81881fe298580da38c5bdb7764c05c03ec278b97 hiram Fri Jan 4 11:54:10 2013 -0800 adding cgiExitTime stderr printout to CGI binaries for apache error_log information diff --git src/hg/hgApi/hgApi.c src/hg/hgApi/hgApi.c index 1c83888..15b1d7d 100644 --- src/hg/hgApi/hgApi.c +++ src/hg/hgApi/hgApi.c @@ -1,223 +1,225 @@ /* hgApi - provide a JSON based API to the browser. Required CGI parameters: db: assembly cmd: command (see below) Optional CGI parameters: jsonp: if present, the returned json is wrapped in a call to the value of the jsonp parameter (e.g. "jsonp=parseResponse"). Supported commands: defaultPos: default position for this assembly metaDb: return list of values for metaDb parameter hgt_mdbVal: return metaDb value control - see code for details tableMetadata: returns an html table with metadata for track parameter codonToPos: returns genomic position for given codon; parameters: codon, table and name (which is gene name). codonToPos: returns genomic position for given exon; parameters: exon, table and name (which is gene name). */ #include "common.h" #include "hdb.h" #include "mdb.h" #include "cheapcgi.h" #include "hPrint.h" #include "dystring.h" #include "hui.h" #include "search.h" #include "cv.h" #include "api.h" int main(int argc, char *argv[]) { +long enteredMainTime = clock1000(); struct dyString *output = newDyString(10000); cgiSpoof(&argc, argv); pushWarnHandler(apiWarnAbortHandler); pushAbortHandler(apiWarnAbortHandler); 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) var = sqlEscapeString(var); else 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) var = sqlEscapeString(var); else 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); safef(query, sizeof(query), "select name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds from %s where name = '%s'", sqlEscapeString(table), sqlEscapeString(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; }