void hapmapPrimateAllelesSaveToDb(struct sqlConnection *conn, struct hapmapPrimateAlleles *el, char *tableName, int updateSize)
/* Save hapmapPrimateAlleles 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. Note that strings must be escaped to allow insertion into the database.
* For example "autosql's features include" --> "autosql\'s features include"
* If worried about this use hapmapPrimateAllelesSaveToDbEscaped() */
{
struct dyString *update = newDyString(updateSize);
dyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%c','%c','%c','%s',%u,'%c','%s',%u,'%s',%u,'%c','%s',%u)",
tableName, el->chrom, el->chromStart, el->chromEnd, el->name, el->score, el->strand, el->refAllele, el->otherAllele, el->chimpChrom, el->chimpPos, el->chimpStrand, el->chimpAllele, el->chimpQual, el->rhesusChrom, el->rhesusPos, el->rhesusStrand, el->rhesusAllele, el->rhesusQual);
sqlUpdate(conn, update->string);
freeDyString(&update);
}
void protVarSaveToDb(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. Arrays of native types are
* converted to comma separated strings and loaded as such, User defined types are
* inserted as NULL. Note that strings must be escaped to allow insertion into the database.
* For example "autosql's features include" --> "autosql\'s features include"
* If worried about this use protVarSaveToDbEscaped() */
{
struct dyString *update = newDyString(updateSize);
dyStringPrintf(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 dbRIPSaveToDb(struct sqlConnection *conn, struct dbRIP *el, char *tableName, int updateSize)
/* Save dbRIP 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. Note that strings must be escaped to allow insertion into the database.
* For example "autosql's features include" --> "autosql\'s features include"
* If worried about this use dbRIPSaveToDbEscaped() */
{
struct dyString *update = newDyString(updateSize);
dyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s','%s','%s','%s','%s','%s',%s,'%s',%s,'%s','%s',%g,%d,%d,'%s','%s')",
tableName, el->chrom, el->chromStart, el->chromEnd, el->name, el->score, el->strand, el->originalId, el->forwardPrimer, el->reversePrimer, el->polyClass, el->polyFamily, el->polySubfamily, el->polySeq, el->polySource, el->reference, el->ascertainingMethod, el->remarks, el->tm, el->filledSize, el->emptySize, el->disease, el->genoRegion);
sqlUpdate(conn, update->string);
freeDyString(&update);
}
void chainStats(char *chains)
{
int lastChainId = -1;
struct lineFile *chainsLf = lineFileOpen(chains, TRUE);
struct cseqPair *cspList = NULL, *csp;
struct dyString *dy = newDyString(512);
struct hash *chainHash = newHash(0); /* Hash keyed by qSeq<strand>tSeq */
struct chain *chain;
struct cBlock *block;
int count;
count = 0;
while ((chain = chainRead(chainsLf)) != NULL)
{
if (chain->id > lastChainId)
lastChainId = chain->id;
dyStringClear(dy);
dyStringPrintf(dy, "%s%c%s", chain->qName, chain->qStrand, chain->tName);
csp = hashFindVal(chainHash, dy->string);
if (csp == NULL)
{
AllocVar(csp);
slAddHead(&cspList, csp);
hashAddSaveName(chainHash, dy->string, csp, &csp->name);
csp->qName = cloneString(chain->qName);
csp->tName = cloneString(chain->tName);
csp->qStrand = chain->qStrand;
}
slAddHead(&csp->chain, chain);
count++;
}
lineFileClose(&chainsLf);
printf("read in %d chains\n",count);
