void vgLoadJax(char *visiGeneDir, char *jaxDb, char *outDir)
/* vgLoadJax - Load visiGene database from jackson database. */
{
struct sqlConnection *conn = sqlConnect(jaxDb);
struct sqlConnection *conn2 = sqlConnect(jaxDb);
struct sqlConnection *connSp = sqlConnect("uniProt");
char inFull[PATH_LEN];
char *jaxPath = "inSitu/Mouse/jax";
char inJax[PATH_LEN];
#ifdef UNUSED
/* won't work yet */
char* host = "genome-test";
char* user = cfgOptionEnv("HGDB_USER", "db.user");
char* password = cfgOptionEnv("HGDB_PASSWORD", "db.password");
connSp = sqlConnectRemote(host, user, password, "uniProt");
#endif
safef(inFull, sizeof(inFull), "%s/full", visiGeneDir);
safef(inJax, sizeof(inJax), "%s/%s", inFull, jaxPath);
submitToDir(conn, conn2, connSp, outDir, inJax);
sqlDisconnect(&connSp);
sqlDisconnect(&conn2);
sqlDisconnect(&conn);
}
void refPepRepair(char *db,
char *accFile,
boolean dryRun)
/* fix dangling repPep gbSeq entries. */
{
struct sqlConnection *conn = sqlConnect(db);
struct brokenRefPepTbl *brpTbl;
struct extFileTbl* extFileTbl;
struct slName *accs = (accFile == NULL) ? NULL : slNameLoadReal(accFile);
if (!checkForRefLink(conn))
{
sqlDisconnect(&conn);
return;
}
gbVerbMsg(1, "%s: repairing refseq protein gbExtFile entries%s",
sqlGetDatabase(conn), (dryRun? " (dry run)" : ""));
extFileTbl = extFileTblLoad(conn);
brpTbl = brokenRefPepTblNew(conn, accs);
brokenRefPepGetSeqScan(conn, extFileTbl, brpTbl);
brokenRefPepGetMrnas(conn, brpTbl);
fillInFastaOffsets(brpTbl, conn, extFileTbl);
if (brpTbl->numToRepair > 0)
makeRepairs(brpTbl, conn, extFileTbl, dryRun);
else
gbVerbMsg(1, "%s: no refseq proteins to repair", sqlGetDatabase(conn));
brokenRefPepTblFree(&brpTbl);
extFileTblFree(&extFileTbl);
sqlDisconnect(&conn);
slFreeList(&accs);
}
void doValidatedEmail(struct edwSubmit *submit, boolean isComplete)
/* Send an email with info on all validated files */
{
struct sqlConnection *conn = edwConnect();
struct edwUser *user = edwUserFromId(conn, submit->userId);
struct dyString *message = dyStringNew(0);
/* Is this submission has no new file at all */
if ((submit->oldFiles != 0) && (submit->newFiles == 0) &&
(submit->metaChangeCount == 0) && isEmpty(submit->errorMessage)
&& (submit->fileIdInTransit == 0))
{
dyStringPrintf(message, "Your submission from %s is completed, but validation was not performed for this submission since all files in validate.txt have been previously submitted and validated.\n", submit->url);
mailViaPipe(user->email, "EDW Validation Results", message->string, edwDaemonEmail);
sqlDisconnect(&conn);
dyStringFree(&message);
return;
}
if (isComplete)
dyStringPrintf(message, "Your submission from %s is completely validated\n", submit->url);
else
dyStringPrintf(message,
"Your submission hasn't validated after 24 hours, something is probably wrong\n"
"at %s\n", submit->url);
dyStringPrintf(message, "\n#accession\tsubmitted_file_name\tnotes\n");
char query[512];
sqlSafef(query, sizeof(query),
"select licensePlate,submitFileName "
" from edwFile left join edwValidFile on edwFile.id = edwValidFile.fileId "
" where edwFile.submitId = %u and edwFile.id != %u"
, submit->id, submit->submitFileId);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
char *licensePlate = row[0];
char *submitFileName = row[1];
dyStringPrintf(message, "%s\t%s\t", naForNull(licensePlate), submitFileName);
if (licensePlate == NULL)
{
