static char *getDbForGenome(char *genome, struct cart *cart)
/*
Function to find the default database for the given Genome.
It looks in the cart first and then, if that database's Genome matches the
passed-in Genome, returns it. If the Genome does not match, it returns the default
database that does match that Genome.
param Genome - The Genome for which to find a database
param cart - The cart to use to first search for a suitable database name
return - The database matching this Genome type
*/
{
char *retDb = cartUsualString(cart, dbCgiName, NULL);
if ((retDb == NULL) || !hDbExists(retDb))
{
retDb = hDefaultDb();
}
/* If genomes don't match, then get the default db for that genome */
if (differentWord(genome, hGenome(retDb)))
{
retDb = hDefaultDbForGenome(genome);
}
return retDb;
}
static void printActiveGenomes()
/* Print out JSON for an object mapping each genome that has at least one db with active=1
* to its taxId. */
{
struct jsonWrite *jw = jsonWriteNew();
jsonWriteObjectStart(jw, NULL);
struct sqlConnection *conn = hConnectCentral();
// Join with defaultDb because in rare cases, different taxIds (species vs. subspecies)
// may be used for different assemblies of the same species. Using defaultDb means that
// we send a taxId consistent with the taxId of the assembly that we'll change to when
// the species is selected from the tree.
char *query = NOSQLINJ "select dbDb.genome, taxId, dbDb.name from dbDb, defaultDb "
"where defaultDb.name = dbDb.name and active = 1 "
"and taxId > 1;"; // filter out experimental hgwdev-only stuff with invalid taxIds
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
char *genome = row[0], *db = row[2];
int taxId = atoi(row[1]);
if (hDbExists(db))
jsonWriteNumber(jw, genome, taxId);
}
hDisconnectCentral(&conn);
jsonWriteObjectEnd(jw);
puts(jw->dy->string);
jsonWriteFree(&jw);
}
int hgSeqChromSize(char *db, char *chromName)
/* get chrom size if there's a database out there,
* otherwise just return 0 */
{
int thisSize = 0;
if (hDbExists(db))
thisSize = hChromSize(db, chromName);
return thisSize;
}
void hgDropSplitTable(char *db, char *oldRoot)
/* hgDropSplitTable - Drop a table, or drop all tables in a split table. */
{
struct slName *tables, *table;
char query[128];
struct sqlConnection *conn;
if (!hDbExists(db))
errAbort("Non-existent database: %s", db);
tables = hSplitTableNames(db, oldRoot);
if (!tables)
errAbort("Can't find table: %s\n", oldRoot);
conn = sqlConnect(db);
for (table = tables; table != NULL; table = table->next)
{
sqlSafef(query, sizeof query, "DROP TABLE %s", table->name);
sqlUpdate(conn, query);
}
}
int main(int argc, char *argv[])
/* Check args and call snpMaskGenes. */
{
if (argc != 5)
usage();
database = argv[1];
if(!hDbExists(database))
errAbort("%s does not exist\n", database);
hSetDb(database);
if(!hTableExistsDb(database, "snp"))
errAbort("no snp table in %s\n", database);
chromName = argv[2];
if(hgOfficialChromName(chromName) == NULL)
errAbort("no such chromosome %s in %s\n", chromName, database);
// check that nib file exists
// or, use hNibForChrom from hdb.c
snpMaskGenes(argv[3], argv[4]);
return 0;
}
static void printSomeGenomeListHtmlNamedMaybeCheck(char *customOrgCgiName,
char *db, struct dbDb *dbList, char *onChangeText, boolean doCheck)
/* Prints to stdout the HTML to render a dropdown list
* containing a list of the possible genomes to choose from.
* param db - a database whose genome will be the default genome.
* If NULL, no default selection.
* param onChangeText - Optional (can be NULL) text to pass in
* any onChange javascript. */
{
char *orgList[1024];
int numGenomes = 0;
struct dbDb *cur = NULL;
struct hash *hash = hashNew(10); // 2^^10 entries = 1024
char *selGenome = hGenomeOrArchive(db);
char *values [1024];
char *cgiName;
for (cur = dbList; cur != NULL; cur = cur->next)
{
if (!hashFindVal(hash, cur->genome) &&
(!doCheck || hDbExists(cur->name)))
{
hashAdd(hash, cur->genome, cur);
orgList[numGenomes] = trackHubSkipHubName(cur->genome);
values[numGenomes] = cur->genome;
numGenomes++;
if (numGenomes >= ArraySize(orgList))
internalErr();
}
}
cgiName = (customOrgCgiName != NULL) ? customOrgCgiName : orgCgiName;
cgiMakeDropListFull(cgiName, orgList, values, numGenomes,
selGenome, onChangeText);
hashFree(&hash);
}
void getDbGenomeClade(struct cart *cart, char **retDb, char **retGenome,
char **retClade, struct hash *oldVars)
/* Examine CGI and cart variables to determine which db, genome, or clade
* has been selected, and then adjust as necessary so that all three are
* consistent. Detect changes and reset db-specific cart variables.
