08a042ae53f8a7ea0b6e15bee0b12fcf48a90a76 hiram Thu Aug 29 14:07:38 2024 -0700 now with proper interface to assembly status, refSeq category, assembly level refs #32596 diff --git src/hg/hubApi/findGenome.c src/hg/hubApi/findGenome.c index b925041..2197680 100644 --- src/hg/hubApi/findGenome.c +++ src/hg/hubApi/findGenome.c @@ -1,357 +1,453 @@ /* 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; +static unsigned specificYear = 0; /* from year=1234 argument */ +/* from category= reference or representative */ +static char *refSeqCategory = NULL; +/* from status= one of: latest, replaced or suppressed */ +static char *versionStatus = NULL; +/* from level= one of complete, chromosome, scaffold or contig */ +static char *assemblyLevel = NULL; /* 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); 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); 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 void addBrowserExists(struct dyString *query) +/* add the AND clauses for browserExist depending upon option */ +{ +if (browserMustExist) + sqlDyStringPrintf(query, " AND browserExists=1"); +else if (browserNotExist) + sqlDyStringPrintf(query, " AND browserExists=0"); +} + +static void addCategory(struct dyString *query) +/* refSeqCategory = reference or representative */ +{ +if (isNotEmpty(refSeqCategory)) + sqlDyStringPrintf(query, " AND refSeqCategory='%s'", refSeqCategory); +} + +static void addStatus(struct dyString *query) +/* versionStatus = latest, replaced or suppressed */ +{ +if (isNotEmpty(versionStatus)) + sqlDyStringPrintf(query, " AND versionStatus='%s'", versionStatus); +} + +static void addLevel(struct dyString *query) +/* assemblyLevel = complete, chromosome, scaffold or contig */ +{ +if (isNotEmpty(assemblyLevel)) + sqlDyStringPrintf(query, " AND assemblyLevel='%s'", assemblyLevel); +} + +static void addConditions(struct dyString *query) +/* add any of the optional conditions */ +{ +addBrowserExists(query); +addCategory(query); +addStatus(query); +addLevel(query); +} + 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"); +addConditions(query); /* add optional SELECT options */ + 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, 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"); + addConditions(query); /* add optional SELECT options */ 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, 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"); +addConditions(query); /* add optional SELECT options */ 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, 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"); + addConditions(query); /* add optional SELECT options */ 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, 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"); + addConditions(query); /* add optional SELECT options */ 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 *yearString = cgiOptionalString(argYear); +char *categoryString = cgiOptionalString(argCategory); +char *statusString = cgiOptionalString(argStatus); +char *levelString = cgiOptionalString(argLevel); +/* protect sqlUnsigned from errors */ +if (isNotEmpty(yearString)) + { + struct errCatch *errCatch = errCatchNew(); + if (errCatchStart(errCatch)) + { + specificYear = sqlUnsigned(yearString); + if ((specificYear < 1800) || (specificYear > 2100)) + apiErrAbort(err400, err400Msg, "year specified '%s' must be >= 1800 and <= 2100", yearString); + } + errCatchEnd(errCatch); + if (errCatch->gotError) + apiErrAbort(err400, err400Msg, "can not recognize year '%s' as a number", yearString); + } +/* probably be better to place this arg checking business into a function + * operating from a list + */ +if (isNotEmpty(categoryString)) + { + refSeqCategory = cloneString(categoryString); + toLowerN(refSeqCategory, strlen(refSeqCategory)); + if (differentWord(refSeqCategory, "reference")) + { + if (differentWord(refSeqCategory, "representative")) + apiErrAbort(err400, err400Msg, "values for argument %s=%s must be 'reference' or 'representative'", argCategory, categoryString); + } + } +if (isNotEmpty(statusString)) + { + versionStatus = cloneString(statusString); + toLowerN(versionStatus, strlen(versionStatus)); + if (differentWord(versionStatus, "latest")) + { + if (differentWord(versionStatus, "replaced")) + if (differentWord(versionStatus, "suppressed")) + apiErrAbort(err400, err400Msg, "values for argument %s=%s must be one of: 'latest', 'replaced' or 'suppressed'", argStatus, statusString); + } + } +if (isNotEmpty(levelString)) + { + assemblyLevel = cloneString(levelString); + toLowerN(assemblyLevel, strlen(assemblyLevel)); + if (differentWord(assemblyLevel, "complete")) + { + if (differentWord(assemblyLevel, "chromosome")) + if (differentWord(assemblyLevel, "scaffold")) + if (differentWord(assemblyLevel, "scaffold")) + apiErrAbort(err400, err400Msg, "values for argument %s=%s must be one of: 'complete', 'chromosome', 'scaffold' or 'contig'", argLevel, levelString); + } + } + char *browserExistString = cgiOptionalString(argBrowser); +if (NULL == browserExistString) /* set default if none given */ + browserExistString = cloneString("mustExist"); + 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(); +/* show options in effect in JSON return */ + jsonWriteString(jw, argBrowser, browserExistString); +if (specificYear > 0) + jsonWriteNumber(jw, argYear, specificYear); +if (isNotEmpty(refSeqCategory)) + jsonWriteString(jw, argCategory, refSeqCategory); +if (isNotEmpty(versionStatus)) + jsonWriteString(jw, argStatus, versionStatus); +if (isNotEmpty(assemblyLevel)) + jsonWriteString(jw, argLevel, assemblyLevel); 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); }