void jsValidateKeysOnDb(struct joiner *joiner, struct joinerSet *js,
char *db, struct hash *keyHash, struct keyHitInfo *khiList)
/* Validate keys pertaining to this database. */
{
struct joinerField *jf;
struct hash *localKeyHash = NULL;
struct keyHitInfo *localKhiList = NULL;
struct joinerField *keyField;
if ((keyField = js->fieldList) == NULL)
return;
if (keyHash == NULL)
{
char *keyDb;
if (slNameInList(keyField->dbList, db))
{
keyDb = db;
}
else if (!dbInAnyField(js->fieldList->next, db))
{
return;
}
else
{
if (slCount(keyField->dbList) == 1)
keyDb = keyField->dbList->name;
else
{
struct slName *lastDb = slLastEl(keyField->dbList);
keyDb = lastDb->name;
verbose(1, " note - using %s database as reference for identifier %s\n",
keyDb, js->name);
}
}
keyHash = localKeyHash = readKeyHash(keyDb, joiner, keyField,
&localKhiList);
khiList = localKhiList;
}
if (keyHash != NULL)
{
for (jf = js->fieldList; jf != NULL; jf = jf->next)
{
if (jf != keyField && slNameInList(jf->dbList, db))
{
doKeyChecks(db, joiner, js, keyHash, khiList, keyField, jf);
}
}
}
hashFree(&localKeyHash);
slFreeList(&localKhiList);
}
static struct joinerField *findJoinerField(struct joinerSet *js,
struct joinerDtf *dtf)
/* Find field in set if any that matches dtf */
{
struct slRef *chain = joinerSetInheritanceChain(js), *link;
struct joinerField *jf, *ret = NULL;
for (link = chain; link != NULL; link = link->next)
{
js = link->val;
for (jf = js->fieldList; jf != NULL; jf = jf->next)
{
if (sameString(dtf->table, jf->table) && sameString(dtf->field, jf->field))
{
if (slNameInList(jf->dbList, dtf->database))
{
ret = jf;
break;
}
}
}
if (ret != NULL)
break;
}
slFreeList(&chain);
return ret;
}
void checkTableForFields(struct sqlConnection *conn, char *tableName)
/* Do basic checks on the table to make sure it's kosher. i.e. */
/* chrom, chromStart, name all exist along with the table itself. */
{
struct slName *fieldList;
if (!sqlTableExists(conn, tableName))
errAbort("table %s not found.", tableName);
fieldList = sqlListFields(conn, tableName);
if (!slNameInList(fieldList, "chrom"))
errAbort("table %s doesn't have a chrom field. It must have chrom, chromStart, and name at the minimum.", tableName);
if (!slNameInList(fieldList, "chromStart"))
errAbort("table %s doesn't have a chrom field. It must have chrom, chromStart, and name at the minimum.", tableName);
if (!slNameInList(fieldList, "name"))
errAbort("table %s doesn't have a chrom field. It must have chrom, chromStart, and name at the minimum.", tableName);
slNameFreeList(&fieldList);
}
void doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
char *database = cgiOptionalString("db");
char *rtdbServer = cfgOption("rtdb.server");
char *rtdbPort = cfgOption("rtdb.port");
char *rtdbChoices = cfgOption("rtdb.databases");
struct slName *dbs = slNameListFromComma(rtdbChoices);
cart = theCart;
cartWebStart(cart, database, "MGC RTDB Update");
if (!rtdbServer)
errAbort("rtdb.update not defined in the hg.conf file. "
"Chances are this CGI isn't meant for this machine.");
if (!rtdbPort)
errAbort("rtdb.update not defined in the hg.conf file. "
"Chances are this CGI isn't meant for this machine.");
/* create HMTL form if button wasn't pressed. Otherwise, run the update */
if (!cgiVarExists("RTDBSubmit"))
makeForm(dbs);
