char *translateName(char *name, boolean toInt)
/* translates external name to internal name format or vice versa */
{
char *transName = NULL;
boolean prefixFound = FALSE;
int i;
for (i = 0; i < NUMPREFIXES && (!prefixFound); i++)
{
if (toInt)
{
if (startsWith(extNamePrefix[i], name))
{
transName = replaceChars(name, extNamePrefix[i], intNamePrefix[i]);
prefixFound = TRUE;
}
}
else
{
if (startsWith(intNamePrefix[i], name))
{
transName = replaceChars(name, intNamePrefix[i], extNamePrefix[i]);
prefixFound = TRUE;
}
}
}
if (prefixFound)
return transName;
else
return NULL;
}
void removeElement(char *el, char ***array, unsigned *count)
/* Add a new element to a array of elements */
{
char *arrayCurr, *arrayCurrDel, del[128];
int sizeOne, size;
char **cArray, **rArray=NULL, ***dArray;
if (*count > 0)
{
size = *count;
arrayCurr = sqlStringArrayToString(*array, *count);
safef(del, ArraySize(del), "%s,", el);
arrayCurrDel = replaceChars(arrayCurr, del, "");
if (differentString(arrayCurr, arrayCurrDel))
size--;
dArray = array;
/* if (*dArray)
freeMem(dArray); */
sqlStringDynamicArray(arrayCurrDel, &cArray, &sizeOne);
assert(sizeOne == size);
*count = size;
if (size > 0)
{
AllocArray(rArray, size);
CopyArray(cArray, rArray, size);
*array = rArray;
}
else
*array = NULL;
}
}
static Color cgColorLikeHgGenome(struct track *tg, struct hvGfx *hvg)
/* Search the cart variables and use the colors corresponding to the hgGenome */
/* graph. */
{
Color ret;
struct hashEl *matchingCartSettings = NULL;
struct hashEl *el;
char cartGenomeWildStr[256];
char *graphCartVarName = NULL;
char *colorCartVarSetting = "black";
safef(cartGenomeWildStr, sizeof(cartGenomeWildStr), "hgGenome_graph_%s_*", database);
/* for ex. hgGenome_graph_hg18_1_1 */
matchingCartSettings = cartFindLike(cart, cartGenomeWildStr);
for (el = matchingCartSettings; el != NULL; el = el->next)
{
char *val = (char *)el->val;
if (val && sameString(val, tg->track))
{
graphCartVarName = el->name;
break;
}
}
if (graphCartVarName)
{
char *colorCartVarName = replaceChars(graphCartVarName, "_graph_", "_graphColor_");
colorCartVarSetting = cartUsualString(cart, colorCartVarName, "black");
freeMem(colorCartVarName);
}
hashElFreeList(&matchingCartSettings);
ret = colorFromAscii(hvg, colorCartVarSetting);
return ret;
}
void setupTable(struct sqlConnection *conn)
/* Set up the autoTest table for testing. Call dropTable() later
to remove table. */
{
struct lineFile *lf = lineFileOpen("output/newTest.sql", TRUE);
char *update = NULL;
char *line = NULL;
struct dyString *ds = newDyString(256);
if(sqlTableExists(conn, testTableName))
errAbort("dbLinkTest.c::setupTable() - Table %s.%s already exists. Can't create another.",
sqlGetDatabase(conn), testTableName);
while(lineFileNextReal(lf, &line))
{
char *tmp = strstr(line, "not null");
if(tmp != NULL)
{
*tmp = ',';
tmp++;
*tmp = '\0';
}
subChar(line, '\t', ' ');
dyStringPrintf(ds, "%s", line);
}
update = replaceChars(ds->string, "PRIMARY KEY", "UNIQUE");
sqlUpdate(conn, update);
freez(&update);
dyStringFree(&ds);
lineFileClose(&lf);
}
u8 convertStringToPin( u8 *ucBuffer )
{
// This function is constant string safe
u8 i, ucPin;
#ifdef __PYGMYNEBULA
for( i = 0; i < PYGMYMAXPINS; i++ ){
if( isStringSame( PYGMYNEBULAPINS[ i ].String, ucBuffer ) ){
return( PYGMYNEBULAPINS[ i ].Value );
} // if
} // for
#endif // __PYGMYNEBULA
// Pin isn't an alias, check for port letter and pin number
if( replaceChars( ucBuffer, "pP", ' ' ) ){
if( replaceChars( ucBuffer, "aA", ' ' ) ){
ucPin = 0;
} else if( replaceChars( ucBuffer, "bB", ' ' ) ){
ucPin = 16;
} else if( replaceChars( ucBuffer, "cC", ' ' ) ){
ucPin = 32;
} else if( replaceChars( ucBuffer, "dD", ' ' ) ){
ucPin = 48;
} else if( replaceChars( ucBuffer, "eE", ' ' ) ){
ucPin = 64;
} else if( replaceChars( ucBuffer, "fF", ' ' ) ){
ucPin = 80;
} else{
return( 0xFF );
} // else
return( ucPin + convertStringToInt( ucBuffer ) );
} // if
return( 0xFF );
}
void replaceTildeWithHome(char **pS)
/* if the path starts with ~ (tilde) char, replace with $HOME */
{
char *s = *pS;
if (s[0] == '~')
{
*pS = replaceChars(s, "~", getenv("HOME"));
}
}
void addVersion(boolean strict, char *database, char *dirName, char *raName,
struct hash *uniqHash,
struct hash *htmlHash,
struct hgFindSpec **pSpecList)
/* Read in specs from raName and add them to list/database if new. */
{
struct hgFindSpec *hfsList = NULL, *hfs = NULL;
struct hgFindSpec *hfsNext = NULL;
hfsList = hgFindSpecFromRa(database, raName, NULL);
/* prune records of the incorrect release */
hfsList = pruneRelease(hfsList);
if (strict)
{
for (hfs = hfsList; hfs != NULL; hfs = hfsNext)
{
hfsNext = hfs->next;
if (! hTableOrSplitExists(database, hfs->searchTable))
{
if (verboseLevel() > 1)
printf("%s missing\n", hfs->searchTable);
slRemoveEl(&hfsList, hfs);
}
else if (hfs->xrefTable[0] != 0)
{
// Use sqlTableExists because xrefTable might be $db.$table,
// not supported by hTableExists / hTableOrSplitExists
// NOTE hfs->xrefTable can sometimes contain a comma-separated table list,
// rather than just a single table.
