXref order by geneSymbol limit 10;", database);
*/
sr2 = sqlMustGetResult(conn2, query2);
row2 = sqlNextRow(sr2);
while (row2 != NULL)
{
kgID = row2[0];
sprintf(query,"select chrom, txSTart, txEnd from %s.knownGene where name='%s'", database, kgID);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
chrom = row[0];
txStart = row[1];
txEnd = row[2];
printf("<A href=\"/cgi-bin/hgGene?db=%s&hgg_gene=%s",
database, kgID);
printf("&hgg_chrom=%s&hgg_start=%s&hgg_end=%s\">", chrom, txStart, txEnd);
printf("%d</A><BR>\n", iCnt);
iCnt++;
if ((iCnt % 1000) == 0) fflush(stdout);
sqlFreeResult(&sr);
row2 = sqlNextRow(sr2);
}
sqlFreeResult(&sr2);
cartWebEnd();
}
void doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
/* struct liftOverChain *chainList = NULL, *chain; */
char *userData;
/* char *dataFile; */
char *dataFormat;
char *organism;
char *db;
float minBlocks, minMatch;
boolean multiple, fudgeThick;
int minSizeQ, minSizeT;
boolean refreshOnly = FALSE;
/* char *err = NULL; */
struct liftOverChain *chainList = NULL, *choice;
cart = theCart;
if (cgiOptionalString(HGLFT_ERRORHELP_VAR))
{
puts("<PRE>");
puts(liftOverErrHelp());
//system("/usr/bin/cal");
puts("</PRE>");
return;
}
/* Get data to convert - from userData variable, or if
* that is empty from a file. */
if (cartOptionalString(cart, "SubmitFile"))
userData = cartOptionalString(cart, HGLFT_DATAFILE_VAR);
else
userData = cartOptionalString(cart, HGLFT_USERDATA_VAR);
dataFormat = cartCgiUsualString(cart, HGLFT_DATAFORMAT_VAR, DEFAULT_FORMAT);
cartWebStart(cart, NULL, "Lift Genome Annotations");
getDbAndGenome(cart, &db, &organism, oldVars);
chainList = liftOverChainListFiltered();
choice = defaultChoices(chainList, db);
if (choice == NULL)
errAbort("Sorry, no conversions available from this assembly\n");
minSizeQ = cartCgiUsualInt(cart, HGLFT_MINSIZEQ, choice->minSizeQ);
minSizeT = cartCgiUsualInt(cart, HGLFT_MINSIZET, choice->minSizeT);
minBlocks = cartCgiUsualDouble(cart, HGLFT_MINBLOCKS, choice->minBlocks);
minMatch = cartCgiUsualDouble(cart, HGLFT_MINMATCH, choice->minMatch);
fudgeThick = cartCgiUsualBoolean(cart, HGLFT_FUDGETHICK, (choice->fudgeThick[0]=='Y') ? TRUE : FALSE);
multiple = cartCgiUsualBoolean(cart, HGLFT_MULTIPLE, (choice->multiple[0]=='Y') ? TRUE : FALSE);
refreshOnly = cartCgiUsualInt(cart, HGLFT_REFRESHONLY_VAR, 0);
webMain(choice, dataFormat, multiple);
liftOverChainFreeList(&chainList);
if (!refreshOnly && userData != NULL && userData[0] != '\0')
{
struct hash *chainHash = newHash(0);
char *chainFile;
struct tempName oldTn, mappedTn, unmappedTn;
FILE *old, *mapped, *unmapped;
char *line;
int lineSize;
char *fromDb, *toDb;
int ct = 0, errCt = 0;
/* read in user data and save to file */
makeTempName(&oldTn, HGLFT, ".user");
old = mustOpen(oldTn.forCgi, "w");
fputs(userData, old);
fputs("\n", old); /* in case user doesn't end last line */
carefulClose(&old);
chmod(oldTn.forCgi, 0666);
/* setup output files -- one for converted lines, the other