dyStringPrintf(message, "Not validating");
}
dyStringPrintf(message, "\n");
}
sqlFreeResult(&sr);
mailViaPipe(user->email, "EDW Validation Results", message->string, edwDaemonEmail);
sqlDisconnect(&conn);
dyStringFree(&message);
}
void mrnaToGene(char *db, char *cdsDb, char *cdsFile, char *pslSpec,
char *genePredFile)
/* convert an PSL mRNA table to a genePred file */
{
struct sqlConnection *conn = NULL;
FILE* genePredFh;
if (db != NULL)
conn = sqlConnect(db);
else if (cdsDb != NULL)
conn = sqlConnect(cdsDb);
genePredFh = mustOpen(genePredFile, "w");
if (cdsFile != NULL)
loadCdsFile(cdsFile);
if (db == NULL)
convertPslFile(conn, pslSpec, genePredFh);
else
convertPslTable(conn, pslSpec, genePredFh);
if (ferror(genePredFh))
errAbort("error writing %s", genePredFile);
carefulClose(&genePredFh);
sqlDisconnect(&conn);
}
void refPepList(char *db,
FILE* outFh)
/* list of sequences needing repair */
{
struct sqlConnection *conn = sqlConnect(db);
struct brokenRefPepTbl *brpTbl;
struct hashCookie cookie;
struct hashEl *hel;
struct extFileTbl* extFileTbl = NULL;
if (!checkForRefLink(conn))
{
sqlDisconnect(&conn);
return;
}
extFileTbl = extFileTblLoad(conn);
brpTbl = brokenRefPepTblNew(conn, NULL);
brokenRefPepGetSeqScan(conn, extFileTbl, brpTbl);
brokenRefPepGetMrnas(conn, brpTbl);
extFileTblFree(&extFileTbl);
cookie = hashFirst(brpTbl->protAccHash);
while ((hel = hashNext(&cookie)) != NULL)
{
struct brokenRefPep *brp = hel->val;
fprintf(outFh, "%s\t%s\t%s\n", sqlGetDatabase(conn), brp->protAcc, (brp->mrnaAcc != NULL)? "repair" : "drop");
}
gbVerbMsg(1, "%s: need to repair %d refseq protein gbExtFile entries",
sqlGetDatabase(conn), brpTbl->numToRepair);
gbVerbMsg(1, "%s: need to drop %d refseq protein gbExtFile entries",
sqlGetDatabase(conn), brpTbl->numToDrop);
}
void docIdReport(char *database)
/* docIdReport - generate report from docIdSub table. */
{
struct sqlConnection *conn = sqlConnect(database);
struct docIdSub *docIdSub;
char query[10 * 1024];
struct sqlResult *sr;
char **row;
safef(query, sizeof query, "select * from %s", docIdTable);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
docIdSub = docIdSubLoad(row);
verbose(2, "ix %d\n", docIdSub->ix);
verbose(2, "submitDate %s\n", docIdSub->submitDate);
verbose(2, "md5sum %s\n", docIdSub->md5sum);
verbose(2, "valReport %s\n", docIdSub->valReport);
verbose(2, "metaData %s\n", docIdSub->metaData);
verbose(2, "submitPath %s\n", docIdSub->submitPath);
verbose(2, "submitter %s\n", docIdSub->submitter);
cgiDecode(docIdSub->metaData, docIdSub->metaData, strlen(docIdSub->metaData));
char *tempFile = "temp";
FILE *f = mustOpen(tempFile, "w");
fwrite(docIdSub->metaData, strlen(docIdSub->metaData), 1, f);
fclose(f);
boolean validated;
struct mdbObj *mdbObj = mdbObjsLoadFromFormattedFile(tempFile, &validated);
printf("%s %s %s %s %s\n", docIdDecorate(docIdSub->ix), mdbObjFindValue(mdbObj, "dataType"), mdbObjFindValue(mdbObj, "view"), mdbObjFindValue(mdbObj, "cell"), mdbObjFindValue(mdbObj, "lab"));
}
sqlFreeResult(&sr);
sqlDisconnect(&conn);
}
struct chromGraph *chromGraphListWithTable(char *fileName, char *db, char *table)
/* Read the chromGraph file and convert to the chr,chromStart format. */
{
struct sqlConnection *conn = sqlConnect(db);
struct hash *posHash = NULL;
struct lineFile *lf;
struct chromGraph *list = NULL;
char *words[2];
checkTableForFields(conn, table);
posHash = posHashFromTable(conn, table);
