static void filterControlsForTableDb(char *db, char *rootTable)
/* Put up filter controls for a single database table. */
{
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(db))
conn = hAllocConn(db);
char *table = chromTable(conn, rootTable);
struct trackDb *tdb = findTdbForTable(db, curTrack, rootTable, ctLookupName);
boolean isSmallWig = isWiggle(db, table);
boolean isBigWig = tdb ? tdbIsBigWig(tdb) : isBigWigTable(table);
boolean isWig = isSmallWig || isBigWig;
boolean isBedGr = tdb ? tdbIsBedGraph(tdb) : isBedGraph(rootTable);
boolean isBb = tdb ? tdbIsBigBed(tdb) : isBigBed(database, table, curTrack, ctLookupName);
boolean isBam = tdb ? tdbIsBam(tdb) : isBamTable(rootTable);
boolean isVcf = tdb ? tdbIsVcf(tdb) : isVcfTable(rootTable, NULL);
int bedGraphColumn = 5; /* default score column */
if (isBedGr)
{
int wordCount;
char *words[8];
char *typeLine = cloneString(tdb->type);
wordCount = chopLine(typeLine,words);
if (wordCount > 1)
bedGraphColumn = sqlUnsigned(words[1]);
freez(&typeLine);
}
if (isWig)
{
hPrintf("<TABLE BORDER=0>\n");
if ((tdb != NULL) && (tdb->type != NULL))
{
double min, max;
wiggleMinMax(tdb,&min,&max);
numericFilterWithLimits(db, rootTable, filterDataValueVar,filterDataValueVar,min,max,"");
hPrintf("<TR><TD COLSPAN=3 ALIGN=RIGHT> (dataValue range: [%g:%g]) "
"</TD></TR></TABLE>\n", min, max);
}
else
{
numericFilter(db, rootTable, filterDataValueVar,filterDataValueVar, "");
hPrintf("</TABLE>\n");
}
}
else
{
struct sqlFieldType *ftList;
if (isBb)
ftList = bigBedListFieldsAndTypes(tdb, conn);
else if (isBam)
ftList = bamListFieldsAndTypes();
else if (isVcf)
ftList = vcfListFieldsAndTypes();
else
ftList = sqlListFieldsAndTypes(conn, table);
printSqlFieldListAsControlTable(ftList, db, rootTable, tdb, isBedGr);
}
/* Printf free-form query row. */
if (!(isWig||isBedGr||isBam||isVcf))
{
char *name;
hPrintf("<TABLE BORDER=0><TR><TD>\n");
name = filterFieldVarName(db, rootTable, "", filterRawLogicVar);
cgiMakeDropList(name, logOpMenu, logOpMenuSize,
cartUsualString(cart, name, logOpMenu[0]));
hPrintf(" Free-form query: ");
name = filterFieldVarName(db, rootTable, "", filterRawQueryVar);
char *val = cartUsualString(cart, name, "");
// escape double quotes to avoid HTML parse trouble in the text input.
val = htmlEncodeText(val, FALSE);
cgiMakeTextVar(name, val, 50);
hPrintf("</TD></TR></TABLE>\n");
}
if (isWig||isBedGr||isBam||isVcf)
{
char *name;
hPrintf("<TABLE BORDER=0><TR><TD> Limit data output to: \n");
name = filterFieldVarName(db, rootTable, "_", filterMaxOutputVar);
cgiMakeDropList(name, maxOutMenu, maxOutMenuSize,
cartUsualString(cart, name, maxOutMenu[0]));
hPrintf(" lines</TD></TR></TABLE>\n");
}
freez(&table);
hFreeConn(&conn);
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoFilterSubmit, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
}
static void hgPositionsJson(struct jsonWrite *jw, char *db, struct hgPositions *hgp, struct cart *cart)
/* Write out JSON description of multiple position matches. */
{
struct hgPosTable *table;
jsonWriteListStart(jw, "positionMatches");
struct trackDb *tdbList = NULL;
for (table = hgp->tableList; table != NULL; table = table->next)
{
if (table->posList != NULL)
{
char *tableName = table->name;
// clear the tdb cache if this track is a hub track
if (isHubTrack(tableName))
tdbList = NULL;
struct trackDb *tdb = tdbForTrack(db, tableName, &tdbList);
if (!tdb && startsWith("all_", tableName))
tdb = tdbForTrack(db, tableName+strlen("all_"), &tdbList);
if (!tdb)
errAbort("no track for table \"%s\" found via a findSpec", tableName);
char *trackName = tdb->track;
jsonWriteObjectStart(jw, NULL);
jsonWriteString(jw, "name", table->name);
jsonWriteString(jw, "trackName", trackName);
jsonWriteString(jw, "description", table->description);
jsonWriteString(jw, "vis", hCarefulTrackOpenVis(db, trackName));
jsonWriteListStart(jw, "matches");
struct hgPos *pos;
for (pos = table->posList; pos != NULL; pos = pos->next)
{
char *encMatches = cgiEncode(pos->browserName);
jsonWriteObjectStart(jw, NULL); // begin one match
if (pos->chrom != NULL)
jsonWriteStringf(jw, "position", "%s:%d-%d",
pos->chrom, pos->chromStart+1, pos->chromEnd);
else
// GenBank results set position to GB accession instead of chr:s-e position.
