void testDb(struct htmlPage *orgPage, char *org, char *db)
/* Test on one database. */
{
struct hash *genomeRa = hgReadRa(org, db, dataDir, "genome.ra", NULL);
char *canonicalTable = hashMustFindVal(genomeRa, "canonicalTable");
char *accColumn = hashMustFindVal(genomeRa, "idColumn");
struct slName *geneList = sqlRandomSampleWithSeed(db, canonicalTable, "transcript", clRepeat, seed);
struct htmlPage *dbPage;
struct slName *ptr;
verbose(1, "genelist:\n");
for (ptr = geneList; ptr != NULL; ptr = ptr->next)
verbose(1, "%s\n", ptr->name);
htmlPageSetVar(orgPage, NULL, "db", db);
htmlPageSetVar(orgPage, NULL, searchVarName, "");
dbPage = quickSubmit(orgPage, NULL, org, db, NULL, NULL, "dbEmptyPage", "submit", "go");
quickErrReport();
if (dbPage != NULL)
{
testDbColumns(dbPage, org, db, geneList);
testDbSorts(dbPage, org, db, accColumn, geneList);
testDbFilters(dbPage, org, db, accColumn, geneList);
}
htmlPageFree(&dbPage);
hashFree(&genomeRa);
slNameFreeList(&geneList);
}
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 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 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 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");
}
struct htmlPage *quickSubmit(struct htmlPage *basePage,
char *sort, char *org, char *db, char *col, char *gene,
char *testName, char *button, char *buttonVal)
/* Submit page and record info. Return NULL if a problem. */
{
struct nearTest *test;
struct qaStatus *qs;
struct htmlPage *page;
if (basePage != NULL)
{
if (db != NULL)
htmlPageSetVar(basePage, NULL, "db", db);
if (org != NULL)
htmlPageSetVar(basePage, NULL, "org", org);
qs = qaPageFromForm(basePage, basePage->forms,
button, buttonVal, &page);
test = nearTestNew(qs, testName, sort, org, db, col, gene);
}
return page;
}
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 testSort(struct htmlPage *emptyConfig, char *org, char *db, char *sort, char *gene, char *accColumn)
/* Test one column. */
{
char accVis[256];
struct htmlPage *printPage = NULL;
safef(accVis, sizeof(accVis), "near.col.%s.vis", accColumn);
htmlPageSetVar(emptyConfig, NULL, accVis, "on");
htmlPageSetVar(emptyConfig, NULL, orderVarName, sort);
htmlPageSetVar(emptyConfig, NULL, countVarName, "25");
htmlPageSetVar(emptyConfig, NULL, searchVarName, gene);
printPage = quickSubmit(emptyConfig, sort, org, db, NULL, gene, "sortType", "submit", "on");
if (printPage != NULL)
{
int lineCount = nearCountRows(printPage);
if (lineCount < 1)
qaStatusSoftError(nearTestList->status, "No rows for sort %s", sort);
}
quickErrReport();
htmlPageFree(&printPage);
}
void hgNearTest(char *url, char *log)
/* hgNearTest - Test hgNear web page. */
{
struct htmlPage *rootPage = htmlPageGet(url);
struct htmlForm *mainForm;
struct htmlFormVar *orgVar;
FILE *f = mustOpen(log, "w");
htmlPageValidateOrAbort(rootPage);
htmlPageSetVar(rootPage, NULL, orderVarName, "geneDistance");
htmlPageSetVar(rootPage, NULL, countVarName, "25");
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, clDb);
else
{
struct slName *org;
for (org = orgVar->values; org != NULL; org = org->next)
{
testOrg(rootPage, mainForm, org->name, clDb);
}
}
htmlPageFree(&rootPage);
slReverse(&nearTestList);
reportSummary(nearTestList, stdout);
fprintf(f,"seed=%d\n",seed);
reportAll(nearTestList, f);
fprintf(f, "---------------------------------------------\n");
reportSummary(nearTestList, f);
slFreeList(&nearTestList);
carefulClose(&f);
}
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 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");
}
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 tablesTest *test;
struct qaStatus *qs;
struct htmlPage *page;
// 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)
{
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 testOrg(struct htmlPage *rootPage, struct htmlForm *rootForm, char *org, char *forceDb)
/* Test on organism. If forceDb is non-null, only test on
* given database. */
{
struct htmlPage *orgPage;
struct htmlForm *mainForm;
struct htmlFormVar *dbVar;
struct slName *db;
htmlPageSetVar(rootPage, rootForm, "org", org);
htmlPageSetVar(rootPage, rootForm, "db", NULL);
htmlPageSetVar(rootPage, rootForm, searchVarName, "");
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; db != NULL; db = db->next)
{
if (forceDb == NULL || sameString(forceDb, db->name))
testDb(orgPage, org, db->name);
}
htmlPageFree(&orgPage);
}
void testCol(struct htmlPage *emptyConfig, char *org, char *db, char *col, char *gene)