struct sqlConnection *conn = hAllocConn(database);
char *tables = replaceChars(hfs->xrefTable, ",", " ");
boolean exists = sqlTablesExist(conn, tables);
hFreeConn(&conn);
freeMem(tables);
if (! exists)
{
if (verboseLevel() > 1)
printf("%s (xref) missing\n", hfs->xrefTable);
slRemoveEl(&hfsList, hfs);
}
}
}
}
for (hfs = hfsList; hfs != NULL; hfs = hfsNext)
{
hfsNext = hfs->next;
if (! hashLookup(uniqHash, hfs->searchName))
{
hashAdd(uniqHash, hfs->searchName, hfs);
slAddHead(pSpecList, hfs);
}
}
}
u8 handler_ATSMSPROMPT( u8 *ucBuffer )
{
u8 *ucParam;
ucParam = getNextSubString( ucBuffer, NEWLINE );
if( replaceChars( ucParam, ">", ' ' ) ){
print( MODEM_COM, "\rATSMSPROMPT", ucParam );
return( TRUE );
} // if
return( TRUE );
}
static void handleCID(char **html, char *ctMain)
/* Handle CID replacements if needed */
{
if (optionExists("cid") && ctMain && sameWord(ctMain,"text/html"))
{
struct hashEl *el, *list = hashElListHash(cidHash);
for(el=list;el;el=el->next)
{
char *cid=addSuffix("cid:",el->name);
if (stringIn(cid,*html))
{
char *new = replaceChars(*html, cid, el->val);
freez(html);
*html = new;
}
freez(&cid);
// support for content-location
if (stringIn(el->name,*html))
{
char *new = replaceChars(*html, el->name, el->val);
freez(html);
*html = new;
}
}
static struct slName *hgFindSpecNameList(char *db)
/* Return the hgFindSpec table name(s) to use (based on trackDb name). */
{
struct slName *trackDbList = hTrackDbList();
struct slName *specNameList = NULL;
struct slName *tdbName;
for (tdbName = trackDbList; tdbName != NULL; tdbName = tdbName->next)
{
char *subbed = replaceChars(tdbName->name, "trackDb", "hgFindSpec");
if (hTableExists(db, subbed))
slNameAddHead(&specNameList, subbed);
freez(&subbed);
}
if (!specNameList)
specNameList = slNameNew("hgFindSpec");
else
slReverse(&specNameList);
return specNameList;
}
void LoadCustomSettings(bool internal)
{
std::string myString = replaceChars(RSP.romname);
bool found = false;
char buffer[256];
char* line;
FILE* fPtr;
std::transform(myString.begin(), myString.end(), myString.begin(), ::toupper);
if (internal) {
line = strtok(customini, "\n");
} else {
const char *pathname = ConfigGetSharedDataFilepath("GLideN64.custom.ini");
if (pathname == NULL || (fPtr = fopen(pathname, "rb")) == NULL)
return;
}
while (true)
{
if (!internal) {
if (fgets(buffer, 255, fPtr) == NULL)
break;
else
line = buffer;
}
ini_line l = ini_parse_line(&line);
switch (l.type)
{
case INI_SECTION:
{
if (myString == replaceChars(l.name))
found = true;
else
found = false;
}
case INI_PROPERTY:
{
if (found) {
if (!strcmp(l.name, "video\\cropMode"))
config.video.cropMode = atoi(l.value);
else if (!strcmp(l.name, "video\\cropWidth"))
config.video.cropWidth = atoi(l.value);
else if (!strcmp(l.name, "video\\cropHeight"))
config.video.cropHeight = atoi(l.value);
else if (!strcmp(l.name, "video\\multisampling"))
config.video.multisampling = atoi(l.value);
else if (!strcmp(l.name, "frameBufferEmulation\\aspect"))
config.frameBufferEmulation.aspect = atoi(l.value);
else if (!strcmp(l.name, "frameBufferEmulation\\nativeResFactor"))
config.frameBufferEmulation.nativeResFactor = atoi(l.value);
else if (!strcmp(l.name, "frameBufferEmulation\\copyToRDRAM"))
config.frameBufferEmulation.copyToRDRAM = atoi(l.value);
else if (!strcmp(l.name, "frameBufferEmulation\\copyFromRDRAM"))
config.frameBufferEmulation.copyFromRDRAM = atoi(l.value);
else if (!strcmp(l.name, "frameBufferEmulation\\copyDepthToRDRAM"))
config.frameBufferEmulation.copyDepthToRDRAM = atoi(l.value);
else if (!strcmp(l.name, "frameBufferEmulation\\copyAuxToRDRAM"))
config.frameBufferEmulation.copyAuxToRDRAM = atoi(l.value);
else if (!strcmp(l.name, "frameBufferEmulation\\N64DepthCompare"))