for(csp = cspList; csp; csp = csp->next)
{
slSort(&csp->chain, chainCmpTarget);
gapChains(csp->chain);
for(chain = csp->chain ; chain ; chain = chain->next)
{
for(block = chain->blockList; block; block = block->next)
{
}
}
}
dyStringFree(&dy);
}
static void testOneSql(int start, int end, char *expected)
{
struct dyString *sqlQuery;
sqlQuery = newDyString(1024);
hAddBinToQuery(start, end, sqlQuery);
if (NULL != expected)
if (differentString(sqlQuery->string,expected))
{
verbose(2,"#\tERROR: SQL incorrect at (%d, %d)\n",
start, end);
++failureCount;
}
verbose(3,"# (%d, %d):\nsql:\"%s\",\n", start, end, sqlQuery->string);
freeDyString(&sqlQuery);
}
char *docIdGetPath(char *docId, char *docIdDir, char *type, char *submitPath)
{
char *ptr = docId + strlen(docId) - 1;
struct dyString *dy = newDyString(20);
char *suffix = docDecorateType(type);
dyStringPrintf(dy, "%s/", docIdDir);
for (; ptr != docId; ptr--)
{
dyStringPrintf(dy, "%c/", *ptr);
}
dyStringPrintf(dy, "%s.%s", docId, suffix);
return dyStringCannibalize(&dy);
}
static char *getDbList(struct trackHub *tHub, int *pCount)
/* calculate dbList for hubStatus table from trackHub */
{
struct hashEl *hel;
struct dyString *dy = newDyString(1024);
struct hashCookie cookie = hashFirst(tHub->genomeHash);
int dbCount = 0;
while ((hel = hashNext(&cookie)) != NULL)
{
dbCount++;
dyStringPrintf(dy,"%s,", hel->name);
}
*pCount = dbCount;
return dy->string;
}
void gtexGeneBedSaveToDb(struct sqlConnection *conn, struct gtexGeneBed *el, char *tableName, int updateSize)
/* Save gtexGeneBed 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. This function automatically escapes quoted strings for mysql. */
{
struct dyString *update = newDyString(updateSize);
char *expScoresArray;
expScoresArray = sqlFloatArrayToString(el->expScores, el->expCount);
sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s','%s',%u,'%s')",
tableName, el->chrom, el->chromStart, el->chromEnd, el->name, el->score, el->strand, el->geneId, el->geneType, el->expCount, expScoresArray );
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&expScoresArray);
}
char *gsUploadUrl(char *gsToken, char *user, char *uploadFileName, off_t contentLength, char *base64Md5, char *contentType)
/* call uploadurl */
{
// UPLOADURLS
// TODO deal with creating parent dirs if uploadFileName contains a path? maybe not.
// old: "https://identity.genomespace.org/datamanager/uploadurls/users/"
// old "https://dm.genomespace.org/datamanager/v1.0/uploadurl/users/" // if this works, use default dir fetched earlier instead
char *dmSvr = getGenomeSpaceConfig("dmServer");
char uploadUrl[1024];
safef(uploadUrl, sizeof(uploadUrl),
"%s/v1.0/uploadurl/users/"
"%s/"
"%s"
"?Content-Length=%lld"
"&Content-MD5=%s"
"&Content-Type=%s"
, dmSvr
, user
, uploadFileName
, (long long) contentLength
, cgiEncode(base64Md5)
, contentType
);
struct dyString *reqExtra = newDyString(256);
dyStringPrintf(reqExtra, "Cookie: gs-token=%s\r\n", gsToken);
int sd = netOpenHttpExt(uploadUrl, "GET", reqExtra->string);
if (sd < 0)
errAbort("failed to open socket for [%s]", uploadUrl);
char *responseCode = NULL;
char *s3UploadUrl = parseResponse(sd, &responseCode);
if (sameString(responseCode, "404 Not Found"))
errAbort("GenomeSpace: %s, if a path was used in the output name, it may indicate the path does not exist in GenomeSpace.", responseCode);
