struct htmlFormVar *htmlPageGetVar(struct htmlPage *page, struct htmlForm *form, char *name)
/* Get named variable. If form is NULL, first form in page is used. */
{
if (form == NULL)
form = page->forms;
return htmlFormVarGet(form, name);
}
void testDbSorts(struct htmlPage *dbPage, char *org, char *db,
char *accColumn, struct slName *geneList)
/* Test on one database. */
{
struct htmlPage *emptyConfig;
struct htmlFormVar *sortVar = htmlFormVarGet(dbPage->forms, orderVarName);
struct slName *gene, *sort;
uglyf("testDbSorts %s %s\n", org, db);
if (sortVar == NULL)
errAbort("Couldn't find var %s", orderVarName);
emptyConfig = emptyConfigPage(dbPage, org, db);
if (emptyConfig != NULL)
{
for (sort = sortVar->values; sort != NULL; sort= sort->next)
{
for (gene = geneList; gene != NULL; gene = gene->next)
{
testSort(emptyConfig, org, db, sort->name, gene->name, accColumn);
}
}
htmlPageFree(&emptyConfig);
}
}
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 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 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);
}
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);
}
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);
}
}
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);
}
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 htmlFormVarSet(struct htmlForm *form, char *name, char *val)
/* Set variable to given value. Create it if it doesn't exist*/
{
struct htmlFormVar *var;
if (form == NULL)
errAbort("Null form passed to htmlFormVarSet");
var = htmlFormVarGet(form, name);
if (var == NULL)
{
AllocVar(var);
var->type = "TEXT";
var->tagName = "INPUT";
var->name = name;
slAddHead(&form->vars, var);
}
freez(&var->curVal);
var->curVal = cloneString(val);
}
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 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 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 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 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);
}
