64cd3197e8c5507c2a3c0f1c4a5b28627183fd8b
tdreszer
  Fri Mar 11 16:11:55 2011 -0800
Changed mdb API required this change.
diff --git src/hg/hgApi/hgApi.c src/hg/hgApi/hgApi.c
index a220ec6..a4ff12d 100644
--- src/hg/hgApi/hgApi.c
+++ src/hg/hgApi/hgApi.c
@@ -1,248 +1,248 @@
 /* hgApi - provide a JSON based API to the browser. */
 
 #include "common.h"
 #include "hdb.h"
 #include "mdb.h"
 #include "cheapcgi.h"
 #include "hPrint.h"
 #include "dystring.h"
 #include "hui.h"
 #include "searchTracks.h"
 
 static char const rcsid[] = "$Id: hgApi.c,v 1.3 2010/05/30 21:11:47 larrym Exp $";
 
 static void fail(char *msg)
 {
 puts("Status: 400\n\n");
 puts(msg);
 exit(-1);
 }
 
 void makeIndent(char *buf, int bufLen, int indent)
 {
 indent = min(indent, bufLen - 2);
 memset(buf, '\t', indent);
 buf[indent] = 0;
 }
 
 static void trackJson(struct dyString *json, struct trackDb *tdb, int *count, int indent)
 {
 char tabs[100];
 makeIndent(tabs, sizeof(tabs), indent);
 if((*count)++)
     dyStringPrintf(json, ",\n");
 dyStringPrintf(json, "%s{\n", tabs);
 makeIndent(tabs, sizeof(tabs), indent + 1);
 dyStringPrintf(json, "%s\"track\": \"%s\",\n%s\"shortLabel\": \"%s\",\n%s\"longLabel\": \"%s\",\n%s\"group\": \"%s\"",
                tabs, tdb->track,
                tabs, tdb->shortLabel, tabs, tdb->longLabel,
                tabs, tdb->grp);
 if(tdbIsComposite(tdb) && tdb->subtracks != NULL)
     {
     struct trackDb *ptr;
     dyStringPrintf(json, ",\n%s\"subtracks\":\n%s[\n", tabs, tabs);
     int count = 0;
     for (ptr = tdb->subtracks; ptr != NULL; ptr = ptr->next)
         {
         trackJson(json, ptr, &count, indent + 2);
         }
     dyStringPrintf(json, "\n%s]", tabs);
     }
 makeIndent(tabs, sizeof(tabs), indent);
 dyStringPrintf(json, "\n%s}", tabs);
 }
 
 int main(int argc, char *argv[])
 {
 struct dyString *output = newDyString(10000);
 char *database = cgiOptionalString("db");
 char *cmd = cgiOptionalString("cmd");
 char *jsonp = cgiOptionalString("jsonp");
 if(database)
     {
     database = sqlEscapeString(database);
     if(!hDbExists(database))
         fail("Invalid database");
     }
 else
     fail("Missing 'db' parameter");
 
 if(!cmd)
     fail("Missing 'cmd' parameter");
 
 if(!strcmp(cmd, "trackList"))
     {
     // Return trackList for this assembly
     // e.g. http://genome.ucsc.edu/hgApi?db=hg18&cmd=trackList
 
     struct trackDb *tdb, *tdbList = NULL;
     tdbList = hTrackDb(database);
     dyStringPrintf(output, "[\n");
     int count = 0;
     for (tdb = tdbList; tdb != NULL; tdb = tdb->next)
         {
         trackJson(output, tdb, &count, 1);
         count++;
         }
     dyStringAppend(output, "\n]\n");
     }
 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
             fail("Missing var parameter");
-        struct slPair *pairs = mdbValLabelSearch(conn, var, MDB_VAL_STD_TRUNCATION, TRUE, FALSE); // Tables not files
+        struct slPair *pairs = mdbValLabelSearch(conn, var, MDB_VAL_STD_TRUNCATION, FALSE, TRUE, FALSE); // not tags, yes tables, not files
         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
         fail("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
             fail("Missing var parameter");
 
         int ix = atoi(cmd+strlen(METADATA_VALUE_PREFIX)); // 1 based index
         if(ix == 0) //
             fail("Unsupported 'cmd' parameter");
 
         enum mdbCvSearchable searchBy = mdbCvSearchMethod(var);
         char name[128];
         safef(name,sizeof name,"%s%i",METADATA_VALUE_PREFIX,ix);
         if (searchBy == cvsSearchBySingleSelect || searchBy == cvsSearchByMultiSelect)
             {
-            struct slPair *pairs = mdbValLabelSearch(conn, var, MDB_VAL_STD_TRUNCATION, TRUE, FALSE); // Tables not files
+            struct slPair *pairs = mdbValLabelSearch(conn, var, MDB_VAL_STD_TRUNCATION, FALSE, TRUE, FALSE); // not tags, yes tables, not files
             if (slCount(pairs) > 0)
                 {
                 char *dropDownHtml = cgiMakeSelectDropList((searchBy == cvsSearchByMultiSelect),
                         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 == cvsSearchByFreeText)
             {
             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 == cvsSearchByDateRange || searchBy == cvsSearchByDateRange)
-        //    {
-        //    // TO BE IMPLEMENTED
-        //    }
+        else if (searchBy == cvsSearchByDateRange || searchBy == cvsSearchByIntegerRange)
+            {
+            // TO BE IMPLEMENTED
+            }
         else
             fail("Metadata variable not searchable");
 
         dyStringPrintf(output,"<span id='helpLink%i'>&nbsp;</span>",ix);
         }
     else
         fail("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)
         {
         struct trackDb *tdb = hTrackDbForTrackAndAncestors(database, trackName); // Doesn't get whole track list
         if (tdb != NULL)
             {
             char * html = metadataAsHtmlTable(database,tdb,showLonglabel,showShortLabel,NULL);
             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("unknwon cmd: %s",cmd);
     fail("Unsupported 'cmd' parameter");
     }
 
 // It's debatable whether the type should be text/plain, text/javascript or application/javascript; I think
 // any of the types containing "javascript" don't work with IE6, so I'm using text/plain
 
 puts("Content-Type:text/javascript\n");
 //puts("\n");
 if(jsonp)
     printf("%s(%s)", jsonp, dyStringContents(output));
 else
     puts(dyStringContents(output));
 
 return 0;
 }