744a3b2e1774459ae0348822c983a24746776f96
jcasper
  Fri Feb 16 12:26:31 2018 -0800
Hub text search now includes metadata tags, behaves better when encountering missing tracks/assemblies, and includes a MySQL index on the track field of hubSearchText refs #20761, #18865, #20694

diff --git src/hg/lib/hubSearchText.c src/hg/lib/hubSearchText.c
index 0a3575a..2ad3045 100644
--- src/hg/lib/hubSearchText.c
+++ src/hg/lib/hubSearchText.c
@@ -1,236 +1,236 @@
 /* hubSearchText.c was originally generated by the autoSql program, which also 
  * generated hubSearchText.h and hubSearchText.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "rangeTree.h"
 #include "hubSearchText.h"
 
 
 
 char *hubSearchTextCommaSepFieldNames = "hubUrl,db,track,textLength,text";
 
 /* definitions for textLength column */
-static char *values_textLength[] = {"Short", "Long", NULL};
+static char *values_textLength[] = {"Short", "Long", "Meta", NULL};
 static struct hash *valhash_textLength = NULL;
 
 void hubSearchTextStaticLoadWithNull(char **row, struct hubSearchText *ret)
 /* Load a row from hubSearchText table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->hubUrl = row[0];
 ret->db = row[1];
 ret->track = row[2];
 ret->label = row[3];
 ret->textLength = sqlEnumParse(row[4], values_textLength, &valhash_textLength);
 ret->text = row[5];
 }
 
 struct hubSearchText *hubSearchTextLoadWithNull(char **row)
 /* Load a hubSearchText from row fetched with select * from hubSearchText
  * from database.  Dispose of this with hubSearchTextFree(). */
 {
 struct hubSearchText *ret;
 
 AllocVar(ret);
 ret->hubUrl = cloneString(row[0]);
 ret->db = cloneString(row[1]);
 ret->track = cloneString(row[2]);
 ret->label = cloneString(row[3]);
 ret->textLength = sqlEnumParse(row[4], values_textLength, &valhash_textLength);
 ret->text = cloneString(row[5]);
 return ret;
 }
 
 struct hubSearchText *hubSearchTextLoadAll(char *fileName) 
 /* Load all hubSearchText from a whitespace-separated file.
  * Dispose of this with hubSearchTextFreeList(). */
 {
 struct hubSearchText *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[6];
 
 while (lineFileRow(lf, row))
     {
     el = hubSearchTextLoadWithNull(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hubSearchText *hubSearchTextLoadAllByChar(char *fileName, char chopper) 
 /* Load all hubSearchText from a chopper separated file.
  * Dispose of this with hubSearchTextFreeList(). */
 {
 struct hubSearchText *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[6];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = hubSearchTextLoadWithNull(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hubSearchText *hubSearchTextCommaIn(char **pS, struct hubSearchText *ret)
 /* Create a hubSearchText out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new hubSearchText */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->hubUrl = sqlStringComma(&s);
 ret->db = sqlStringComma(&s);
 ret->track = sqlStringComma(&s);
 ret->label = sqlStringComma(&s);
 ret->textLength = sqlEnumComma(&s, values_textLength, &valhash_textLength);
 ret->text = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void hubSearchTextFree(struct hubSearchText **pEl)
 /* Free a single dynamically allocated hubSearchText such as created
  * with hubSearchTextLoad(). */
 {
 struct hubSearchText *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->hubUrl);
 freeMem(el->db);
 freeMem(el->track);
 freeMem(el->label);
 freeMem(el->text);
 freez(pEl);
 }
 
 void hubSearchTextFreeList(struct hubSearchText **pList)
 /* Free a list of dynamically allocated hubSearchText's */
 {
 struct hubSearchText *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     hubSearchTextFree(&el);
     }
 *pList = NULL;
 }
 
 void hubSearchTextOutput(struct hubSearchText *el, FILE *f, char sep, char lastSep) 
 /* Print out hubSearchText.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->hubUrl);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->db);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->track);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->label);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 sqlEnumPrint(f, el->textLength, values_textLength);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->text);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 /* Restrictions on the size of context chunks returned by getTextContext() */
 #define HST_MAXCONTEXTLENGTH 300
 #define HST_CONTEXTRADIUS 70
 
 static char *getTextContext(char *text, char *searchTerms)
 /* Look for instances of words from searchTerms in the supplied text, grab some surrounding
  * context, and stitch them together into a string that combines overlapping regions. */
 {
 struct dyString *contextString = dyStringNew(0);
 struct rbTree *contextTree = rangeTreeNew();
 char *splitTerms[1024];
 char *cloneTerms = cloneString(searchTerms);
 if (isNotEmpty(cloneTerms))
     strLower(cloneTerms);
 char *lowText = cloneString(text);
 if (isNotEmpty(lowText))
     strLower(lowText);
 int termCount = chopByWhiteRespectDoubleQuotes(cloneTerms, splitTerms, 1024);
 int i;
 for (i=0; i<termCount; i++)
     {
     char *thisTerm = splitTerms[i];
     if (thisTerm[0] == '"')
         {
         thisTerm++;
         trimLastChar(thisTerm);
         }
     char *position = stringIn(thisTerm, lowText);
     if (position == NULL)
         continue;
     int termStart = position - HST_CONTEXTRADIUS - lowText;
     if (termStart < 0)
         termStart = 0;
     int termEnd = position + strlen(thisTerm) + HST_CONTEXTRADIUS - lowText;
     if (termEnd > strlen(lowText))
         termEnd = strlen(lowText);
     rangeTreeAdd(contextTree, termStart, termEnd);
     }
 struct range *rangeResult = rangeTreeList(contextTree);
 int cumulativeSize = 0;
 if (rangeResult != NULL)
     dyStringPrintf(contextString, "...");
 while (rangeResult != NULL)
     {
     char contextChunk[HST_MAXCONTEXTLENGTH+1];
     int copySize = rangeResult->end - rangeResult->start;
     if (copySize > HST_MAXCONTEXTLENGTH)
         copySize = HST_MAXCONTEXTLENGTH;
     safencpy(contextChunk, sizeof(contextChunk), text+rangeResult->start, copySize);
     dyStringPrintf(contextString, " %s ...", contextChunk);
     cumulativeSize += copySize;
     if (cumulativeSize >= HST_MAXCONTEXTLENGTH)
         break;
     rangeResult = rangeResult->next;
     }
 return dyStringCannibalize(&contextString);
 }
 
 
 struct hubSearchText *hubSearchTextLoadWithNullGiveContext(char **row, char *searchTerms)
 /* Load a hubSearchText from row fetched with select * from hubSearchText
  * from database, but instead of loading the entire text field for long text results,
  * only load the pieces that provide context for the supplied searchTerms.
  * Dispose of this with hubSearchTextFree(). */
 {
 struct hubSearchText *hst = hubSearchTextLoadWithNull(row);
 if (hst->textLength == hubSearchTextLong)
     {
     char *longTextContext = getTextContext(hst->text, searchTerms);
     freeMem(hst->text);
     hst->text = longTextContext;
     }
 return hst;
 }