if (!sameString(responseCode, "200 OK"))
errAbort("GenomeSpace: %s", responseCode);
dyStringFree(&reqExtra);
return s3UploadUrl;
}
static char *getGsPersonalDirectory(char *gsToken)
/* Get User's default directory from GenomeSpace DM
* Returns a url like [https://identity.genomespace.org/datamanager/files/users/<user>]
*/
{
// DEFAULT DIRECTORY
// old1 char *defaultDirectoryUrl = "https://identity.genomespace.org/datamanager/defaultdirectory";
// old2 char *defaultDirectoryUrl = "https://dmtest.genomespace.org:8444/datamanager/defaultdirectory";
// old3 char *defaultDirectoryUrl = "https://dm.genomespace.org/datamanager/v1.0/defaultdirectory";
// NOTE the defaultdirectory method got renamed to personaldirectory
// old4 char *personalDirectoryUrl = "https://dm.genomespace.org/datamanager/v1.0/personaldirectory";
char *dmSvr = getGenomeSpaceConfig("dmServer");
char personalDirectoryUrl[1024];
safef(personalDirectoryUrl, sizeof personalDirectoryUrl, "%s/v1.0/personaldirectory", dmSvr);
struct dyString *reqExtra = newDyString(256);
dyStringPrintf(reqExtra, "Cookie: gs-token=%s\r\n", gsToken);
int sd = netOpenHttpExt(personalDirectoryUrl, "GET", reqExtra->string);
if (sd < 0)
errAbort("failed to open socket for [%s]", personalDirectoryUrl);
struct dyString *dy = netSlurpFile(sd);
close(sd);
char *personalDirectory = NULL;
if (strstr(dy->string, "HTTP/1.1 303 See Other"))
{
char *valStart = strstr(dy->string, "Location: ");
if (valStart)
{
valStart += strlen("Location: ");
char *valEnd = strstr(valStart, "\r\n");
if (!valEnd)
errAbort("location not found in response headers");
personalDirectory = cloneStringZ(valStart, valEnd - valStart);
}
}
dyStringFree(&dy);
dyStringFree(&reqExtra);
return personalDirectory;
}
void omimParseRec(char *omimTextFile, FILE *recFh, FILE *fieldFh)
/* omimParseRec - parse OMIM flat text file. */
{
struct lineFile *lf = lineFileOpen(omimTextFile, TRUE);
struct omimRecord *omimr;
struct dyString *dy = newDyString(4096);
for (;;)
{
struct lm *lm = lmInit(8*1024);
omimr = omimRecordNext(lf, lm, dy, recFh, fieldFh);
if (omimr == NULL)
break;
lmCleanup(&lm);
}
dyStringFree(&dy);
}
int main(int argc, char** argv)
{
FILE *infile;
struct dyString *path = newDyString(128);
usage(argv);
if(argv[2] != NULL)
{
dyStringAppend(path, argv[2]);
if(!endsWith(path->string, "/"))
dyStringAppend(path, "/");
}
infile = mustOpen(argv[1], "r");
getTransFromFile(infile, path->string);
carefulClose(&infile);
freeDyString(&path);
return 0;
}
void populateXMLFile(FILE *outfile, int tmNumber, char *proteinID, char *path)
/** Adds the number of TM helices and sequence the the xml file */
{
struct dyString *filename = newDyString(128);
if(path == NULL)
dyStringPrintf(filename, "%s.seq", proteinID);
else
dyStringPrintf(filename, "%s%s.seq", path, proteinID);
fprintf(outfile,
"%d\" id-prefix=\"TM\" nterm-id=\"N-term\" cterm-id=\"C-term\" direction=\"down\" />\n\n"
"\t</diagram-layout>\n\n\t<protein>\n\n\t\t<name>%s</name>\n\n\t\t<residue-codes>\n\n",
tmNumber, proteinID
);
catSeqFile(outfile, filename->string);
fprintf(outfile, "\n\n\t\t</residue-codes>\n\n\t\t<secondary-structure>\n\n");
freeDyString(&filename);
}
void updatePath(struct hash *hash, char *userPath,
char *homeDir, char *sysPath)
/* Prepend userPath and system path to existing path.