sqlDisconnect(&conn);
lf = lineFileOpen(fileName, TRUE);
while (lineFileRow(lf, words))
{
struct chromGraph *cg;
/* Look up ID in hash. */
struct slPair *infoFromHash = hashFindVal(posHash, words[0]);
if (!infoFromHash)
warn("%s line %d: %s not found in %s table", fileName, lf->lineIx, words[0], table);
else
{
AllocVar(cg);
cg->chrom = cloneString(infoFromHash->name);
cg->chromStart = ptToInt(infoFromHash->val);
cg->val = sqlDouble(words[1]);
slAddHead(&list, cg);
}
}
slReverse(&list);
/* Free stuff up. */
lineFileClose(&lf);
hashFreeWithVals(&posHash, slPairFree);
return list;
}
int searchProteinsInSwissProtByGene(char *queryGeneID)
/* search Swiss-Prot database to see if it contains the protein
Input: queryGeneID
return: number of proteins found in Swiss-Prot
*/
{
int proteinCnt;
struct sqlConnection *conn;
char query[256];
struct sqlResult *sr;
char **row;
conn = sqlConnect(UNIPROT_DB_NAME);
sqlSafef(query, sizeof(query),
"select count(*) from gene, displayId, accToTaxon,taxon "
"where gene.val='%s' and gene.acc=displayId.acc and accToTaxon.taxon=taxon.id "
"and accToTaxon.acc=gene.acc order by taxon.id",
queryGeneID);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
if (row == NULL)
{
errAbort("Error occured during mySQL query: %s\n", query);
}
proteinCnt = atoi(row[0]);
sqlFreeResult(&sr);
sqlDisconnect(&conn);
return(proteinCnt);
}
void saveClonePos(struct clonePos *cloneList, char *database)
/* Save sorted clone position list to database. */
{
struct sqlConnection *conn = sqlConnect(database);
struct clonePos *clone;
struct tempName tn;
FILE *f;
struct dyString *ds = newDyString(2048);
/* Create tab file from clone list. */
printf("Creating tab file\n");
makeTempName(&tn, "hgCP", ".tab");
f = mustOpen(tn.forCgi, "w");
for (clone = cloneList; clone != NULL; clone = clone->next)
clonePosTabOut(clone, f);
fclose(f);
/* Create table if it doesn't exist, delete whatever is
* already in it, and fill it up from tab file. */
printf("Loading clonePos table\n");
sqlMaybeMakeTable(conn, "clonePos", createClonePos);
sqlUpdate(conn, "NOSQLINJ DELETE from clonePos");
sqlDyStringPrintf(ds, "LOAD data local infile '%s' into table clonePos",
tn.forCgi);
sqlUpdate(conn, ds->string);
/* Clean up. */
remove(tn.forCgi);
sqlDisconnect(&conn);
}
static void ccdsMkTables(char *ccdsDb, char *hgDb, int ccdsBuildId, char *ccdsInfoOut, char *ccdsNotesOut, char *ccdsGeneOut)
/* create tables for hg db from imported CCDS database */
{
if (verboseLevel() >= 2)
sqlMonitorEnable(JKSQL_TRACE);
struct sqlConnection *ccdsConn = ccdsSqlConn(ccdsDb);
struct genomeInfo *genome = getGenomeInfo(hgDb, ccdsBuildId);
struct hash *infoCcds = hashNew(20);
struct hash *geneCcds = hashNew(20);
struct hash* ignoreTbl = buildIgnoreTbl(ccdsConn, genome);
char ccdsInfoFile[PATH_LEN], ccdsInfoTbl[PATH_LEN];
ccdsGetTblFileNames(ccdsInfoOut, ccdsInfoTbl, ccdsInfoFile);
createCcdsInfo(ccdsConn, ccdsInfoFile, genome, ignoreTbl, infoCcds);
char ccdsNotesFile[PATH_LEN], ccdsNotesTbl[PATH_LEN];
ccdsGetTblFileNames(ccdsNotesOut, ccdsNotesTbl, ccdsNotesFile);
createCcdsNotes(ccdsConn, ccdsNotesFile, genome, infoCcds);
char ccdsGeneFile[PATH_LEN], ccdsGeneTbl[PATH_LEN];
ccdsGetTblFileNames(ccdsGeneOut, ccdsGeneTbl, ccdsGeneFile);
createCcdsGene(ccdsConn, ccdsGeneFile, genome, ignoreTbl, geneCcds);
sqlDisconnect(&ccdsConn);
sqlMonitorDisable();
gotCcdsValidate(infoCcds, geneCcds);
