Index: src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/encode/hgEncodeVocab/hgEncodeVocab.c,v
retrieving revision 1.28
retrieving revision 1.29
diff -b -B -U 1000000 -r1.28 -r1.29
--- src/hg/encode/hgEncodeVocab/hgEncodeVocab.c	3 Dec 2009 22:11:44 -0000	1.28
+++ src/hg/encode/hgEncodeVocab/hgEncodeVocab.c	4 Dec 2009 01:31:44 -0000	1.29
@@ -1,421 +1,427 @@
 /* hgEncodeVocab - print table of controlled vocabulary from ENCODE configuration files */
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "cheapcgi.h"
 #include "hCommon.h"
 #include "htmshell.h"
 #include "ra.h"
 #include "hui.h"
 
 /* hgEncodeVocab - A CGI script to display the different types of encode controlled vocabulary.
  * usage:
  *   hgEncodeVocab [ra=cv.ra] type=[Antibody|"Cell Line"|localization|rnaExtract|"Gene Type"] [tier=(1|2|3)]
  * options:\n"
  *    ra=cv.ra       : Path to cv.ra file (default cv_file())
  *    type=TypeName  : Type to display
  *    tier=N         : If type="Cell Line" then this is the tier to display
  *    bgcolor=RRGGBB : Change background color (hex digits)
+ *    organism=Human|Mouse : If type="Cell Line", then set 'Mouse' to override default Human
+ *    term=a         : Display row for a single term
+ *    TODO: terms=a,b,c    : Display rows for listed terms.  Must use with 'type'.
+ *    tag=a          : Display row for a single term, using tag as identifier
+ *    TODO:  tags=a,b,c    : Display rows for listed terms, using tags as identifiers.  Must use with 'type'.
  */
 
-//#define HANDLE_IMPLICIT_CONTROL
-
 static char const rcsid[] = "$Id$";
 
+//options that apply to all vocab types
+
+static char *termOpt = NULL;
+static char *tagOpt = NULL;
+static char *typeOpt = NULL;
+static char *organismOpt = "Human"; // default, uses naming convention from dbDb table
+
 static char *cv_file()
 {
 /* return default location of cv.ra (can specify as cgi var: ra=cv.ra) */
 
 static char filePath[PATH_LEN];
 safef(filePath, sizeof(filePath), "%s/encode/cv.ra", hCgiRoot());
 if(!fileExists(filePath))
     errAbort("Error: can't locate cv.ra; %s doesn't exist\n", filePath);
 return filePath;
 }
 
 
 int termCmp(const void *va, const void *vb)
 /* Compare controlled vocab based on term value */
 {
 const struct hash *a = *((struct hash **)va);
 const struct hash *b = *((struct hash **)vb);
 char *termA = hashMustFindVal((struct hash *)a, "term");
 char *termB = hashMustFindVal((struct hash *)b, "term");
 return (strcasecmp(termA, termB));
 }
 
 void doTypeHeader(char *type)
 {
 if (sameString(type,"Antibody"))
     {
     puts("  <TH>Term</TH><TH>Target Description</TH><TH>Antibody Description</TH><TH>Vendor ID</TH><TH>Lab</TH><TH>Lots</TH><TH>Target Link</TH>");
     }
 else if (sameString(type,"ripAntibody"))
     {
     puts("  <TH>Term</TH><TH>Antibody Description</TH><TH>Target Description</TH><TH>Vendor ID</TH>");
     }
 else if (sameString(type,"ripTgtProtein"))
     {
     puts("  <TH>Term</TH><TH>Alternative Symbols</TH><TH>Description</TH>");
     }
 else if (sameString(type,"localization"))
     {
     puts("  <TH>Term</TH><TH>Description</TH><TH>GO ID</TH>");
     }
 else if (sameString(type,"Cell Line"))
     {
     puts("  <TH>Term</TH><TH>Tier</TH><TH>Description</TH><TH>Lineage</TH><TH>Karyotype</TH><TH>Documents</TH><TH>Vendor ID</TH><TH>Term ID</TH>");
     }
-#ifdef HANDLE_IMPLICIT_CONTROL
-else if (sameWord(type,"control") || sameWord(type,"input"))
-    {
-    puts("  <TH>Term</TH><TH>Description</TH></TR><TR>");
-    printf("  <Td>%s</Td><Td>This data represents a control being compared with the other tracks in the set.</Td>\n",type);
-    }
-#endif//def HANDLE_IMPLICIT_CONTROL
 else
     puts("  <TH>Term</TH><TH>Description</TH>");
 }
 
 void doTypeRow(struct hash *ra, char *type, int *total)
 {
-char *s, *u;
+char *term;
+char *s, *t, *u;
 
