void xpFree(struct xp **pXp)
/* Free up an xp parser. */
{
int i;
struct xp *xp = *pXp;
if (xp != NULL)
{
struct xpStack *stack;
for (stack = xp->stackBufEnd; --stack >= xp->stackBuf; )
{
if (stack->tag == NULL)
break;
freeDyString(&stack->tag);
freeDyString(&stack->text);
}
for (i=0; i<ArraySize(xp->attDyBuf); ++i)
{
if (xp->attDyBuf[i] == NULL)
break;
freeDyString(&xp->attDyBuf[i]);
}
freeDyString(&xp->endTag);
freeMem(xp->fileName);
hashFree(&xp->symHash);
freez(pXp);
}
}
void taxonGeneticCodeSaveToDbEscaped(struct sqlConnection *conn, struct taxonGeneticCode *el, char *tableName, int updateSize)
/* Save taxonGeneticCode as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than taxonGeneticCodeSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *abbr, *name, *tranlsation, *starts, *comments;
abbr = sqlEscapeString(el->abbr);
name = sqlEscapeString(el->name);
tranlsation = sqlEscapeString(el->tranlsation);
starts = sqlEscapeString(el->starts);
comments = sqlEscapeString(el->comments);
dyStringPrintf(update, "insert into %s values ( %u,'%s','%s','%s','%s','%s')",
tableName, el->id , abbr, name, tranlsation, starts, comments);
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&abbr);
freez(&name);
freez(&tranlsation);
freez(&starts);
freez(&comments);
}
void paraNodeStart(char *machineList)
/* Start node servers on all machines in list. */
{
char *exe = optionVal("exe", "paraNode");
char *rsh = optionVal("rsh", "rsh");
struct lineFile *lf = lineFileOpen(machineList, TRUE);
char *row[2];
struct dyString *dy = newDyString(256);
while (lineFileRow(lf, row))
{
char *name = row[0];
int cpu = atoi(row[1]);
if (cpu <= 0)
errAbort("Expecting cpu count in second column, line %d of %s\n",
lf->lineIx, lf->fileName);
dyStringClear(dy);
dyStringPrintf(dy, "%s %s %s start -cpu=%d", rsh, name, exe, cpu);
carryOption("logFacility", dy);
carryOption("logMinPriority", dy);
carryOption("log", dy);
carryOption("hub", dy);
carryOption("umask", dy);
carryOption("sysPath", dy);
carryOption("userPath", dy);
carryMultiOption("env", dy);
carryOption("randomDelay", dy);
printf("%s\n", dy->string);
system(dy->string);
}
lineFileClose(&lf);
freeDyString(&dy);
}
void makeItemsItemSaveToDbEscaped(struct sqlConnection *conn, struct makeItemsItem *el, char *tableName, int updateSize)
/* Save makeItemsItem as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than makeItemsItemSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *chrom, *name, *strand, *description;
chrom = sqlEscapeString(el->chrom);
name = sqlEscapeString(el->name);
strand = sqlEscapeString(el->strand);
description = sqlEscapeString(el->description);
dyStringPrintf(update, "insert into %s values ( %u,'%s',%u,%u,'%s',%u,'%s',%u,%u,%u,'%s',%u)",
tableName, el->bin, chrom, el->chromStart, el->chromEnd, name, el->score, strand, el->thickStart, el->thickEnd, el->itemRgb, description, el->id);
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&chrom);
freez(&name);
freez(&strand);
freez(&description);
}
void protVarSaveToDbEscaped(struct sqlConnection *conn, struct protVar *el, char *tableName, int updateSize)
/* Save protVar as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than protVarSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *id, *name, *srcId, *baseChangeType, *location;
id = sqlEscapeString(el->id);
name = sqlEscapeString(el->name);
srcId = sqlEscapeString(el->srcId);
baseChangeType = sqlEscapeString(el->baseChangeType);
location = sqlEscapeString(el->location);
dyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s',%u)",
tableName, id, name, srcId, baseChangeType, location, el->coordinateAccuracy);
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&id);
freez(&name);
freez(&srcId);
freez(&baseChangeType);
freez(&location);
}
int nextRepeatPos(char *chrom, int desiredPos, struct sqlConnection *conn)