* for lines that could not be mapped */
makeTempName(&mappedTn, HGLFT, ".bed");
makeTempName(&unmappedTn, HGLFT, ".err");
mapped = mustOpen(mappedTn.forCgi, "w");
chmod(mappedTn.forCgi, 0666);
unmapped = mustOpen(unmappedTn.forCgi, "w");
chmod(unmappedTn.forCgi, 0666);
fromDb = cgiString(HGLFT_FROMDB_VAR);
toDb = cgiString(HGLFT_TODB_VAR);
chainFile = liftOverChainFile(fromDb, toDb);
if (chainFile == NULL)
errAbort("ERROR: Can't convert from %s to %s: no chain file loaded",
fromDb, toDb);
readLiftOverMap(chainFile, chainHash);
if (sameString(dataFormat, WIGGLE_FORMAT))
/* TODO: implement Wiggle */
{}
else if (sameString(dataFormat, POSITION_FORMAT))
{
/* minSizeT here and in liftOverChain.c/h has been renamed minChainT in liftOver.c */
/* ignore multiple, it must be false when position is used */
ct = liftOverPositions(oldTn.forCgi, chainHash,
minMatch, minBlocks, 0, minSizeQ,
minSizeT, 0,
fudgeThick, mapped, unmapped, FALSE, NULL, &errCt);
}
else if (sameString(dataFormat, BED_FORMAT))
{
/* minSizeT here and in liftOverChain.c/h has been renamed minChainT in liftOver.c */
ct = liftOverBed(oldTn.forCgi, chainHash,
minMatch, minBlocks, 0, minSizeQ,
minSizeT, 0,
fudgeThick, mapped, unmapped, multiple, NULL, &errCt);
}
else
/* programming error */
errAbort("ERROR: Unsupported data format: %s\n", dataFormat);
webNewSection("Results");
if (ct)
{
/* some records succesfully converted */
cgiParagraph("");
printf("Successfully converted %d record", ct);
printf("%s: ", ct > 1 ? "s" : "");
printf("<A HREF=%s TARGET=_blank>View Conversions</A>\n", mappedTn.forCgi);
}
if (errCt)
{
/* some records not converted */
cgiParagraph("");
printf("Conversion failed on %d record", errCt);
printf("%s. ", errCt > 1 ? "s" : "");
printf("<A HREF=%s TARGET=_blank>Display failure file</A> \n",
unmappedTn.forCgi);
printf("<A HREF=\"../cgi-bin/hgLiftOver?%s=1\" TARGET=_blank>Explain failure messages</A>\n", HGLFT_ERRORHELP_VAR);
puts("<P>Failed input regions:\n");
struct lineFile *errFile = lineFileOpen(unmappedTn.forCgi, TRUE);
puts("<BLOCKQUOTE><PRE>\n");
while (lineFileNext(errFile, &line, &lineSize))
puts(line);
lineFileClose(&errFile);
puts("</PRE></BLOCKQUOTE>\n");
}
if (sameString(dataFormat, POSITION_FORMAT) && multiple)
{
puts("<BLOCKQUOTE><PRE>\n");
puts("Note: multiple checkbox ignored since it is not supported for position format.");
puts("</PRE></BLOCKQUOTE>\n");
}
carefulClose(&unmapped);
}
webDataFormats();
webDownloads();
cartWebEnd();
}
static void webStartWrapperDetailedInternal(struct cart *theCart,
char *db, char *headerText, char *textOutBuf,
boolean withHttpHeader, boolean withLogo, boolean skipSectionHeader,
boolean withHtmlHeader)
/* output a CGI and HTML header with the given title in printf format */
{
char uiState[256];
char *scriptName = cgiScriptName();
boolean isEncode = FALSE;
if (theCart)
{
char *theGenome = NULL;
char *genomeEnc = NULL;
getDbAndGenome(theCart, &db, &theGenome, NULL);
genomeEnc = cgiEncode(theGenome);