else if ((database == NULL) || (!slNameInList(dbs, database)))
{
makeForm(dbs);
printf("<br>Error: Select one of databases listed.");
}
else
updateServer(rtdbServer, rtdbPort, database);
cartWebEnd();
slNameFreeList(&dbs);
}
void checkOneDependency(struct joiner *joiner,
struct joinerDependency *dep, struct sqlConnection *conn, char *dbName)
/* Check out one dependency in one database. */
{
char *tableToCheck = dep->table->table;
if (sqlWildcardIn(tableToCheck))
{
errAbort("Can't handle wildCards in dependency tables line %d of %s",
dep->lineIx, joiner->fileName);
}
if (slNameInList(dep->table->dbList, dbName)
&& sqlTableExists(conn, tableToCheck))
{
time_t tableTime = sqlTableUpdateTime(conn, tableToCheck);
struct joinerTable *dependsOn;
for (dependsOn = dep->dependsOnList; dependsOn != NULL;
dependsOn = dependsOn->next)
{
if (slNameInList(dependsOn->dbList, dbName))
{
if (!sqlTableExists(conn, dependsOn->table))
{
warn("Error: %s.%s doesn't exist line %d of %s",
dbName, dependsOn->table,
dep->lineIx, joiner->fileName);
}
else
{
time_t depTime = sqlTableUpdateTime(conn, dependsOn->table);
if (depTime > tableTime)
{
char *depStr = sqlUnixTimeToDate(&depTime, FALSE);
char *tableStr = sqlUnixTimeToDate(&tableTime, FALSE);
warn("Error: %s.%s updated after %s.%s line %d of %s",
dbName, dependsOn->table, dbName, tableToCheck,
dep->lineIx, joiner->fileName);
warn("\t%s vs. %s", depStr, tableStr);
freeMem(depStr);
freeMem(tableStr);
}
}
}
}
}
}
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);
}
static boolean filterColumnFail(struct vcfRecord *record, struct slName *filterValues)
/* Return TRUE if record's FILTER column value(s) matches one of filterValues (from cart). */
{
int i;
for (i = 0; i < record->filterCount; i++)
if (slNameInList(filterValues, record->filters[i]))
return TRUE;
return FALSE;
}
char *findSelDb()
/* Find user selected database (as opposed to genome database). */
{
struct slName *dbList = getDbListForGenome();
char *selDb = cartUsualString(cart, hgtaTrack, NULL);
if (!slNameInList(dbList, selDb))
selDb = cloneString(dbList->name);
slFreeList(&dbList);
return selDb;
}
boolean dbInAnyField(struct joinerField *fieldList, char *db)
/* Return TRUE if database is used in any field. */
{
struct joinerField *field;
for (field = fieldList; field != NULL; field = field->next)
{
if (slNameInList(field->dbList, db))
return TRUE;
}
return FALSE;
}
static struct chromSize *getChroms(char *db)
/* get list of chroms to use in tests */
{
struct slName *specs = optionMultiVal("chrom", NULL);
if (specs == NULL)
return getLongestChrom(db);
else if (slNameInList(specs, "all"))
return getAllChroms(db);
else
return getChromsFromSpecs(db, specs);
}
static struct hash *getCoveredTables(struct joiner *joiner, char *db,
struct sqlConnection *conn)
/* Get list of tables covered in database. */
{
struct hash *hash = hashNew(0);
struct joinerIgnore *ig;
struct slName *spec;
struct joinerSet *js;
struct joinerField *jf;
/* First put in all the ignored tables. */
for (ig = joiner->tablesIgnored; ig != NULL; ig = ig->next)
{
if (slNameInList(ig->dbList, db))
{
for (spec = ig->tableList; spec != NULL; spec = spec->next)
{
verbose(3,"ignoreTable: '%s'\n", spec->name);
addTablesLike(hash, conn, spec->name);
}
}
}
/* Now put in tables that are in one of the identifiers. */
