7544fd2a03bf573a9a12195d86a2fc082a88de78
tdreszer
  Tue Apr 5 15:17:56 2011 -0700
Tightened the screws on searching by mdb vars where the search is either for files or tables
diff --git src/hg/lib/cv.c src/hg/lib/cv.c
index f4c8cba..e0273fc 100644
--- src/hg/lib/cv.c
+++ src/hg/lib/cv.c
@@ -1,260 +1,203 @@
 
 
 // cv.c stands for Controlled Vocabullary and this file contains the
 // library APIs for reading and making sense of the contents of cv.ra.
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "ra.h"
 #include "hui.h"
 #include "mdb.h"
 
 // CV Defines that should not necessarily be public
 
 // CV UGLY TERMS (NOTE: These should be hiddne inside cv.c APIS and callers should use non-UGLY terms)
 #define CV_UGLY_TOT_CELLTYPE    "cellType"
 #define CV_UGLY_TERM_CELL_LINE  "Cell Line"
 #define CV_UGLY_TERM_ANTIBODY   "Antibody"
 
 // Type of Terms searchable defines
 #define CV_SEARCHABLE               "searchable"
 #define CV_SEARCHABLE_SINGLE_SELECT "select"
 #define CV_SEARCHABLE_MULTI_SELECT  "multiSelect"
 #define CV_SEARCHABLE_FREE_TEXT     "freeText"
 
 char *cvTypeNormalized(char *sloppyTerm)
 // returns (on stack) the proper term to use when requesting a typeOfTerm
 {
 if (sameWord(sloppyTerm,CV_TERM_CELL) || sameWord(sloppyTerm,CV_UGLY_TERM_CELL_LINE))
     return CV_UGLY_TOT_CELLTYPE;
 if (sameWord(sloppyTerm,CV_TERM_ANTIBODY))
     return CV_UGLY_TERM_ANTIBODY;
 
 return sloppyTerm;
 }
 
 char *cvTermNormalized(char *sloppyTerm)
 // returns (on stack) the proper term to use when requesting a cvTerm hash
 {
 if (sameWord(sloppyTerm,CV_UGLY_TOT_CELLTYPE) || sameWord(sloppyTerm,CV_UGLY_TERM_CELL_LINE))
     return CV_TERM_CELL;
 if (sameWord(sloppyTerm,CV_UGLY_TERM_ANTIBODY))
     return CV_TERM_ANTIBODY;
 
 return sloppyTerm;
 }
 
 // TODO: decide to make this public or hide it away inside the one function so far that uses it.
 static char *cv_file()
 // return default location of cv.ra
 {
 static char filePath[PATH_LEN];
 char *root = hCgiRoot();
 if (root == NULL || *root == 0)
     root = "/usr/local/apache/cgi-bin/"; // Make this check out sandboxes?
 //    root = "/cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/cv/alpha/"; // Make this check out sandboxes?
 safef(filePath, sizeof(filePath), "%s/encode/%s", root,CV_FILE_NAME);
 if(!fileExists(filePath))
     errAbort("Error: can't locate %s; %s doesn't exist\n", CV_FILE_NAME, filePath);
 return filePath;
 }
 
 const struct hash *cvTermHash(char *term)
 // returns a hash of hashes of a term which should be defined in cv.ra
 // NOTE: in static memory: DO NOT FREE
 {
 static struct hash *cvHashOfHashOfHashes = NULL;
 if (sameString(term,CV_TERM_CELL))
     term = CV_UGLY_TERM_CELL_LINE;
 else if (sameString(term,CV_TERM_ANTIBODY))
     term = CV_UGLY_TERM_ANTIBODY;
 
 if (cvHashOfHashOfHashes == NULL)
     cvHashOfHashOfHashes = hashNew(0);
 
 struct hash *cvHashForTerm = hashFindVal(cvHashOfHashOfHashes,term);
 // Establish cv hash of Term Types if it doesn't already exist
 if (cvHashForTerm == NULL)
     {
     cvHashForTerm = raReadWithFilter(cv_file(), CV_TERM,CV_TYPE,term);
     if (cvHashForTerm != NULL)
         hashAdd(cvHashOfHashOfHashes,term,cvHashForTerm);
     }
 
 return cvHashForTerm;
 }
 
-struct slPair *mdbValLabelSearch(struct sqlConnection *conn, char *var, int limit, boolean tags, boolean tables, boolean files)
-// Search the metaDb table for vals by var and returns val (as pair->name) and controlled vocabulary (cv) label
-// (if it exists) (as pair->val).  Can impose (non-zero) limit on returned string size of name.
-// if requested, return cv tag instead of mdb val.  If requested, limit to table objs or file objs
-// Return is case insensitive sorted on label (cv label or else val).
-{  // TODO: Change this to use normal mdb struct routines?
-if (!tables && !files)
-    errAbort("mdbValSearch requests values for neither table nor file objects.\n");
-
-char *tableName = mdbTableName(conn,TRUE); // Look for sandBox name first
-
-struct dyString *dyQuery = dyStringNew(512);
-if (limit > 0)
-    dyStringPrintf(dyQuery,"select distinct LEFT(val,%d)",limit);
-else
-    dyStringPrintf(dyQuery,"select distinct val");
-
-dyStringPrintf(dyQuery," from %s l1 where l1.var='%s' ",tableName,var);
-
-if (!tables || !files)
-    dyStringPrintf(dyQuery,"and exists (select l2.obj from %s l2 where l2.obj = l1.obj and l2.var='objType' and l2.val='%s')",
-                   tableName,tables?MDB_OBJ_TYPE_TABLE:MDB_OBJ_TYPE_FILE);
-
-struct hash *varHash = (struct hash *)cvTermHash(var);
-
-struct slPair *pairs = NULL;
-struct sqlResult *sr = sqlGetResult(conn, dyStringContents(dyQuery));
-dyStringFree(&dyQuery);
-char **row;
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    char *val = row[0];
-    char *label = NULL;
-    if (varHash != NULL)
-        {
-        struct hash *valHash = hashFindVal(varHash,val);
-        if (valHash != NULL)
-            {
-            label = cloneString(hashOptionalVal(valHash,CV_LABEL,row[0]));
-            if (tags)
-                {
-                char *tag = hashFindVal(valHash,CV_TAG);
-                if (tag != NULL)
-                    val = tag;
-                }
-            }
-        }
-    if (label == NULL);
-        label = cloneString(row[0]);
-    label = strSwapChar(label,'_',' ');  // vestigial _ meaning space
-    slPairAdd(&pairs,val,label);
-    }
-sqlFreeResult(&sr);
-slPairValSortCase(&pairs);
-return pairs;
-}
-
 const struct hash *cvTermTypeHash()
 // returns a hash of hashes of mdb and controlled vocabulary (cv) term types
 // Those terms should contain label,description,searchable,cvDefined,hidden
 // NOTE: in static memory: DO NOT FREE
 { // NOTE: "typeOfTerm" is specialized, so don't use cvTermHash
 static struct hash *cvHashOfTermTypes = NULL;
 
