a52bdc2dcb5068501fbc48696d7ad85e8fb2608e hiram Tue Aug 13 17:57:48 2024 -0700 eliminate the DBG statements and get the query string construction into a dyPrintf refs #32897 diff --git src/hg/hubApi/findGenome.c src/hg/hubApi/findGenome.c index 4efd1d1..267e352 100644 --- src/hg/hubApi/findGenome.c +++ src/hg/hubApi/findGenome.c @@ -1,272 +1,275 @@ /* findGenome search functions */ #include "dataApi.h" #include "hgFind.h" #include "cartTrackDb.h" #include "cartJson.h" #include "genark.h" #include "asmAlias.h" #include "asmSummary.h" #include "assemblyList.h" struct combinedSummary /* may have information from any of: asmSummary, genark or dbDb */ { struct combinedSummary *next; /* Next in singly linked list */ struct asmSummary *summary; /* from asmSummary table */ struct genark *genArk; /* from genark table */ struct dbDb *dbDb; /* from dbDb table */ }; /* will be initialized as this function begins */ static char *genarkTable = NULL; static char *asmListTable = NULL; static boolean statsOnly = FALSE; static boolean allowAll = FALSE; /* default only show existing browsers*/ /* hgsql -e 'desc assemblyList;' hgcentraltest +----------------+---------------------+------+-----+---------+-------+ | Field | Type | Null | Key | Default | Extra | +----------------+---------------------+------+-----+---------+-------+ | name | varchar(255) | NO | PRI | NULL | | | priority | int(10) unsigned | YES | | NULL | | | commonName | varchar(511) | YES | | NULL | | | scientificName | varchar(511) | YES | | NULL | | | taxId | int(10) unsigned | YES | | NULL | | | clade | varchar(255) | YES | | NULL | | | description | varchar(1023) | YES | | NULL | | | browserExists | tinyint(3) unsigned | YES | | NULL | | | hubUrl | varchar(511) | YES | | NULL | | +----------------+---------------------+------+-----+---------+-------+ */ static long long sqlJsonOut(struct jsonWrite *jw, struct sqlResult *sr) /* given a sqlResult, walk through the rows and output the json */ { int itemCount = 0; char **row; if (statsOnly) // only counting, nothing returned { while ((row = sqlNextRow(sr)) != NULL) ++itemCount; } else { while ((row = sqlNextRow(sr)) != NULL) { struct assemblyList *el = assemblyListLoadWithNull(row); jsonWriteObjectStart(jw, el->name); jsonWriteNumber(jw, "priority", (long long)el->priority); jsonWriteString(jw, "commonName", el->commonName); jsonWriteString(jw, "scientificName", el->scientificName); jsonWriteNumber(jw, "taxId", (long long)el->taxId); jsonWriteString(jw, "clade", el->clade); jsonWriteString(jw, "description", el->description); if (1 == *el->browserExists) jsonWriteBoolean(jw, "browserExists", TRUE); else jsonWriteBoolean(jw, "browserExists", FALSE); if (isEmpty(el->hubUrl)) jsonWriteString(jw, "hubUrl", NULL); else jsonWriteString(jw, "hubUrl", el->hubUrl); jsonWriteObjectEnd(jw); ++itemCount; } } return (itemCount); } static long long multipleWordSearch(struct sqlConnection *conn, char **words, int wordCount, struct jsonWrite *jw, long long *totalMatchCount) /* perform search on multiple words, prepare json and return number of matches */ { long long itemCount = 0; *totalMatchCount = 0; if (wordCount < 0) return itemCount; /* get the words[] into a single string */ struct dyString *queryDy = dyStringNew(128); dyStringPrintf(queryDy, "%s", words[0]); for (int i = 1; i < wordCount; ++i) dyStringPrintf(queryDy, " %s", words[i]); -char query[4096]; -if (allowAll) - sqlSafef(query, sizeof(query), "SELECT COUNT(*) FROM %s WHERE MATCH(name, commonName, scientificName, clade, description) AGAINST ('%s' IN BOOLEAN MODE);", asmListTable, queryDy->string); -else - sqlSafef(query, sizeof(query), "SELECT COUNT(*) FROM %s WHERE MATCH(name, commonName, scientificName, clade, description) AGAINST ('%s' IN BOOLEAN MODE) AND browserExists=1;", asmListTable, queryDy->string); -long long matchCount = sqlQuickLongLong(conn, query); +struct dyString *query = dyStringNew(64); +sqlDyStringPrintf(query, "SELECT COUNT(*) FROM %s WHERE MATCH(name, commonName, scientificName, clade, description) AGAINST ('%s' IN BOOLEAN MODE)", asmListTable, queryDy->string); +if (!allowAll) + sqlDyStringPrintf(query, " AND browserExists=1"); +long long matchCount = sqlQuickLongLong(conn, query->string); if (matchCount > 0) { - verbose(1, "DBG: matchCount: %lld from search '%s'\n", matchCount, query); *totalMatchCount = matchCount; - if (allowAll) - sqlSafef(query, sizeof(query), "SELECT * FROM %s WHERE MATCH(name, commonName, scientificName, clade, description) AGAINST ('%s' IN BOOLEAN MODE) ORDER BY priority LIMIT %d;", asmListTable, queryDy->string, maxItemsOutput); - else - sqlSafef(query, sizeof(query), "SELECT * FROM %s WHERE MATCH(name, commonName, scientificName, clade, description) AGAINST ('%s' IN BOOLEAN MODE) AND browserExists=1 ORDER BY priority LIMIT %d;", asmListTable, queryDy->string, maxItemsOutput); - struct sqlResult *sr = sqlGetResult(conn, query); + dyStringFree(&query); + query = dyStringNew(64); + sqlDyStringPrintf(query, "SELECT * FROM %s WHERE MATCH(name, commonName, scientificName, clade, description) AGAINST ('%s' IN BOOLEAN MODE)", asmListTable, queryDy->string); + if (!allowAll) + sqlDyStringPrintf(query, " AND browserExists=1"); + sqlDyStringPrintf(query, " ORDER BY priority LIMIT %d;", maxItemsOutput); + struct sqlResult *sr = sqlGetResult(conn, query->string); itemCount = sqlJsonOut(jw, sr); - verbose(1, "DBG: itemCount: %lld from search '%s'\n", itemCount, query); sqlFreeResult(&sr); + dyStringFree(&query); } return itemCount; } static long long oneWordSearch(struct sqlConnection *conn, char *searchWord, struct jsonWrite *jw, long long *totalMatchCount) /* perform search on a single word, prepare json and return number of matches * and number of potential matches totalMatchCount */ { -char query[4096]; long long itemCount = 0; *totalMatchCount = 0; -if (allowAll) - sqlSafef(query, sizeof(query), "SELECT COUNT(*) FROM %s WHERE MATCH(name, commonName, scientificName, clade, description) AGAINST ('%s' IN BOOLEAN MODE);", asmListTable, searchWord); -else - sqlSafef(query, sizeof(query), "SELECT COUNT(*) FROM %s WHERE MATCH(name, commonName, scientificName, clade, description) AGAINST ('%s' IN BOOLEAN MODE) AND browserExists=1;", asmListTable, searchWord); +struct dyString *query = dyStringNew(64); +sqlDyStringPrintf(query, "SELECT COUNT(*) FROM %s WHERE MATCH(name, commonName, scientificName, clade, description) AGAINST ('%s' IN BOOLEAN MODE)", asmListTable, searchWord); +if (!allowAll) + sqlDyStringPrintf(query, " AND browserExists=1"); -verbose(1, "DBG '%s'\n", query); -long long matchCount = sqlQuickLongLong(conn, query); +long long matchCount = sqlQuickLongLong(conn, query->string); boolean prefixSearch = FALSE; if (matchCount < 1) /* no match, add the * wild card match to make a prefix match */ { - if (allowAll) - sqlSafef(query, sizeof(query), "SELECT COUNT(*) FROM %s WHERE MATCH(name, commonName, scientificName, clade, description) AGAINST ('%s*' IN BOOLEAN MODE);", asmListTable, searchWord); - else - sqlSafef(query, sizeof(query), "SELECT COUNT(*) FROM %s WHERE MATCH(name, commonName, scientificName, clade, description) AGAINST ('%s*' IN BOOLEAN MODE) AND browserExists=1;", asmListTable, searchWord); - matchCount = sqlQuickLongLong(conn, query); + dyStringFree(&query); + query = dyStringNew(64); + sqlDyStringPrintf(query, "SELECT COUNT(*) FROM %s WHERE MATCH(name, commonName, scientificName, clade, description) AGAINST ('%s*' IN BOOLEAN MODE)", asmListTable, searchWord); + if (!allowAll) + sqlDyStringPrintf(query, " AND browserExists=1"); + matchCount = sqlQuickLongLong(conn, query->string); if (matchCount > 0) prefixSearch = TRUE; } if (matchCount < 1) return itemCount; *totalMatchCount = matchCount; -if (allowAll) - sqlSafef(query, sizeof(query), "SELECT * FROM %s WHERE MATCH(name, commonName, scientificName, clade, description) AGAINST ('%s%s' IN BOOLEAN MODE) ORDER BY priority LIMIT %d;", asmListTable, searchWord, prefixSearch ? "*" : "", maxItemsOutput); -else - sqlSafef(query, sizeof(query), "SELECT * FROM %s WHERE MATCH(name, commonName, scientificName, clade, description) AGAINST ('%s%s' IN BOOLEAN MODE) AND browserExists=1 ORDER BY priority LIMIT %d;", asmListTable, searchWord, prefixSearch ? "*" : "", maxItemsOutput); -struct sqlResult *sr = sqlGetResult(conn, query); +dyStringFree(&query); +query = dyStringNew(64); + +sqlDyStringPrintf(query, "SELECT * FROM %s WHERE MATCH(name, commonName, scientificName, clade, description) AGAINST ('%s%s' IN BOOLEAN MODE)", asmListTable, searchWord, prefixSearch ? "*" : ""); +if (!allowAll) + sqlDyStringPrintf(query, " AND browserExists=1"); +sqlDyStringPrintf(query, " ORDER BY priority LIMIT %d;", maxItemsOutput); +struct sqlResult *sr = sqlGetResult(conn, query->string); itemCount = sqlJsonOut(jw, sr); sqlFreeResult(&sr); +dyStringFree(&query); return itemCount; } /* static long long oneWordSearch(struct sqlConnection *conn, char *searchWord, struct jsonWrite *jw) */ static void elapsedTime(struct jsonWrite *jw) { long nowTime = clock1000(); long elapsedTimeMs = nowTime - enteredMainTime; jsonWriteNumber(jw, "elapsedTimeMs", elapsedTimeMs); } void apiFindGenome(char *pathString[MAX_PATH_INFO]) /* 'findGenome' function */ { char *searchString = cgiOptionalString(argGenomeSearchTerm); char *inputSearchString = cloneString(searchString); char *extraArgs = verifyLegalArgs(argFindGenome); genarkTable = genarkTableName(); asmListTable = assemblyListTableName(); if (extraArgs) apiErrAbort(err400, err400Msg, "extraneous arguments found for function /findGenome'%s'", extraArgs); boolean asmListExists = hTableExists("hgcentraltest", asmListTable); if (!asmListExists) apiErrAbort(err400, err400Msg, "table hgcentraltest.assemblyList does not exist for /findGenome"); boolean asmSummaryExists = hTableExists("hgcentraltest", "asmSummary"); if (!asmSummaryExists) apiErrAbort(err400, err400Msg, "table hgcentraltest.asmSummary does not exist for /findGenome"); boolean genArkExists = hTableExists("hgcentraltest", genarkTable); if (!genArkExists) apiErrAbort(err400, err400Msg, "table hgcentraltest.%s does not exist for /findGenome", genarkTable); char *allowAllString = cgiOptionalString(argAllowAll); if (isNotEmpty(allowAllString)) { if (sameString("1", allowAllString)) allowAll = TRUE; else if (sameString("0", allowAllString)) allowAll = FALSE; else apiErrAbort(err400, err400Msg, "unrecognized '%s=%s' argument, can only be =1 or =0", argAllowAll, allowAllString); } char *statsOnlyString = cgiOptionalString(argStatsOnly); if (isNotEmpty(statsOnlyString)) { if (sameString("1", statsOnlyString)) statsOnly = TRUE; else if (sameString("0", statsOnlyString)) statsOnly = FALSE; else apiErrAbort(err400, err400Msg, "unrecognized '%s=%s' argument, can only be =1 or =0", argStatsOnly, statsOnlyString); } struct sqlConnection *conn = hConnectCentral(); if (!sqlTableExists(conn, asmListTable)) apiErrAbort(err500, err500Msg, "missing central.assemblyList table in function /findGenome'%s'", extraArgs); int wordCount = 0; /* verify number of words in search string is legal */ wordCount = chopByWhite(searchString, NULL, 0); if (wordCount < 1) apiErrAbort(err400, err400Msg, "search term '%s' does not contain a word ? for function /findGenome", argGenomeSearchTerm); if (wordCount > 5) apiErrAbort(err400, err400Msg, "search term '%s=%s' should not have more than 5 words for function /findGenome", argGenomeSearchTerm, searchString); struct jsonWrite *jw = apiStartOutput(); jsonWriteString(jw, argGenomeSearchTerm, searchString); if (allowAll) jsonWriteBoolean(jw, argAllowAll, allowAll); long long itemCount = 0; long long totalMatchCount = 0; char **words; AllocArray(words, wordCount); (void) chopByWhite(searchString, words, wordCount); if (1 == wordCount) itemCount = oneWordSearch(conn, words[0], jw, &totalMatchCount); else /* multiple word search */ itemCount = multipleWordSearch(conn, words, wordCount, jw, &totalMatchCount); /* rules about what can be in the search string: * + sign before a word indicates the word must be in the result * - sign before a word indicates it must not be in the result * * at end of word makes the word be a prefix search * "double quotes" to group words together as a phrase to match exactly * < or > adjust the words contribution to the relevance value * >moreImportant <lessImportant * ~ negates the word's contribution to the relevance value without * excluding it from the results * (parens clauses) to groups words together for more complex queries * | OR operator 'thisWord | otherWord' */ elapsedTime(jw); if (statsOnly) jsonWriteBoolean(jw, "statsOnly", TRUE); if (itemCount) { jsonWriteNumber(jw, "itemCount", itemCount); jsonWriteNumber(jw, "totalMatchCount", totalMatchCount); if (totalMatchCount > itemCount) jsonWriteBoolean(jw, "maxItemsLimit", TRUE); apiFinishOutput(0, NULL, jw); } else apiErrAbort(err400, err400Msg, "no genomes found matching search term %s='%s' for endpoint: /findGenome", argGenomeSearchTerm, inputSearchString); hDisconnectCentral(&conn); }