safef(uiState, sizeof(uiState), "?%s=%s&%s=%s&%s=%s",
orgCgiName, genomeEnc,
dbCgiName, db,
cartSessionVarName(), cartSessionId(theCart));
}
else
{
uiState[0] = 0;
uiState[1] = 0;
}
if (db == NULL)
db = hDefaultDb();
boolean dbIsFound = hDbExists(db);
boolean haveBlat = FALSE;
if (dbIsFound)
haveBlat = hIsBlatIndexedDatabase(db);
if (scriptName == NULL)
scriptName = cloneString("");
/* don't output two headers */
if(webHeadAlreadyOutputed)
return;
if (sameString(cgiUsualString("action",""),"encodeReleaseLog") ||
rStringIn("EncodeDataVersions", scriptName))
isEncode = TRUE;
/* Preamble. */
dnaUtilOpen();
if (withHttpHeader)
puts("Content-type:text/html\n");
if (withHtmlHeader)
{
char *newString, *ptr1, *ptr2;
char *browserVersion;
if (btIE == cgiClientBrowser(&browserVersion, NULL, NULL) && *browserVersion < '8')
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 3.2//EN\">");
else
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" "
"\"http://www.w3.org/TR/html4/loose.dtd\">");
// Strict would be nice since it fixes atleast one IE problem (use of :hover CSS pseudoclass)
puts(
"<HTML>" "\n"
"<HEAD>" "\n"
);
printf("\t%s\n", headerText);
webPragmasEtc();
printf("\t<TITLE>");
/* we need to take any HTML formatting out of the titlebar string */
newString = cloneString(textOutBuf);
for(ptr1=newString, ptr2=textOutBuf; *ptr2 ; ptr2++)
{
if (*ptr2 == '<')
{
for(; *ptr2 && (*ptr2 != '>'); ptr2++)
;
}
else
*ptr1++ = *ptr2;
}
*ptr1 = 0;
htmlTextOut(newString);
printf(" </TITLE>\n ");
webIncludeResourceFile("HGStyle.css");
if (extraStyle != NULL)
puts(extraStyle);
printf("</HEAD>\n");
printBodyTag(stdout);
htmlWarnBoxSetup(stdout);// Sets up a warning box which can be filled with errors as they occur
puts(commonCssStyles());
}
webStartSectionTables();
if (withLogo)
{
puts("<TR><TH COLSPAN=1 ALIGN=\"left\">");
if (isEncode)
{
puts("<A HREF=\"http://www.genome.gov/10005107\" TARGET=\"_BLANK\">"
"<IMG SRC=\"../images/ENCODE_scaleup_logo.png\" height=50 ALT=\"ENCODE Project at NHGRI\">"
"</A>");
puts("<IMG SRC=\"../images/encodeDcc.jpg\" ALT=\"ENCODE Project at UCSC\">");
}
else
{
puts("<IMG SRC=\"../images/title.jpg\">");
}
puts("</TH></TR>" "\n"
"" "\n" );
}
/* Put up the hot links bar. */
char *menuStr = menuBar(theCart, db);
if(menuStr)
{
puts(menuStr);
}
if(!skipSectionHeader)
/* this HTML must be in calling code if skipSectionHeader is TRUE */
{
webFirstSection(textOutBuf);
};
webPushErrHandlers();
/* set the flag */
webHeadAlreadyOutputed = TRUE;
errAbortSetDoContentType(FALSE);
} /* static void webStartWrapperDetailedInternal() */
void doMiddle(struct cart *theCart)
/* Write header and body of html page. */
{
boolean gotDisconnect = FALSE;
cart = theCart;
if (cartVarExists(cart, hgHubDoClear))
{
doClearHub(cart);
cartWebEnd();
return;
}
if (cartVarExists(cart, hgHubDoDisconnect))
{
gotDisconnect = TRUE;
doDisconnectHub(cart);
// now rebuild the cart variable ("trackHubs") that has which lists which
// hubs are on.