for (js = joiner->jsList; js != NULL; js = js->next)
{
for (jf = js->fieldList; jf != NULL; jf = jf->next)
{
if (slNameInList(jf->dbList, db))
{
char spec[512];
safef(spec, sizeof(spec), "%s%s%s",
emptyForNull(jf->splitPrefix), jf->table,
emptyForNull(jf->splitSuffix));
addTablesLike(hash, conn, spec);
verbose(4,"ident: '%s', table: '%s'\n", js->name, spec);
}
}
}
return hash;
}
static struct joinerField *joinerSetIncludesTable(struct joinerSet *js,
char *database, char *table)
/* If joiner set includes database and table, return the associated field. */
{
struct joinerField *jf;
for (jf = js->fieldList; jf != NULL; jf = jf->next)
{
if (sameString(table, jf->table) && slNameInList(jf->dbList, database))
return jf;
}
return NULL;
}
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 cullCutters(struct cutter **enzList, boolean semicolon, struct slName *justThese, int matchSize)
/* Reduce the list of enzymes based on different options. */
{
struct cutter *enz = *enzList, *next;
while (enz != NULL)
{
next = enz->next;
if ((justThese && !slNameInList(justThese, enz->name)) ||
(enz->matchSize < matchSize) || (!semicolon && enz->semicolon))
{
slRemoveEl(enzList, enz);
cutterFree(&enz);
}
enz = next;
}
}
void kvtWriteAll(struct kvt *kvt, FILE *f, struct slName *hideList)
/* Write all keys to file except the ones in hideList */
{
int i;
static char lf = '\n';
struct keyVal *kv = kvt->table;
int keyCount = kvt->used;
for (i=0; i<keyCount; ++i)
{
char *key = kv->key;
if (kv->val != NULL && !slNameInList(hideList, key))
fprintf(f, "%s %s\n", key, kv->val);
++kv;
}
mustWrite(f, &lf, 1); /* Instead of fputc for error checking. */
}
struct grp *groupsFilterForTdbList(struct grp **grps,struct trackDb *tdbList)
{
struct grp *grpList = *grps;
*grps = NULL;
struct slName *tdbGroups = tdbListGetGroups(tdbList);
if (tdbList == NULL)
return *grps;
while (grpList != NULL)
{
struct grp *grp = slPopHead(&grpList);
if (slNameInList(tdbGroups,grp->name))
slAddHead(grps,grp);
}
slNameFreeList(&tdbGroups);
slReverse(grps);
return *grps;
}
static void addHitMiss(struct hash *keyHash, char *id, struct joinerField *jf,
int *pHits, char **pMiss, int *pTotal)
/* Record info about one hit or miss to keyHash */
{
id = doChopsAndUpper(jf, id);
if (jf->exclude == NULL || !slNameInList(jf->exclude, id))
{
struct keyHitInfo *khi;
if ((khi = hashFindVal(keyHash, id)) != NULL)
{
*pHits += 1;
khi->count += 1;
}
else
{
if (*pMiss == NULL)
*pMiss = cloneString(id);
}
*pTotal += 1;
}
}
void cleanup(struct mahoney *mahoneyList, char *mouseDb, char *pcrBed)
/* Look up gene names in refLink table where possible and use these instead
* of embedded names. */
{
struct mahoney *m;
struct hash *refHash = refGeneToNameHash(mouseDb);
struct hash *llHash = locusLinkToRefSeq(mouseDb);
struct hash *pcrHash = mtfToRnaHash(pcrBed);
int refWinsByPcr = 0, llWinsByPcr = 0, noWin = 0, bothWin = 0, noWinNoPcr = 0;
int refWinsByName = 0, llWinsByName = 0;
int refWinsByDefault = 0, llWinsByDefault = 0, noWinByDefault = 0;
int locusLinkFromPcr = 0, genbankFromPcr = 0;
for (m = mahoneyList; m != NULL; m = m->next)
{
char mtf[8];
char buf[9];
safef(mtf, sizeof(mtf), "%d", m->mtf);
struct rnaList *rl;
boolean gotConflict = FALSE;
rl = hashFindVal(pcrHash, mtf);
/* Look for conflicts between refSeq and locusLink representations.
