e70152e44cc66cc599ff6b699eb8adc07f3e656a kent Sat May 24 21:09:34 2014 -0700 Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment. diff --git src/hg/hgTablesTest/hgTablesTest.c src/hg/hgTablesTest/hgTablesTest.c index 7685fe4..b9698c8 100644 --- src/hg/hgTablesTest/hgTablesTest.c +++ src/hg/hgTablesTest/hgTablesTest.c @@ -1,1190 +1,1193 @@ /* hgTablesTest - Test hgTables web page. */ + +/* Copyright (C) 2014 The Regents of the University of California + * See README in this or parent directory for licensing information. */ #include "common.h" #include "memalloc.h" #include "linefile.h" #include "hash.h" #include "htmshell.h" #include "portable.h" #include "options.h" #include "errCatch.h" #include "ra.h" #include "htmlPage.h" #include "../hgTables/hgTables.h" #include "hdb.h" #include "qa.h" #include "chromInfo.h" #define MAX_ATTEMPTS 10 /* Command line variables. */ char *clOrg = NULL; /* Organism from command line. */ char *clDb = NULL; /* DB from command line */ char *clGroup = NULL; /* Group from command line. */ char *clTrack = NULL; /* Track from command line. */ char *clTable = NULL; /* Table from command line. */ int clGroups = BIGNUM; /* Number of groups to test. */ int clTracks = 4; /* Number of track to test. */ int clTables = 2; /* Number of tables to test. */ int clDbs = 1; /* Number of databases per organism. */ int clOrgs = 2; /* Number of organisms to test. */ boolean appendLog; /* append to log rather than create it */ void usage() /* Explain usage and exit. */ { errAbort( "hgTablesTest - Test hgTables web page\n" "usage:\n" " hgTablesTest url log\n" "Where url is something like hgwbeta.cse.ucsc.edu/cgi-bin/hgTables\n" "and log is a file where error messages and statistics will be written\n" "options:\n" " -org=Human - Restrict to Human (or Mouse, Fruitfly, etc.)\n" " -db=hg17 - Restrict to particular database\n" " -group=genes - Restrict to a particular group\n" " -track=knownGene - Restrict to a particular track\n" " -table=knownGeneMrna - Restrict to a particular table\n" " -orgs=N - Number of organisms to test. Default %d\n" " -dbs=N - Number of databases per organism to test. Default %d\n" " -groups=N - Number of groups to test (default all)\n" " -tracks=N - Number of tracks per group to test (default %d)\n" " -tables=N - Number of tables per track to test (deault %d)\n" " -verbose=N - Set to 0 for silent operation, 2 or 3 for debugging\n" " -appendLog - Append to log file rather than creating it\n" , clOrgs, clDbs, clTracks, clTables); } FILE *logFile; /* Log file. */ static struct optionSpec options[] = { {"org", OPTION_STRING}, {"db", OPTION_STRING}, {"group", OPTION_STRING}, {"track", OPTION_STRING}, {"table", OPTION_STRING}, {"orgs", OPTION_INT}, {"dbs", OPTION_INT}, {"search", OPTION_STRING}, {"groups", OPTION_INT}, {"tracks", OPTION_INT}, {"tables", OPTION_INT}, {"appendLog", OPTION_BOOLEAN}, {NULL, 0}, }; struct tablesTest /* Test on one column. */ { struct tablesTest *next; struct qaStatus *status; /* Result of test. */ char *info[6]; }; enum tablesTestInfoIx { ntiiType, ntiiOrg, ntiiDb, ntiiGroup, ntiiTrack, ntiiTable, ntiiTotalCount, }; char *tablesTestInfoTypes[] = { "type", "organism", "db", "group", "track", "table"}; struct tablesTest *tablesTestList = NULL; /* List of all tests, latest on top. */ struct tablesTest *tablesTestNew(struct qaStatus *status, char *type, char *org, char *db, char *group, char *track, char *table) /* Save away test test results. */ { struct tablesTest *test; AllocVar(test); test->status = status; test->info[ntiiType] = cloneString(naForNull(type)); test->info[ntiiOrg] = cloneString(naForNull(org)); test->info[ntiiDb] = cloneString(naForNull(db)); test->info[ntiiGroup] = cloneString(naForNull(group)); test->info[ntiiTrack] = cloneString(naForNull(track)); test->info[ntiiTable] = cloneString(naForNull(table)); slAddHead(&tablesTestList, test); return test; } void tablesTestLogOne(struct tablesTest *test, FILE *f) /* Log test result to file. */ { int i; for (i=0; i<ArraySize(test->info); ++i) fprintf(f, "%s ", test->info[i]); fprintf(f, "%s\n", test->status->errMessage); } struct htmlPage *quickSubmit(struct htmlPage *basePage, char *org, char *db, char *group, char *track, char *table, char *testName, char *button, char *buttonVal) /* Submit page and record info. Return NULL if a