if (loadDb)
loadTables(hgDb, ccdsInfoTbl, ccdsInfoFile, ccdsGeneTbl, ccdsGeneFile, ccdsNotesTbl, ccdsNotesFile);
}
void readTableTask(char *db, char *table)
/* Implements the readTable task */
{
FILE *outFh = NULL;
struct sqlConnection *conn = sqlConnect(db);
struct pslReader* pr = pslReaderQuery(conn, table, gWhere);
struct psl* psl;
int numRows = 0;
if (gOutput != NULL)
outFh = mustOpen(gOutput, "w");
while ((numRows < gMaxRows) && ((psl = pslReaderNext(pr)) != NULL))
{
if (outFh != NULL)
pslTabOut(psl, outFh);
pslFree(&psl);
numRows++;
}
carefulClose(&outFh);
pslReaderFree(&pr);
sqlDisconnect(&conn);
checkNumRows(table, numRows);
}
void saveCtgPos(struct ctgPos *ctgList, char *database)
/* Save ctgList to database. */
{
struct sqlConnection *conn = sqlConnect(database);
struct ctgPos *ctg;
char *tabFileName = "ctgPos.tab";
FILE *f;
struct dyString *ds = newDyString(2048);
/* Create tab file from ctg list. */
printf("Creating tab file\n");
f = mustOpen(tabFileName, "w");
for (ctg = ctgList; ctg != NULL; ctg = ctg->next)
ctgPosTabOut(ctg, f);
fclose(f);
/* Create table if it doesn't exist, delete whatever is
* already in it, and fill it up from tab file. */
printf("Loading ctgPos table\n");
sqlMaybeMakeTable(conn, "ctgPos", createCtgPos);
sqlUpdate(conn, "NOSQLINJ DELETE from ctgPos");
sqlDyStringPrintf(ds, "LOAD data local infile '%s' into table ctgPos",
tabFileName);
sqlUpdate(conn, ds->string);
/* Clean up. */
remove(tabFileName);
sqlDisconnect(&conn);
}
boolean chromSeqFileExists(char *db, char *chrom)
/* Check whether chromInfo exists for a database, find the path of the */
/* sequence file for this chromosome and check if the file exists. */
{
char seqFile[512];
struct sqlConnection *conn = sqlConnect(db);
char query[256];
char *res = NULL;
boolean exists = FALSE;
/* if the database exists, check for the chromInfo file */
if (sqlDatabaseExists(db))
{
sqlSafef(query, sizeof(query), "select fileName from chromInfo where chrom = '%s'", chrom);
res = sqlQuickQuery(conn, query, seqFile, 512);
sqlDisconnect(&conn);
}
/* if there is not table or no information in the table or if the table */
/* exists but the file can not be opened return false, otherwise sequence */
/* file exists and return true */
if (res != NULL)
{
char *seqFile2 = hReplaceGbdb(seqFile);
exists = udcExists(seqFile2);
freeMem(seqFile2);
}
return exists;
}
void hgMaxExp(char *database, char *table)
/* Output maximum expScore in table */
{
struct sqlConnection *conn = sqlConnect(database);
struct sqlResult *sr;
char query[256];
char **row;
/* Get list of all items with expression values. */
char *fieldNames = "name, expCount, expScores";
sqlSafef(query, sizeof(query), "select %s from %s", fieldNames, table);
sr = sqlGetResult(conn, query);
float maxScore = 0.0;
float minScore = 100000.0;
while ((row = sqlNextRow(sr)) != NULL)
{
char *name = row[0];
int expCount = sqlUnsigned(row[1]);
int commaCount;
float *expScores = NULL;
sqlFloatDynamicArray(row[2], &expScores, &commaCount);
if (expCount != commaCount)
errAbort("expCount and expScores don't match on %s in %s", name, table);
int i;
for (i=0; i<expCount; i++)
{
maxScore = max(maxScore, expScores[i]);
minScore = min(minScore, expScores[i]);
}
}
sqlFreeResult(&sr);
conn = sqlConnect(database);
sqlDisconnect(&conn); /* Disconnect because next step is slow. */
printf("max: %0.2f min: %0.2f\n", maxScore, minScore);