/* Find next 0% diverged repeat on the chrom and return midpoint */
{
struct sqlResult *sr;
char **row;
int pos = -1;
int start, end;
struct hTableInfo *hti = hFindTableInfo(db, chrom, "rmsk");
struct dyString *query = newDyString(1024);
if (hti == NULL)
errAbort("table %s.rmsk doesn't exist", db);
dyStringPrintf(query, "select genoStart,genoEnd from ");
if (hti->isSplit)
dyStringPrintf(query, "%s_rmsk where ", chrom);
else
dyStringPrintf(query, "rmsk where %s='%s' AND ", hti->chromField, chrom);
dyStringPrintf(query,
"(genoStart >= %d AND \
milliDiv=0 AND \
repClass<>'Simple_repeat' AND repClass<>'Low_complexity' AND \
genoEnd-genoStart>%d) order by genoStart limit 1",
desiredPos, minRepeat);
sr = sqlGetResult(conn, query->string);
freeDyString(&query);
if ((row = sqlNextRow(sr)) != NULL)
{
start = sqlSigned(row[0]);
end = sqlSigned(row[1]);
pos = start + (end - start)/2;
}
sqlFreeResult(&sr);
return pos;
}
void affy10KDetailsSaveToDbEscaped(struct sqlConnection *conn, struct affy10KDetails *el, char *tableName, int updateSize)
/* Save affy10KDetails as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than affy10KDetailsSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *affyId, *rsId, *tscId, *baseA, *baseB, *sequenceA, *sequenceB, *enzyme;
affyId = sqlEscapeString(el->affyId);
rsId = sqlEscapeString(el->rsId);
tscId = sqlEscapeString(el->tscId);
baseA = sqlEscapeString(el->baseA);
baseB = sqlEscapeString(el->baseB);
sequenceA = sqlEscapeString(el->sequenceA);
sequenceB = sqlEscapeString(el->sequenceB);
enzyme = sqlEscapeString(el->enzyme);
dyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s','%s','%s','%s')",
tableName, affyId, rsId, tscId, baseA, baseB, sequenceA, sequenceB, enzyme);
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&affyId);
freez(&rsId);
freez(&tscId);
freez(&baseA);
freez(&baseB);
freez(&sequenceA);
freez(&sequenceB);
freez(&enzyme);
}
void protVarLinkSaveToDbEscaped(struct sqlConnection *conn, struct protVarLink *el, char *tableName, int updateSize)
/* Save protVarLink as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than protVarLinkSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *id, *attrType, *raKey, *acc, *displayVal;
id = sqlEscapeString(el->id);
attrType = sqlEscapeString(el->attrType);
raKey = sqlEscapeString(el->raKey);
acc = sqlEscapeString(el->acc);
displayVal = sqlEscapeString(el->displayVal);
dyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s')",
tableName, id, attrType, raKey, acc, displayVal);
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&id);
freez(&attrType);
freez(&raKey);
freez(&acc);
freez(&displayVal);
}
static char *ccFreezeDbConversion(char *database, char *freeze, char *org)
/* Find freeze given database or vice versa. Pass in NULL
* for parameter that is unknown and it will be returned
* as a result. This result can be freeMem'd when done. */
{
struct sqlConnection *conn = hConnectCentral();
struct sqlResult *sr;
char **row;
char *ret = NULL;
struct dyString *dy = newDyString(128);
if (database != NULL)
dyStringPrintf(dy, "select description from dbDb where name = '%s' and (genome like '%s' or genome like 'Zoo')",
database, org);
else if (freeze != NULL)
dyStringPrintf(dy, "select name from dbDb where description = '%s' and (genome like '%s' or genome like 'Zoo')",
freeze, org);
else
internalErr();
sr = sqlGetResult(conn, dy->string);
if ((row = sqlNextRow(sr)) != NULL)
ret = cloneString(row[0]);
sqlFreeResult(&sr);
hDisconnectCentral(&conn);
freeDyString(&dy);
return ret;
}
int nextGapPos(char *chrom, int desiredPos, struct sqlConnection *conn)
{
/* Find next gap on the chrom and return midpoint */
struct sqlResult *sr;
char **row;
int pos = -1;
int start, end;
struct hTableInfo *hti = hFindTableInfo(db, chrom, "gap");
struct dyString *query = newDyString(1024);
if (hti == NULL)
errAbort("table %s.gap doesn't exist", db);