config.frameBufferEmulation.N64DepthCompare = atoi(l.value);
else if (!strcmp(l.name, "frameBufferEmulation\\bufferSwapMode"))
config.frameBufferEmulation.bufferSwapMode = atoi(l.value);
else if (!strcmp(l.name, "texture\\bilinearMode"))
config.texture.bilinearMode = atoi(l.value);
else if (!strcmp(l.name, "texture\\maxAnisotropy"))
config.texture.maxAnisotropy = atoi(l.value);
else if (!strcmp(l.name, "generalEmulation\\enableNativeResTexrects"))
config.generalEmulation.enableNativeResTexrects = atoi(l.value);
else if (!strcmp(l.name, "generalEmulation\\correctTexrectCoords"))
config.generalEmulation.correctTexrectCoords = atoi(l.value);
else if (!strcmp(l.name, "generalEmulation\\enableLegacyBlending"))
config.generalEmulation.enableLegacyBlending = atoi(l.value);
else if (!strcmp(l.name, "generalEmulation\\enableFragmentDepthWrite"))
config.generalEmulation.enableFragmentDepthWrite = atoi(l.value);
}
}
}
if (internal) {
line = strtok(NULL, "\n");
if (line == NULL)
break;
}
}
}
void sortGenes(struct sqlConnection *conn)
/* Put up sort gene page. */
{
cartWebStart(cart, database, "Finding Candidate Genes for Gene Sorter");
if (!hgNearOk(database))
errAbort("Sorry, gene sorter not available for this database.");
/* Get list of regions. */
struct genoGraph *gg = ggFirstVisible();
double threshold = getThreshold();
struct bed3 *bed, *bedList = regionsOverThreshold(gg);
/* Figure out what table and column are the sorter's main gene set. */
struct hash *genomeRa = hgReadRa(genome, database, "hgNearData",
"genome.ra", NULL);
char *geneTable = hashMustFindVal(genomeRa, "geneTable");
char *idColumn = hashMustFindVal(genomeRa, "idColumn");
/* if marker labels were present when the file was uploaded, they are saved here */
char cgmName[256];
safef(cgmName, sizeof(cgmName), "%s.cgm", gg->binFileName);
struct lineFile *m = lineFileMayOpen(cgmName, TRUE);
char *cgmRow[4];
cgmRow[0] = ""; /* dummy row */
cgmRow[1] = "";
cgmRow[2] = "0";
cgmRow[3] = "0";
FILE *g = NULL;
int markerCount = 0;
struct tempName snpTn;
if (m)
{
/* Create custom column output file. */
trashDirFile(&snpTn, "hgg", "marker", ".mrk");
g = mustOpen(snpTn.forCgi, "w");
fprintf(g,
"column name=\"%s Markers\" shortLabel=\"%s Markers over threshold\" longLabel=\"%s Markers in regions over threshold\" "
"visibility=on priority=99 "
"\n"
, gg->shortLabel
, gg->shortLabel
, gg->shortLabel
);
}
/*** Build up hash of all transcriptHash that are in region. */
struct hash *transcriptHash = hashNew(16);
/* This loop handles one chromosome at a time. It depends on
* the bedList being sorted by chromosome. */
for (bed = bedList; bed != NULL; )
{
/* Make binKeeper and stuff in all regions in this chromosome into it. */
char *chrom = bed->chrom;
int chromSize = hChromSize(database, chrom);
struct binKeeper *bk = binKeeperNew(0, chromSize);
while (bed != NULL && sameString(chrom, bed->chrom))
{
binKeeperAdd(bk, bed->chromStart, bed->chromEnd, bed);
bed = bed->next;
}
struct binKeeper *bkGenes = NULL;
if (m)
bkGenes = binKeeperNew(0, chromSize);
/* Query database to find out bounds of all genes on this chromosome
* and if they overlap any of the regions then put them in the hash. */
char query[512];
safef(query, sizeof(query),
"select name,txStart,txEnd from %s where chrom='%s'", geneTable, chrom);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
char *name = row[0];
int start = sqlUnsigned(row[1]);
int end = sqlUnsigned(row[2]);
if (binKeeperAnyOverlap(bk, start, end))
{
hashStore(transcriptHash, name);
if (m)
binKeeperAdd(bkGenes, start, end, cloneString(name));
}
}
sqlFreeResult(&sr);
if (m)
{
/* Read cgm file if it exists, looking at all markers on this chromosome
* and if they overlap any of the regions and genes then output them. */
do
{
// marker, chrom, chromStart, val
