748b06ac95ff2a3957be3845bd3594984e3cc3cf
chmalee
  Wed Aug 17 19:21:48 2022 -0700
Rename test cgi to official name. Always search everything, only show
categories that have matches in the result list. Add /search endpoint to
hubApi, add code to search help docs in hgSuggest but don't call it yet
in autoComplete.js. Minor fixups so search result links work correctly.

Fixing up old programs that call hgPositionsFind

diff --git src/hg/qa/testSearch.c src/hg/qa/testSearch.c
index 48df809..7688b85 100644
--- src/hg/qa/testSearch.c
+++ src/hg/qa/testSearch.c
@@ -1,297 +1,297 @@
 /* testSearch - test the search functionality */
 
 /* Copyright (C) 2011 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 #include "common.h"
 #include "cart.h"
 #include "cheapcgi.h"
 #include "hgFind.h"
 #include "hdb.h"
 #include "hui.h"
 
 
 /* Need to get a cart in order to use hgFind. */
 struct cart *cart = NULL;
 char *excludeVars[] = { NULL };
 
 struct searchTestCase 
     {
     struct searchTestCase *next;
     char *searchTerm;
     char *database;
     int posCount;
     struct searchResults *results;
     };
 
 struct searchResults
     {
     struct searchResults *next;
     char *tableName;
     char *chrom;
     int start;
     int end;
     char *browserName;
     };
 
 
 void usage()
 {
 errAbort("testSearch - test search functionality.\n"
     "usage:\n"
     "  testSearch inputFile\n");
 }
 
 struct searchTestCase *readInput(char *fileName)
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *line;
 char *headerLine[3];
 char *resultLine[5];
 struct searchTestCase *testCase;
 struct searchTestCase *testCaseList = NULL;
 struct searchResults *result;
 struct searchResults *resultList;
 int elementCount;
 int matchCount;
 int pos = 0;
 
 while (lineFileNext(lf, &line, NULL))
     {
     elementCount = chopString(line, " ", headerLine, ArraySize(headerLine));
     if (elementCount != 3)
         {
 	fprintf(stderr, "Error: formatting problem, exitting\n");
 	return NULL;
 	}
     resultList = NULL;
     matchCount = sqlUnsigned(headerLine[2]);
     for (pos = 0; pos < matchCount; pos++)
         {
 	lineFileNext(lf, &line, NULL);
 	elementCount = chopString(line, " ", resultLine, ArraySize(resultLine));
 	if (elementCount != 5)
 	    {
 	    fprintf(stderr, "Error: formatting problem, exitting\n");
 	    return NULL;
 	    }
 	AllocVar(result);
         result->tableName = cloneString(resultLine[0]);
         result->chrom = cloneString(resultLine[1]);
 	result->start = sqlUnsigned(resultLine[2]);
 	result->end = sqlUnsigned(resultLine[3]);
         result->browserName = cloneString(resultLine[4]);
         slAddHead(&resultList, result);
 	}
     AllocVar(testCase);
     testCase->searchTerm = headerLine[0];
     testCase->database = headerLine[1];
     testCase->posCount = matchCount;
     testCase->results = resultList;
     slAddHead(&testCaseList, testCase);
     }
 return testCaseList;
 }
 
 struct searchTestCase *morph(char *database, char *searchTerm, struct hgPositions *hgpList)
 /* convert an hgpList into a searchTestCase */
 {
 struct hgPositions *hgp = NULL;
 struct hgPosTable *table = NULL;
 struct hgPos *pos = NULL;
 struct searchTestCase *testCase = NULL;
 struct searchResults *result = NULL;
 struct searchResults *resultList = NULL;
 int count = 0;
 
 AllocVar(testCase);
 testCase->database = cloneString(database);
 testCase->searchTerm = cloneString(searchTerm);
 
 for (hgp = hgpList; hgp != NULL; hgp = hgp->next)
     {
     if (hgp->tableList != NULL)
         {
         for (table = hgp->tableList; table != NULL; table = table->next)
             {
 	    if (table->posList != NULL)
 	        {
 	        for (pos = table->posList; pos != NULL; pos = pos->next)
 	            {
 		    count++;
 		    AllocVar(result);
 		    result->tableName = cloneString(table->name);
 		    result->chrom = cloneString(pos->chrom);
 		    result->start = pos->chromStart;
 		    result->end = pos->chromEnd;
 		    result->browserName = cloneString(pos->browserName);
 		    slAddHead(&resultList, result);
 		    }
 	        }
 	    }
 	}
     }
 testCase->posCount = count;
 testCase->results = resultList;
 return testCase;
 }
 
 
 void compareResults(struct searchTestCase *expected, struct searchTestCase *actual)
 /* don't assume the results are in the same order */
 /* for each excepted, just do a linear read of the actual list */
 /* all of these lists should be small enough so performance isn't an issue */
 {
 struct searchResults *result1, *result2;
 