dyStringPrintf(query, "select chromStart,chromEnd from ");
if (hti->isSplit)
dyStringPrintf(query, "%s_gap where ", chrom);
else
dyStringPrintf(query, "gap where %s='%s' AND ", hti->chromField, chrom);
dyStringPrintf(query, "(chromStart >= %d and chromEnd-chromStart > %d)\
order by chromStart limit 1",
desiredPos, minGap);
sr = sqlGetResult(conn, query->string);
freeDyString(&query);
if ((row = sqlNextRow(sr)) != NULL)
{
start = sqlSigned(row[0]);
end = sqlSigned(row[1]);
pos = start + (end - start)/2;
}
sqlFreeResult(&sr);
return pos;
}
void cutterSaveToDbEscaped(struct sqlConnection *conn, struct cutter *el, char *tableName, int updateSize)
/* Save cutter as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than cutterSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *name, *seq, *scizsArray, *companiesArray, *refsArray;
name = sqlEscapeString(el->name);
seq = sqlEscapeString(el->seq);
scizsArray = sqlStringArrayToString(el->scizs, el->numSciz);
companiesArray = sqlCharArrayToString(el->companies, el->numCompanies);
refsArray = sqlUnsignedArrayToString(el->refs, el->numRefs);
dyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,%d,%u,%u,%u,'%s',%u,'%s',%u,'%s')",
tableName, name, el->size , el->matchSize , seq, el->cut , el->overhang , el->palindromic , el->semicolon , el->numSciz , scizsArray , el->numCompanies , companiesArray , el->numRefs , refsArray );
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&name);
freez(&seq);
freez(&scizsArray);
freez(&companiesArray);
freez(&refsArray);
}
void affyAtlasSaveToDbEscaped(struct sqlConnection *conn, struct affyAtlas *el, char *tableName, int updateSize)
/* Save affyAtlas as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than affyAtlasSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *annName, *probeSet, *detection, *tissue;
annName = sqlEscapeString(el->annName);
probeSet = sqlEscapeString(el->probeSet);
detection = sqlEscapeString(el->detection);
tissue = sqlEscapeString(el->tissue);
dyStringPrintf(update, "insert into %s values ( '%s','%s',%f,'%s',%f,'%s')",
tableName, annName, probeSet, el->signal , detection, el->pval , tissue);
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&annName);
freez(&probeSet);
freez(&detection);
freez(&tissue);
}
void tfbsConsSaveToDbEscaped(struct sqlConnection *conn, struct tfbsCons *el, char *tableName, int updateSize)
/* Save tfbsCons as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than tfbsConsSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *chrom, *name, *strand, *species, *factor, *id;
chrom = sqlEscapeString(el->chrom);
name = sqlEscapeString(el->name);
strand = sqlEscapeString(el->strand);
species = sqlEscapeString(el->species);
factor = sqlEscapeString(el->factor);
id = sqlEscapeString(el->id);
dyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s','%s','%s')",
tableName, chrom, el->chromStart , el->chromEnd , name, el->score , strand, species, factor, id);
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&chrom);
freez(&name);
freez(&strand);
freez(&species);
freez(&factor);
freez(&id);
}
void doSubmitToGreat(const char *path)
/* Send a URL to GREAT that it can use to retrieve the results. */
{
struct dyString *requestName = getRequestName();
struct dyString *requestURL = dyStringCreate("http://%s/%s", cgiServerNamePort(), path);
struct dyString *greatRequest;
greatRequest = dyStringCreate(
"<meta http-equiv='refresh' content='0;url=http://great.stanford.edu/public/cgi-bin/greatStart.php?requestURL=%s&requestSpecies=%s&requestName=%s&requestSender=UCSC%20Table%20Browser'>",
dyStringContents(requestURL), database, dyStringContents(requestName));
hPrintf("<b>GREAT</b> is processing BED data from \"%s\"...please wait.\n", dyStringContents(requestName));
hWrites(dyStringContents(greatRequest));
freeDyString(&greatRequest);
freeDyString(&requestName);