char *marker = cgmRow[0];
char *chr = cgmRow[1];
int start = sqlUnsigned(cgmRow[2]);
int end = start+1;
double val = sqlDouble(cgmRow[3]);
int cmp = strcmp(chr,chrom);
if (cmp > 0)
break;
if (cmp == 0)
{
if (val >= threshold)
{
struct binElement *el, *bkList = binKeeperFind(bkGenes, start, end);
for (el = bkList; el; el=el->next)
{
/* output to custom column trash file */
fprintf(g, "%s %s\n", (char *)el->val, marker);
}
if (bkList)
{
++markerCount;
slFreeList(&bkList);
}
}
}
}
while (lineFileRow(m, cgmRow));
}
/* Clean up for this chromosome. */
binKeeperFree(&bk);
if (m)
{
/* For speed, we do not free up the values (cloned the kg names earlier) */
binKeeperFree(&bkGenes);
}
}
/* Get list of all transcripts in regions. */
struct hashEl *el, *list = hashElListHash(transcriptHash);
/* Create file with all matching gene IDs. */
struct tempName keyTn;
trashDirFile(&keyTn, "hgg", "key", ".key");
FILE *f = mustOpen(keyTn.forCgi, "w");
for (el = list; el != NULL; el = el->next)
fprintf(f, "%s\n", el->name);
carefulClose(&f);
/* Print out some info. */
hPrintf("Thresholding <i>%s</i> at %g. ", gg->shortLabel, threshold);
hPrintf("There are %d regions covering %lld bases.<BR>\n",
slCount(bedList), bedTotalSize((struct bed*)bedList) );
hPrintf("Installed a Gene Sorter filter that selects only genes in these regions.<BR>\n");
if (m)
{
hPrintf("There are %d markers in the regions over threshold that overlap knownGenes.<BR>\n", markerCount);
hPrintf("Installed a Gene Sorter custom column called \"%s Markers\" with these markers.<BR>\n", gg->shortLabel);
}
/* close custom column output file */
if (m)
{
lineFileClose(&m);
carefulClose(&g);
}
/* Stuff cart variable with name of file. */
char keyCartName[256];
safef(keyCartName, sizeof(keyCartName), "%s%s.keyFile",
advFilterPrefix, idColumn);
cartSetString(cart, keyCartName, keyTn.forCgi);
cartSetString(cart, customFileVarName, snpTn.forCgi);
char snpVisCartNameTemp[256];
char *snpVisCartName = NULL;
safef(snpVisCartNameTemp, sizeof(snpVisCartNameTemp), "%s%s Markers.vis",
colConfigPrefix, gg->shortLabel);
snpVisCartName = replaceChars(snpVisCartNameTemp, " ", "_");
cartSetString(cart, snpVisCartName, "1");
freeMem(snpVisCartName);
hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" METHOD=GET>\n");
cartSaveSession(cart);
hPrintf("<CENTER>");
cgiMakeButton("submit", "go to gene sorter");
hPrintf("</CENTER>");
hPrintf("</FORM>");
cartWebEnd();
}
char *menuBar(struct cart *cart, char *db)
// Return HTML for the menu bar (read from a configuration file);
// we fixup internal CGI's to add hgsid's and include the appropriate js and css files.
//
// Note this function is also called by hgTracks which extends the menu bar
// with a View menu defined in hgTracks/menu.c
{
char *docRoot = hDocumentRoot();
char *menuStr, buf[4096], uiVars[128];
FILE *fd;
char *navBarFile = "inc/globalNavBar.inc";
struct stat statBuf;
char *scriptName = cgiScriptName();
if (cart)
safef(uiVars, sizeof(uiVars), "%s=%s", cartSessionVarName(), cartSessionId(cart));
else
uiVars[0] = 0;
if(docRoot == NULL)
// tolerate missing docRoot (i.e. don't bother with menu when running from command line)
return NULL;
jsIncludeFile("jquery.js", NULL);
jsIncludeFile("jquery.plugins.js", NULL);
webIncludeResourceFile("nice_menu.css");
// Read in menu bar html
safef(buf, sizeof(buf), "%s/%s", docRoot, navBarFile);
fd = mustOpen(buf, "r");
fstat(fileno(fd), &statBuf);
int len = statBuf.st_size;
menuStr = needMem(len + 1);
mustRead(fd, menuStr, statBuf.st_size);
menuStr[len] = 0;
carefulClose(&fd);
if (cart)
{
char *newMenuStr = menuBarAddUiVars(menuStr, "/cgi-bin/hg", uiVars);
freez(&menuStr);
menuStr = newMenuStr;
}
if(scriptName)
{
// Provide hgTables options for some CGIs.