* Save db, genome and clade in the cart so it will be consistent hereafter.
* The order of preference here is as follows:
* If we got a request that explicitly names the db, that takes
* highest priority, and we synch the organism to that db.
* If we get a cgi request for a specific organism then we use that
* organism to choose the DB. If just clade, go from there.
* In the cart only, we use the same order of preference.
* If someone requests an Genome we try to give them the same db as
* was in their cart, unless the Genome doesn't match.
*/
{
boolean gotClade = hGotClade();
*retDb = cgiOptionalString(dbCgiName);
*retGenome = cgiOptionalString(orgCgiName);
*retClade = cgiOptionalString(cladeCgiName);
/* phoneHome business */
phoneHome();
/* Was the database passed in as a cgi param?
* If so, it takes precedence and determines the genome. */
if (*retDb && hDbExists(*retDb))
{
*retGenome = hGenome(*retDb);
}
/* If no db was passed in as a cgi param then was the organism (a.k.a. genome)
* passed in as a cgi param?
* If so, the we use the proper database for that genome. */
else if (*retGenome && !sameWord(*retGenome, "0"))
{
*retDb = getDbForGenome(*retGenome, cart);
*retGenome = hGenome(*retDb);
}
else if (*retClade && gotClade)
{
*retGenome = hDefaultGenomeForClade(*retClade);
*retDb = getDbForGenome(*retGenome, cart);
}
/* If no cgi params passed in then we need to inspect the session */
else
{
*retDb = cartOptionalString(cart, dbCgiName);
*retGenome = cartOptionalString(cart, orgCgiName);
*retClade = cartOptionalString(cart, cladeCgiName);
/* If there was a db found in the session that determines everything. */
if (*retDb && hDbExists(*retDb))
{
*retGenome = hGenome(*retDb);
}
else if (*retGenome && !sameWord(*retGenome, "0"))
{
*retDb = hDefaultDbForGenome(*retGenome);
}
else if (*retClade && gotClade)
{
*retGenome = hDefaultGenomeForClade(*retClade);
*retDb = getDbForGenome(*retGenome, cart);
}
/* If no organism in the session then get the default db and organism. */
else
{
*retDb = hDefaultDb();
*retGenome = hGenome(*retDb);
}
}
*retDb = cloneString(*retDb);
*retGenome = cloneString(*retGenome);
*retClade = hClade(*retGenome);
/* Detect change of database and reset db-specific cart variables: */
if (oldVars)
{
char *oldDb = hashFindVal(oldVars, "db");
char *oldOrg = hashFindVal(oldVars, "org");
char *oldClade = hashFindVal(oldVars, "clade");
if ((!IS_CART_VAR_EMPTY(oldDb) && differentWord(oldDb, *retDb)) ||
(!IS_CART_VAR_EMPTY(oldOrg) && differentWord(oldOrg, *retGenome)) ||
(!IS_CART_VAR_EMPTY(oldClade) && differentWord(oldClade, *retClade)))
{
/* Change position to default -- unless it was passed in via CGI: */
if (cgiOptionalString("position") == NULL)
cartSetString(cart, "position", hDefaultPos(*retDb));
/* hgNear search term -- unless it was passed in via CGI: */
if (cgiOptionalString("near_search") == NULL)
cartRemove(cart, "near_search");
/* hgBlat results (hgUserPsl track): */
cartRemove(cart, "ss");
/* hgTables correlate: */
cartRemove(cart, "hgta_correlateTrack");
cartRemove(cart, "hgta_correlateTable");
cartRemove(cart, "hgta_correlateGroup");
cartRemove(cart, "hgta_correlateOp");
cartRemove(cart, "hgta_nextCorrelateTrack");
cartRemove(cart, "hgta_nextCorrelateTable");
cartRemove(cart, "hgta_nextCorrelateGroup");
cartRemove(cart, "hgta_nextCorrelateOp");
cartRemove(cart, "hgta_corrWinSize");