jsonWriteString(jw, "position", pos->name);
// this is magic to tell the browser to make the
// composite and this subTrack visible
if (tdb->parent)
{
if (tdbIsSuperTrackChild(tdb))
jsonWriteStringf(jw, "extraSel", "%s=show&", tdb->parent->track);
else
{
// tdb is a subtrack of a composite or a view
jsonWriteStringf(jw, "extraSel", "%s_sel=1&%s_sel=1&",
trackName, tdb->parent->track);
}
}
jsonWriteString(jw, "hgFindMatches", encMatches);
jsonWriteString(jw, "posName", htmlEncodeText(pos->name, FALSE));
if (pos->description)
{
stripString(pos->description, "\n");
jsonWriteString(jw, "description", stripAnchor(pos->description));
}
jsonWriteObjectEnd(jw); // end one match
}
jsonWriteListEnd(jw); // end matches
jsonWriteObjectEnd(jw); // end one table
}
}
jsonWriteListEnd(jw); // end positionMatches
}
int documentLink(struct hash *ra, char *term, char *docTerm,char *dir,
char *title,boolean genericDoc)
// Compare controlled vocab based on term value
{
boolean docsPrinted = 0;
char *s;
if (title == NULL)
title = docTerm;
//can use hg.conf to direct links back to main UCSC server if a mirror doesn't
//want all the PDFs
char *baseUrl = cfgOptionDefault("hgEncodeVocabDocBaseUrl", "");
// add links to protocol doc if it exists
char docUrl[PATH_LEN];
char docFile[PATH_LEN];
// parse setting
s = hashFindVal(ra,docTerm);
if (s != NULL)
{
if (sameWord(s,"missing"))
printf(" <em>missing</em>\n");
else
{
char *docSetting = cloneString(s);
char *settings=docSetting;
int count=0;
while ((s = nextWord(&settings)) != NULL)
{
char *docTitle = NULL;
char *fileName = NULL;
if (strchr(s,':')) // lab Specific setting
{
docTitle = strSwapChar(s,':',0);
fileName = docTitle + strlen(docTitle) + 1;
}
else
{
docTitle = title;
fileName = s;
}
if (count>0)
printf("<BR>");
count++;
docTitle = htmlEncodeText(strSwapChar(docTitle,'_',' '),FALSE);
if (sameWord(fileName,"missing"))
printf("%s<em>missing</em>\n",docTitle);
else
{
safef(docUrl, sizeof(docUrl), "%s%s%s", baseUrl, dir, fileName);
safef(docFile, sizeof(docFile), "%s%s", hDocumentRoot(), docUrl);
printf(" <A TARGET=_BLANK HREF=%s>%s</A>\n", docUrl,docTitle);
docsPrinted++;
}
freeMem(docTitle);
}
freeMem(docSetting);
}
}
else if (genericDoc)
{ // generate a standard name
safef(docUrl, sizeof(docUrl), "%s%s%s_protocol.pdf", baseUrl, dir, term);
safef(docFile, sizeof(docFile), "%s%s", hDocumentRoot(), docUrl);
if (fileExists(docFile))
{
printf(" <A TARGET=_BLANK HREF=%s>%s</A>\n", docUrl,title);
docsPrinted++;
}
}
return docsPrinted;
}