 if (differentString(expected->searchTerm, actual->searchTerm))
     {
     fprintf(stderr, "Error: mismatched search terms: expected = %s, actual = %s\n", 
             expected->searchTerm, actual->searchTerm);
     return;
     }
 if (differentString(expected->database, actual->database))
     {
     fprintf(stderr, "Error: mismatched databases: expected = %s, actual = %s\n", expected->database, actual->database);
     return;
     }
 if (expected->posCount != actual->posCount)
     {
     fprintf(stderr, "Error: mismatched posCount: expected = %d, actual = %d\n", expected->posCount, actual->posCount);
     return;
     }
 
 result1 = expected->results;
 while (result1)
     {
     boolean matchFound = FALSE;
     result2 = actual->results;
     while (result2)
         {
 	if (differentString(result1->tableName, result2->tableName)) 
 	    {
 	    result2 = result2->next;
 	    continue;
 	    }
 	if (differentString(result1->chrom, result2->chrom)) 
 	    {
 	    result2 = result2->next;
 	    continue;
 	    }
 	if (result1->start != result2->start)
 	    {
 	    result2 = result2->next;
 	    continue;
 	    }
 	if (result1->end != result2->end)
 	    {
 	    result2 = result2->next;
 	    continue;
 	    }
 	if (differentString(result1->browserName, result2->browserName)) 
 	    {
 	    result2 = result2->next;
 	    continue;
 	    }
 	matchFound = TRUE;
 	break;
         }
     if (!matchFound)
         {
 	fprintf(stderr, "Error: no match found for expected result %s\n", result1->tableName);
         fprintf(stderr, "position = %s:%d-%d\n", result1->chrom, result1->start, result1->end);
         fprintf(stderr, "browserName = %s\n", result1->browserName);
 	}
     result1 = result1->next;
     }
 
 result1 = actual->results;
 while (result1)
     {
     boolean matchFound = FALSE;
     result2 = expected->results;
     while (result2)
         {
 	if (differentString(result1->tableName, result2->tableName)) 
 	    {
 	    result2 = result2->next;
 	    continue;
 	    }
 	if (differentString(result1->chrom, result2->chrom)) 
 	    {
 	    result2 = result2->next;
 	    continue;
 	    }
 	if (result1->start != result2->start)
 	    {
 	    result2 = result2->next;
 	    continue;
 	    }
 	if (result1->end != result2->end)
 	    {
 	    result2 = result2->next;
 	    continue;
 	    }
 	if (differentString(result1->browserName, result2->browserName)) 
 	    {
 	    result2 = result2->next;
 	    continue;
 	    }
 	matchFound = TRUE;
 	break;
         }
     if (!matchFound)
         {
 	fprintf(stderr, "Error: no match found for actual result %s\n", result1->tableName);
         fprintf(stderr, "position = %s:%d-%d\n", result1->chrom, result1->start, result1->end);
         fprintf(stderr, "browserName = %s\n", result1->browserName);
 	}
     result1 = result1->next;
     }
 
 }
 
 void searchAndCompare(struct searchTestCase *testCaseList)
 /* Read testCaseList.  Execute each search.  Report unexpected results. */
 {
 struct hgPositions *hgpList = NULL;
 struct searchTestCase *morphOutput = NULL;
 
 while (testCaseList)
     {
     verbose(1, "database = %s, searchTerm = %s\n", testCaseList->database, testCaseList->searchTerm);
-    hgpList = hgPositionsFind(testCaseList->database, testCaseList->searchTerm, "", "hgTracks", cart, FALSE);
+    hgpList = hgPositionsFind(testCaseList->database, testCaseList->searchTerm, "", "hgTracks", cart, FALSE, FALSE, NULL);
     /* handle cases where there are no expected matches */
     if (testCaseList->posCount == 0)
         {
         if (hgpList == NULL || hgpList->posCount == 0) 
 	    {
 	    testCaseList = testCaseList->next;
 	    continue;
 	    }
 	fprintf(stderr, "Error: expected no matches, got some\n");
 	fprintf(stderr, "database = %s, searchTerm = %s\n", 
 	        testCaseList->database, testCaseList->searchTerm);
 	continue;
 	}
     morphOutput = morph(testCaseList->database, testCaseList->searchTerm, hgpList);
     compareResults(testCaseList, morphOutput);
     testCaseList = testCaseList->next;
     }
 }
 
 
 int main(int argc, char *argv[])
 {
 struct searchTestCase *testCases =  NULL;
 
 cgiSpoof(&argc, argv);
 cart = cartForSession(hUserCookie(), excludeVars, NULL);
 
 if (argc != 2)
     usage();
 
 testCases = readInput(argv[1]);
 searchAndCompare(testCases);
 
 return 0;
 }