* Use PCR and names to try to resolve them. (Ultimately this proves to
* be futile though). On unresolved ones axe the locusLink and refSeq
* id's */
if (startsWith("NM_", m->genbank) && m->locusId[0] != 0)
{
struct refSeqInfo *rsRsi = hashFindVal(refHash, m->genbank);
struct refSeqInfo *llRsi = hashFindVal(llHash, m->locusId);
boolean resolved = FALSE;
if (rsRsi != NULL && llRsi != NULL)
{
if (rsRsi->locusLink == llRsi->locusLink)
{
++bothWin;
resolved = TRUE;
}
else
{
if (conflictLog != NULL)
fprintf(conflictLog,
"MTF #%d locusLink %d (from %s) doesn't match %s\n",
m->mtf, rsRsi->locusLink, m->genbank, m->locusId);
}
if (!resolved)
{
if (rl != NULL)
{
if (slNameInList(rl->accList, rsRsi->refSeq))
{
safef(buf, sizeof(buf), "%d", rsRsi->locusLink);
m->locusId = cloneString(buf);
++refWinsByPcr;
if (conflictLog != NULL)
fprintf(conflictLog, " picking %d by PCR\n",
rsRsi->locusLink);
resolved = TRUE;
}
else if (slNameInList(rl->accList, llRsi->refSeq))
{
m->genbank = cloneString(llRsi->refSeq);
++llWinsByPcr;
if (conflictLog != NULL)
fprintf(conflictLog, " picking %d by PCR\n",
llRsi->locusLink);
resolved = TRUE;
}
else
{
++noWin;
}
}
}
else
{
++noWinNoPcr;
}
if (!resolved)
{
if (mahoneyNameAgrees(m->geneName, rsRsi->geneName))
{
safef(buf, sizeof(buf), "%d", rsRsi->locusLink);
m->locusId = cloneString(buf);
++refWinsByName;
if (conflictLog != NULL)
fprintf(conflictLog, " picking %d by name\n",
rsRsi->locusLink);
resolved = TRUE;
}
else if (mahoneyNameAgrees(m->geneName, llRsi->geneName))
{
m->genbank = cloneString(llRsi->refSeq);
++llWinsByName;
if (conflictLog != NULL)
fprintf(conflictLog, " picking %d by name\n",
llRsi->locusLink);
resolved = TRUE;
}
else
{
verbose(3, "No resolution MTF%d by name or PCR\n", m->mtf);
}
}
}
else if (rsRsi == NULL && llRsi == NULL)
{
verbose(3, "refSeq %s, locusLink %s not found in refLink\n", m->genbank, m->locusId);
if (conflictLog != NULL)
fprintf(conflictLog,
"MTF #%d neither locusLink %s nor refSeq %s exist for mouse\n",
m->mtf, m->locusId, m->genbank);
++noWinByDefault;
}
else if (llRsi == NULL)
{
if (conflictLog != NULL)
{
fprintf(conflictLog,
"MTF #%d locusLink %d (from %s) doesn't match %s\n",
m->mtf, rsRsi->locusLink, m->genbank, m->locusId);
fprintf(conflictLog, " picking %d since %s not in mouse\n",
rsRsi->locusLink, m->locusId);
}
verbose(3, "locusId %s not found in refLink (refSeq %s)\n", m->locusId, m->genbank);
safef(buf, sizeof(buf), "%d", rsRsi->locusLink);
m->locusId = cloneString(buf);
++refWinsByDefault;
resolved = TRUE;
}
else if (rsRsi == NULL)
{
if (conflictLog != NULL)
{
fprintf(conflictLog,
"MTF #%d refSeq %s doesn't exist in mouse\n",
m->mtf, m->genbank);
fprintf(conflictLog, " replacing with %s from locusLink %s\n",
llRsi->refSeq, m->locusId);
}
verbose(3, "refSeq %s not found in refLink (locusLink %s)\n", m->genbank, m->locusId);
m->genbank = cloneString(llRsi->refSeq);
++llWinsByDefault;
resolved = TRUE;
}
else
{
internalErr();
}
}
/* If no locusLink, try to get it from PCR */
if (m->locusId == NULL || m->locusId[0] == 0)