/* Test one column. */
{
struct htmlPage *printPage = NULL;
char visVar[256];
safef(visVar, sizeof(visVar), "near.col.%s.vis", col);
htmlPageSetVar(emptyConfig, NULL, visVar, "on");
htmlPageSetVar(emptyConfig, NULL, orderVarName, "nameSimilarity");
htmlPageSetVar(emptyConfig, NULL, countVarName, "25");
printPage = quickSubmit(emptyConfig, NULL, org, db, col, gene, "colPrint", "Submit", "on");
if (printPage != NULL)
{
int expectCount = 25;
int lineCount = nearCountRows(printPage);
if (lineCount != expectCount)
qaStatusSoftError(nearTestList->status,
"Got %d rows, expected %d", lineCount, expectCount);
}
quickErrReport();
htmlPageFree(&printPage);
htmlPageSetVar(emptyConfig, NULL, visVar, NULL);
}
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 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;
}
void testDbColumns(struct htmlPage *dbPage, char *org, char *db,
struct slName *geneList)
/* Test on one database. */
{
struct htmlPage *emptyConfig;
struct slName *colList = NULL, *col;
struct htmlFormVar *var;
struct slName *gene;
uglyf("testDbColumns %s %s\n", org, db);
emptyConfig = emptyConfigPage(dbPage, org, db);
if (emptyConfig != NULL )
{
for (var = emptyConfig->forms->vars; var != NULL; var = var->next)
{
if (startsWith("near.col.", var->name) && endsWith(var->name, ".vis"))
{
char *colNameStart = var->name + strlen("near.col.");
char *colNameEnd = strchr(colNameStart, '.');
*colNameEnd = 0;
col = slNameNew(colNameStart);
slAddHead(&colList, col);
*colNameEnd = '.';
}
}
slReverse(&colList);
for (gene = geneList; gene != NULL; gene = gene->next)
{
htmlPageSetVar(emptyConfig, NULL, searchVarName, gene->name);
for (col = colList; col != NULL; col = col->next)
{
testCol(emptyConfig, org, db, col->name, gene->name);
}
}
for (col = colList; col != NULL; col = col->next)
{
testColInfo(dbPage, org, db, col->name);
}
}
htmlPageFree(&emptyConfig);
}
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 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 testDbFilters(struct htmlPage *dbPage, char *org, char *db,
char *accColumn, struct slName *geneList)
/* Test filter that returns just geneList. */
{
struct slName *gene;
int rowCount;
char accFilter[256];
/* Start out with filter page. */
struct htmlPage *page = quickSubmit(dbPage, NULL, org, db, accColumn, NULL,
"accOneFilterPage", advFilterVarName, "on");
verbose(1, "testFilters %s %s\n", org, db);
if (page == NULL)
return;
/* Set up to filter exactly one gene. */
safef(accFilter, sizeof(accFilter), "near.as.%s.wild", accColumn);
{
htmlPageSetVar(page, NULL, accFilter, geneList->name);
htmlPageSetVar(page, NULL, searchVarName, geneList->name);
serialSubmit(&page, NULL, org, db, accColumn, geneList->name,
"accOneFilterSubmit", "Submit", "on");
if (page == NULL)
return;
/* Make sure really got one gene. */
rowCount = nearCountUniqAccRows(page);
if (rowCount != 1)
{
qaStatusSoftError(nearTestList->status,
"Acc exact filter returned %d items", rowCount);
}
}
/* Set up filter for all genes in list. */
{
struct dyString *dy = newDyString(0);
int geneCount = slCount(geneList);
for (gene = geneList; gene != NULL; gene = gene->next)
dyStringPrintf(dy, "%s ", gene->name);
htmlPageSetVar(page, NULL, accFilter, dy->string);
htmlPageSetVar(page, NULL, countVarName, "all"); /* despite 3 genes requested, must see all if many dupes */
serialSubmit(&page, NULL, org, db, accColumn, dy->string,
"accMultiFilterSubmit", "Submit", "on");
dyStringFree(&dy);
if (page == NULL)
return;
rowCount = nearCountUniqAccRows(page);
if (rowCount != geneCount)
{
qaStatusSoftError(nearTestList->status,
"Acc multi filter expecting %d, got %d items", geneCount, rowCount);
}
}
/* Set up filter for wildcard in list. */
{
struct dyString *dy = newDyString(0);
char len = strlen(geneList->name);
dyStringAppendN(dy, geneList->name, len-1);
dyStringAppendC(dy, '*');
htmlPageSetVar(page, NULL, accFilter, dy->string);
serialSubmit(&page, NULL, org, db, accColumn, dy->string,
"accWildFilterSubmit", "Submit", "on");
dyStringFree(&dy);
if (page == NULL)
return;
rowCount = nearCountRows(page);
if (rowCount < 1)
{
qaStatusSoftError(nearTestList->status,
"Acc wild filter no match");
}
}
/* Clear out advanced filters. */
{
htmlPageFree(&page);
page = quickSubmit(dbPage, NULL, org, db, NULL, NULL,
"advFilterClear", advFilterClearVarName, "on");
}
htmlPageFree(&page);
}
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);
}