-// Skip all rows that do not match term
-char *term = cgiOptionalString("term");
-if(term)
+// Skip all rows that do not match term or tag if specified
+char *optVal = termOpt;
+char *optType = "term";
+if (tagOpt)
     {
-    (void)stripChar(term,'\"');
-    if(differentWord(term,hashMustFindVal(ra,"term")))
+    optVal = tagOpt;
+    optType = "tag";
+    }
+if (optVal)
+    {
+    (void)stripChar(optVal,'\"');
+    if (differentWord(optVal, hashMustFindVal(ra, optType)))
         return;
     }
-else
-    term = hashMustFindVal(ra,"term");
-
+term = (char *)hashMustFindVal(ra, "term");
 if (sameString(type,"Antibody"))
     {
     ++(*total);
     puts("<TR>");
     printf("  <TD>%s</TD>\n", term);
     s = hashFindVal(ra, "targetDescription");
     printf("  <TD>%s</TD>\n", s ? s : "&nbsp;");
     s = hashFindVal(ra, "antibodyDescription");
     printf("  <TD>%s</TD>\n", s ? s : "&nbsp;");
 
     s = hashFindVal(ra, "vendorName");
-    char *t = hashFindVal(ra, "vendorId");
-    char *u = hashFindVal(ra, "orderUrl");
+    t = hashFindVal(ra, "vendorId");
+    u = hashFindVal(ra, "orderUrl");
     printf("  <TD>");
     if (u)
         printf("<A TARGET=_BLANK HREF=%s>", u);
     printf("%s %s", s ? s : "&nbsp;", t ? t : "&nbsp;");
     if (u)
         printf("</A>");
     puts("</TD>");
 
     s = hashFindVal(ra, "lab");
     printf("  <TD>%s</TD>\n", s ? s : "&nbsp;");
 
     s = hashFindVal(ra, "lots");
     printf("  <TD>%s</TD>\n", s ? s : "&nbsp;");
 
     t = hashFindVal(ra, "targetId");
     u = hashFindVal(ra, "targetUrl");
     printf("  <TD>");
     if (u)
         printf("<A TARGET=_BLANK HREF=%s>", u);
     printf("%s", t ? t : "&nbsp;");
     if (u)
         printf("</A>");
     puts("</TD>");
 
     puts("</TR>");
     }
 else if (sameString(type,"ripAntibody"))
     {
     ++(*total);
     puts("<TR>");
     printf("  <TD>%s</TD>\n", term);
     s = hashFindVal(ra, "antibodyDescription");
     printf("  <TD>%s</TD>\n", s ? s : "&nbsp;");
     s = hashFindVal(ra, "targetDescription");
     printf("  <TD>%s</TD>\n", s ? s : "&nbsp;");
     s = hashFindVal(ra, "vendorName");
-    char *t = hashFindVal(ra, "vendorId");
-    char *u = hashFindVal(ra, "orderUrl");
+    t = hashFindVal(ra, "vendorId");
+    u = hashFindVal(ra, "orderUrl");
     printf("  <TD>");
     if (u)
         printf("<A TARGET=_BLANK HREF=%s>", u);
     printf("%s %s", s ? s : "&nbsp;", t ? t : "&nbsp;");
     if (u)
         printf("</A>");
     puts("</TD>");
 
     puts("</TR>");
     }
 else if (sameString(type,"ripTgtProtein"))
     {
     ++(*total);
     puts("<TR>");
     s = hashFindVal(ra, "url");
     if (s)
 	printf("  <TD><A TARGET=_BLANK HREF=\"%s\">%s</A></TD>\n", s, term);
     else
 	printf("  <TD>%s</TD>\n", term);
     s = hashFindVal(ra, "alternativeSymbols");
     printf("  <TD>%s</TD>\n", s ? s : "&nbsp;");
     s = hashFindVal(ra, "description");
     printf("  <TD>%s</TD>\n", s ? s : "&nbsp;");
     puts("</TR>");
     }
 else if (sameString(type,"localization"))
     {
     ++(*total);
     puts("<TR>");
     printf("  <TD>%s</TD>\n", term);
     s = hashMustFindVal(ra, "description");
     printf("  <TD>%s</TD>\n", s);
     s = hashFindVal(ra, "termId");
     u = hashFindVal(ra, "termUrl");
     printf("  <TD>");
     if (u)
         printf("<A TARGET=_BLANK HREF=%s>", u);
     printf("%s", s ? s : "&nbsp;");
     if (u)
         printf("</A>");
     puts("</TD>");
 