problem. */ { struct htmlPage *page = NULL; // don't get ahead of the botDelay sleep1000(5000); verbose(2, "quickSubmit(%p, %s, %s, %s, %s, %s, %s, %s, %s)\n", basePage, naForNull(org), naForNull(db), naForNull(group), naForNull(track), naForNull(table), naForNull(testName), naForNull(button), naForNull(buttonVal)); if (basePage != NULL) { struct qaStatus *qs; struct tablesTest *test; if (db != NULL) htmlPageSetVar(basePage, NULL, "db", db); if (org != NULL) htmlPageSetVar(basePage, NULL, "org", org); if (group != NULL) htmlPageSetVar(basePage, NULL, hgtaGroup, group); if (track != NULL) htmlPageSetVar(basePage, NULL, hgtaTrack, track); if (table != NULL) htmlPageSetVar(basePage, NULL, hgtaTable, table); qs = qaPageFromForm(basePage, basePage->forms, button, buttonVal, &page); /* if (page->forms != NULL) htmlFormPrint(page->forms, stdout); */ test = tablesTestNew(qs, testName, org, db, group, track, table); } return page; } void serialSubmit(struct htmlPage **pPage, char *org, char *db, char *group, char *track, char *table, char *testName, char *button, char *buttonVal) /* Submit page, replacing old page with new one. */ { struct htmlPage *oldPage = *pPage; if (oldPage != NULL) { *pPage = quickSubmit(oldPage, org, db, group, track, table, testName, button, buttonVal); htmlPageFree(&oldPage); } } int tableSize(char *db, char *table) /* Return number of rows in table. */ { struct sqlConnection *conn = sqlConnect(db); int size = sqlTableSize(conn, table); sqlDisconnect(&conn); return size; } void quickErrReport() /* Report error at head of list if any */ { struct tablesTest *test = tablesTestList; if (test->status->errMessage != NULL) tablesTestLogOne(test, stderr); } void testSchema(struct htmlPage *tablePage, struct htmlForm *mainForm, char *org, char *db, char *group, char *track, char *table) /* Make sure schema page comes up. */ /* mainForm not used */ { struct htmlPage *schemaPage = quickSubmit(tablePage, org, db, group, track, table, "schema", hgtaDoSchema, "submit"); htmlPageFree(&schemaPage); } void testSummaryStats(struct htmlPage *tablePage, struct htmlForm *mainForm, char *org, char *db, char *group, char *track, char *table) /* Make sure summary stats page comes up. */ { if (htmlFormVarGet(mainForm, hgtaDoSummaryStats) != NULL) { struct htmlPage *statsPage = quickSubmit(tablePage, org, db, group, track, table, "summaryStats", hgtaDoSummaryStats, "submit"); htmlPageFree(&statsPage); } } boolean varIncludesType(struct htmlForm *form, char *var, char *value) /* Return TRUE if value is one of the options for var. */ { struct htmlFormVar *formVar = htmlFormVarGet(form, var); if (formVar == NULL) errAbort("Couldn't find %s variable in form", var); return slNameInList(formVar->values, value); } boolean outTypeAvailable(struct htmlForm *form, char *value) /* Return true if outType options include value. */ { return varIncludesType(form, hgtaOutputType, value); } int countNoncommentLines(char *s) /* Count number of lines in s that don't start with # */ { int count = 0; s = skipLeadingSpaces(s); while (s != NULL && s[0] != 0) { if (s[0] != '#') ++count; s = strchr(s, '\n'); s = skipLeadingSpaces(s); } return count; } int testAllFields(struct htmlPage *tablePage, struct htmlForm *mainForm, char *org, char *db, char *group, char *track, char *table) /* Get all fields and return count of rows. */ /* mainForm not used */ { struct htmlPage *outPage; int rowCount = 0; htmlPageSetVar(tablePage, NULL, hgtaOutputType, "primaryTable"); outPage = quickSubmit(tablePage, org, db, group, track, table, "allFields", hgtaDoTopSubmit, "submit"); /* check for NULL outPage */ if (outPage == NULL) errAbort("Null page in testAllFields"); rowCount = countNoncommentLines(outPage->htmlText); htmlPageFree(&outPage); return rowCount; } struct htmlFormVar *findPrefixedVar(struct htmlFormVar *list, char *prefix) /* Find first var with given prefix in list. */ { struct htmlFormVar *var; for (var = list; var != NULL; var = var->next) { if (startsWith(prefix, var->name)) return var; } return NULL; } void checkExpectedSimpleRows(struct htmlPage *outPage, int expectedRows) /* Make sure we got the number of rows we expect. */ { if (outPage != NULL) { int rowCount = countNoncommentLines(outPage->htmlText); if (rowCount != expectedRows) qaStatusSoftError(tablesTestList->status, "Got %d