freeDyString(&requestURL);
}
void correctOne(struct dnaSeq *est, struct psl *psl, char *nibDir,
struct hash *nibHash, FILE *f)
/* Write one corrected EST to file. */
{
struct dnaSeq *geno = readCachedNib(nibHash, nibDir, psl->tName,
psl->tStart, psl->tEnd - psl->tStart);
struct dyString *t = newDyString(est->size+20);
int qSize = psl->qSize;
int tSize = psl->tSize;
int qLastEnd = 0;
int blockIx;
struct mrnaBlock *mbList, *mb;
int genoOffset = psl->tStart;
boolean isRc = FALSE;
/* Load sequence and alignment blocks, coping with reverse
* strand as necessary. */
toUpperN(geno->dna, geno->size); /* This helps debug... */
mbList = mrnaBlockFromPsl(psl);
if (psl->strand[0] == '-')
{
reverseComplement(geno->dna, geno->size);
genoOffset = tSize - psl->tEnd;
for (mb = mbList; mb != NULL; mb = mb->next)
{
reverseIntRange(&mb->tStart, &mb->tEnd, tSize);
reverseIntRange(&mb->qStart, &mb->qEnd, qSize);
}
slReverse(&mbList);
isRc = TRUE;
}
/* Make t have corrected sequence. */
for (mb = mbList; mb != NULL; mb = mb->next)
{
int qStart = mb->qStart;
int qEnd = mb->qEnd;
int uncovSize = qStart - qLastEnd;
if (uncovSize > 0)
dyStringAppendN(t, est->dna + qLastEnd, uncovSize);
dyStringAppendN(t, geno->dna + mb->tStart - genoOffset,
mb->tEnd - mb->tStart);
qLastEnd = qEnd;
}
if (qLastEnd != qSize)
{
int uncovSize = qSize - qLastEnd;
dyStringAppendN(t, est->dna + qLastEnd, uncovSize);
}
/* Output */
faWriteNext(f, est->name, t->string, t->stringSize);
/* Clean up time. */
slFreeList(&mbList);
freeDyString(&t);
freeDnaSeq(&geno);
}
void getTransFromFile(FILE* infile, char *path)
{
FILE* outfile = NULL;
int start, end, tmNumber, count, seqLength;
char *line, *token;
struct dyString *proteinID = newDyString(24);
start = end = tmNumber = count = seqLength = 0;
while( ( line = readLine(infile) ) != NULL )
{ /*grab the protein ID after each <PRE> tag*/
while( (token = nextWord(&line)) != NULL )
{
if( sameString(token,"<PRE>#"))
{ /*create a new xml file*/
token = nextWord(&line);
dyStringAppend(proteinID, token);
token = lastWordInLine(line);
seqLength = atoi(token);
}
if( sameString(token,"predicted") )
{ /*grab the number of transmembrane helices*/
token = lastWordInLine(line);
tmNumber = atoi(token);
if(tmNumber > 0)
{
outfile = createXMLFile(proteinID->string, path);
populateXMLFile(outfile, tmNumber, proteinID->string, path);
}
}
if( sameString(token,"</PRE>") )
{ /*close the xml file*/
carefulClose(&outfile);
dyStringClear(proteinID);
count = 0;
}
if( sameString(token,"TMhelix") )
{
if( (token = nextWord(&line)) != NULL )
{ /*get the start*/
start = atoi(token);
if( (token = nextWord(&line)) != NULL )
end = atoi(token);
}
if( count == 0)
addCoordinatesToXMLFile(outfile, 1, start-1, "N-term", count);
count++;
addCoordinatesToXMLFile(outfile, start, end, "TM", count);
if( count == tmNumber && outfile != NULL )
{
addCoordinatesToXMLFile(outfile,end+1,seqLength,"C-term",count);
finishXMLFile(outfile, proteinID->string, seqLength);
}
}
} /*end inner while*/
} /*end outer while*/
freeMem(line);
freeDyString(&proteinID);
}
static struct mimePart * cgiParseMultipart(int fd, FILE *out, boolean autoBoundary)
/* process a multipart form */
{
char h[1024]; /* hold mime header line */
char *s = NULL;
struct dyString *dy = newDyString(256);
struct mimeBuf *mb = NULL;
struct mimePart *mp = NULL;
char **env = NULL;
if (altHeader)
{
/* find the CONTENT_ environment strings, use to make Alternate Header string for MIME */
for(env=environ; *env; env++)
if (startsWith("CONTENT_",*env))
{
//debug
//fprintf(stderr,"%s\n",*env); //debug
safef(h,sizeof(h),"%s",*env);
/* change env syntax to MIME style header, from _ to - */
s = strchr(h,'_');
if (!s)
errAbort("expecting '_' parsing env var %s for MIME alt header", *env);
*s = '-';
/* change env syntax to MIME style header, from = to : */
s = strchr(h,'=');
if (!s)