{
struct rnaList *rl = hashFindVal(pcrHash, mtf);
if (rl != NULL)
{
char *refSeq = findRefSeqInList(rl, NULL);
if (refSeq != NULL)
{
struct refSeqInfo *rsi = hashFindVal(refHash, refSeq);
if (rsi != NULL)
{
char buf[8];
++locusLinkFromPcr;
safef(buf, sizeof(buf), "%d", rsi->locusLink);
verbose(3, "MTF%d from PCR refSeq %s\n", m->mtf, refSeq);
if (conflictLog != NULL)
{
fprintf(conflictLog,
"MTF #%d setting locusLink/refseq to %d/%s from PCR\n",
m->mtf, rsi->locusLink, refSeq);
fprintf(conflictLog, " replacing with %s from locusLink %s\n",
rsi->refSeq, m->locusId);
}
m->locusId = cloneString(buf);
m->genbank = refSeq;
}
}
}
}
/* If have locusLink, use it to update name. */
{
struct refSeqInfo *llRsi = hashFindVal(llHash, m->locusId);
if (llRsi != NULL && llRsi->geneName != NULL && llRsi->geneName[0] != 0)
m->geneName = llRsi->geneName;
}
/* If no genbank, use PCR to fill in genbank. */
if ( (m->genbank == NULL || m->genbank[0] == 0)
&& (m->locusId == NULL || m->locusId[0] == 0)
&& (m->geneName == NULL || m->geneName[0] == 0))
{
struct rnaList *rl = hashFindVal(pcrHash, mtf);
if (rl != NULL)
{
m->genbank = rl->accList->name;
verbose(2, "MTF%d - filling in genbank %s from PCR\n", m->mtf, m->genbank);
++genbankFromPcr;
}
}
}
verbose(2, "RefSeq conflicts: refWinsByPcr %d, llWinsByPcr %d, noWin %d, noWinNoPcr %d, bothWin %d\n", refWinsByPcr, llWinsByPcr, noWin, noWinNoPcr, bothWin);
verbose(2, " refWinsByName %d, llWinsByName %d\n", refWinsByName, llWinsByName);
verbose(2, " refWinsByDefault %d, llWinsByDefault %d, noWinByDefault %d\n", refWinsByDefault, llWinsByDefault, noWinByDefault);
verbose(2, "Filled by PCR: locusLink %d, genbank %d\n", locusLinkFromPcr, genbankFromPcr);
}
void cdwCheckDataset(char *outputFile)
/* cdwCheckDataset - Look at all the submissions for a given dataset and print helpful stats.. */
{
FILE *f = mustOpen(outputFile,"w");
struct sqlConnection *conn = sqlConnect("cdw");
char query[1024];
struct cdwSubmitDir *submitDir;
// Get the id associated with the submission directory.
if (gWorkingDir == NULL)
{
char cwd[1024];
getcwd(cwd, sizeof(cwd));
sqlSafef(query, sizeof(query), "select * from cdwSubmitDir where url = '%s';", cwd);
submitDir = cdwSubmitDirLoadByQuery(conn, query);
}
else
{
sqlSafef(query, sizeof(query), "select * from cdwSubmitDir where url = '%s';", gWorkingDir);
submitDir = cdwSubmitDirLoadByQuery(conn, query);
}
if (!submitDir)
uglyAbort("There are no submissions associated with the submission directory provided.");
// Get all cdwSubmit entries associated with the submission directory.
sqlSafef(query, sizeof(query), "select * from cdwSubmit where submitDirId = '%i';", submitDir->id);
struct cdwSubmit *submitList = cdwSubmitLoadByQuery(conn, query);
struct cdwSubmit *submission;
// Keep track of the # of submissions, meta files and mani files.
int count = 0;
long long int totalFiles = 0, totalBytes = 0; // Count the total files and bytes.
struct slName *submitters = NULL, *user; // Keep track of the submitters.