char hgTablesOptions[1024] = "";
char *track = (cart == NULL ? NULL :
(endsWith(scriptName, "hgGene") ?
cartOptionalString(cart, "hgg_type") :
cartOptionalString(cart, "g")));
if (track && cart && db &&
(endsWith(scriptName, "hgc") || endsWith(scriptName, "hgTrackUi") ||
endsWith(scriptName, "hgGene")))
{
struct trackDb *tdb = hTrackDbForTrack(db, track);
if (tdb)
{
struct trackDb *topLevel = trackDbTopLevelSelfOrParent(tdb);
safef(hgTablesOptions, sizeof hgTablesOptions,
"../cgi-bin/hgTables?hgta_doMainPage=1&hgta_group=%s&hgta_track=%s&hgta_table=%s&",
topLevel->grp, topLevel->track, tdb->table);
menuStr = replaceChars(menuStr, "../cgi-bin/hgTables?", hgTablesOptions);
trackDbFree(&tdb);
}
}
}
if(!loginSystemEnabled())
stripRegEx(menuStr, "<\\!-- LOGIN_START -->.*<\\!-- LOGIN_END -->", REG_ICASE);
if(scriptName)
{ // Provide optional official mirror servers menu items
char *geoMenu = geoMirrorMenu();
char *pattern = "<!-- OPTIONAL_MIRROR_MENU -->";
char *newMenuStr = replaceChars(menuStr, pattern, geoMenu);
freez(&menuStr);
menuStr = newMenuStr;
}
if(scriptName)
{
// Provide view menu for some CGIs.
struct dyString *viewItems = dyStringCreate("");
boolean hasViewMenu = TRUE;
if (endsWith(scriptName, "hgGenome"))
{
safef(buf, sizeof(buf), "../cgi-bin/hgGenome?%s&hgGenome_doPsOutput=1", uiVars);
dyStringPrintf(viewItems, "<li><a href='%s' id='%s'>%s</a></li>\n", buf, "pdfLink", "PDF/PS");
}
else
{
hasViewMenu = FALSE;
}
if (hasViewMenu)
{
struct dyString *viewMenu = dyStringCreate("<li class='menuparent' id='view'><span>View</span>\n<ul style='display: none; visibility: hidden;'>\n");
dyStringAppend(viewMenu, viewItems->string);
dyStringAppend(viewMenu, "</ul>\n</li>\n");
menuStr = replaceChars(menuStr, "<!-- OPTIONAL_VIEW_MENU -->", viewMenu->string);
dyStringFree(&viewMenu);
}
else if (!endsWith(scriptName, "hgTracks"))
{
replaceChars(menuStr, "<!-- OPTIONAL_VIEW_MENU -->", "");
}
dyStringFree(&viewItems);
}
if(scriptName)
{
// Provide context sensitive help links for some CGIs.
char *link = NULL;
char *label = NULL;
if (endsWith(scriptName, "hgBlat"))
{
link = "../goldenPath/help/hgTracksHelp.html#BLATAlign";
label = "Help on Blat";
}
else if (endsWith(scriptName, "hgHubConnect"))
{
link = "../goldenPath/help/hgTrackHubHelp.html";
label = "Help on Track Hubs";
}
else if (endsWith(scriptName, "hgNear"))
{
link = "../goldenPath/help/hgNearHelp.html";
label = "Help on Gene Sorter";
}
else if (endsWith(scriptName, "hgTables"))
{
link = "../goldenPath/help/hgTablesHelp.html";
label = "Help on Table Browser";
}
else if (endsWith(scriptName, "hgGenome"))
{
link = "../goldenPath/help/hgGenomeHelp.html";
label = "Help on Genome Graphs";
}
else if (endsWith(scriptName, "hgSession"))
{
link = "../goldenPath/help/hgSessionHelp.html";
label = "Help on Sessions";
}
else if (endsWith(scriptName, "hgVisiGene"))
{
link = "../goldenPath/help/hgTracksHelp.html#VisiGeneHelp";
label = "Help on VisiGene";
}
else if (endsWith(scriptName, "hgCustom"))
{
link = "../goldenPath/help/customTrack.html";
label = "Help on Custom Tracks";
}
// Don't overwrite any previously set defaults
if(!contextSpecificHelpLink && link)
contextSpecificHelpLink = link;
if(!contextSpecificHelpLabel && label)
contextSpecificHelpLabel = label;
}
if(contextSpecificHelpLink)
{
char buf[1024];
safef(buf, sizeof(buf), "<li><a href='%s'>%s</a></li>", contextSpecificHelpLink, contextSpecificHelpLabel);
menuStr = replaceChars(menuStr, "<!-- CONTEXT_SPECIFIC_HELP -->", buf);
}
return menuStr;
}
static void gadPrint(struct section *section,
