6b90bc1b27dafa410579a6cbb479cd4ab44403c8 hiram Sun Feb 4 20:54:17 2024 -0800 add stats output function and timing measure refs #32897 diff --git src/hg/hubApi/findGenome.c src/hg/hubApi/findGenome.c index 92c9b5c..fc5d195 100644 --- src/hg/hubApi/findGenome.c +++ src/hg/hubApi/findGenome.c @@ -7,30 +7,31 @@ #include "genark.h" #include "asmAlias.h" #include "asmSummary.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 boolean statsOnly = FALSE; 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); @@ -269,59 +270,155 @@ comboOutput->dbDb = dbDbEntry; itemCount = outputCombo(jw, comboOutput); } } /* checked genArk and UCSC database */ if (0 == itemCount) /* not found in genark or ucsc db, check asmSummary */ { 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); } return itemCount; -} /* static void singleWordSearch(struct sqlConnection *conn, char *searchWord) */ +} /* static int singleWordSearch(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(); if (extraArgs) apiErrAbort(err400, err400Msg, "extraneous arguments found for function /findGenome'%s'", extraArgs); +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 *statsOnlyArg = cgiOptionalString("statsOnly"); +if (isNotEmpty(statsOnlyArg)) + { + if (sameString("1", statsOnlyArg)) + statsOnly = TRUE; + else if (sameString("0", statsOnlyArg)) + statsOnly = FALSE; + else + apiErrAbort(err400, err400Msg, "unrecognized 'statsOnly=%s' argument, can only be =1 or =0", statsOnlyArg); + } + struct sqlConnection *conn = hConnectCentral(); -genarkTable = genarkTableName(); if (!sqlTableExists(conn, genarkTable)) apiErrAbort(err500, err500Msg, "missing central.genark table in function /findGenome'%s'", extraArgs); +int wordCount = 0; + +if (! statsOnly) + { /* verify number of words in search string is legal */ -int wordCount = chopByWhite(searchString, NULL, 0); + 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); int itemCount = 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 @@ -334,23 +431,24 @@ 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); } +elapsedTime(jw); if (itemCount) apiFinishOutput(0, NULL, jw); else apiErrAbort(err400, err400Msg, "no genomes found matching search term %s='%s' for endpoint: /findGenome", argGenomeSearchTerm, inputSearchString); hDisconnectCentral(&conn); }