f8c0ad0bbd396785452c18d9fc3473cfb75c73a5 hiram Tue Aug 13 15:47:21 2024 -0700 much cleaner at this time removed all the previous experiments refs #32897 diff --git src/hg/hubApi/findGenome.c src/hg/hubApi/findGenome.c index 123ffd1..4efd1d1 100644 --- src/hg/hubApi/findGenome.c +++ src/hg/hubApi/findGenome.c @@ -1,592 +1,272 @@ /* 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*/ -static void startGenomes(struct jsonWrite *jw) -/* begin the list output */ -{ -if (jsonOutputArrays) - jsonWriteListStart(jw, "genomes"); -else - jsonWriteObjectStart(jw, "genomes"); -} - -static void endGenomes(struct jsonWrite *jw) -/* end the list output */ -{ -if (jsonOutputArrays) - jsonWriteListEnd(jw); -else - jsonWriteObjectEnd(jw); -} - -static void finiGenArk(struct jsonWrite *jw, struct genark *el) -/* output of a genark item has started, finish it off */ -{ -jsonWriteBoolean(jw, "isGenArkBrowser", TRUE); -jsonWriteString(jw, "hubUrl", el->hubUrl); -jsonWriteString(jw, "asmName", el->asmName); -jsonWriteString(jw, "scientificName", el->scientificName); -jsonWriteString(jw, "commonName", el->commonName); -} - -static void finiSummary(struct jsonWrite *jw, struct asmSummary *el) -/* output of a summary item has started, finish it off */ -{ -jsonWriteString(jw, "bioProject", el->bioproject); -jsonWriteString(jw, "bioSample", el->biosample); -jsonWriteString(jw, "wgsMaster", el->wgsMaster); -jsonWriteString(jw, "refseqCategory", el->refseqCategory); -jsonWriteNumber(jw, "taxId", (long long)el->taxId); -jsonWriteNumber(jw, "speciesTaxid", (long long)el->speciesTaxid); -jsonWriteString(jw, "organismName", el->organismName); -jsonWriteString(jw, "infraspecificName", el->infraspecificName); -jsonWriteString(jw, "isolate", el->isolate); -jsonWriteString(jw, "versionStatus", el->versionStatus); -jsonWriteString(jw, "assemblyLevel", el->assemblyLevel); -jsonWriteString(jw, "releaseType", el->releaseType); -jsonWriteString(jw, "genomeRep", el->genomeRep); -jsonWriteString(jw, "seqRelDate", el->seqRelDate); -jsonWriteString(jw, "asmName", el->asmName); -jsonWriteString(jw, "asmSubmitter", el->asmSubmitter); -jsonWriteString(jw, "gbrsPairedAsm", el->gbrsPairedAsm); -jsonWriteString(jw, "pairedAsmComp", el->pairedAsmComp); -jsonWriteString(jw, "ftpPath", el->ftpPath); -jsonWriteString(jw, "excludedFromRefseq", el->excludedFromRefseq); -jsonWriteString(jw, "relationToTypeMaterial", el->relationToTypeMaterial); -jsonWriteString(jw, "assemblyType", el->assemblyType); -jsonWriteString(jw, "phyloGroup", el->phyloGroup); -jsonWriteNumber(jw, "genomeSize", (long long)el->genomeSize); -jsonWriteNumber(jw, "genomeSizeUngapped", (long long)el->genomeSizeUngapped); -jsonWriteDouble(jw, "gcPercent", (double)el->gcPercent); -jsonWriteNumber(jw, "repliconCount", (long long)el->repliconCount); -jsonWriteNumber(jw, "scaffoldCount", (long long)el->scaffoldCount); -jsonWriteNumber(jw, "contigCount", (long long)el->contigCount); -jsonWriteString(jw, "annotationProvider", el->annotationProvider); -jsonWriteString(jw, "annotationName", el->annotationName); -jsonWriteString(jw, "annotationDate", el->annotationDate); -jsonWriteNumber(jw, "totalGeneCount", (long long)el->totalGeneCount); -jsonWriteNumber(jw, "proteinCodingGeneCount", (long long)el->proteinCodingGeneCount); -jsonWriteNumber(jw, "nonCodingGeneCount", (long long)el->nonCodingGeneCount); -jsonWriteString(jw, "pubmedId", el->pubmedId); -} - -static void setBrowserUrl(struct jsonWrite *jw, char *browserId) -{ -char* host = getenv("HTTP_HOST"); -char browserUrl[1024]; -if (startsWith("GC", browserId)) - { - if (host) - safef(browserUrl, sizeof(browserUrl), "https://%s/h/%s", host, browserId); - else - safef(browserUrl, sizeof(browserUrl), "https://genome.ucsc.edu/h/%s", browserId); - } -else - { - if (host) - safef(browserUrl, sizeof(browserUrl), "https://%s/cgi-bin/hgTracks?db=%s", host, browserId); - else - safef(browserUrl, sizeof(browserUrl), "https://genome.ucsc.edu/cgi-bin/hgTracks?db=%s", browserId); - } -jsonWriteString(jw, "browserUrl", browserUrl); -} +/* +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 