struct sqlConnection *conn, char *geneId)
/* Print out GAD section. */
{
int refPrinted = 0;
boolean showCompleteGadList;
char condStr[256];
char query[256];
struct sqlResult *sr;
char **row;
struct dyString *currentCgiUrl;
char *upperDisease;
char *url =
cloneString("http://geneticassociationdb.nih.gov/cgi-bin/tableview.cgi?table=allview&cond=gene=");
char *itemName;
if (url != NULL && url[0] != 0)
{
safef(condStr, sizeof(condStr),
"k.kgId='%s' and k.geneSymbol = g.geneSymbol", geneId);
itemName = sqlGetField(database, "kgXref k, gadAll g", "k.geneSymbol", condStr);
showCompleteGadList = FALSE;
if (cgiOptionalString("showAllRef") != NULL)
{
if (sameWord(cgiOptionalString("showAllRef"), "Y") ||
sameWord(cgiOptionalString("showAllRef"), "y") )
{
showCompleteGadList = TRUE;
}
}
currentCgiUrl = cgiUrlString();
printf("<B>Genetic Association Database: ");
printf("<A HREF=\"%s'%s'\" target=_blank>", url, itemName);
printf("%s</B></A>\n", itemName);
printf("<BR><B>CDC HuGE Published Literature: ");
printf("<A HREF=\"%s%s%s\" target=_blank>",
"http://hugenavigator.net/HuGENavigator/searchSummary.do?firstQuery=",
itemName,
"&publitSearchType=now&whichContinue=firststart&check=n&dbType=publit&Mysubmit=go");
printf("%s</B></A>\n", itemName);
/* List diseases associated with the gene */
safef(query, sizeof(query),
"select distinct broadPhen from gadAll where geneSymbol='%s' and association = 'Y' order by broadPhen",
itemName);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL)
{
upperDisease = replaceChars(row[0], "'", "''");
touppers(upperDisease);
printf("<BR><B>Positive Disease Associations: </B>");
printf("<A HREF=\"%s%s%s%s%s\" target=_blank>",
"http://geneticassociationdb.nih.gov/cgi-bin/tableview.cgi?table=allview&cond=upper(DISEASE)%20like%20'%25",
cgiEncode(upperDisease), "%25'%20AND%20upper(GENE)%20%20like%20'%25", itemName, "%25'");
printf("%s</B></A>\n", row[0]);
row = sqlNextRow(sr);
}
while (row != NULL)
{
upperDisease = replaceChars(row[0], "'", "''");
touppers(upperDisease);
printf(", <A HREF=\"%s%s%s%s%s\" target=_blank>",
"http://geneticassociationdb.nih.gov/cgi-bin/tableview.cgi?table=allview&cond=upper(DISEASE)%20like%20'%25",
cgiEncode(upperDisease), "%25'%20AND%20upper(GENE)%20%20like%20'%25", itemName, "%25'");
printf("%s</B></A>\n", row[0]);
row = sqlNextRow(sr);
}
sqlFreeResult(&sr);
refPrinted = 0;
safef(query, sizeof(query),
"select broadPhen,reference,title,journal, pubMed, conclusion from gadAll where geneSymbol='%s' and association = 'Y' order by broadPhen",
itemName);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL) printf("<BR><B>Related Studies: </B><OL>");
while (row != NULL)
{
printf("<LI><B>%s </B>", row[0]);
printf("<br>%s, %s, %s.\n", row[1], row[2], row[3]);
if (!sameWord(row[4], ""))
{
printf(" [PubMed ");
printf("<A HREF=\"%s%s%s'\" target=_blank>",
"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=",
row[4],"&query_hl=1&itool=genome.ucsc.edu");
printf("%s</B></A>]\n", row[4]);
}
printf("<br><i>%s</i>\n", row[5]);
printf("</LI>\n");
refPrinted++;
if ((!showCompleteGadList) && (refPrinted >= 3)) break;
row = sqlNextRow(sr);
}
sqlFreeResult(&sr);
printf("</OL>");
if ((!showCompleteGadList) && (row != NULL))
{
printf("<B>   more ... </B>");
printf(
"<A HREF=\"%s?showAllRef=Y&%s#gad\">click here to view the complete list</A> ",
"hgGene", currentCgiUrl->string);
}
}
}
char *menuBar(struct cart *cart)
// Return HTML for the menu bar (read from a configuration file);
// we fixup internal CGI's to add hgsid's and include the appropriate js and css files.