* Add homeDir in front of all elements of user path. */
{
struct dyString *dy = newDyString(1024);
char *s, *e;
char *oldPath;
/* Go through user path - which is colon separated
* and prepend homeDir to it. */
userPath = cloneString(userPath);
s = userPath;
for (;;)
{
if (s == NULL || s[0] == 0)
break;
e = strchr(s, ':');
if (e != NULL)
*e++ = 0;
dyStringAppend(dy, homeDir);
dyStringAppend(dy, "/");
dyStringAppend(dy, s);
dyStringAppend(dy, ":");
s = e;
}
/* Add system path next. */
if (sysPath != NULL && sysPath[0] != 0)
{
dyStringAppend(dy, sysPath);
if (lastChar(sysPath) != ':')
dyStringAppend(dy, ":");
}
/* Add paths we inherited from root. */
oldPath = hashFindVal(hash, "PATH");
if (oldPath == NULL || oldPath[0] == 0)
oldPath = "/bin:/usr/bin";
dyStringAppend(dy, oldPath);
hashUpdate(hash, "PATH", dy->string);
freez(&userPath);
dyStringFree(&dy);
}
char *associationCellVal(struct column *col, struct genePos *gp,
struct sqlConnection *conn)
/* Make comma separated list of matches to association table. */
{
char query[1024];
struct sqlResult *sr;
char **row;
boolean gotOne = FALSE;
struct dyString *dy = newDyString(512);
char *result = NULL;
char *key = (col->protKey
? (kgVersion == KG_III ? lookupProtein(conn, gp->name) : gp->protein)
: gp->name);
struct hash *uniqHash = NULL;
if (col->weedDupes) uniqHash = newHash(8);
safef(query, sizeof(query), col->queryOne, key);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
char *s = row[0];
boolean needQuote;
if (uniqHash != NULL)
{
if (hashLookup(uniqHash, s))
continue;
else
hashAdd(uniqHash, s, NULL);
}
needQuote = hasWhiteSpace(s);
if (needQuote)
dyStringAppendC(dy, '\'');
dyStringAppend(dy, s);
if (needQuote)
dyStringAppendC(dy, '\'');
dyStringAppend(dy, ",");
gotOne = TRUE;
}
sqlFreeResult(&sr);
if (gotOne)
result = cloneString(dy->string);
dyStringFree(&dy);
freeHash(&uniqHash);
return result;
}
void userSettingsSaveForm(struct userSettings *us)
/* Put up controls that let user name and save the current
* set. */
{
char buf[1024];
struct hashEl *list = cartFindPrefix(us->cart, us->savePrefix);
safef(buf, sizeof(buf), "Save %s", us->formTitle);
makeTitle(buf, NULL);
/* Start form/save session/print title. */
hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" NAME=\"usForm\" METHOD=GET>\n");
cartSaveSession(us->cart);
/* Put up controls that are always there. */
hPrintf("Please name this setup:\n");
cartMakeTextVar(us->cart, us->nameVar, "", 16);
hPrintf(" ");
cgiMakeButton(us->formVar, "save");
hPrintf(" ");
cgiMakeButton(us->formVar, "cancel");
/* Put up additional controls if have saved settings already. */
if (list != NULL)
{
struct dyString *js = newDyString(0);
htmlHorizontalLine();
slSort(&list, hashElCmp);
hPrintf("Existing Setups:");
dyStringPrintf(js, "document.usForm.%s.value=", us->nameVar);
dyStringPrintf(js, "document.usForm.%s.options", us->listDisplayVar);
dyStringPrintf(js, "[document.usForm.%s.selectedIndex].value;", us->listDisplayVar);
hPrintf("<SELECT NAME=\"%s\" SIZE=%d onchange=\"%s\">",
us->listDisplayVar, slCount(list), js->string);
printLabelList(us, list);
hPrintf("</SELECT>\n");
cgiMakeButton(us->formVar, "delete existing setup");
}
/* Cleanup. */
hPrintf("</FORM>\n");
slFreeList(&list);
}
void warnWithBackTrace(char *format, ...)
/* Issue a warning message and append backtrace. */
{
va_list args;
va_start(args, format);
struct dyString *dy = newDyString(255);
dyStringAppend(dy, format);
#define STACK_LIMIT 20
char **strings = NULL;
int count = 0;
// developer: this is an occasionally useful means of getting stack info without crashing
// however, it is not supported on cygwin. Conditionally compile this in when desired.