int outputCombo(struct jsonWrite *jw, struct combinedSummary *summaryList) -/* may be information from any of the three tables */ +static long long sqlJsonOut(struct jsonWrite *jw, struct sqlResult *sr) +/* given a sqlResult, walk through the rows and output the json */ { int itemCount = 0; -struct combinedSummary *el = NULL; -startGenomes(jw); -for (el=summaryList; el != NULL; el=el->next) - { - if (el->summary) - { - if (jsonOutputArrays) - { - jsonWriteObjectStart(jw, NULL); - jsonWriteString(jw, "accession", el->summary->assemblyAccession); - } - else - jsonWriteObjectStart(jw, el->summary->assemblyAccession); - - finiSummary(jw, el->summary); - boolean sciNameDone = FALSE; - boolean comNameDone = FALSE; - if (el->genArk) - { -// jsonWriteString(jw, "gcAccession", el->genArk->gcAccession); - /* some of these are going to be dups of the asmSummary */ - setBrowserUrl(jw, el->genArk->gcAccession); - finiGenArk(jw, el->genArk); - sciNameDone = TRUE; - comNameDone = TRUE; -// jsonWriteNumber(jw, "taxId", (long long)genome->taxId); - } - if (el->dbDb) - { - setBrowserUrl(jw, el->dbDb->name); - jsonWriteString(jw, "database", el->dbDb->name); - jsonWriteString(jw, "description", el->dbDb->description); - jsonWriteString(jw, "sourceName", el->dbDb->sourceName); - if (!sciNameDone) - jsonWriteString(jw, "scientificName", el->dbDb->scientificName); - if (!comNameDone) - jsonWriteString(jw, "commonName", el->dbDb->organism); -// jsonWriteNumber(jw, "taxId", (long long)dbDbEntry->taxId); - } - } - else if (el->genArk) /* ONLY genArk ?? - should have asmSummary TBD */ - { - if (jsonOutputArrays) - { - jsonWriteObjectStart(jw, NULL); - jsonWriteString(jw, "gcAccession", el->genArk->gcAccession); - } - else - jsonWriteObjectStart(jw, el->genArk->gcAccession); - setBrowserUrl(jw, el->genArk->gcAccession); - finiGenArk(jw, el->genArk); - if (el->dbDb) - { - jsonWriteBoolean(jw, "isUcscDatabase", TRUE); - jsonWriteString(jw, "database", el->dbDb->name); - jsonWriteString(jw, "description", el->dbDb->description); - jsonWriteString(jw, "sourceName", el->dbDb->sourceName); -// if (!sciNameDone) -// jsonWriteString(jw, "scientificName", el->dbDb->scientificName); -// if (!comNameDone) -// jsonWriteString(jw, "commonName", el->dbDb->organism); -// jsonWriteNumber(jw, "taxId", (long long)dbDbEntry->taxId); - } - } - else if (el->dbDb) /* ONLY dbDb ? - should have the other two TBD */ - { - if (jsonOutputArrays) +char **row; +if (statsOnly) // only counting, nothing returned { - jsonWriteObjectStart(jw, NULL); - jsonWriteString(jw, "database", el->dbDb->name); - } - else - jsonWriteObjectStart(jw, el->dbDb->name); - - setBrowserUrl(jw, el->dbDb->name); - jsonWriteBoolean(jw, "isUcscDatabase", TRUE); - jsonWriteString(jw, "description", el->dbDb->description); - jsonWriteString(jw, "sourceName", el->dbDb->sourceName); - jsonWriteString(jw, "scientificName", el->dbDb->scientificName); - jsonWriteString(jw, "commonName", el->dbDb->organism); - jsonWriteNumber(jw, "taxId", (long long)el->dbDb->taxId); - } - - jsonWriteObjectEnd(jw); + while ((row = sqlNextRow(sr)) != NULL) ++itemCount; } -endGenomes(jw); -return (itemCount); -} /* static int outputCombo(struct jsonWrite *jw, struct combinedSummary *summaryList) */ - -static struct combinedSummary *checkForGenArk(struct sqlConnection *conn, struct asmSummary *list) -/* given an asmSummary list, see if any match to genArk genomes */ -/* TBD - should also check here for UCSC database matching */ -{ -struct combinedSummary *comboSumary = NULL; -if (list) - { - struct asmSummary *el = NULL; - for (el=list; el != NULL; el=el->next) - { - struct combinedSummary *cs = NULL; - AllocVar(cs); - cs->summary = el; - cs->genArk = NULL; - cs->dbDb = NULL; - char query[4096]; - sqlSafef(query, sizeof(query), "SELECT * FROM %s WHERE gcAccession = \"%s\"", genarkTable, el->assemblyAccession); - struct genark *gA = genarkLoadByQuery(conn, query); - if (gA) - cs->genArk = gA; - slAddHead(&comboSumary, cs); - } - } -if (comboSumary) - slReverse(&comboSumary); -return