cartRemove(cart, "hgta_corrMaxLimitCount");
}
}
/* Save db, genome (as org) and clade in cart. */
cartSetString(cart, "db", *retDb);
cartSetString(cart, "org", *retGenome);
if (gotClade)
cartSetString(cart, "clade", *retClade);
}
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() */
void mafPrettyOut(FILE *f, struct mafAli *maf, int lineSize,
boolean onlyDiff, int blockNo)
{
int ii, ch;
int srcChars = 0;
struct mafComp *mc;
int lineStart, lineEnd;
char *summaryLine = needMem(lineSize+1);
char *referenceText;
int startChars, sizeChars, srcSizeChars;
boolean haveInserts = FALSE;
struct mafComp *masterMc = maf->components;
startChars = sizeChars = srcSizeChars = 0;
for (mc = maf->components; mc != NULL; mc = mc->next)
{
/* Figure out length of source (species) field. */
/*if (mc->size != 0)*/
{
char dbOnly[128];
int len;
char *org;
memset(dbOnly, 0, sizeof(dbOnly));
safef(dbOnly, sizeof(dbOnly), "%s", mc->src);
chopPrefix(dbOnly);
if ((org = hOrganism(dbOnly)) == NULL)
len = strlen(dbOnly);
else
len = strlen(org);
if (srcChars < len)
srcChars = len;
len = digitsBaseTen(mc->start);
if (startChars < len)
startChars = len;
len = digitsBaseTen(mc->size);
if (sizeChars < len)
sizeChars = len;
len = digitsBaseTen(mc->srcSize);
if (srcSizeChars < len)
srcSizeChars = len;
if (mc->text && (mc->rightStatus == MAF_INSERT_STATUS) && (masterMc->start + masterMc->size < winEnd))
haveInserts = TRUE;
#ifdef REVERSESTRAND
/* complement bases if hgTracks is on reverse strand */
if (mc->size && cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE))
complement(mc->text, maf->textSize);
#endif
}
}
/* first sequence in the alignment */
referenceText = maf->components->text;
for (lineStart = 0; lineStart < maf->textSize; lineStart = lineEnd)
{
int size;
lineEnd = lineStart + lineSize;
if (lineEnd >= maf->textSize)
lineEnd = maf->textSize;
size = lineEnd - lineStart;
initSummaryLine(summaryLine, size, '*');
for (mc = maf->components; mc != NULL; mc = mc->next)
{
char dbOnly[128], *chrom;
int s = mc->start;
int e = s + mc->size;
char *org;
char *revComp = "";
char strand = mc->strand;
struct dyString *dy = newDyString(512);
#ifdef REVERSESTRAND
if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE))
strand = (strand == '+') ? '-' : '+';
#endif
if (strand == '-') revComp = "&hgSeq.revComp=on";
dyStringClear(dy);
safef(dbOnly, sizeof(dbOnly), "%s", mc->src);
chrom = chopPrefix(dbOnly);
if ((org = hOrganism(dbOnly)) == NULL)
org = dbOnly;
if (mc->strand == '-')
reverseIntRange(&s, &e, mc->srcSize);
if (mc->text != NULL)
{
if (lineStart == 0)
{
if (hDbIsActive(dbOnly))
{
dyStringPrintf(dy, "%s Browser %s:%d-%d %c %*dbps",hOrganism(dbOnly),chrom, s+1, e, mc->strand,sizeChars, mc->size);
linkToOtherBrowserTitle(dbOnly, chrom, s, e, dy->string);
dyStringClear(dy);
fprintf(f, "B</A> ");
}
else
fprintf(f, " ");
if (hDbExists(dbOnly))
{
dyStringPrintf(dy, "Get %s DNA %s:%d-%d %c %*dbps",hOrganism(dbOnly),chrom, s+1, e, mc->strand,sizeChars, mc->size);
printf("<A TITLE=\"%s\" TARGET=\"_blank\" HREF=\"%s?o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d&db=%s%s\">D</A> ", dy->string,hgcName(),
s, cgiEncode(chrom),
chrom, s, e, dbOnly, revComp);
}
else
fprintf(f, " ");
}
else
{
fprintf(f, " ");
}
dyStringClear(dy);
dyStringPrintf(dy, "%s:%d-%d %c %*dbps",chrom, s+1, e, mc->strand,sizeChars, mc->size);
fprintf(f, "<A TITLE=\"%s\"> %*s </A> ", dy->string, srcChars, org);