// The define is at top to include execinfo.h
#ifdef BACKTRACE_EXISTS
void *buffer[STACK_LIMIT];
count = backtrace(buffer, STACK_LIMIT);
strings = backtrace_symbols(buffer, count);
#endif///def BACKTRACE_EXISTS
if (strings == NULL)
dyStringAppend(dy,"\nno backtrace_symbols available in errabort::warnWithBackTrace().");
else
{
int ix = 1;
dyStringAppend(dy,"\nBACKTRACE (use on cmdLine):");
if (strings[1] != NULL)
{
strSwapChar(strings[1],' ','\0');
dyStringPrintf(dy,"\naddr2line -Cfise %s",strings[1]);
strings[1] += strlen(strings[1]) + 1;
}
for (; ix < count && strings[ix] != NULL; ix++)
{
strings[ix] = skipBeyondDelimit(strings[ix],'[');
strSwapChar(strings[ix],']','\0');
dyStringPrintf(dy," %s",strings[ix]);
}
free(strings);
}
vaWarn(dyStringCannibalize(&dy), args);
va_end(args);
}
FILE* createXMLFile(char* proteinID, char *path)
{
FILE* outfile;
struct dyString *filename = newDyString(128);
if(path == NULL)
dyStringPrintf(filename, "%s.xml", proteinID);
else
dyStringPrintf(filename, "%s%s.xml", path, proteinID);
outfile = mustOpen(filename->string, "w");
fprintf(outfile,
"<?xml version=\"1.0\" encoding=\"UTF-8\" ?>\n\n"
"<rbde-diagram xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\""
" xsi:noNamespaceSchemaLocation=\"H:\\dev\\crover\\xml\\xsd\\residue-based-diagram.xsd\">\n\n"
"\t<diagram-layout>\n\n\t\t<tm-bundle tm-number=\""
);
freeDyString(&filename);
return outfile;
}
static char *transcriptToCanonical(struct sqlConnection *conn, char *transcript)
/* Translate transcript to canonical ID if possible, otherwise just return
* a copy of transcript. */
{
struct dyString *dy = newDyString(1024);
char *cannon = genomeSetting("canonicalTable");
char *isoform = genomeSetting("isoformTable");
char buf[128];
char *result = NULL;
sqlDyStringPrintf(dy, "select %s.transcript from %s,%s where %s.transcript = '%s'",
cannon, isoform, cannon, isoform, transcript);
sqlDyStringPrintf(dy, " and %s.clusterId = %s.clusterId", isoform, cannon);
result = sqlQuickQuery(conn, dy->string, buf, sizeof(buf));
if (result != NULL)
return(cloneString(result));
else
return(cloneString(transcript));
}
void encodeErgeSaveToDb(struct sqlConnection *conn, struct encodeErge *el, char *tableName, int updateSize)
/* Save encodeErge 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);
char *blockSizesArray, *chromStartsArray;
blockSizesArray = sqlUnsignedArrayToString(el->blockSizes, el->blockCount);
chromStartsArray = sqlUnsignedArrayToString(el->chromStarts, el->blockCount);
sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s',%u,%u,%u,%u,'%s','%s','%s','%s')",
tableName, el->chrom, el->chromStart, el->chromEnd, el->name, el->score, el->strand, el->thickStart, el->thickEnd, el->reserved, el->blockCount, blockSizesArray , chromStartsArray , el->Id, el->color);
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&blockSizesArray);
freez(&chromStartsArray);
}
void newStitch3(char *axtFile, char *output)
/* newStitch3 - Another stitching experiment - with kd-trees.. */
{
struct hash *pairHash = newHash(0); /* Hash keyed by qSeq<strand>tSeq */
struct dyString *dy = newDyString(512);
struct lineFile *lf = lineFileOpen(axtFile, TRUE);
struct axt *axt;
struct seqPair *spList = NULL, *sp;
FILE *f = mustOpen(output, "w");
/* Read input file and divide alignments into various parts. */
while ((axt = axtRead(lf)) != NULL)
{
struct cBlock *block;
if (axt->score < 500)
{
axtFree(&axt);
continue;
}
dyStringClear(dy);
