3a3e7f9931622d8837bf08c3de5dfb328c384203
tdreszer
  Fri Jun 22 15:59:56 2012 -0700
Third batch of many checkins as dictated by Jim's OCD.  Formatting space after if and limiting lines to 100 chars.  Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history.  None of these changes should affect executables in any way.  Only affect is to my sanity and Jim's.
diff --git src/hg/hgApi/hgApi.c src/hg/hgApi/hgApi.c
index ae5a8b6..abd570a 100644
--- src/hg/hgApi/hgApi.c
+++ src/hg/hgApi/hgApi.c
@@ -1,213 +1,221 @@
 /* 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[])
 {
 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); // not tags, either a file or table search
+        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, "['%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); // not tags, either a file or table search
+            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);'");
+                                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);
+            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);
+            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'>&nbsp;</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)
         {
-        struct trackDb *tdb = hTrackDbForTrackAndAncestors(database, trackName); // Doesn't get whole track list
+        // 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);
 return 0;
 }