     puts("</TR>");
     }
 else if (sameString(type,"Cell Line"))
     {
     printf("<!-- Cell Line table: contains links to protocol file and vendor description page -->");
+    s = hashFindVal(ra, "organism");
+    if (s && differentString(s, organismOpt))
+        return;
     if (cgiOptionalInt("tier",0))
         {
         if (hashFindVal(ra,"tier") == NULL)
             return;
         if (atoi(hashFindVal(ra,"tier"))!=cgiOptionalInt("tier",0))
             return;
         }
     if (cgiOptionalString("tiers"))
         {
         if (hashFindVal(ra,"tier") == NULL)
             return;
         boolean found=FALSE;
         char *tiers=cloneString(cgiOptionalString("tiers"));
         char *tier;
         (void)strSwapChar(tiers,',',' ');
         while((tier=nextWord(&tiers)))
             {
             if (atoi(hashFindVal(ra,"tier"))==atoi(tier))
                 {
                 found=TRUE;
                 break;
                 }
             }
         if(!found)
             return;
         }
     ++(*total);
     puts("<TR>");
 
     printf("  <TD>%s</TD>\n", term);
 
     s = hashFindVal(ra, "tier");
     printf("  <TD>%s</TD>\n", s ? s : "&nbsp;" );
     s = hashFindVal(ra, "description");
     printf("  <TD>%s</TD>\n", s ? s : "&nbsp;" );
     s = hashFindVal(ra, "lineage");
     printf("  <TD>%s</TD>\n", s ? s : "&nbsp;" );
     s = hashFindVal(ra, "karyotype");
     printf("  <TD>%s</TD>\n", s ? s : "&nbsp;" );
 
 #define PROTOCOL_DIR "/ENCODE/protocols/cell/"
 #define PROTOCOL_TITLE "protocol"
     // add links to protocol doc if it exists
     printf("  <TD>");
     char protocolUrl[PATH_LEN];
     char protocolFile[PATH_LEN];
     // parse Protocol setting
     s = hashFindVal(ra,"protocol");
     if(s != NULL)
         {
         char *protocolSetting = cloneString(s);
         char *settings=protocolSetting;
         while((s = nextWord(&settings)) != NULL)
             {
             char *title = NULL;
             char *fileName = NULL;
             if(strchr(s,':')) // lab Specific setting
                 {
                 title = strSwapChar(s,':',0);
                 fileName = title + strlen(title) + 1;
                 }
             else
                 {
                 title = PROTOCOL_TITLE;
                 fileName = s;
                 }
             safef(protocolUrl, sizeof(protocolUrl), "%s%s", PROTOCOL_DIR, fileName);
             safef(protocolFile, sizeof(protocolFile), "%s%s", hDocumentRoot(), protocolUrl);
             if (fileExists(protocolFile))
                 printf(" <A TARGET=_BLANK HREF=%s>%s</A>\n", protocolUrl,title);
             }
         freeMem(protocolSetting);
         }
     else
         { // generate a standard name
         safef(protocolUrl, sizeof(protocolUrl), "%s%s_protocol.pdf", PROTOCOL_DIR, term);
         safef(protocolFile, sizeof(protocolFile), "%s%s", hDocumentRoot(), protocolUrl);
         if (fileExists(protocolFile))
             printf(" <A TARGET=_BLANK HREF=%s>%s</A>\n", protocolUrl,PROTOCOL_TITLE);
         }
     printf("  &nbsp;</TD>\n");
 
     s = hashFindVal(ra, "vendorName");
-    char *t = hashFindVal(ra, "vendorId");
-    char *u = hashFindVal(ra, "orderUrl");
+    t = hashFindVal(ra, "vendorId");
+    u = hashFindVal(ra, "orderUrl");
     printf("  <TD>");
     if (u)
         printf("<A TARGET=_BLANK HREF=%s>", u);
     printf("%s %s", s ? s : "&nbsp;", t ? t : "&nbsp;");
     if (u)
         printf("</A>");
     puts("</TD>");
 
     s = hashFindVal(ra, "termId");
     u = hashFindVal(ra, "termUrl");
     printf("  <TD>");
     if (u)
         printf("<A TARGET=_BLANK HREF=%s>", u);
     printf("%s", s ? s : "&nbsp;");
     if (u)
         printf("</A>");
     puts("</TD>");
     puts("</TR>");
     }
 else
     {
     s = hashFindVal(ra, "description");
     if(s != NULL)
         {
         ++(*total);
         puts("<TR>");
         printf("  <TD>%s</TD>\n", term);
         printf("  <TD>%s</TD>\n", s);
         puts("</TR>");
         }
     else
         {
         printf("<TR>\n  <TD>%s</TD>\n  <TD>Unrecognised term</TD>\n</TR>\n", term);
         errAbort("Error: Unrecognised type (%s)\n", type);
         }
     }
 }
 
