5a00dc1ab5eaaaf1776558e2fedc99997471eb73 hiram Tue Aug 13 14:38:20 2024 -0700 ready to start cleaning up refs #32897 diff --git src/hg/hubApi/findGenome.c src/hg/hubApi/findGenome.c index 5bb88a8..123ffd1 100644 --- src/hg/hubApi/findGenome.c +++ src/hg/hubApi/findGenome.c @@ -1,575 +1,592 @@ /* 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); } static int outputCombo(struct jsonWrite *jw, struct combinedSummary *summaryList) /* may be information from any of the three tables */ { 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) { 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); ++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 singleWordSearch(struct sqlConnection *conn, char *searchWord, struct jsonWrite *jw) -/* conn is a connection to hgcentral, searching for one word, - * might be a UCSC database or a GenArk hub accession, or just some word. - */ +static int sqlJsonOut(struct jsonWrite *jw, struct sqlResult *sr) +/* given a sqlResult, walk through the rows and output the json */ { -/* the input word might be a database alias - * asmAliasFind returns the searchWord if no alias found - */ -char *perhapsAlias = asmAliasFind(searchWord); - int itemCount = 0; - -if (startsWith("GC", perhapsAlias)) - { - struct asmSummary *asmSumFound = NULL; - struct hash *asmSummaryHash = NULL; - asmSumFound = checkAsmSummary(conn, perhapsAlias, FALSE, 0); - if (asmSumFound) - { - struct asmSummary *el; - asmSummaryHash = newHash(0); - for (el = asmSumFound; el != NULL; el = el->next) - hashAdd(asmSummaryHash, el->assemblyAccession, (void *)el); - } - char query[4096]; - sqlSafef(query, sizeof(query), "SELECT * FROM %s WHERE gcAccession LIKE \"%s%%\"", genarkTable, perhapsAlias); - struct sqlResult *sr = sqlGetResult(conn, query); char **row; - struct combinedSummary *comboOutput = NULL; while ((row = sqlNextRow(sr)) != NULL) { - struct genark *genome = genarkLoad(row); - struct combinedSummary *cs = NULL; - AllocVar(cs); - cs->genArk = genome; - cs->dbDb = NULL; - if (asmSummaryHash) - { - cs->summary = hashFindVal(asmSummaryHash, genome->gcAccession); - if (cs->summary) - hashRemove(asmSummaryHash, genome->gcAccession); + 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; } - slAddHead(&comboOutput, cs); +return (itemCount); } - sqlFreeResult(&sr); - if (allowAll && asmSummaryHash) + +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 */ { - /* check if all asmSummaryHash has been used up */ - struct hashCookie cookie = hashFirst(asmSummaryHash); - struct hashEl *hel; - while ((hel = hashNext(&cookie)) != NULL) +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); +long long matchCount = sqlQuickLongLong(conn, query); +if (matchCount > 0) { - struct combinedSummary *cs = NULL; - AllocVar(cs); - cs->genArk = NULL; - cs->dbDb = NULL; - cs->summary = hel->val; - slAddHead(&comboOutput, cs); + verbose(1, "DBG: matchCount: %lld from search '%s'\n", matchCount, query); + *totalMatchCount = matchCount; + 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); + 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; } - if (comboOutput) + +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 + */ { - slReverse(&comboOutput); - itemCount = outputCombo(jw, comboOutput); - } - } /* if (startsWith("GC", perhapsAlias)) */ -else - { /* not a GC genArk name, perhaps a UCSC database */ - if (hDbIsActive(perhapsAlias)) - { - struct combinedSummary *comboOutput = NULL; - AllocVar(comboOutput); - comboOutput->summary = NULL; - comboOutput->genArk = NULL; - struct dbDb *dbDbEntry = hDbDb(perhapsAlias); - comboOutput->dbDb = dbDbEntry; - struct asmSummary *sumList = dbDbAsmEquivalent(conn, perhapsAlias); - if (sumList) - comboOutput->summary = sumList; - itemCount = outputCombo(jw, comboOutput); - } - } /* checked genArk and UCSC database */ -if (0 == itemCount) /* not found in genark or ucsc db, check asmSummary */ +char query[4096]; +int 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); +long long matchCount = sqlQuickLongLong(conn, query); +boolean prefixSearch = FALSE; +if (matchCount < 1) /* no match, add the * wild card match to make a prefix match */ { - long long totalMatch = 0; - /* no more than 100 items result please */ - struct asmSummary *summaryList = asmSummaryFullText(conn, perhapsAlias, (long long) 100, &totalMatch); - /* now check the genark table to see if there are any of those */ - struct combinedSummary *comboOutput = checkForGenArk(conn, summaryList); - if (comboOutput) - itemCount = outputCombo(jw, comboOutput); + sqlSafef(query, sizeof(query), "SELECT count(*) FROM %s WHERE MATCH(name, commonName, scientificName, clade, description) AGAINST ('%s*' IN BOOLEAN MODE);", asmListTable, searchWord); + matchCount = sqlQuickLongLong(conn, query); + if (matchCount > 0) + prefixSearch = TRUE; } +if (matchCount < 1) + return itemCount; +*totalMatchCount = matchCount; + +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); +struct sqlResult *sr = sqlGetResult(conn, query); +itemCount = sqlJsonOut(jw, sr); +sqlFreeResult(&sr); + return itemCount; -} /* static int singleWordSearch(struct sqlConnection *conn, char *searchWord, struct jsonWrite *jw) */ +} /* 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, genarkTable)) - apiErrAbort(err500, err500Msg, "missing central.genark table in function /findGenome'%s'", extraArgs); +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); } -genarkTable = genarkTableName(); - 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); -int itemCount = 0; +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 = singleWordSearch(conn, words[0], jw); - if (itemCount) - jsonWriteNumber(jw, "itemCount", itemCount); - else - verbose(0, "# DBG need to search this word %s somewhere else\n", words[0]); - } + itemCount = oneWordSearch(conn, words[0], jw, &totalMatchCount); else /* multiple word search */ +/* 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 (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); }