5d9ee32b367b0cce28e02c83b20101ecbd8e8c3d hiram Fri Aug 16 00:09:46 2024 -0700 now with the browserExists argument to eliminate the allowAll refs #32897 diff --git src/hg/hubApi/findGenome.c src/hg/hubApi/findGenome.c index e4d0825..9cf70a9 100644 --- src/hg/hubApi/findGenome.c +++ src/hg/hubApi/findGenome.c @@ -11,30 +11,34 @@ 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*/ +/* these three are radio button states, only one of these three can be TRUE */ +static boolean browserMustExist = TRUE; /* default: browser must exist */ +static boolean browserMayExist = FALSE; +static boolean browserNotExist = FALSE; /* 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 | | @@ -72,101 +76,116 @@ 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]); +/* initial SELECT allows any browser exist status, existing or not */ 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) +/* add specific browserExists depending upon options */ +if (browserMustExist) sqlDyStringPrintf(query, " AND browserExists=1"); +else if (browserNotExist) + sqlDyStringPrintf(query, " AND browserExists=0"); long long matchCount = sqlQuickLongLong(conn, query->string); if (matchCount > 0) { *totalMatchCount = matchCount; if (statsOnly) // only counting, nothing returned { // the LIMIT would limit results to maxItemsOutput itemCount = min(maxItemsOutput, matchCount); } // when less than totalMatchCount else { 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) + /* add specific browserExists depending upon options */ + if (browserMustExist) sqlDyStringPrintf(query, " AND browserExists=1"); + else if (browserNotExist) + sqlDyStringPrintf(query, " AND browserExists=0"); 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, long long *totalMatchCount) /* perform search on a single word, prepare json and return number of matches * and number of potential matches totalMatchCount */ { long long itemCount = 0; *totalMatchCount = 0; 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) +if (browserMustExist) sqlDyStringPrintf(query, " AND browserExists=1"); +else if (browserNotExist) + sqlDyStringPrintf(query, " AND browserExists=0"); 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 */ { 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) + /* add specific browserExists depending upon options */ + if (browserMustExist) sqlDyStringPrintf(query, " AND browserExists=1"); + else if (browserNotExist) + sqlDyStringPrintf(query, " AND browserExists=0"); matchCount = sqlQuickLongLong(conn, query->string); if (matchCount > 0) prefixSearch = TRUE; } if (matchCount < 1) // nothing found, returning zero return itemCount; *totalMatchCount = matchCount; if (statsOnly) // only counting, nothing returned { // the LIMIT would limit results to maxItemsOutput itemCount = min(maxItemsOutput, matchCount); } // when less than totalMatchCount else { 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) + /* add specific browserExists depending upon options */ + if (browserMustExist) sqlDyStringPrintf(query, " AND browserExists=1"); + else if (browserNotExist) + sqlDyStringPrintf(query, " AND browserExists=0"); 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); @@ -184,70 +203,95 @@ 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 *browserExistString = cgiOptionalString(argBrowser); +if (isNotEmpty(browserExistString)) + { /* from radio buttons, only one can be on */ + if (sameWord(browserExistString, "mustExist")) + { + browserMustExist = TRUE; /* default: browser must exist */ + browserMayExist = FALSE; + browserNotExist = FALSE; + } + else if (sameWord(browserExistString, "mayExist")) + { + browserMustExist = FALSE; + browserMayExist = TRUE; + browserNotExist = FALSE; + } + else if (sameWord(browserExistString, "notExist")) + { + browserMustExist = FALSE; + browserMayExist = FALSE; + browserNotExist = TRUE; + } + else + apiErrAbort(err400, err400Msg, "unrecognized '%s=%s' argument, must be one of: mustExist, mayExist or notExist", argBrowser, browserExistString); + } char *allowAllString = cgiOptionalString(argAllowAll); if (isNotEmpty(allowAllString)) { - if (sameString("1", allowAllString)) + if (SETTING_IS_ON(allowAllString)) allowAll = TRUE; - else if (sameString("0", allowAllString)) + else if (SETTING_IS_OFF(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)) + if (SETTING_IS_ON(statsOnlyString)) statsOnly = TRUE; - else if (sameString("0", statsOnlyString)) + else if (SETTING_IS_OFF(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); +jsonWriteString(jw, argBrowser, browserExistString); 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