}
void hgSoftberryHom(char *database, int fileCount, char *files[])
/* hgSoftberryHom - Make table storing Softberry protein homology information. */
{
int i;
char *fileName;
char *table = "softberryHom";
char *tabFileName = "softberryHom.tab";
FILE *f = mustOpen(tabFileName, "w");
struct sqlConnection *conn = NULL;
struct dyString *ds = newDyString(2048);
for (i=0; i<fileCount; ++i)
{
fileName = files[i];
printf("Processing %s\n", fileName);
makeTabLines(fileName, f);
}
carefulClose(&f);
/* Create table if it doesn't exist, delete whatever is
* already in it, and fill it up from tab file. */
conn = sqlConnect(database);
printf("Loading %s table\n", table);
sqlMaybeMakeTable(conn, table, createTable);
sqlDyStringPrintf(ds, "DELETE from %s", table);
sqlUpdate(conn, ds->string);
dyStringClear(ds);
sqlDyStringPrintf(ds, "LOAD data local infile '%s' into table %s",
tabFileName, table);
sqlUpdate(conn, ds->string);
sqlDisconnect(&conn);
}
void relationRecon(char *fileName)
/* Do relationship based reconstruction. */
{
char **words;
long start, end;
struct sqlConnection *conn = sqlConnect(database);
struct sqlResult *sr;
char **row;
FILE *f = mustOpen(fileName, "w");
int lineCount;
int i;
char query[256];
start = clock1000();
words = loadWords();
end = clock1000();
printf("Time to load words: %4.3f\n", 0.001*(end-start));
start = clock1000();
lineCount = sqlTableSize(conn, "lineSize");
for (i=0; i<lineCount; ++i)
{
sprintf(query, "select * from lineWords where line = %d", i);
sr = sqlQuery(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
fileOutput(f,words[sqlUnsigned(row[1])]);
sqlFreeResult(&sr);
}
end = clock1000();
printf("Time to relation reconstruct file: %4.3f\n", 0.001*(end-start));
sqlDisconnect(&conn);
}
void doLabContacts(struct cart *theCart)
{
char *subId = cartString(theCart, "lab");
cartWebStart(cart, database, "ENCODE DCC: Contacts for submission: %s",subId);
struct sqlConnection *conn = sqlConnect(database);
char query[10 * 1024];
struct sqlResult *sr;
char **row;
printf("<a href=docIdView?db=%s> Return </a><BR>", database);
safef(query, sizeof query, "select user_id from %s where id = %s ", "projects",subId);
char *userId = sqlQuickString(conn, query);
safef(query, sizeof query, "select name,email,pi from %s where id = '%s' ", "users",userId);
sr = sqlGetResult(conn, query);
printf("<pre>");
while ((row = sqlNextRow(sr)) != NULL)
{
printf("Name: %s\nEmail: %s\nPI: %s", row[0], row[1], row[2]);
}
sqlFreeResult(&sr);
sqlDisconnect(&conn);
cartWebEnd();
}
boolean chromSeqFileExists(char *db, char *chrom)
/* Check whether chromInfo exists for a database, find the path of the */
/* sequence file for this chromosome and check if the file exists. */
{
char seqFile[512];
struct sqlConnection *conn = sqlConnect(db);
char query[256];
char *res = NULL;
boolean exists = FALSE;
/* if the database exists, check for the chromInfo file */
if (sqlDatabaseExists(db))
{
safef(query, sizeof(query), "select fileName from chromInfo where chrom = '%s'", chrom);
res = sqlQuickQuery(conn, query, seqFile, 512);
sqlDisconnect(&conn);
}
/* if there is not table or no information in the table or if the table */
/* exists but the file can not be opened return false, otherwise sequence */
/* file exists and return true */
if (res != NULL)
{
/* chromInfo table exists so check that sequence file can be opened */