rows, expected %d", rowCount, expectedRows); } } void testOneField(struct htmlPage *tablePage, struct htmlForm *mainForm, char *org, char *db, char *group, char *track, char *table, int expectedRows) /* Get one field and make sure the count agrees with expected. */ /* mainForm not used */ { struct htmlPage *outPage; struct htmlForm *form; struct htmlFormVar *var; int attempts = 0; int rowCount = 0; if (tablePage->forms == NULL) errAbort("testOneField: Missing form (tablePage)"); htmlPageSetVar(tablePage, NULL, hgtaOutputType, "selectedFields"); outPage = quickSubmit(tablePage, org, db, group, track, table, "selFieldsPage", hgtaDoTopSubmit, "submit"); while (outPage == NULL && attempts < MAX_ATTEMPTS) { printf("testOneField: trying again to get selFieldsPage\n"); outPage = quickSubmit(tablePage, org, db, group, track, table, "selFieldsPage", hgtaDoTopSubmit, "submit"); attempts++; } if (outPage == NULL) { qaStatusSoftError(tablesTestList->status, "Error in testOneField - couldn't get outPage."); return; } if (outPage->forms == NULL) { qaStatusSoftError(tablesTestList->status, "Error in testOneField - missing form."); htmlPageFree(&outPage); return; } form = outPage->forms; rowCount = 0; var = findPrefixedVar(form->vars, "hgta_fs.check."); if (var == NULL) errAbort("No hgta_fs.check. vars in form"); htmlPageSetVar(outPage, NULL, var->name, "on"); serialSubmit(&outPage, org, db, group, track, table, "oneField", hgtaDoPrintSelectedFields, "submit"); // check that outPage != NULL checkExpectedSimpleRows(outPage, expectedRows); htmlPageFree(&outPage); } void testOutBed(struct htmlPage *tablePage, struct htmlForm *mainForm, char *org, char *db, char *group, char *track, char *table, int expectedRows) /* Get as bed and make sure count agrees with expected. */ /* mainForm not used */ { struct htmlPage *outPage; int attempts = 0; if (tablePage->forms == NULL) errAbort("testOutBed: Missing form (tablePage)"); htmlPageSetVar(tablePage, NULL, hgtaOutputType, "bed"); outPage = quickSubmit(tablePage, org, db, group, track, table, "bedUiPage", hgtaDoTopSubmit, "submit"); while (outPage == NULL && attempts < MAX_ATTEMPTS) { printf("testOutBed: trying again to get bedUiPage\n"); outPage = quickSubmit(tablePage, org, db, group, track, table, "bedUiPage", hgtaDoTopSubmit, "submit"); attempts++; } if (outPage == NULL) { qaStatusSoftError(tablesTestList->status, "Error in testOneBed - couldn't get outPage."); return; } if (outPage->forms == NULL) { qaStatusSoftError(tablesTestList->status, "Error in testOneBed - missing form."); htmlPageFree(&outPage); return; } serialSubmit(&outPage, org, db, group, track, table, "outBed", hgtaDoGetBed, "submit"); // check that outPage != NULL checkExpectedSimpleRows(outPage, expectedRows); htmlPageFree(&outPage); } void testOutGff(struct htmlPage *tablePage, struct htmlForm *mainForm, char *org, char *db, char *group, char *track, char *table) /* Get as GFF and make sure no crash. */ /* mainForm not used */ { struct htmlPage *outPage; if (tablePage->forms == NULL) errAbort("testOutGff: Missing form (tablePage)"); htmlPageSetVar(tablePage, NULL, hgtaOutputType, "gff"); outPage = quickSubmit(tablePage, org, db, group, track, table, "outGff", hgtaDoTopSubmit, "submit"); /* no checking here */ if (outPage != NULL) htmlPageFree(&outPage); } int countTagsBetween(struct htmlPage *page, char *start, char *end, char *type) /* Count number of tags of given type (which should be upper case) * between start and end. If start is NULL it will start from * beginning of page. If end is NULL it will end at end of page. */ { int count = 0; struct htmlTag *tag; if (start == NULL) start = page->htmlText; if (end == NULL) end = start + strlen(start); for (tag = page->tags; tag != NULL; tag = tag->next) { if (tag->start >= start && tag->start < end && sameString(tag->name, type)) { ++count; } } return count; } void testOutHyperlink(struct htmlPage *tablePage, struct htmlForm *mainForm, char *org, char *db, char *group, char *track, char *table, int expectedRows) /* Get as hyperlink and make sure count agrees with expected. */ /* mainForm not used */ { struct htmlPage *outPage; int attempts = 0; char *s; int rowCount; if (tablePage->forms == NULL) errAbort("testOutHyperlink: Missing form (tablePage)"); htmlPageSetVar(tablePage, NULL, hgtaOutputType, "hyperlinks"); outPage = quickSubmit(tablePage, org, db, group, track, table, "outHyperlinks", hgtaDoTopSubmit, "submit"); while (outPage == NULL && attempts < MAX_ATTEMPTS) { printf("testOutHyperLink: trying again to get outHyperLinks\n"); outPage = quickSubmit(tablePage, org, db, group, track, table, "outHyperlinks", hgtaDoTopSubmit, "submit"); attempts++; } if (outPage == NULL) { qaStatusSoftError(tablesTestList->status, "Error in testOutHyperLink - couldn't get outPage."); return; } s = stringIn("<!