static int getTermArray(struct sqlConnection *conn, char ***pLabels, char ***pTerms, char *type)
// Pull out all term fields from ra entries with given type
// Returns count of items found and items via the terms argument.
{
int ix = 0, count = 0;
char **labels;
char **values;
struct slPair *pairs = mdbValLabelSearch(conn, type, MDB_VAL_STD_TRUNCATION, TRUE, FALSE); // Tables not files
count = slCount(pairs) + 1; // make room for "Any"
AllocArray(labels, count);
AllocArray(values, count);
labels[ix] = cloneString(ANYLABEL);
values[ix] = cloneString(ANYLABEL);
struct slPair *pair = NULL;
while((pair = slPopHead(&pairs)) != NULL)
{
ix++;
labels[ix] = pair->name;
values[ix] = pair->val;
freeMem(pair);
}
*pLabels = labels;
*pTerms = values;
return count;
}
char *mdbSelectsHtmlRows(struct sqlConnection *conn,struct slPair *mdbSelects,
struct slPair *mdbVars,int cols,boolean fileSearch)
// genereates the html for the table rows containing mdb var and val selects.
// Assume tableSearch unless fileSearch
{
struct dyString *output = dyStringNew(1024);
dyStringPrintf(output,"<tr><td colspan='%d' align='right' class='lineOnTop' style='height:20px; "
"max-height:20px;'><em style='color:%s; width:200px;'>ENCODE terms</em>"
"</td></tr>\n", cols,COLOR_DARKGREY);
struct slPair *mdbSelect = mdbSelects;
int row = 0;
for (;mdbSelect != NULL; mdbSelect = mdbSelect->next)
{
char buf[256];
char *dropDownHtml = NULL;
#define PLUS_MINUS_BUTTON "<input type='button' id='%sButton%d' value='%c' " \
"style='font-size:.7em;' title='%s' " \
"onclick='findTracks.mdbSelectPlusMinus(this,%d)'>"
#define ADD_PM_BUTTON(type,num,value) \
dyStringPrintf(output,PLUS_MINUS_BUTTON, (type), (num), (value), \
((value) == '+' ? "add another row after":"delete"), (num))
dyStringAppend(output,"<tr valign='top' class='mdbSelect'><td nowrap>\n");
row++;
if (slCount(mdbSelects) > 2 || row > 2)
ADD_PM_BUTTON("minus", row, '-');
else
dyStringAppend(output," ");
ADD_PM_BUTTON("plus", row, '+');
dyStringAppend(output,"</td><td>and </td><td colspan=3 nowrap>\n");
safef(buf, sizeof(buf), "%s%i", METADATA_NAME_PREFIX, row);
// Left side select of vars
dropDownHtml = cgiMakeSingleSelectDropList(buf, mdbVars,mdbSelect->name, NULL,"mdbVar",
"style='font-size:.9em;' onchange='findTracks.mdbVarChanged(this);'");
if (dropDownHtml)
{
dyStringAppend(output,dropDownHtml);
freeMem(dropDownHtml);
}
// Right side select of vals
safef(buf, sizeof(buf), "%s%i", METADATA_VALUE_PREFIX, row);
enum cvSearchable searchBy = cvSearchMethod(mdbSelect->name);
if (searchBy == cvSearchBySingleSelect || searchBy == cvSearchByMultiSelect)
{
dyStringPrintf(output,"</td>\n<td align='right' id='isLike%i' style='width:10px; "
"white-space:nowrap;'>is%s</td>\n<td nowrap id='%s' "
"style='max-width:600px;'>\n",
row,(searchBy == cvSearchByMultiSelect?" among":""),buf);
struct slPair *pairs = mdbValLabelSearch(conn, mdbSelect->name, MDB_VAL_STD_TRUNCATION,
FALSE, !fileSearch, fileSearch);
// not tags, either a file or table search
if (slCount(pairs) > 0)
{
char *dropDownHtml = cgiMakeSelectDropList((searchBy == cvSearchByMultiSelect),
buf, pairs,mdbSelect->val, ANYLABEL,"mdbVal",
"style='min-width:200px; font-size:.9em;' "
"onchange='findTracks.mdbValChanged(this);'");
if (dropDownHtml)
{
dyStringAppend(output,dropDownHtml);
freeMem(dropDownHtml);
}
slPairFreeList(&pairs);
}
}
else if (searchBy == cvSearchByFreeText)
{
dyStringPrintf(output,"</td><td align='right' id='isLike%i' style='width:10px; "
"white-space:nowrap;'>contains</td>\n<td nowrap id='%s' "
"style='max-width:600px;'>\n",row,buf);
dyStringPrintf(output,"<input type='text' name='%s' value='%s' class='mdbVal freeText' "
"style='max-width:310px; width:310px; font-size:.9em;' "
"onchange='findTracks.mdbVarChanged(true);'>\n",
buf,(mdbSelect->val ? (char *)mdbSelect->val: ""));
}
else if (searchBy == cvSearchByWildList)
{
dyStringPrintf(output,"</td><td align='right' id='isLike%i' style='width:10px; "
"white-space:nowrap;'>is among</td>\n<td nowrap id='%s' "
"style='max-width:600px;'>\n",row,buf);
dyStringPrintf(output,"<input type='text' name='%s' value='%s' class='mdbVal wildList' "
"title='enter comma separated list of values' "
"style='max-width:310px; width:310px; font-size:.9em;' "
"onchange='findTracks.mdbVarChanged(true);'>\n",
buf,(mdbSelect->val ? (char *)mdbSelect->val: ""));
}
//else if (searchBy == cvSearchByDateRange || searchBy == cvSearchByIntegerRange)
// {
// // TO BE IMPLEMENTED
// }
dyStringPrintf(output,"<span id='helpLink%i'> </span></td>\n", row);
dyStringPrintf(output,"</tr>\n");
}
dyStringPrintf(output,"<tr><td colspan='%d' align='right' style='height:10px; "
"max-height:10px;'> </td></tr>", cols);
return dyStringCannibalize(&output);
}
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;
}