errAbort("expecting '=' parsing env var %s for MIME alt header", *env);
*s = ':';
dyStringPrintf(dy,"%s\r\n",h);
}
dyStringAppend(dy,"\r\n"); /* blank line at end means end of headers */
fprintf(out,"Alternate Header Text:\n%s",dy->string);
}
mb = initMimeBuf(fd);
if (altHeader)
mp = parseMultiParts(mb, cloneString(dy->string)); /* The Alternate Header will get freed */
else if (autoBoundary)
mp = parseMultiParts(mb, "autoBoundary");
else
mp = parseMultiParts(mb, NULL);
if(!mp->multi) /* expecting multipart child parts */
errAbort("Malformatted multipart-form.");
freeDyString(&dy);
freez(&mb);
printMimeInfo(mp, out, 0);
return mp;
}
void sshSelf(char *hostList, char *host, int start, char *destFile, char *lockDir)
/* Execute ssh command to invoke self. */
{
struct dyString *dy = newDyString(512);
dyStringPrintf(dy,
"ssh -x %s /projects/compbio/experiments/hg/bin/i386/ccCp %s %s %d %s &",
host, destFile, hostList, start, lockDir);
system(dy->string);
freeDyString(&dy);
}
void rshSelf(char *hostList, char *host, int start, char *destFile, char *lockDir)
/* Execute rsh command to invoke self. */
{
struct dyString *dy = newDyString(512);
dyStringPrintf(dy,
"rsh %s /cse/guests/kent/bin/i386/ccCp %s %s %d %s &",
host, destFile, hostList, start, lockDir);
system(dy->string);
freeDyString(&dy);
}
int cpFile(char *source, char *destFile)
/* Execute cp command to copy file to host. */
{
struct dyString *dy = newDyString(512);
int ret;
dyStringPrintf(dy, "cp %s %s", source, destFile);
ret = system(dy->string);
freeDyString(&dy);
return ret;
}
void freeDyStringList(struct dyString **pDs)
/* free up a list of dyStrings */
{
struct dyString *ds, *next;
for(ds = *pDs; ds != NULL; ds = next)
{
next = ds->next;
freeDyString(&ds);
}
*pDs = NULL;
}
void loadTableFromTabFile(char *database, char *table, char *tabFile)
/* Load up table from tab file. */
{
struct sqlConnection *conn = sqlConnect(database);
struct dyString *ds = newDyString(2048);
sqlDyStringPrintf(ds,
"load data local infile '%s' into table %s", tabFile, table);
sqlUpdate(conn, ds->string);
sqlDisconnect(&conn);
freeDyString(&ds);
}
void makeCustomTable(char *database, char *table, char *defString)
/* create/recreate table. */
{
struct sqlConnection *conn = sqlConnect(database);
struct dyString *ds = newDyString(2048);
sqlDyStringPrintf(ds, defString, table);
sqlRemakeTable(conn, table, ds->string);
sqlDisconnect(&conn);
freeDyString(&ds);
}
int scpFile(char *source, char *destHost, char *destFile)
/* Execute scp command to copy source file to host. */
{
struct dyString *dy = newDyString(512);
int ret;
dyStringPrintf(dy, "scp %s %s:/%s >/dev/null", source, destHost, destFile);
ret = system(dy->string);
freeDyString(&dy);
return ret;
}
void gapFileToTable(struct sqlConnection *conn, char *gapFileName,
char *gapTableName)
/* Build a single gap table from a single gap file. */
{
struct lineFile *lf = lineFileOpen(gapFileName, TRUE);
char tabFileName[256];
FILE *tabFile = NULL;
char *words[16];
int wordCount;
safef(tabFileName, sizeof(tabFileName), "%s.tab", gapTableName);
tabFile = mustOpen(tabFileName, "w");
while ((wordCount = lineFileChop(lf, words)) > 0)
{
if (wordCount < 5)
errAbort("Short line %d of %s", lf->lineIx, lf->fileName);
if (words[4][0] == 'N' || words[4][0] == 'U')
{
int len = strlen(words[0]);
if (len > maxChromNameSize)
{
maxChromNameSize = len;
if (maxChromNameSize > 254)
errAbort("ERROR: chrom name size is over 254(%d) characters: "
"'%s'", maxChromNameSize, words[0]);
}
struct agpGap gap;
agpGapStaticLoad(words, &gap);
gap.chromStart -= 1;
fprintf(tabFile, "%u\t", hFindBin(gap.chromStart, gap.chromEnd));
agpGapTabOut(&gap, tabFile);
}
}
lineFileClose(&lf);
fclose(tabFile);
if (! noLoad)
{
struct dyString *ds = newDyString(2048);
if (unsplit)
sqlDyStringPrintf(ds, createGapUnsplit, gapTableName,
maxChromNameSize, maxChromNameSize);