hubConnectHubsInCart(cart);
}
if (cartVarExists(cart, hgHubDoReset))
{
doResetHub(cart);
}
cartWebStart(cart, NULL, "%s", pageTitle);
jsIncludeFile("jquery.js", NULL);
jsIncludeFile("utils.js", NULL);
jsIncludeFile("jquery-ui.js", NULL);
webIncludeResourceFile("jquery-ui.css");
jsIncludeFile("ajax.js", NULL);
jsIncludeFile("hgHubConnect.js", NULL);
jsIncludeFile("jquery.cookie.js", NULL);
printf("<div id=\"hgHubConnectUI\"> <div id=\"description\"> \n");
printf(
"<P>Track data hubs are collections of tracks from outside of UCSC that "
"can be imported into the Genome Browser. To import a public hub check "
"the box in the list below. "
"After import the hub will show up as a group of tracks with its own blue "
"bar and label underneath the main browser graphic, and in the "
"configure page. For more information, see the "
"<A HREF=\"../goldenPath/help/hgTrackHubHelp.html\" TARGET=_blank>"
"User's Guide</A>.</P>\n"
"<P><B>NOTE: Because Track Hubs are created and maintained by external sources,"
" UCSC is not responsible for their content.</B></P>"
);
printf("</div>\n");
getDbAndGenome(cart, &database, &organism, oldVars);
char *survey = cfgOptionEnv("HGDB_HUB_SURVEY", "hubSurvey");
char *surveyLabel = cfgOptionEnv("HGDB_HUB_SURVEY_LABEL", "hubSurveyLabel");
if (survey && differentWord(survey, "off"))
hPrintf("<span style='background-color:yellow;'><A HREF='%s' TARGET=_BLANK><EM><B>%s</EM></B></A></span>\n", survey, surveyLabel ? surveyLabel : "Take survey");
hPutc('\n');
// check to see if we have any new hubs
hubCheckForNew(cart);
// grab all the hubs that are listed in the cart
struct hubConnectStatus *hubList = hubConnectStatusListFromCartAll(cart);
checkTrackDbs(hubList);
// here's a little form for the add new hub button
printf("<FORM ACTION=\"%s\" NAME=\"addHubForm\">\n", "../cgi-bin/hgHubConnect");
cgiMakeHiddenVar("hubUrl", "");
cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
puts("</FORM>");
// this the form for the disconnect hub button
printf("<FORM ACTION=\"%s\" NAME=\"disconnectHubForm\">\n", "../cgi-bin/hgHubConnect");
cgiMakeHiddenVar("hubId", "");
cgiMakeHiddenVar(hgHubDoDisconnect, "on");
cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
puts("</FORM>");
// this the form for the reset hub button
printf("<FORM ACTION=\"%s\" NAME=\"resetHubForm\">\n", "../cgi-bin/hgHubConnect");
cgiMakeHiddenVar("hubUrl", "");
cgiMakeHiddenVar(hgHubDoReset, "on");
cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
puts("</FORM>");
// ... and now the main form
if (cartVarExists(cart, hgHubConnectCgiDestUrl))
destUrl = cartOptionalString(cart, hgHubConnectCgiDestUrl);
printf("<FORM ACTION=\"%s\" METHOD=\"POST\" NAME=\"mainForm\">\n", destUrl);
cartSaveSession(cart);
// we have two tabs for the public and unlisted hubs
printf("<div id=\"tabs\">"
"<ul> <li><a href=\"#publicHubs\">Public Hubs</a></li>"
"<li><a href=\"#unlistedHubs\">My Hubs</a></li> "
"</ul> ");
struct hash *publicHash = hgHubConnectPublic();
hgHubConnectUnlisted(hubList, publicHash);
printf("</div>");
printf("<div class=\"tabFooter\">");
cgiMakeButton("Submit", "Use Selected Hubs");
char *emailAddress = cfgOptionDefault("hub.emailAddress","*****@*****.**");
printf("<span class=\"small\">"
"Contact <A HREF=\"mailto:%s\">%s</A> to add a public hub."
"</span>\n", emailAddress,emailAddress);
printf("</div>");
cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
printf("</div>\n");
puts("</FORM>");
cartWebEnd();
}