updateSummaryLine(summaryLine, referenceText + lineStart, mc->text + lineStart, size);
blueCapWrite(f, mc->text + lineStart, size,
(onlyDiff && mc != maf->components) ? referenceText + lineStart : NULL);
fprintf(f, "\n");
}
else
{
if (((mc->leftStatus == MAF_CONTIG_STATUS) && (mc->rightStatus == MAF_CONTIG_STATUS) )
|| ((mc->leftStatus == MAF_TANDEM_STATUS) && (mc->rightStatus == MAF_TANDEM_STATUS) )
|| ((mc->leftStatus == MAF_INSERT_STATUS) && (mc->rightStatus == MAF_INSERT_STATUS) )
|| ((mc->leftStatus == MAF_MISSING_STATUS) && (mc->rightStatus == MAF_MISSING_STATUS) ))
{
if (lineStart == 0)
{
int s = mc->start;
int e = s + mc->rightLen;
struct dyString *dy = newDyString(512);
if (mc->strand == '-')
reverseIntRange(&s, &e, mc->srcSize);
if ( hDbIsActive(dbOnly))
{
dyStringPrintf(dy, "%s Browser %s:%d-%d %c %d bps Unaligned",hOrganism(dbOnly),chrom, s+1, e, mc->strand, e-s);
linkToOtherBrowserTitle(dbOnly, chrom, s, e, dy->string);
fprintf(f,"B</A> ");
dyStringClear(dy);
}
else
fprintf(f," ");
if (hDbExists(dbOnly))
{
dyStringPrintf(dy, "Get %s DNA %s:%d-%d %c %d bps Unaligned",hOrganism(dbOnly),chrom, s+1, e, mc->strand, e-s);
printf("<A TITLE=\"%s\" TARGET=\"_blank\" HREF=\"%s?o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d&db=%s%s\">D</A> ", dy->string, hgcName(),
s, cgiEncode(chrom),
chrom, s, e, dbOnly,revComp);
}
else
fprintf(f, " ");
}
else
fprintf(f, " ");
initSummaryLine(summaryLine, size, ' ');
dyStringClear(dy);
dyStringPrintf(dy, "%s:%d-%d %c %*dbps",chrom, s+1, e, mc->strand,sizeChars, mc->size);
fprintf(f, "<A TITLE=\"%s\">%*s</A> ", dy->string, srcChars, org);
ch = '-';
switch(mc->rightStatus)
{
case MAF_INSERT_STATUS:
ch = '=';
break;
case MAF_MISSING_STATUS:
ch = 'N';
break;
case MAF_TANDEM_STATUS:
case MAF_CONTIG_STATUS:
ch = '-';
break;
}
for(ii=lineStart; ii < lineEnd ; ii++)
fputc(ch,f);
fprintf(f,"\n");
}
}
}
#ifdef ADDMATCHLINE
if (lineStart == 0)
fprintf(f, " %-*s %s\n", srcChars, "", summaryLine);
else
fprintf(f, "%-*s %s\n", srcChars, "", summaryLine);
#else
fprintf(f, "\n");
#endif
}
if (haveInserts)
{
fprintf(f, "<B>Inserts between block %d and %d in window</B>\n",blockNo, blockNo+1);
for (mc = maf->components; mc != NULL; mc = mc->next)
{
char dbOnly[128], *chrom;
int s = mc->start + mc->size;
int e = s + mc->rightLen;
char *org;
if (mc->text == NULL)
continue;
if (mc->strand == '-')
reverseIntRange(&s, &e, mc->srcSize);
safef(dbOnly, sizeof(dbOnly), "%s", mc->src);
chrom = chopPrefix(dbOnly);
if ((org = hOrganism(dbOnly)) == NULL)
org = dbOnly;
if (mc->rightStatus == MAF_INSERT_STATUS)
{
char *revComp = "";
if (hDbIsActive(dbOnly))
{
char strand = mc->strand;
#ifdef REVERSESTRAND
if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE))
strand = (strand == '+') ? '-' : '+';
#endif
if (strand == '-') revComp = "&hgSeq.revComp=on";
linkToOtherBrowser(dbOnly, chrom, s, e);
fprintf(f,"B");
fprintf(f, "</A>");
fprintf(f, " ");
}
else
fprintf(f, " ");
if (hDbExists(dbOnly))
{
printf("<A TARGET=\"_blank\" HREF=\"%s?o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d"
"&db=%s%s\">D</A> ", hgcName(), s, cgiEncode(chrom), chrom, s,
e, dbOnly,revComp);
}
else
fprintf(f, " ");
fprintf(f, "%*s %dbp\n", srcChars, org,mc->rightLen);
}
}
fprintf(f, "\n");
}
freeMem(summaryLine);
}
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;
}
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() */