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 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 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);
}
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 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 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 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 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 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 testColInfo(struct htmlPage *dbPage, char *org, char *db, char *col)
/* Click on all colInfo columns. */
{
struct htmlPage *infoPage =
quickSubmit(dbPage, NULL, org, db, col, NULL, "colInfo", colInfoVarName, col);
if (infoPage != NULL)
{
if (stringIn("No additional info available", infoPage->htmlText))
qaStatusSoftError(nearTestList->status,
"%s failed - no %s.html?", colInfoVarName, col);
}
quickErrReport();
htmlPageFree(&infoPage);
}
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 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 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 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);
}
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();
}
}