dyStringPrintf(dy, "%s%c%s", axt->qName, axt->qStrand, axt->tName);
sp = hashFindVal(pairHash, dy->string);
if (sp == NULL)
{
AllocVar(sp);
slAddHead(&spList, sp);
hashAddSaveName(pairHash, dy->string, sp, &sp->name);
}
AllocVar(block);
block->qStart = axt->qStart;
block->qEnd = axt->qEnd;
block->tStart = axt->tStart;
block->tEnd = axt->tEnd;
block->score = axt->score;
slAddHead(&sp->blockList, block);
axtFree(&axt);
}
for (sp = spList; sp != NULL; sp = sp->next)
{
slReverse(&sp->blockList);
chainPair(sp, f);
}
dyStringFree(&dy);
}
boolean testingFileIdentical(char *file1, char *file2)
/** Check to see if two files are the same. */
{
struct dyString *command = newDyString(2048);
char *resultsFile = "_testingFileIdentical.tmp";
int result = 0;
boolean identical = FALSE;
int numDiff = 0;
dyStringPrintf(command, "diff -b %s %s | wc > %s", file1, file2,resultsFile );
result = system(command->string);
if(result != 0)
errAbort("testing::testingFileIdentical() - Failed running diff on %s and %s", file1, file2);
numDiff = countWcDiff(resultsFile);
if(numDiff ==0)
identical = TRUE;
freeDyString(&command);
remove(resultsFile);
return identical;
}
struct kgProtAlias *findKGProtAlias(char *dataBase, char *spec, char *mode)
{
/* findKGProtAlias looks up protein aliases for Known Genes, given a seach spec
mode "E" is for Exact match
mode "F" is for Fuzzy match
mode "P" is for Prefix match
it returns a link list of kgProtAlias nodes, which contain kgID, displayID, and alias
*/
struct sqlConnection *conn = hAllocConn(dataBase);
struct dyString *ds = newDyString(256);
struct kgProtAlias *kapList = NULL;
char fullTableName[256];
safef(fullTableName, 250, "%s.%s", dataBase, "kgProtAlias");
if (!sqlTableExists(conn, fullTableName))
{
errAbort("Table %s.kgProtAlias does not exist.\n", dataBase);
}
if (sameString(mode, "E"))
{
sqlDyStringPrintf(ds, "select * from %s.kgProtAlias where alias = '%s'", dataBase, spec);
}
else if (sameString(mode, "F"))
{
sqlDyStringPrintf(ds, "select * from %s.kgProtAlias where alias like '%%%s%%'", dataBase, spec);
}
else if (sameString(mode, "P"))
{
sqlDyStringPrintf(ds, "select * from %s.kgProtAlias where alias like '%s%%'", dataBase, spec);
}
else
{
errAbort("%s is not a valid mode for findKGAlias()\n", mode);
}
addKGProtAlias(conn, ds, &kapList);
hFreeConn(&conn);
return(kapList);
}
struct hash *readInfoFile(char *fileName)
/* Read in 'info' file into hash keyed by gene field and
* containing a partial sanger22extra. */
{
struct hash *infoHash = newHash(0);
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *line, *type, *val;
struct dyString *dy = newDyString(512);
struct sanger22extra *sx = NULL;
while (lineFileNext(lf, &line, NULL))
{
line = skipLeadingSpaces(line);
if (line[0] == 0)
{
finishRecord(sx, dy);
sx = NULL;
}
else
{
if (sx == NULL)
AllocVar(sx);
type = nextWord(&line);
val = strchr(line, '"');
if (val == NULL)
errAbort("No quoted value line %d of %s\n", lf->lineIx, lf->fileName);
parseQuotedString(val, val, &line);
if (sameString("Gene", type))
{
sx->name = cloneString(val);
hashAdd(infoHash, val, sx);
}
else if (sameString("Remark", type))
{
dyStringAppend(dy, val);
dyStringAppend(dy, ". ");
}
}
}
finishRecord(sx, dy);
lineFileClose(&lf);
return infoHash;
}
void affy10KSaveToDbEscaped(struct sqlConnection *conn, struct affy10K *el, char *tableName, int updateSize)
/* Save affy10K 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 affy10KSaveToDb().