else
sqlDyStringPrintf(ds, createGapSplit, gapTableName);
char query[1024];
sqlRemakeTable(conn, gapTableName, ds->string);
sqlSafef(query, sizeof(query), "LOAD data local infile '%s' into table %s",
tabFileName, gapTableName);
sqlUpdate(conn, query);
remove(tabFileName);
freeDyString(&ds);
}
}
void gvSaveToDb(struct sqlConnection *conn, struct gv *el, char *tableName, int updateSize)
/* Save gv as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size
* of a string that would contain the entire query. Arrays of native types are
* converted to comma separated strings and loaded as such, User defined types are
* inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
{
struct dyString *update = newDyString(updateSize);
sqlDyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s',%u)",
tableName, el->id, el->name, el->srcId, el->baseChangeType, el->location, el->coordinateAccuracy);
sqlUpdate(conn, update->string);
freeDyString(&update);
}
void trackVersionSaveToDb(struct sqlConnection *conn, struct trackVersion *el, char *tableName, int updateSize)
/* Save trackVersion as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size
* of a string that would contain the entire query. Arrays of native types are
* converted to comma separated strings and loaded as such, User defined types are
* inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
{
struct dyString *update = newDyString(updateSize);
sqlDyStringPrintf(update, "insert into %s values ( %d,'%s','%s','%s','%s','%s','%s','%s','%s')",
tableName, el->ix, el->db, el->name, el->who, el->version, el->updateTime, el->comment, el->source, el->dateReference);
sqlUpdate(conn, update->string);
freeDyString(&update);
}
void makeItemsItemSaveToDb(struct sqlConnection *conn, struct makeItemsItem *el, char *tableName, int updateSize)
/* Save makeItemsItem as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size
* of a string that would contain the entire query. Arrays of native types are
* converted to comma separated strings and loaded as such, User defined types are
* inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
{
struct dyString *update = newDyString(updateSize);
sqlDyStringPrintf(update, "insert into %s values ( %u,'%s',%u,%u,'%s',%u,'%s',%u,%u,%u,%s,%u)",
tableName, el->bin, el->chrom, el->chromStart, el->chromEnd, el->name, el->score, el->strand, el->thickStart, el->thickEnd, el->itemRgb, el->description, el->id);
sqlUpdate(conn, update->string);
freeDyString(&update);
}
void taxonGeneticCodeSaveToDb(struct sqlConnection *conn, struct taxonGeneticCode *el, char *tableName, int updateSize)
/* Save taxonGeneticCode as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size
* of a string that would contain the entire query. Arrays of native types are
* converted to comma separated strings and loaded as such, User defined types are
* inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
{
struct dyString *update = newDyString(updateSize);
sqlDyStringPrintf(update, "insert into %s values ( %u,'%s','%s','%s','%s','%s')",
tableName, el->id, el->abbr, el->name, el->tranlsation, el->starts, el->comments);
sqlUpdate(conn, update->string);
freeDyString(&update);
}
void snpExceptionsSaveToDb(struct sqlConnection *conn, struct snpExceptions *el, char *tableName, int updateSize)
/* Save snpExceptions as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size
* of a string that would contain the entire query. Arrays of native types are
* converted to comma separated strings and loaded as such, User defined types are
* inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
{
struct dyString *update = newDyString(updateSize);
sqlDyStringPrintf(update, "insert into %s values ( %u,'%s',%u,'%s','%s')",
tableName, el->exceptionId, el->query, el->num, el->description, el->resultPath);
sqlUpdate(conn, update->string);
freeDyString(&update);
}