comboSumary; -} - -static struct asmSummary *checkAsmSummary(struct sqlConnection *conn, char *oneAccession, boolean exactMatch, long long limit) -/* check the asmSummary table for oneAccession, mayby exact, maybe a limit */ -{ -char query[4096]; -if (limit > 0) - { - if (exactMatch) - sqlSafef(query, sizeof(query), "SELECT * FROM asmSummary WHERE assemblyAccession = '%s' LIMIT %lld", oneAccession, limit); - else - sqlSafef(query, sizeof(query), "SELECT * FROM asmSummary WHERE assemblyAccession LIKE '%s%%' LIMIT %lld", oneAccession, limit); - } else { - if (exactMatch) - sqlSafef(query, sizeof(query), "SELECT * FROM asmSummary WHERE assemblyAccession = '%s'", oneAccession); - else - sqlSafef(query, sizeof(query), "SELECT * FROM asmSummary WHERE assemblyAccession LIKE '%s%%'", oneAccession); - } - -struct asmSummary *list = asmSummaryLoadByQuery(conn, query); -return list; -} - -// Field Type Null Key Default Extra -// source varchar(255) NO MUL NULL -// destination varchar(255) NO MUL NULL -// sourceAuthority enum('ensembl','ucsc','genbank','refseq') NO NULL -// destinationAuthority enum('ensembl','ucsc','genbank','refseq') NO NULL -// matchCount bigint(20) NO NULL -// sourceCount bigint(20) NO NULL -// destinationCount bigint(20) NO NULL - -struct asmSummary *dbDbAsmEquivalent(struct sqlConnection *centConn, char *dbDbName) -{ -struct asmSummary *itemReturn = NULL; -struct sqlConnection *conn = hAllocConn("hgFixed"); -char query[4096]; -sqlSafef(query, sizeof(query), "SELECT destination from asmEquivalent WHERE source='%s' AND sourceAuthority='ucsc' AND destinationAuthority='refseq' LIMIT 1", dbDbName); -char *asmIdFound = NULL; -char *genBank = NULL; -char *refSeq = sqlQuickString(conn, query); -if (refSeq) - asmIdFound = refSeq; -else - { - sqlSafef(query, sizeof(query), "SELECT destination from asmEquivalent WHERE source='%s' AND sourceAuthority='ucsc' AND destinationAuthority='genbank' LIMIT 1", dbDbName); - genBank = sqlQuickString(conn, query); - if (genBank) - asmIdFound = genBank; - } -if (asmIdFound) - { - char *words[3]; - int wordCount = chopString(asmIdFound, "_", words, ArraySize(words)); - if (wordCount > 2) - { - safef(query, sizeof(query), "%s_%s", words[0], words[1]); - itemReturn = checkAsmSummary(centConn, query, TRUE, 1); - } - } -return itemReturn; -} - -static int sqlJsonOut(struct jsonWrite *jw, struct sqlResult *sr) -/* given a sqlResult, walk through the rows and output the json */ -{ -int itemCount = 0; -char **row; while ((row = sqlNextRow(sr)) != NULL) { struct assemblyList *el = assemblyListLoadWithNull(row); jsonWriteObjectStart(jw, el->name); -// jsonWriteString(jw, "name", 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]; -sqlSafef(query, sizeof(query), "SELECT count(*) FROM %s WHERE MATCH(name, commonName, scientificName, clade, description) AGAINST ('%s' IN BOOLEAN MODE);", asmListTable, queryDy->string); +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); 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); itemCount = sqlJsonOut(jw, sr); verbose(1, "DBG: itemCount: %lld from search '%s'\n", itemCount, query); sqlFreeResult(&sr); } 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]; -int itemCount = 0; +long long itemCount = 0; *totalMatchCount = 0; -sqlSafef(query, sizeof(query), "SELECT count(*) FROM %s WHERE MATCH(name, commonName, scientificName, clade, description) AGAINST ('%s' IN BOOLEAN MODE);", asmListTable, searchWord); +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); + +verbose(1, "DBG '%s'\n", query); long long matchCount = sqlQuickLongLong(conn, query); boolean prefixSearch = FALSE; if (matchCount < 1) /* no match, add the * wild card match to make a prefix match */ { - sqlSafef(query, sizeof(query), "SELECT count(*) FROM %s WHERE MATCH(name, commonName, scientificName, clade, description) AGAINST ('%s*' IN BOOLEAN MODE);", asmListTable, searchWord); + 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); 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); itemCount = sqlJsonOut(jw, sr); sqlFreeResult(&sr); return