-- +++++++++++++++++++++ CONTENT TABLES +++++++++++++++++++ -->", outPage->htmlText); if (s == NULL) errAbort("Can't find <!-- +++++++++++++++++++++ CONTENT TABLES +++++++++++++++++++ -->"); rowCount = countTagsBetween(outPage, s, NULL, "A"); if (rowCount != expectedRows) qaStatusSoftError(tablesTestList->status, "Got %d rows, expected %d", rowCount, expectedRows); htmlPageFree(&outPage); } void testOutCustomTrack(struct htmlPage *tablePage, struct htmlForm *mainForm, char *org, char *db, char *group, char *track, char *table) /* Get as customTrack and make sure nothing explodes. */ /* mainForm not used */ { struct htmlPage *outPage; int attempts = 0; struct htmlFormVar *groupVar; if (tablePage->forms == NULL) errAbort("testOutCustomTrack: Missing form (tablePage)"); htmlPageSetVar(tablePage, NULL, hgtaOutputType, "customTrack"); outPage = quickSubmit(tablePage, org, db, group, track, table, "customTrackUi", hgtaDoTopSubmit, "submit"); while (outPage == NULL && attempts < MAX_ATTEMPTS) { printf("testOutCustomTrack: trying again to get customTrackUi\n"); outPage = quickSubmit(tablePage, org, db, group, track, table, "customTrackUi", hgtaDoTopSubmit, "submit"); attempts++; } if (outPage == NULL) { qaStatusSoftError(tablesTestList->status, "Error in testOutCustomTrack - couldn't get outPage."); return; } serialSubmit(&outPage, org, db, group, track, table, "outCustom", hgtaDoGetCustomTrackTb, "submit"); if (outPage == NULL) { qaStatusSoftError(tablesTestList->status, "Error in testOutCustomTrack - serialSubmit returned null page."); return; } if (outPage->forms == NULL) { qaStatusSoftError(tablesTestList->status, "Error in custom track - no form produced."); htmlPageFree(&outPage); return; } groupVar = htmlFormVarGet(outPage->forms, hgtaGroup); if (!slNameInList(groupVar->values, "user")) { qaStatusSoftError(tablesTestList->status, "No custom track group after custom track submission"); } htmlPageFree(&outPage); } void checkFaOutput(struct htmlPage *page, int expectedCount, boolean lessOk) /* Check that page contains expected number of sequences. If lessOk is set * (needed to handle some multiply mapped cases in refSeq) then just check * that have at least one if expecting any. */ { if (page != NULL) { int count = countChars(page->htmlText, '>'); if (count != expectedCount) { if (!lessOk || count > expectedCount || (expectedCount > 0 && count <= 0)) qaStatusSoftError(tablesTestList->status, "Got %d sequences, expected %d", count, expectedCount); } } } void testOutSequence(struct htmlPage *tablePage, struct htmlForm *mainForm, char *org, char *db, char *group, char *track, char *table, int expectedRows) /* Get as sequence and make sure count agrees with expected. */ /* mainForm not used */ { struct htmlPage *outPage; int attempts = 0; struct htmlFormVar *typeVar; if (tablePage->forms == NULL) errAbort("testOutSequence: Missing form (tablePage)"); htmlPageSetVar(tablePage, NULL, hgtaOutputType, "sequence"); outPage = quickSubmit(tablePage, org, db, group, track, table, "seqUi1", hgtaDoTopSubmit, "submit"); while (outPage == NULL && attempts < MAX_ATTEMPTS) { printf("testOutSequence: trying again to get seqUi1\n"); outPage = quickSubmit(tablePage, org, db, group, track, table, "seqUi1", hgtaDoTopSubmit, "submit"); attempts++; } if (outPage == NULL) { qaStatusSoftError(tablesTestList->status, "Error in testOutSequence - couldn't get outPage"); return; } if (outPage->forms == NULL) { qaStatusSoftError(tablesTestList->status, "Error in testOutSequence - missing form"); htmlPageFree(&outPage); return; } /* Since some genomic sequence things are huge, this will * only test in case where it's a gene prediction. */ typeVar = htmlFormVarGet(outPage->forms, hgtaGeneSeqType); if (typeVar != NULL) { struct htmlPage *seqPage; static char *types[] = {"protein", "mRNA"}; int i; for (i=0; i<ArraySize(types); ++i) { char *type = types[i]; if (slNameInList(typeVar->values, type)) { struct htmlPage *page; char testName[128]; htmlPageSetVar(outPage, NULL, hgtaGeneSeqType, type); safef(testName, sizeof(testName), "%sSeq", type); page = quickSubmit(outPage, org, db, group, track, table, testName, hgtaDoGenePredSequence, "submit"); checkFaOutput(page, expectedRows, TRUE); htmlPageFree(&page); } } htmlPageSetVar(outPage, NULL, hgtaGeneSeqType, "genomic"); serialSubmit(&outPage, org, db, group, track, table, "seqUi2", hgtaDoGenePredSequence, "submit"); // check that outPage != NULL /* On genomic page uncheck intron if it's there, then get results * and count them. */ if (htmlFormVarGet(outPage->forms, "hgSeq.intron") != NULL) htmlPageSetVar(outPage, NULL, "hgSeq.intron", NULL); seqPage = quickSubmit(outPage, org, db, group, track, table, "genomicSeq", hgtaDoGenomicDna, "submit"); // check that seqPage != NULL checkFaOutput(seqPage, expectedRows, FALSE); htmlPageFree(&seqPage); } htmlPageFree(&outPage); } boolean isObsolete(char *table) /* Some old table types we can't handle. Just warn that * they are there and skip. */ { boolean obsolete = sameString(table, "wabaCbr"); if (obsolete) qaStatusSoftError(tablesTestList->status, "Skipping obsolete table %s", table); return obsolete; } void testOneTable(struct htmlPage *trackPage, char *org, char *db, char *group, char *track, char *table) /* Test stuff on one table if we haven't already tested this table. */ { /* Why declared here and not globally? */ static struct hash *uniqHash = NULL; char fullName[256]; if (uniqHash == NULL) uniqHash = newHash(0); safef(fullName, sizeof(fullName), "%s.%s", db, table); if (!hashLookup(uniqHash, fullName)) { struct htmlPage *tablePage; struct htmlForm *mainForm; hashAdd(uniqHash, fullName, NULL); verbose(1, "Testing %s %s %s %s %s\n", naForNull(org), db, group, track, table); tablePage = quickSubmit(trackPage, org, db, group, track, table, "selectTable", hgtaTable, table); if (!isObsolete(table) && tablePage != NULL) { if ((mainForm = htmlFormGet(tablePage, "mainForm")) == NULL) { qaStatusSoftError(tablesTestList->status, "Couldn't get main form on tablePage for %s %s %s %s", db, group, track, table); } else { testSchema(tablePage, mainForm, org, db, group, track, table); testSummaryStats(tablePage, mainForm, org, db, group, track, table); if (outTypeAvailable(mainForm, "bed")) { if (outTypeAvailable(mainForm, "primaryTable")) { int rowCount; rowCount = testAllFields(tablePage, mainForm, org, db, group, track, table); testOneField(tablePage, mainForm, org, db, group, track, table, rowCount); testOutSequence(tablePage, mainForm, org, db, group, track, table, rowCount); testOutBed(tablePage, mainForm, org, db, group, track, table, rowCount); testOutHyperlink(tablePage, mainForm, org, db, group, track, table, rowCount); testOutGff(tablePage, mainForm, org, db, group, track, table); if (rowCount > 0) testOutCustomTrack(tablePage, mainForm, org, db, group, track, table); } } else if (outTypeAvailable(mainForm, "primaryTable")) { /* If BED type is not available then the region will be ignored, and * we'll end up scanning whole table. Make sure table is not huge * before proceeding. */ if (tableSize(db, table) < 500000) { int rowCount; rowCount = testAllFields(tablePage, mainForm, org, db, group, track, table); testOneField(tablePage, mainForm, org, db, group, track, table, rowCount); } } } htmlPageFree(&tablePage); } carefulCheckHeap(); } } void testOneTrack(struct htmlPage *groupPage, char *org, char *db, char *group, char *track, int maxTables) /* Test a little something on up to maxTables in one track. */ { struct htmlPage *trackPage = quickSubmit(groupPage, org, db, group, track, NULL, "selectTrack", hgtaTrack, track); struct htmlForm *mainForm; struct htmlFormVar *tableVar; struct slName *table; int tableIx; if (trackPage == NULL) errAbort("Couldn't select track %s", track); if ((mainForm = htmlFormGet(trackPage, "mainForm")) == NULL) errAbort("Couldn't get main form on trackPage"); if ((tableVar = htmlFormVarGet(mainForm, hgtaTable)) == NULL) errAbort("Can't find table var"); for (table = tableVar->values, tableIx = 0; table != NULL && tableIx < maxTables; table = table->next, ++tableIx) { if (clTable == NULL || sameString(clTable, table->name)) testOneTable(trackPage, org, db, group, track, table->name); } /* Clean up. */ htmlPageFree(&trackPage); } void testOneGroup(struct htmlPage *dbPage, char *org, char *db, char *group, int maxTracks) /* Test a little something on up to maxTracks in one group */ { struct htmlPage *groupPage = quickSubmit(dbPage, org, db, group, NULL, NULL, "selectGroup", hgtaGroup, group); struct htmlForm *mainForm; struct htmlFormVar *trackVar; struct slName *track; int trackIx; if ((mainForm = htmlFormGet(groupPage, "mainForm")) == NULL) errAbort("Couldn't get main form on groupPage"); if ((trackVar = htmlFormVarGet(mainForm, hgtaTrack)) == NULL) errAbort("Can't find track var"); for (track = trackVar->values, trackIx = 0; track != NULL && trackIx < maxTracks; track = track->next, ++trackIx) { if (clTrack == NULL || sameString(track->name, clTrack)) testOneTrack(groupPage, org, db, group, track->name, clTables); } /* Clean up. */ htmlPageFree(&groupPage); } void testGroups(struct htmlPage *dbPage, char *org, char *db, int maxGroups) /* Test a little something in all groups for dbPage. */ { struct htmlForm *mainForm; struct htmlFormVar *groupVar; struct slName *group; int groupIx; if ((mainForm = htmlFormGet(dbPage, "mainForm")) == NULL) errAbort("Couldn't get main form on dbPage"); if ((groupVar = htmlFormVarGet(mainForm, hgtaGroup)) == NULL) errAbort("Can't find group var"); for (group = groupVar->values, groupIx=0; group != NULL && groupIx < maxGroups; group = group->next, ++groupIx) { if (!sameString("allTables", group->name)) { if (clGroup == NULL || sameString(clGroup, group->name)) testOneGroup(dbPage, org, db, group->name, clTracks); } } } void getTestRegion(char *db, char region[256], int regionSize) /* Look up first chromosome in database and grab five million bases * from the middle of it. */ { struct sqlConnection *conn = sqlConnect(db); struct sqlResult *sr = sqlGetResult(conn, "NOSQLINJ select * from chromInfo limit 1"); char **row; struct chromInfo ci; int start,end,middle; if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't get one row from chromInfo"); chromInfoStaticLoad(row, &ci); middle = ci.size/2; start = middle-2500000; end = middle+2500000; if (start < 0) start = 0; if (end > ci.size) end = ci.size; safef(region, regionSize, "%s:%d-%d", ci.chrom, start+1, end); verbose(1, "Testing %s at position %s\n", db, region); fprintf(logFile, "Testing %s at position %s\n", db, region); sqlFreeResult(&sr); sqlDisconnect(&conn); } void testDb(struct htmlPage *orgPage, char *org, char *db) /* Test on one database. */ { struct htmlPage *dbPage; char region[256]; htmlPageSetVar(orgPage, NULL, "db", db); getTestRegion(db, region, sizeof(region)); htmlPageSetVar(orgPage, NULL, "position", region); htmlPageSetVar(orgPage, NULL, hgtaRegionType, "range"); dbPage = quickSubmit(orgPage, org, db, NULL, NULL, NULL, "selectDb", "submit", "go"); if (dbPage != NULL) testGroups(dbPage, org, db, clGroups); htmlPageFree(&dbPage); } void testOrg(struct htmlPage *rootPage, struct htmlForm *rootForm, char *org) /* Test on organism. */ { struct htmlPage *orgPage; struct htmlForm *mainForm; struct htmlFormVar *dbVar; struct slName *db; int dbIx; /* Get page with little selected beyond organism. This page * will get whacked around a little by testDb, so set range * position and db to something safe each time through. */ htmlPageSetVar(rootPage, rootForm, "org", org); htmlPageSetVar(rootPage, NULL, "db", NULL); htmlPageSetVar(rootPage, NULL, hgtaRegionType, NULL); htmlPageSetVar(rootPage, NULL, "position", NULL); orgPage = htmlPageFromForm(rootPage, rootPage->forms, "submit", "Go"); if ((mainForm = htmlFormGet(orgPage, "mainForm")) == NULL) { errAbort("Couldn't get main form on orgPage"); } if ((dbVar = htmlFormVarGet(mainForm, "db")) == NULL) errAbort("Couldn't get org var"); for (db = dbVar->values, dbIx=0; db != NULL && dbIx < clDbs; db = db->next, ++dbIx) { testDb(orgPage, org, db->name); } htmlPageFree(&orgPage); } void verifyJoinedFormat(char *s) /* Verify that s consists of lines with two tab-separated fields, * and that the second field has some n/a and some comma-separated lists. */ { char *e; int lineIx = 0; boolean gotCommas = FALSE, gotNa = FALSE; while (s != NULL && s[0] != 0) { char *row[3]; int fieldCount; ++lineIx; e = strchr(s, '\n'); if (e != NULL) *e++ = 0; if (s[0] != '#') { fieldCount = chopTabs(s, row); if (fieldCount != 2) { qaStatusSoftError(tablesTestList->status, "Got %d fields line %d of joined result, expected 2", fieldCount, lineIx); break; } if (sameString(row[1], "n/a")) gotNa = TRUE; if (countChars(s, ',') >= 2) gotCommas = TRUE; } s = e; } if (!gotCommas) qaStatusSoftError(tablesTestList->status, "Expected some rows in join to have comma separated lists."); if (!gotNa) qaStatusSoftError(tablesTestList->status, "Expected some rows in joint to have n/a."); } void testJoining(struct htmlPage *rootPage) /* Simulate pressing buttons to get a reasonable join on a * couple of uniProt tables. */ { struct htmlPage *allPage, *page; char *org = NULL, *db = NULL, *group = "allTables", *track="uniProt"; int expectedCount = tableSize("uniProt", "taxon"); allPage = quickSubmit(rootPage, org, db, group, "uniProt", "uniProt.taxon", "taxonJoin1", NULL, NULL); if (allPage != NULL) { if (allPage->forms == NULL) { errAbort("uniProt page with no form"); } else { int count = testAllFields(allPage, allPage->forms, org, db, group, track, "uniProt.taxon"); if (count != expectedCount) qaStatusSoftError(tablesTestList->status, "Got %d rows in uniProt.taxon, expected %d", count, expectedCount); htmlPageSetVar(allPage, NULL, hgtaOutputType, "selectedFields"); page = quickSubmit(allPage, org, db, group, track, "uniProt.taxon", "taxonJoin2", hgtaDoTopSubmit, "submit"); htmlPageSetVar(page, NULL, "hgta_fs.linked.uniProt.commonName", "on"); serialSubmit(&page, org, db, group, track, NULL, "taxonJoin3", hgtaDoSelectFieldsMore, "submit"); if (page != NULL) { htmlPageSetVar(page, NULL, "hgta_fs.check.uniProt.taxon.binomial", "on"); htmlPageSetVar(page, NULL, "hgta_fs.check.uniProt.commonName.val", "on"); serialSubmit(&page, org, db, group, track, NULL, "taxonJoin4", hgtaDoPrintSelectedFields, "submit"); if (page != NULL) { checkExpectedSimpleRows(page, expectedCount); verifyJoinedFormat(page->htmlText); htmlPageFree(&page); } } } } htmlPageFree(&allPage); verbose(1, "Tested joining on uniProt.taxon & commonName\n"); } void checkXenopus(char *s) /* Check that all lines start with xenopus, and that we * see laevis in there somewhere. */ { char *e; boolean gotLaevis = FALSE; while (s != NULL && s[0] != 0) { s = skipLeadingSpaces(s); e = strchr(s, '\n'); if (e != NULL) *e++ = 0; if (s[0] != '#') { char *t = strchr(s, '\t'); if (t != NULL) *t = 0; if (!startsWith("Xenopus", s)) { qaStatusSoftError(tablesTestList->status, "Xenopus filter passing non-Xenopus"); return; } if (sameString(s, "Xenopus laevis")) gotLaevis = TRUE; } s = e; } if (!gotLaevis) qaStatusSoftError(tablesTestList->status, "Can't find Xenopus laevis in filtered uniProt.taxon"); } void testFilter(struct htmlPage *rootPage) /* Simulate pressing buttons to get a reasonable filter on * uniProt taxon. */ { char *org = NULL, *db = NULL, *group = "allTables", *track="uniProt", *table = "uniProt.taxon"; struct htmlPage *page; page = quickSubmit(rootPage, org, db, group, "uniProt", table, "taxonFilter1", hgtaDoFilterPage, "submit"); if (page != NULL) { struct htmlFormVar *var = htmlFormVarGet(page->forms, "hgta_fil.v.uniProt.taxon.binomial.pat"); if (var == NULL) internalErr(); htmlPageSetVar(page, NULL, "hgta_fil.v.uniProt.taxon.binomial.pat", "Xenopus*"); serialSubmit(&page, org, db, group, track, table, "taxonFilter2", hgtaDoFilterSubmit, "submit"); if (page != NULL) { htmlPageSetVar(page, NULL, hgtaOutputType, "selectedFields"); serialSubmit(&page, org, db, group, track, table, "taxonFilter3", hgtaDoTopSubmit, "submit"); if (page != NULL) { htmlPageSetVar(page, NULL, "hgta_fs.check.uniProt.taxon.binomial", "on"); serialSubmit(&page, org, db, group, track, table, "taxonFilter4", hgtaDoPrintSelectedFields, "submit"); if (page != NULL) checkXenopus(page->htmlText); htmlPageFree(&page); } } } verbose(1, "Tested filter on uniProt.taxon\n"); } void testIdentifier(struct htmlPage *rootPage) /* Do simple check on identifiers. Relies on * 8355 Xenopus laevis being stable taxon (and not being filtered out * by testFilter). */ { char *org = NULL, *db = NULL, *group = "allTables", *track="uniProt", *table = "uniProt.taxon"; struct htmlPage *page; page = quickSubmit(rootPage, org, db, group, "uniProt", table, "taxonId1", hgtaDoPasteIdentifiers, "submit"); if (page != NULL) { htmlPageSetVar(page, NULL, hgtaPastedIdentifiers, "8355"); serialSubmit(&page, org, db, group, track, table, "taxonId2", hgtaDoPastedIdentifiers, "submit"); if (page != NULL) { htmlPageSetVar(page, NULL, hgtaOutputType, "selectedFields"); serialSubmit(&page, org, db, group, track, table, "taxonId3", hgtaDoTopSubmit, "submit"); if (page != NULL) { htmlPageSetVar(page, NULL, "hgta_fs.check.uniProt.taxon.binomial", "on"); serialSubmit(&page, org, db, group, track, table, "taxonId4", hgtaDoPrintSelectedFields, "submit"); if (page != NULL) { if (!stringIn("Xenopus laevis", page->htmlText)) { qaStatusSoftError(tablesTestList->status, "Can't find Xenopus laevis in uniProt.taxon #8355"); } checkExpectedSimpleRows(page, 1); } htmlPageFree(&page); } } } verbose(1, "Tested identifier on uniProt.taxon\n"); } void statsOnSubsets(struct tablesTest *list, int subIx, FILE *f) /* Report tests of certain subtype. */ { struct tablesTest *test; struct hash *hash = newHash(0); struct slName *typeList = NULL, *type; fprintf(f, "\n%s subtotals\n", tablesTestInfoTypes[subIx]); /* Get list of all types in this field. */ for (test = list; test != NULL; test = test->next) { char *info = test->info[subIx]; if (!hashLookup(hash, info)) { type = slNameNew(info); hashAdd(hash, info, type); slAddHead(&typeList, type); } } slNameSort(&typeList); hashFree(&hash); for (type = typeList; type != NULL; type = type->next) { struct qaStatistics *stats; AllocVar(stats); for (test = list; test != NULL; test = test->next) { if (sameString(type->name, test->info[subIx])) { qaStatisticsAdd(stats, test->status); } } qaStatisticsReport(stats, type->name, f); freez(&stats); } } void reportSummary(struct tablesTest *list, FILE *f) /* Report summary of test results. */ { struct qaStatistics *stats; struct tablesTest *test; int i; AllocVar(stats); for (i=0; i<ntiiTotalCount; ++i) statsOnSubsets(list, i, f); for (test = list; test != NULL; test = test->next) qaStatisticsAdd(stats, test->status); fprintf(f, "\ngrand total\n"); qaStatisticsReport(stats, "Total", f); } void reportAll(struct tablesTest *list, FILE *f) /* Report all tests. */ { struct tablesTest *test; for (test = list; test != NULL; test = test->next) { if (test->status->errMessage != NULL) tablesTestLogOne(test, f); } } void hgTablesTest(char *url, char *logName) /* hgTablesTest - Test hgTables web page. */ { /* Get default page, and open log. */ struct htmlPage *rootPage = htmlPageGet(url); if (appendLog) logFile = mustOpen(logName, "a"); else logFile = mustOpen(logName, "w"); if (! endsWith(url, "hgTables")) warn("Warning: first argument should be a complete URL to hgTables, " "but doesn't look like one (%s)", url); htmlPageValidateOrAbort(rootPage); /* Go test what they've specified in command line. */ if (clDb != NULL) { testDb(rootPage, NULL, clDb); } else { struct htmlForm *mainForm; struct htmlFormVar *orgVar; if ((mainForm = htmlFormGet(rootPage, "mainForm")) == NULL) errAbort("Couldn't get main form"); if ((orgVar = htmlFormVarGet(mainForm, "org")) == NULL) errAbort("Couldn't get org var"); if (clOrg != NULL) testOrg(rootPage, mainForm, clOrg); else { struct slName *org; int orgIx; for (org = orgVar->values, orgIx=0; org != NULL && orgIx < clOrgs; org = org->next, ++orgIx) { testOrg(rootPage, mainForm, org->name); } } } /* Do some more complex tests on uniProt. */ testJoining(rootPage); testFilter(rootPage); testIdentifier(rootPage); /* Clean up and report. */ htmlPageFree(&rootPage); slReverse(&tablesTestList); reportSummary(tablesTestList, stdout); reportAll(tablesTestList, logFile); fprintf(logFile, "---------------------------------------------\n"); reportSummary(tablesTestList, logFile); } int main(int argc, char *argv[]) /* Process command line. */ { pushCarefulMemHandler(500000000); optionInit(&argc, argv, options); if (argc != 3) usage(); clDb = optionVal("db", clDb); clOrg = optionVal("org", clOrg); clGroup = optionVal("group", clGroup); clTrack = optionVal("track", clTrack); clTable = optionVal("table", clTable); clDbs = optionInt("dbs", clDbs); clOrgs = optionInt("orgs", clOrgs); clGroups = optionInt("groups", clGroups); clTracks = optionInt("tracks", clTracks); clTables = optionInt("tables", clTables); appendLog = optionExists("appendLog"); if (clOrg != NULL) clOrgs = BIGNUM; hgTablesTest(argv[1], argv[2]); carefulCheckHeap(); return 0; }