{
char *docRoot = hDocumentRoot();
char *menuStr, buf[4096], uiVars[128];
FILE *fd;
int len, offset, err;
char *navBarFile = "inc/globalNavBar.inc";
struct stat statBuf;
regex_t re;
regmatch_t match[2];
char *scriptName = cgiScriptName();
if (cart)
safef(uiVars, sizeof(uiVars), "%s=%u", cartSessionVarName(), cartSessionId(cart));
else
uiVars[0] = 0;
if(docRoot == NULL)
// tolerate missing docRoot (i.e. don't bother with menu when running from command line)
return NULL;
jsIncludeFile("jquery.js", NULL);
jsIncludeFile("jquery.plugins.js", NULL);
webIncludeResourceFile("nice_menu.css");
// Read in menu bar html
safef(buf, sizeof(buf), "%s/%s", docRoot, navBarFile);
fd = mustOpen(buf, "r");
fstat(fileno(fd), &statBuf);
len = statBuf.st_size;
menuStr = needMem(len + 1);
mustRead(fd, menuStr, statBuf.st_size);
menuStr[len] = 0;
carefulClose(&fd);
if (cart)
{
// fixup internal CGIs to have hgsid
safef(buf, sizeof(buf), "/cgi-bin/hg[A-Za-z]+(%c%c?)", '\\', '?');
err = regcomp(&re, buf, REG_EXTENDED);
if(err)
errAbort("regcomp failed; err: %d", err);
struct dyString *dy = newDyString(0);
for(offset = 0; offset < len && !regexec(&re, menuStr + offset, ArraySize(match), match, 0); offset += match[0].rm_eo)
{
dyStringAppendN(dy, menuStr + offset, match[0].rm_eo);
if(match[1].rm_so == match[1].rm_eo)
dyStringAppend(dy, "?");
dyStringAppend(dy, uiVars);
if(match[1].rm_so != match[1].rm_eo)
dyStringAppend(dy, "&");
}
if(offset < len)
dyStringAppend(dy, menuStr + offset);
freez(&menuStr);
menuStr = dyStringCannibalize(&dy);
}
if(!loginSystemEnabled())
stripRegEx(menuStr, "<\\!-- LOGIN_START -->.*<\\!-- LOGIN_END -->", REG_ICASE);
if(scriptName)
{ // Provide optional official mirror servers menu items
char *geoMenu = geoMirrorMenu();
char *pattern = "<!-- OPTIONAL_MIRROR_MENU -->";
char *newMenuStr = replaceChars(menuStr, pattern, geoMenu);
freez(&menuStr);
menuStr = newMenuStr;
}
if(scriptName)
{
// Provide view menu for some CGIs.
struct dyString *viewItems = dyStringCreate("");
boolean hasViewMenu = TRUE;
if (endsWith(scriptName, "hgGenome"))
{
safef(buf, sizeof(buf), "../cgi-bin/hgGenome?%s&hgGenome_doPsOutput=1", uiVars);
dyStringPrintf(viewItems, "<li><a href='%s' id='%s'>%s</a></li>\n", buf, "pdfLink", "PDF/PS");
}
else
{
hasViewMenu = FALSE;
}
if (hasViewMenu)
{
struct dyString *viewMenu = dyStringCreate("<li class='menuparent' id='view'><span>View</span>\n<ul style='display: none; visibility: hidden;'>\n");
dyStringAppend(viewMenu, viewItems->string);
dyStringAppend(viewMenu, "</ul>\n</li>\n");
menuStr = replaceChars(menuStr, "<!-- OPTIONAL_VIEW_MENU -->", viewMenu->string);
dyStringFree(&viewMenu);
}
dyStringFree(&viewItems);
}
if(scriptName)
{
// Provide context sensitive help links for some CGIs.
char *link = NULL;
char *label = NULL;
if (endsWith(scriptName, "hgBlat"))
{
link = "../goldenPath/help/hgTracksHelp.html#BLATAlign";
label = "Help on Blat";
}
else if (endsWith(scriptName, "hgHubConnect"))
{
link = "../goldenPath/help/hgTrackHubHelp.html";
label = "Help on Track Hubs";
}
else if (endsWith(scriptName, "hgNear"))
{
link = "../goldenPath/help/hgNearHelp.html";
label = "Help on Gene Sorter";
}
else if (endsWith(scriptName, "hgTables"))
{
link = "../goldenPath/help/hgTablesHelp.html";
label = "Help on Table Browser";
}
else if (endsWith(scriptName, "hgGenome"))
{
link = "../goldenPath/help/hgGenomeHelp.html";
label = "Help on Genome Graphs";
}
else if (endsWith(scriptName, "hgSession"))
{
link = "../goldenPath/help/hgSessionHelp.html";
label = "Help on Sessions";
}
else if (endsWith(scriptName, "hgVisiGene"))
{
link = "../goldenPath/help/hgTracksHelp.html#VisiGeneHelp";
label = "Help on VisiGene";
}
else if (endsWith(scriptName, "hgCustom"))
{
link = "../goldenPath/help/customTrack.html";
label = "Help on Custom Tracks";
}
// Don't overwrite any previously set defaults
if(!contextSpecificHelpLink && link)
contextSpecificHelpLink = link;