FILE *f = fopen(seqFile, "rb");
if (f != NULL)
{
exists = TRUE;
fclose(f);
}
}
return exists;
}
void checkDbTables(char *database, char *composite, struct hash *mdbHash, struct hash *allBbiNames)
// search the database for tables that begin with composite and call checkTable
{
struct sqlConnection *conn = sqlConnect(database);
char buffer[10 * 1024];
verbose(1, "----------------------------------------------\n");
verbose(1, "Checking that tables starting with composite in db are in metaDb\n (also checks dummy table and the bbi symlink and its target)\n");
verbose(1, "----------------------------------------------\n");
sqlSafef(buffer, sizeof buffer, "show tables like '%s%%'", composite);
struct sqlResult *sr;
sr = sqlGetResult(conn, buffer);
char **row;
struct slName *list = NULL;
while ((row = sqlNextRow(sr)) != NULL)
{
struct slName *el = slNameNew(row[0]);
slAddHead(&list, el);
}
sqlFreeResult(&sr);
for(; list; list = list->next)
checkTable(conn, list->name, mdbHash, allBbiNames);
sqlDisconnect(&conn);
}
int main(int argc, char *argv[]) {
// sql vars
SQLHENV henv = SQL_NULL_HENV; // environment
SQLHDBC hdbc = SQL_NULL_HDBC; // connection
SQLHSTMT hstmt = SQL_NULL_HSTMT; // statement
// sql connect
sqlConnect(&henv, &hdbc, &hstmt);
// input vars
char beruf[BERUFSIZE + 1];
char mitID[MITIDSIZE + 1];
// program logic
while (getBerufe(&henv, &hdbc, &hstmt, beruf)) {
if (getMitarbeiter(&henv, &hdbc, &hstmt, beruf, mitID)) {
if (getMitDetails(&henv, &hdbc, &hstmt, beruf, mitID)) {
getProjektDetails(&henv, &hdbc, &hstmt, beruf, mitID);
}
}
}
puts("");
// sql disconnect
sqlDisconnect(&henv, &hdbc, &hstmt);
return 0;
}
void writeSplitTables()
/* sequentially read ContigLocFilter, writing to appropriate chrom file */
/* we are storing chromName in the table just as a sanity check */
/* It is dropped in the next step of the pipeline */
{
char query[512];
struct sqlConnection *conn = hAllocConn();
struct sqlResult *sr;
char **row;
struct hashEl *hel;
char *chromName;
verbose(1, "reading ContigLocFilter...\n");
sqlSafef(query, sizeof(query),
"select snp_id, ctg_id, chromName, loc_type, phys_pos_from, phys_pos, orientation, allele from ContigLocFilter");
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
hel = hashLookup(chromHash,row[2]);
if (hel == NULL)
{
verbose(1, "%s not found\n", row[2]);
continue;
}
fprintf(hel->val, "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n", row[0], row[1], row[2], row[3], row[4], row[5], row[6], row[7]);
}
sqlFreeResult(&sr);
sqlDisconnect(&conn);
}
void createAll()
/* Define all tables. */
{
struct sqlConnection *conn = sqlConnect(database);
sqlGetResult(conn,
"CREATE table word ("
"id smallint not null primary key,"
"word varchar(250) not null"
")" );
sqlGetResult(conn,
"CREATE table lineSize ("
"id int(8) not null primary key,"
"size smallint not null"
")" );
sqlGetResult(conn,
"CREATE table lineWords ("
"line int(8) not null,"
"word smallint not null,"
"pos smallint not null"
")" );
sqlGetResult(conn,
"CREATE table commaLine ("
"id int(8) not null primary key,"
"size smallint not null,"
"wordList blob not null"
")" );
sqlDisconnect(&conn);
}
void cartMain(struct cart *theCart)
/* We got the persistent/CGI variable cart. Now
* set up the globals and make a web page. */
{
cart = theCart;
/* Break out new block after have set cart */
{
int id = cartUsualInt(cart, hgbiId, 1);