 static char *normalizeType(char *type)
 /* Strips any quotation marks and converts common synonyms */
 {
 (void)stripChar(type,'\"');
 if ((sameWord(type,"Cell Line"))
 ||  (sameWord(type,"cellLine" ))
 ||  (sameWord(type,"Cell Type"))
 ||  (sameWord(type,"cellType" )))
     return cloneString("Cell Line");
 else if (sameWord(type,"Factor"))
     return cloneString("Antibody");
 
 return type;
 }
 
 static char *findType(struct hash *cvHash)
 /* returns the type that was requested or else the type associated with the term requested */
 {
 struct hashCookie hc = hashFirst(cvHash);
 struct hashEl *hEl;
 struct hash *ra;
-char *type = cgiOptionalString("type");
+char *type = typeOpt;
 
-if(type==NULL)    // If not type, but term, then search for first term and use it's type
+if (type == NULL)    // If not type, but term (or tag), then search for match and use its type
     {
-    char *term = cgiOptionalString("term");
-    if(term==NULL)
-        errAbort("Error: Required 'term' or 'type' argument not found\n");
-    (void)stripChar(term,'\"');
-#ifdef HANDLE_IMPLICIT_CONTROL
-    if(sameWord(term,"control") || sameWord(term,"input"))
+    char *optType = "tag";
+    char *optVal = tagOpt;
+    if (optVal == NULL)
         {
-        type = term;
+        optVal = termOpt;
+        if (optVal == NULL)
+            errAbort("Error: Required 'term', 'tag', or 'type' optument not found\n");
+        optType = "term";
         }
-    else
-#endif//def HANDLE_IMPLICIT_CONTROL
-        {
+    (void)stripChar(optVal,'\"');
         while ((hEl = hashNext(&hc)) != NULL)
             {
             ra = (struct hash *)hEl->val;
-            char *cmpTerm = hashFindVal(ra, "term");
-            if (cmpTerm == NULL || differentWord(cmpTerm, term))
-                continue;
-            type = hashFindVal(ra, "type");
+        char *val = hashMustFindVal(ra, optType);
+        if (sameWord(val, optVal))
+            {
+            type = hashMustFindVal(ra, "type");
             break;
             }
-        //hc = hashFirst(cvHash);
         }
     }
-if(type==NULL)    // Still not type? abort
-    errAbort("Error: Required 'type' or 'term' argument not found\n");
+if (type == NULL)    // Still not type? abort
+    errAbort("Error: Required 'type', 'tag', or 'term' argument not found\n");
 return normalizeType(type);
 }
 
 void doMiddle()
 {
 struct hash *cvHash = raReadAll(cgiUsualString("ra", cv_file()), "term");
 struct hashCookie hc = hashFirst(cvHash);
 struct hashEl *hEl;
 struct slList *termList = NULL;
 struct hash *ra;
 char *type;
 int total = 0;
 
 puts("<TABLE BORDER=1 BGCOLOR=#FFFEE8 CELLSPACING=0 CELLPADDING=2>");
 puts("<TR style=\"background:#D9E4F8\">");
 type = findType(cvHash);
 doTypeHeader(type);
 puts("</TR>");
-
-#ifdef HANDLE_IMPLICIT_CONTROL
-if(differentWord(type,"control") && differentWord(type,"input"))
-#endif//def HANDLE_IMPLICIT_CONTROL
-    {
-    while ((hEl = hashNext(&hc)) != NULL)
+while ((hEl = hashNext(&hc)) != NULL)
         {
         ra = (struct hash *)hEl->val;
         if (differentString(hashMustFindVal(ra, "type"), type))
             continue;
         slAddTail(&termList, ra);
         }
-    slSort(&termList, termCmp);
-    while((ra = slPopHead(&termList)) != NULL)
+slSort(&termList, termCmp);
+while((ra = slPopHead(&termList)) != NULL)
         {
         // TODO: Add check for unknown tags in cv.ra
         doTypeRow(ra, type, &total);
         }
-    }
 puts("</TABLE><BR>");
 if(total > 1)
     printf("Total = %d\n", total);
 }
 
 int main(int argc, char *argv[])
 /* Process command line */
 {
 cgiSpoof(&argc, argv);
+termOpt = cgiOptionalString("term");
+tagOpt = cgiOptionalString("tag");
+typeOpt = cgiOptionalString("type");
+organismOpt = cgiUsualString("organism", organismOpt);
 char *bgColor = cgiOptionalString("bgcolor");
 if (bgColor)
     htmlSetBgColor(strtol(bgColor, 0, 16));
 htmlSetStyle(htmlStyleUndecoratedLink);
 htmShell("ENCODE Controlled Vocabulary", doMiddle, "get");
 return 0;
 }
 