// Loop over all cdwSubmit entries and gather/print out stats.
for (submission = submitList; ; submission = submission->next)
{
++count;
sqlSafef(query,sizeof(query), "select * from cdwUser where id = '%i';", (int)submission->userId);
struct cdwUser *user = cdwUserLoadByQuery(conn,query);
if(!slNameInList(submitters, user->email)) // If a submitter has not been seen add it.
slNameAddHead(&submitters, user->email);
// Print out submission stats.
fprintf(f, "Sub #: %i | Sub id: %i | New files: %i | New bytes: %lld | Mani id: %i |",
count, submission->id, submission->newFiles, submission->newBytes, submission->manifestFileId);
fprintf(f, " Meta id: %i | Files with new meta data values: %i | User email: %s | Wrangler: %s\n",
submission->metaFileId, submission->metaChangeCount, user->email, submission->wrangler);
totalFiles += submission->newFiles;
totalBytes += submission->newBytes;
if (submission->next == NULL)
break;
}
sqlSafef(query, sizeof(query), "select distinct metaFileId from cdwSubmit where submitDirId=%i", submitDir->id);
fprintf(f,"Total submissions:\t%i\n", count);
fprintf(f,"Total files:\t%lld\n",totalFiles);
// Math magic for pretty printing the file size.
long long int tBytes, gBytes, mBytes, kBytes, bytes;
tBytes = totalBytes/1000000000000;
gBytes = (totalBytes - tBytes * 1000000000000)/1000000000;
mBytes = (totalBytes - tBytes * 1000000000000 - gBytes * 1000000000)/1000000;
kBytes = (totalBytes - tBytes * 1000000000000 - gBytes * 1000000000 - mBytes * 1000000)/1000;
bytes = totalBytes - tBytes * 1000000000000 - gBytes * 1000000000 - mBytes * 1000000 - kBytes * 1000;
fprintf(f,"Total bytes:\t%lld T %lld G %lld M %lld K %lld B\n", tBytes, gBytes, mBytes, kBytes, bytes);
fprintf(f,"Submitters: ");
// Print out the submitters, ideally it will only be one person but in practice... Not so much.
for (user = submitters; ; user = user->next)
{
fprintf(f,"%s", user->name);
if (user->next == NULL)
break;
fprintf(f,", ");
}
fprintf(f,"\n");
sqlDisconnect(&conn);
}
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);
}
struct hash *readKeyHash(char *db, struct joiner *joiner,
struct joinerField *keyField, struct keyHitInfo **retList)
/* Read key-field into hash. Check for dupes if need be. */
{
struct sqlConnection *conn = sqlWarnConnect(db);
struct hash *keyHash = NULL;
struct keyHitInfo *khiList = NULL, *khi;
if (conn == NULL)
{
return NULL;
}
else
{
struct slName *table;
struct slName *tableList = getTablesForField(conn,keyField->splitPrefix,
keyField->table,
keyField->splitSuffix);
int rowCount = totalTableRows(conn, tableList);
int hashSize = digitsBaseTwo(rowCount)+1;
char query[256], **row;
struct sqlResult *sr;
int itemCount = 0;
int dupeCount = 0;
char *dupe = NULL;
if (rowCount > 0)
{
if (hashSize > hashMaxSize)
hashSize = hashMaxSize;
keyHash = hashNew(hashSize);
for (table = tableList; table != NULL; table = table->next)
{
safef(query, sizeof(query), "select %s from %s",
keyField->field, table->name);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
char *id = doChopsAndUpper(keyField, row[0]);
if (hashLookup(keyHash, id))
{
if (keyField->unique)
{
if (keyField->exclude == NULL ||
!slNameInList(keyField->exclude, id))
{
if (dupeCount == 0)
dupe = cloneString(id);
++dupeCount;
}
}
}
else
{
AllocVar(khi);
hashAddSaveName(keyHash, id, khi, &khi->name);
slAddHead(&khiList, khi);
++itemCount;
}
}
sqlFreeResult(&sr);
}
if (dupe != NULL)
{
warn("Error: %d duplicates in %s.%s.%s including '%s'",
dupeCount, db, keyField->table, keyField->field, dupe);
freez(&dupe);
}
verbose(2, " %s.%s.%s - %d unique identifiers\n",
db, keyField->table, keyField->field, itemCount);
}
slFreeList(&tableList);
}
sqlDisconnect(&conn);
*retList = khiList;
return keyHash;
}