struct sqlConnection *conn = sqlConnect("bioImage");
char *geneName = bioImageGeneName(conn, id);
if (cartVarExists(cart, hgbiDoFullSize))
{
htmStart(stdout, "BioImage Full Sized Image");
printf("<IMG SRC=\"/%s\"><BR>\n", bioImageFullSizePath(conn, id));
printCaption(conn, id, geneName);
htmlEnd();
}
else /* Default case - start fancy web page. */
{
mainPage(conn, id, geneName);
}
cartRemovePrefix(cart, hgbiDoPrefix);
sqlDisconnect(&conn);
}
}
void encode2ExpDumpFlat(char *outFile, char *viewSql, char *flatTable)
/* encode2ExpDumpFlat - Dump the experiment table in a semi-flat way from a relationalized Encode2 metadatabase.. */
{
FILE *f = mustOpen(outFile, "w");
struct sqlConnection *conn = sqlConnect(database);
struct starTableInfo **stiArray;
AllocArray(stiArray, ArraySize(starFields));
int i;
for (i=0; i<ArraySize(starFields); ++i)
stiArray[i] = starTableInfoNew(conn, starFields[i]);
struct dyString *query = dyStringNew(2000);
sqlDyStringPrintf(query, "select ");
for (i=0; i<ArraySize(flatFields); ++i)
{
if (i != 0)
dyStringAppendC(query, ',');
sqlDyStringPrintf(query, "%s", flatFields[i]);
}
for (i=0; i<ArraySize(starFields); ++i)
{
dyStringAppendC(query, ',');
sqlDyStringPrintf(query, "%s", starFields[i]);
}
dyStringPrintf(query, " from %s%s", tablePrefix, "experiment");
struct sqlResult *sr = sqlGetResult(conn, query->string);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
int flatSize = ArraySize(flatFields);
int starSize = ArraySize(starFields);
int i;
for (i=0; i<flatSize; ++i)
{
if (i != 0)
fputc('\t', f);
fputs(row[i], f);
}
for (i=0; i<starSize; ++i)
{
int id = sqlUnsigned(row[i+flatSize]);
fputc('\t', f);
if (id == 0)
fputs("n/a", f);
else
fputs(stiArray[i]->termsForIds[id], f);
}
fputc('\n', f);
}
sqlFreeResult(&sr);
sqlDisconnect(&conn);
carefulClose(&f);
makeViewSql(viewSql);
makeFlatTableSql(flatTable);
}
int tableSize(char *db, char *table)
/* Return number of rows in table. */
{
struct sqlConnection *conn = sqlConnect(db);
int size = sqlTableSize(conn, table);
sqlDisconnect(&conn);
return size;
}
struct mdbObj *getMdbList(char *database)
/* Get list of metaDb objects for a database. */
{
struct sqlConnection *conn = sqlConnect(database);
struct mdbObj *list = mdbObjsQueryAll(conn, metaTable);
sqlDisconnect(&conn);
return list;
}
void localWebWrap(struct cart *theCart)
/* We got the http stuff handled, and a cart. */
{
cart = theCart;
struct sqlConnection *conn = sqlConnect(cdwDatabase);
dispatch(conn);
sqlDisconnect(&conn);
}
void createFakeEntries(char *host, char *user, char *password, char *database, int count)
/* create count new fake entries in database. */
{
struct sqlConnection *conn = sqlConnectRemote(host, user, password, database);
int i;
for (i=0; i<count; ++i)
createFakeEntry(conn, randomFakeSize());
sqlDisconnect(&conn);
}
void createEmptyDatabase(char *host, char *user, char *password, char *database)
/* Create a new database with no tables. */
{
struct sqlConnection *conn = sqlConnectRemote(host, user, password, NULL);
char query[512];
sqlSafef(query, sizeof(query), "create database %s", database);
sqlUpdate(conn, query);
sqlDisconnect(&conn);
}
boolean databaseExists(char *host, char *user, char *password, char *database)
/* Return TRUE if database exists. */
{
struct sqlConnection *conn = sqlMayConnectRemote(host, user, password, database);
if (conn == NULL)
return FALSE;
sqlDisconnect(&conn);
return TRUE;
}