 // Establish cv hash of Term Types if it doesn't already exist
 if (cvHashOfTermTypes == NULL)
     {
     cvHashOfTermTypes = raReadWithFilter(cv_file(), CV_TERM,CV_TYPE,CV_TOT);
     // Patch up an ugly inconsistency with 'cell'
     struct hash *cellHash = hashRemove(cvHashOfTermTypes,CV_UGLY_TOT_CELLTYPE);
     if (cellHash)
         {
         hashAdd(cvHashOfTermTypes,CV_TERM_CELL,cellHash);
         hashReplace(cellHash, CV_TERM, cloneString(CV_TERM_CELL)); // spilling memory of 'cellType' val
         }
     struct hash *abHash = hashRemove(cvHashOfTermTypes,CV_UGLY_TERM_ANTIBODY);
     if (abHash)
         {
         hashAdd(cvHashOfTermTypes,CV_TERM_ANTIBODY,abHash);
         hashReplace(abHash, CV_TERM, cloneString(CV_TERM_ANTIBODY)); // spilling memory of 'Antibody' val
         }
     }
 
 return cvHashOfTermTypes;
 }
 
 struct slPair *cvWhiteList(boolean searchTracks, boolean cvDefined)
 // returns the official mdb/controlled vocabulary terms that have been whitelisted for certain uses.
 // TODO: change to return struct that includes searchable!
 {
 struct slPair *whitePairs = NULL;
 
 // Get the list of term types from thew cv
 struct hash *termTypeHash = (struct hash *)cvTermTypeHash();
 struct hashCookie hc = hashFirst(termTypeHash);
 struct hashEl *hEl;
 while ((hEl = hashNext(&hc)) != NULL)
     {
     char *setting = NULL;
     struct hash *typeHash = (struct hash *)hEl->val;
     //if (!includeHidden)
         {
         setting = hashFindVal(typeHash,CV_TOT_HIDDEN);
         if(SETTING_IS_ON(setting))
             continue;
         }
     if (searchTracks)
         {
         setting = hashFindVal(typeHash,CV_SEARCHABLE);
         if (setting == NULL
         || (   differentWord(setting,CV_SEARCHABLE_SINGLE_SELECT)
             && differentWord(setting,CV_SEARCHABLE_MULTI_SELECT)
             && differentWord(setting,CV_SEARCHABLE_FREE_TEXT)))
            continue;
         }
     if (cvDefined)
         {
         setting = hashFindVal(typeHash,CV_TOT_CV_DEFINED);
         if(SETTING_NOT_ON(setting))
             continue;
         }
     char *term  = hEl->name;
     char *label = hashFindVal(typeHash,CV_LABEL);
     if (label == NULL)
         label = term;
     slPairAdd(&whitePairs, term, cloneString(label)); // Term gets cloned in slPairAdd
     }
 if (whitePairs != NULL)
     slPairValSortCase(&whitePairs);
 
 return whitePairs;
 }
 
 enum cvSearchable cvSearchMethod(char *term)
 // returns whether the term is searchable
 {
 // Get the list of term types from thew cv
 struct hash *termTypeHash = (struct hash *)cvTermTypeHash();
 struct hash *termHash = hashFindVal(termTypeHash,term);
 if (termHash != NULL)
     {
     char *searchable = hashFindVal(termHash,CV_SEARCHABLE);
     if (searchable != NULL)
         {
         if (sameWord(searchable,CV_SEARCHABLE_SINGLE_SELECT))
             return cvSearchBySingleSelect;
         if (sameWord(searchable,CV_SEARCHABLE_MULTI_SELECT))
             return cvSearchByMultiSelect;
         if (sameWord(searchable,CV_SEARCHABLE_FREE_TEXT))
             return cvSearchByFreeText;
         if (sameWord(searchable,"date"))
             return cvSearchByDateRange;
         if (sameWord(searchable,"numeric"))
             return cvSearchByIntegerRange;
         }
     }
 return cvNotSearchable;
 }
 
 const char *cvLabel(char *term)
 // returns cv label if term found or else just term
 {
 // Get the list of term types from thew cv
 struct hash *termTypeHash = (struct hash *)cvTermTypeHash();
 struct hash *termHash = hashFindVal(termTypeHash,term);
 if (termHash != NULL)
     {
     char *label = hashFindVal(termHash,CV_LABEL);
     if (label != NULL)
         return label;
     }
 return term;
 }