* 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;
chrom = sqlEscapeString(el->chrom);
dyStringPrintf(update, "insert into %s values ( '%s',%u,%u,%u)",
tableName, chrom, el->chromStart , el->chromEnd , el->affyId );
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&chrom);
}
void cnpSharpCutoffSaveToDbEscaped(struct sqlConnection *conn, struct cnpSharpCutoff *el, char *tableName, int updateSize)
/* Save cnpSharpCutoff 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 cnpSharpCutoffSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *sample;
sample = sqlEscapeString(el->sample);
dyStringPrintf(update, "insert into %s values ( '%s',%u,%g)",
tableName, sample, el->batch , el->value );
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&sample);
}
void loadDatabase(char *database, char *track, char *tabName)
/* Load up database from tab-file. */
{
struct sqlConnection *conn = sqlConnect(database);
struct dyString *dy = newDyString(1024);
if (!cgiBoolean("add"))
{
sqlDyStringPrintf(dy, createString, track);
sqlRemakeTable(conn, track, dy->string);
dyStringClear(dy);
}
sqlDyStringPrintf(dy, "load data local infile '%s' into table %s",
tabName, track);
sqlUpdate(conn, dy->string);
dyStringFree(&dy);
sqlDisconnect(&conn);
}
int main(int argc, char *argv[])
/* Process command line. */
{
struct dyString *ds = newDyString(1024);
int i;
optionInit(&argc, argv, options);
cgi = optionExists("cgi");
jkhgap = optionExists("jkhgap");
if (argc < 3)
usage();
for (i=2; i<argc; ++i)
{
dyStringAppend(ds, argv[i]);
if (i != argc-1)
dyStringAppend(ds, " ");
}
newProg(argv[1], ds->string);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
long enteredMainTime = clock1000();
struct dyString *headText = newDyString(512);
char *destination = cgiUsualString("destination", defaultDestination);
if (strstr(destination, "://"))
errAbort("To stop Open Redirect abuse, only relative URLs are supported. "
"Request for destination=[%s] rejected.\n", destination);
dyStringPrintf(headText,
"<META HTTP-EQUIV=\"REFRESH\" CONTENT=\"0;URL=%s\">"
"<META HTTP-EQUIV=\"Pragma\" CONTENT=\"no-cache\">"
"<META HTTP-EQUIV=\"Expires\" CONTENT=\"-1\">"
,destination);
htmShellWithHead("Reset Cart", headText->string, doMiddle, NULL);
dyStringFree(&headText);
cgiExitTime("cartReset", enteredMainTime);
return 0;
}
void tigrCmrGeneSaveToDbEscaped(struct sqlConnection *conn, struct tigrCmrGene *el, char *tableName, int updateSize)
/* Save tigrCmrGene 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 tigrCmrGeneSaveToDb().
* 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, *tigrCommon, *tigrGene, *tigrECN, *primLocus, *tigrMainRole, *tigrSubRole, *swissProt, *genbank, *goTerm;
chrom = sqlEscapeString(el->chrom);
name = sqlEscapeString(el->name);
strand = sqlEscapeString(el->strand);
tigrCommon = sqlEscapeString(el->tigrCommon);
tigrGene = sqlEscapeString(el->tigrGene);
tigrECN = sqlEscapeString(el->tigrECN);
primLocus = sqlEscapeString(el->primLocus);
tigrMainRole = sqlEscapeString(el->tigrMainRole);
tigrSubRole = sqlEscapeString(el->tigrSubRole);
swissProt = sqlEscapeString(el->swissProt);
genbank = sqlEscapeString(el->genbank);
goTerm = sqlEscapeString(el->goTerm);
dyStringPrintf(update, "insert into %s values ( %d,'%s',%u,%u,'%s',%u,'%s','%s','%s','%s','%s',%u,%u,'%s','%s','%s','%s',%f,%f,%f,'%s')",
tableName, el->bin , chrom, el->chromStart , el->chromEnd , name, el->score , strand, tigrCommon, tigrGene, tigrECN, primLocus, el->tigrLength , el->tigrPepLength , tigrMainRole, tigrSubRole, swissProt, genbank, el->tigrMw , el->tigrPi , el->tigrGc , goTerm);
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&chrom);
freez(&name);
freez(&strand);
freez(&tigrCommon);
freez(&tigrGene);
freez(&tigrECN);
freez(&primLocus);
freez(&tigrMainRole);
freez(&tigrSubRole);
freez(&swissProt);
freez(&genbank);
freez(&goTerm);
}