e39d2c40cdc3e17273b158602400481ae7d2d03d hiram Wed Aug 28 18:44:07 2024 -0700 correspond with the new table structure and properly output the number values refs #32596 diff --git src/hg/hubApi/findGenome.c src/hg/hubApi/findGenome.c index d1251b6..b925041 100644 --- src/hg/hubApi/findGenome.c +++ src/hg/hubApi/findGenome.c @@ -1,335 +1,357 @@ /* 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; /* 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 | | +----------------+---------------------+------+-----+---------+-------+ */ static long long sqlJsonOut(struct jsonWrite *jw, struct sqlResult *sr) /* given a sqlResult, walk through the rows and output the json */ { long long itemCount = 0; char **row; while ((row = sqlNextRow(sr)) != NULL) { struct assemblyList *el = assemblyListLoadWithNull(row); jsonWriteObjectStart(jw, el->name); - jsonWriteNumber(jw, "priority", (long long)el->priority); + if (el->priority) + jsonWriteNumber(jw, "priority", (long long)*el->priority); + else + jsonWriteNumber(jw, "priority", (long long)0); jsonWriteString(jw, "commonName", el->commonName); jsonWriteString(jw, "scientificName", el->scientificName); - jsonWriteNumber(jw, "taxId", (long long)el->taxId); + if (el->taxId) + jsonWriteNumber(jw, "taxId", (long long)*el->taxId); + else + jsonWriteNumber(jw, "taxId", (long long)0); 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); + if (el->year) + jsonWriteNumber(jw, "year", (long long)*el->year); + else + jsonWriteNumber(jw, "year", (long long)0); + if (isEmpty(el->refSeqCategory)) + jsonWriteString(jw, "refSeqCategory", NULL); + else + jsonWriteString(jw, "refSeqCategory", el->refSeqCategory); + if (isEmpty(el->versionStatus)) + jsonWriteString(jw, "versionStatus", NULL); + else + jsonWriteString(jw, "versionStatus", el->versionStatus); + if (isEmpty(el->assemblyLevel)) + jsonWriteString(jw, "assemblyLevel", NULL); + else + jsonWriteString(jw, "assemblyLevel", el->assemblyLevel); 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]); /* 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); /* 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); + sqlDyStringPrintf(query, "SELECT * FROM %s WHERE MATCH(name, commonName, scientificName, clade, description, refSeqCategory, versionStatus, assemblyLevel) AGAINST ('%s' IN BOOLEAN MODE)", asmListTable, queryDy->string); /* 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, boolean *prefixSearch) /* 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); +sqlDyStringPrintf(query, "SELECT COUNT(*) FROM %s WHERE MATCH(name, commonName, scientificName, clade, description, refSeqCategory, versionStatus, assemblyLevel) AGAINST ('%s' IN BOOLEAN MODE)", asmListTable, searchWord); if (browserMustExist) sqlDyStringPrintf(query, " AND browserExists=1"); else if (browserNotExist) sqlDyStringPrintf(query, " AND browserExists=0"); long long matchCount = sqlQuickLongLong(conn, query->string); *prefixSearch = FALSE; /* assume not */ 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); + sqlDyStringPrintf(query, "SELECT COUNT(*) FROM %s WHERE MATCH(name, commonName, scientificName, clade, description, refSeqCategory, versionStatus, assemblyLevel) AGAINST ('%s*' IN BOOLEAN MODE)", asmListTable, searchWord); /* 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 ? "*" : ""); + sqlDyStringPrintf(query, "SELECT * FROM %s WHERE MATCH(name, commonName, scientificName, clade, description, refSeqCategory, versionStatus, assemblyLevel) AGAINST ('%s%s' IN BOOLEAN MODE)", asmListTable, searchWord, *prefixSearch ? "*" : ""); /* 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, boolean *prefixSearch) */ static long elapsedTime(struct jsonWrite *jw) { long nowTime = clock1000(); long elapsedTimeMs = nowTime - enteredMainTime; jsonWriteNumber(jw, "elapsedTimeMs", elapsedTimeMs); return elapsedTimeMs; } void apiFindGenome(char *pathString[MAX_PATH_INFO]) /* 'findGenome' function */ { char *searchString = cgiOptionalString(argQ); char *inputSearchString = cloneString(searchString); char *endResultSearchString = NULL; boolean prefixSearch = FALSE; 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 *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 *statsOnlyString = cgiOptionalString(argStatsOnly); if (isNotEmpty(statsOnlyString)) { if (SETTING_IS_ON(statsOnlyString)) statsOnly = TRUE; 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", argQ); if (wordCount > 5) apiErrAbort(err400, err400Msg, "search term '%s=%s' should not have more than 5 words for function /findGenome", argQ, searchString); struct jsonWrite *jw = apiStartOutput(); jsonWriteString(jw, argBrowser, browserExistString); 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, &prefixSearch); else /* multiple word search */ itemCount = multipleWordSearch(conn, words, wordCount, jw, &totalMatchCount); if (prefixSearch) { struct dyString *addedStar = dyStringNew(64); dyStringPrintf(addedStar, "%s*", inputSearchString); endResultSearchString = dyStringCannibalize(&addedStar); jsonWriteString(jw, argQ, endResultSearchString); } else { endResultSearchString = inputSearchString; jsonWriteString(jw, argQ, inputSearchString); } /* 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' */ struct dyString *query = dyStringNew(64); sqlDyStringPrintf(query, "SELECT COUNT(*) FROM %s", asmListTable); long long universeCount = sqlQuickLongLong(conn, query->string); dyStringFree(&query); long elapTimeMs = elapsedTime(jw); /* apache error_log recording */ fprintf(stderr, "findGenome: '%s' found %lld returned %lld in %ld ms\n", endResultSearchString, totalMatchCount, itemCount, elapTimeMs); if (statsOnly) jsonWriteBoolean(jw, "statsOnly", TRUE); if (itemCount) { jsonWriteNumber(jw, "itemCount", itemCount); jsonWriteNumber(jw, "totalMatchCount", totalMatchCount); jsonWriteNumber(jw, "availableAssemblies", universeCount); 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", argQ, inputSearchString); hDisconnectCentral(&conn); }