itemCount; } /* static long long oneWordSearch(struct sqlConnection *conn, char *searchWord, struct jsonWrite *jw) */ -static void asmSummaryGroup(struct sqlConnection *conn, struct jsonWrite *jw, char *field) -/* show a grouping count for a field in asmSummary table */ -{ -char query[4096]; -jsonWriteObjectStart(jw, field); -sqlSafef(query, sizeof(query), "SELECT %s, COUNT(*) FROM asmSummary GROUP by %s", field, field); -struct sqlResult *sr = sqlGetResult(conn, query); -char **row; -while ((row = sqlNextRow(sr)) != NULL) - { - if (strlen(row[0]) < 1) - jsonWriteNumber(jw, "na", sqlLongLong(row[1])); - else - jsonWriteNumber(jw, row[0], sqlLongLong(row[1])); - } -sqlFreeResult(&sr); -jsonWriteObjectEnd(jw); -} - -static void doStatsOnly(struct sqlConnection *conn, struct jsonWrite *jw) -/* only count the items in each database */ -{ -jsonWriteString(jw, "description", "counting items in tables: asmSummary, genark and dbDb for number of genomes available"); - -char query[4096]; -sqlSafef(query, sizeof(query), "SELECT count(*) FROM %s", genarkTable); -long long genArkCount = sqlQuickLongLong(conn, query); -sqlSafef(query, sizeof(query), "SELECT count(*) FROM asmSummary"); -long long asmSummaryTotal = sqlQuickLongLong(conn, query); -sqlSafef(query, sizeof(query), "SELECT count(*) FROM dbDb where active=1"); -long long dbDbCount = sqlQuickLongLong(conn, query); -long long totalCount = genArkCount + asmSummaryTotal + dbDbCount; -jsonWriteNumber(jw, "totalCount", totalCount); -jsonWriteObjectStart(jw, "genark"); -jsonWriteString(jw, "TBD", "the genark table can count GCF vs. GCA and will have a clade category to couint\n"); -jsonWriteNumber(jw, "itemCount", genArkCount); -jsonWriteObjectEnd(jw); -jsonWriteObjectStart(jw, "dbDb"); -jsonWriteString(jw, "description", "the dbDb table is a count of UCSC 'database' browser instances"); -jsonWriteNumber(jw, "itemCount", dbDbCount); -jsonWriteObjectEnd(jw); -jsonWriteObjectStart(jw, "asmSummary"); -jsonWriteString(jw, "description", "the asmSummary is the contents of the NCBI genbank/refseq assembly_summary.txt information"); -jsonWriteString(jw, "seeAlso", "https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/README_assembly_summary.txt"); -jsonWriteNumber(jw, "asmSummaryTotal", asmSummaryTotal); -asmSummaryGroup(conn, jw, "refseqCategory"); -asmSummaryGroup(conn, jw, "versionStatus"); -asmSummaryGroup(conn, jw, "assemblyLevel"); -asmSummaryGroup(conn, jw, "releaseType"); -asmSummaryGroup(conn, jw, "genomeRep"); -asmSummaryGroup(conn, jw, "pairedAsmComp"); -asmSummaryGroup(conn, jw, "assemblyType"); -asmSummaryGroup(conn, jw, "phyloGroup"); -jsonWriteObjectEnd(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; -if (! statsOnly) - { /* 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(); -if (statsOnly) - { - doStatsOnly(conn, jw); - elapsedTime(jw); - apiFinishOutput(0, NULL, jw); - hDisconnectCentral(&conn); - return; - } jsonWriteString(jw, argGenomeSearchTerm, searchString); if (allowAll) jsonWriteBoolean(jw, argAllowAll, allowAll); long long itemCount = 0; long long totalMatchCount = 0; -/* save the search string before it is chopped */ -char *pristineSearchString = cloneString(searchString); - 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' */ - { - itemCount = multipleWordSearch(conn, words, wordCount, jw, &totalMatchCount); - if ( 1 == 0 ) { - long long totalMatch = 0; - /* no more than 100 items result please */ - struct asmSummary *summaryList = asmSummaryFullText(conn, pristineSearchString, (long long) 100, &totalMatch); - if (summaryList) - { - struct combinedSummary *comboOutput = checkForGenArk(conn, summaryList); - if (comboOutput) - itemCount = outputCombo(jw, comboOutput); - if (itemCount) - jsonWriteNumber(jw, "itemCount", itemCount); - else - verbose(0, "# DBG need to search this string '%s' somewhere else\n", pristineSearchString); - } - else - verbose(0, "# DBG need to search this string '%s' somewhere else\n", pristineSearchString); - } /* if ( 1 == 0 ) */ - } 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); }