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 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 syncOneRecord(struct sqlConnection *conn, char *type, struct jsonWrite *json,
char *table, long long id)
/* Send over one record and save UUID result to row of table defined by id in idField. */
{
/* Construct dyString for URL */
struct dyString *dyUrl = dyStringNew(0);
dyStringPrintf(dyUrl, "http://%s:%s@%s/%s/", gUserId, gPassword, gHost, type);
verbose(2, "%s\n", dyUrl->string);
/* Construct dyString for http header */
struct dyString *dyHeader = dyStringNew(0);
dyStringPrintf(dyHeader, "Content-length: %d\r\n", json->dy->stringSize);
dyStringPrintf(dyHeader, "Content-type: text/javascript\r\n");
/* Send header and then JSON */
int sd = netOpenHttpExt(dyUrl->string, "POST", dyHeader->string);
mustWriteFd(sd, json->dy->string, json->dy->stringSize);
/* Grab response */
struct dyString *dyText = netSlurpFile(sd);
close(sd);
uglyf("%s\n", dyText->string);
/* Turn it into htmlPage structure - this will also parse out http header */
struct htmlPage *response = htmlPageParse(dyUrl->string, dyText->string);
uglyf("status %s %d\n", response->status->version, response->status->status);
/* If we got bad status abort with hopefully very informative message. */
int status = response->status->status;
if (status != 200 && status != 201) // HTTP codes
{
errAbort("ERROR - Metadatabase returns %d to our post request\n"
"POSTED JSON: %s\n"
"URL: %s\n"
"FULL RESPONSE: %s\n", status, json->dy->string, dyUrl->string, dyText->string);
}
/* Parse uuid out of json response. It should look something like
{
"status": "success",
"@graph": [
{
"description": "The macs2 peak calling software from Tao Liu.",
"name": "macs2", "title": "macs2", "url": "https://github.com/taoliu/MACS/",
"uuid": "9bda84fd-9872-49e3-9aa0-b71adbf9f31d",
"schema_version": "1",
"source_url": "https://github.com/taoliu/MACS/",
"references": [],
"@id": "/software/9bda84fd-9872-49e3-9aa0-b71adbf9f31d/",
"@type": ["software", "item"],
"aliases": []
}
],
"@type": ["result"]
}
*/
struct jsonElement *jsonRoot = jsonParse(response->htmlText);
struct jsonElement *graph = jsonMustFindNamedField(jsonRoot, "", "@graph");
struct slRef *ref = jsonListVal(graph, "@graph");
assert(slCount(ref) == 1);
struct jsonElement *graphEl = ref->val;
char *uuid = jsonStringField(graphEl, "uuid");
uglyf("Got uuid %s\n", uuid);
/* Save uuid to table */
char query[256];
sqlSafef(query, sizeof(query),
"update %s set metaUuid='%s' where id=%lld", table, uuid, id);
sqlUpdate(conn, query);
/* Clean up */
dyStringFree(&dyUrl);
dyStringFree(&dyHeader);
dyStringFree(&dyText);
response->fullText = NULL; // avoid double free of this
htmlPageFree(&response);
}
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 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);
}