a019cec925f0e902a6eb2ddeb781dd549c7e9406
chmalee
  Fri Mar 5 15:54:25 2021 -0800
Add public track hub results to track search, refs #26179

diff --git src/hg/lib/hubSearchText.c src/hg/lib/hubSearchText.c
index c7b92d8..5442219 100644
--- src/hg/lib/hubSearchText.c
+++ src/hg/lib/hubSearchText.c
@@ -1,253 +1,397 @@
 /* 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"
-
+#include "hubPublic.h"
+#include "hgConfig.h"
 
 
 char *hubSearchTextCommaSepFieldNames = "hubUrl,db,track,label,textLength,text,parents,parentTypes";
 
 /* definitions for textLength column */
 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];
 ret->parents = row[6];
 ret->parentTypes = row[7];
 }
 
 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]);
 ret->parents = cloneString(row[6]);
 ret->parentTypes = cloneString(row[7]);
 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[8];
 
 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[8];
 
 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);
 ret->parents = sqlStringComma(&s);
 ret->parentTypes = 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);
 freeMem(el->parents);
 freeMem(el->parentTypes);
 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(sep, f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->parents);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->parentTypes);
 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;
 }
+
+char *modifyTermsForHubSearch(char *hubSearchTerms, bool isStrictSearch)
+/* This won't exactly be pretty.  MySQL treats any sequence of alphanumerics and underscores
+ * as a word, and single apostrophes are allowed as long as they don't come back-to-back.
+ * Cut down to those characters, then add initial + (for requiring word) and * (for word
+ * expansion) as appropriate. */
+{
+char *cloneTerms = cloneString(hubSearchTerms);
+struct dyString *modifiedTerms = dyStringNew(0);
+if (isNotEmpty(cloneTerms))
+    {
+    int i;
+    for (i=0; i<strlen(cloneTerms); i++)
+        {
+        // allowed punctuation is underscore and apostrophe, and we'll do special handling for hyphen
+        if (!isalnum(cloneTerms[i]) && cloneTerms[i] != '_' && cloneTerms[i] != '\'' &&
+                cloneTerms[i] != '-')
+            cloneTerms[i] = ' ';
+        }
+    char *splitTerms[1024];
+    int termCount = chopByWhite(cloneTerms, splitTerms, sizeof(splitTerms));
+    for (i=0; i<termCount; i++)
+        {
+        char *hyphenatedTerms[1024];
+        int hyphenTerms = chopString(splitTerms[i], "-", hyphenatedTerms, sizeof(hyphenatedTerms));
+        int j;
+        for (j=0; j<hyphenTerms-1; j++)
+            {
+            dyStringPrintf(modifiedTerms, "+%s ", hyphenatedTerms[j]);
+            }
+        if (isStrictSearch)
+            dyStringPrintf(modifiedTerms, "+%s ", hyphenatedTerms[j]);
+        else
+            {
+            dyStringPrintf(modifiedTerms, "+%s* ", hyphenatedTerms[j]);
+            }
+        }
+    }
+return dyStringCannibalize(&modifiedTerms);
+}
+
+void getHubSearchResults(struct sqlConnection *conn, char *hubSearchTableName,
+        char *hubSearchTerms, bool checkLongText, char *dbFilter, struct hash *hubLookup,
+        struct hash **searchResultHashRet, struct slName **hubsToPrintRet, char *extra)
+/* Find hubs, genomes, and tracks that match the provided search terms.
+ * Return all hits that satisfy the (optional) supplied assembly filter.
+ * if checkLongText is FALSE, skip searching within the long description text entries */
+{
+char *cleanSearchTerms = cloneString(hubSearchTerms);
+if (isNotEmpty(cleanSearchTerms))
+    tolowers(cleanSearchTerms);
+bool isStrictSearch = FALSE;
+char *modifiedSearchTerms = modifyTermsForHubSearch(cleanSearchTerms, isStrictSearch);
+struct hubSearchText *hubSearchResultsList = NULL;
+struct dyString *query = dyStringNew(100);
+char *noLongText = NULL;
+
+if (!checkLongText)
+    noLongText = cloneString("textLength = 'Short' and");
+else
+    noLongText = cloneString("");
+
+sqlDyStringPrintf(query, "select * from %s where ", hubSearchTableName);
+// sqlDyStringPrintf complains about spaces in %s strings and
+// extra has already been escaped so add it on here
+dyStringPrintf(query, "%s %s", noLongText, extra);
+if (isNotEmpty(modifiedSearchTerms))
+    {
+    if (isNotEmpty(extra))
+        {
+        sqlDyStringPrintf(query, " and ");
+        }
+    sqlDyStringPrintf(query, "match(text) against ('%s' in boolean mode)"
+        " order by match(text) against ('%s' in boolean mode)",
+        modifiedSearchTerms, modifiedSearchTerms);
+    }
+
+struct sqlResult *sr = sqlGetResult(conn, dyStringContents(query));
+char **row;
+while ((row = sqlNextRow(sr)) != NULL)
+    {
+    struct hubSearchText *hst = hubSearchTextLoadWithNullGiveContext(row, cleanSearchTerms);
+    // Skip rows where the long text matched the more lax MySQL search (punctuation just
+    // splits terms into two words, so "rna-seq" finds "rna" and "seq" separately, but
+    // not the more strict rules used to find context for the search terms.
+    if ((hst->textLength == hubSearchTextLong) && isEmpty(hst->text))
+        continue;
+    char *hubUrl = hst->hubUrl;
+    struct hubEntry *hubInfo = hashFindVal(hubLookup, hubUrl);
+    if (hubInfo == NULL)
+        continue; // Search table evidently includes a hub that's not on this server.  Skip it.
+    char *db = cloneString(hst->db);
+    tolowers(db);
+    if (isNotEmpty(dbFilter))
+        {
+        if (isNotEmpty(db))
+            {
+            if (stringIn(dbFilter, db) == NULL)
+                continue;
+            }
+        else
+            {
+            // no db in the hubSearchText means this is a top-level hub hit.
+            // filter by the db list associated with the hub instead
+            char *dbList = cloneString(hubInfo->dbList);
+            tolowers(dbList);
+            if (stringIn(dbFilter, dbList) == NULL)
+                continue;
+            }
+        }
+    // Add hst to the list to be returned
+    slAddHead(&hubSearchResultsList, hst);
+    }
+slReverse(&hubSearchResultsList);
+struct slName *hubsToPrint = NULL;
+struct hash *searchResultHash = hashNew(0);
+struct hubSearchText *hst = hubSearchResultsList;
+while (hst != NULL)
+    {
+    struct hubSearchText *nextHst = hst->next;
+    hst->next = NULL;
+    struct hashEl *hubHashEnt = hashLookup(searchResultHash, hst->hubUrl);
+    if (hubHashEnt == NULL)
+        {
+        slNameAddHead(&hubsToPrint, hst->hubUrl);
+        hashAdd(searchResultHash, hst->hubUrl, hst);
+        }
+    else
+        slAddHead(&(hubHashEnt->val), hst);
+    hst = nextHst;
+    }
+struct hashEl *hel;
+struct hashCookie cookie = hashFirst(searchResultHash);
+while ((hel = hashNext(&cookie)) != NULL)
+    slReverse(&(hel->val));
+*searchResultHashRet = searchResultHash;
+*hubsToPrintRet = hubsToPrint;
+}
+
+char *hubSearchTextTableName()
+{
+return cfgOptionDefault("hubSearchTextTable", "hubSearchText");
+}