if(!contextSpecificHelpLabel && label)
contextSpecificHelpLabel = label;
}
if(contextSpecificHelpLink)
{
char buf[1024];
safef(buf, sizeof(buf), "<li><a href='%s'>%s</a></li>", contextSpecificHelpLink, contextSpecificHelpLabel);
menuStr = replaceChars(menuStr, "<!-- CONTEXT_SPECIFIC_HELP -->", buf);
}
return menuStr;
}
void doUserFiles(char *u, struct commit *commits)
/* process one user's files-view (or all if u is NULL) */
{
// http://hgwdev.cse.ucsc.edu/cvs-reports/branch/user/galt/index-by-file.html
// if u is NULL
// http://hgwdev.cse.ucsc.edu/cvs-reports/branch/file/index.html
char userPath[1024];
if (u)
safef(userPath, sizeof(userPath), "%s/%s/%s/%s/index-by-file.html", outDir, outPrefix, "user", u);
else
safef(userPath, sizeof(userPath), "%s/%s/%s/index.html", outDir, outPrefix, "file");
FILE *h = mustOpen(userPath, "w");
if (u)
{
fprintf(h, "<html>\n<head>\n<title>File Changes for %s</title>\n</head>\n</body>\n", u);
fprintf(h, "<h1>File Changes for %s</h1>\n", u);
fprintf(h, "switch to <A href=\"index.html\">commits view</A>, <A href=\"../index.html\">user index</A>");
}
else
{
fprintf(h, "<html>\n<head>\n<title>All File Changes</title>\n</head>\n</body>\n");
fprintf(h, "<h1>All File Changes</h1>\n");
}
fprintf(h, "<h3>%s to %s (%s to %s) %s</h3>\n", startTag, endTag, startDate, endDate, title);
fprintf(h, "<ul>\n");
int totalLinesChanged = 0;
int totalFileCount = 0;
char *cDiff = NULL, *cHtml = NULL, *fDiff = NULL, *fHtml = NULL;
char *relativePath = NULL;
struct commit *c = NULL;
struct files *f = NULL;
struct comFile *comFiles = NULL, *cf = NULL;
// pre-filter for u if u is not NULL
for(c = commits; c; c = c->next)
{
if (!u || (u && sameString(c->author, u)))
{
for(f = c->files; f; f = f->next)
{
AllocVar(cf);
cf->f = f;
cf->commit = c;
slAddHead(&comFiles, cf);
}
}
}
// sort by file path, and then by commitNumber
// so that newest commit is on the bottom.
slSort(&comFiles, slComFileCmp);
char *lastPath = "";
char *closure = "";
for(cf = comFiles; cf; cf = cf->next)
{
c = cf->commit;
f = cf->f;
if (!sameString(f->path, lastPath))
{
fprintf(h, "%s", closure);
lastPath = f->path;
fprintf(h, "<li>%s\n", f->path);
closure = "</li>\n";
}
char path[1024];
// context unified
if (u)
safef(path, sizeof(path), "%s/%s%s", "context", f->path, c->commitId);
else
safef(path, sizeof(path), "../user/%s/%s/%s%s", c->author, "context", f->path, c->commitId);
relativePath = cloneString(path);
safef(path, sizeof(path), "%s.html", relativePath);
cHtml = cloneString(path);
safef(path, sizeof(path), "%s.diff", relativePath);
cDiff = cloneString(path);
// full text (up to 10,000 lines)
freeMem(relativePath);
if (u)
safef(path, sizeof(path), "%s/%s%s", "full", f->path, c->commitId);
else
safef(path, sizeof(path), "../user/%s/%s/%s%s", c->author, "context", f->path, c->commitId);
relativePath = cloneString(path);
safef(path, sizeof(path), "%s.html", relativePath);
fHtml = cloneString(path);
safef(path, sizeof(path), "%s.diff", relativePath);
fDiff = cloneString(path);
// make file view links
fprintf(h, "<ul><li>");
fprintf(h, " lines changed %d, "
"context: <A href=\"%s\">html</A>, <A href=\"%s\">text</A>, "
"full: <A href=\"%s\">html</A>, <A href=\"%s\">text</A><br>\n"
, f->linesChanged
, cHtml, cDiff, fHtml, fDiff);
//fprintf(h, " %s\n", c->commitId);
//fprintf(h, " %s\n", c->date);
char *cc = htmlEncode(c->comment);
char *ccc = replaceChars(cc, "\n", "<br>\n");
fprintf(h, " %s\n", ccc);
freeMem(cc);
freeMem(ccc);
fprintf(h, "</li></ul>\n");
freeMem(relativePath);
freeMem(cDiff);
freeMem(cHtml);
freeMem(fDiff);
freeMem(fHtml);
totalLinesChanged += f->linesChanged;
++totalFileCount;
fprintf(h, "\n");
}
fprintf(h, "%s", closure);
fprintf(h, "</ul>\n");
if (u)
{
fprintf(h, "switch to <A href=\"index.html\">commits view</A>, <A href=\"../index.html\">user index</A>");
}
else
{
fprintf(h, "<ul>\n");
fprintf(h, "<li> lines changed: %d</li>\n", totalLinesChanged);
fprintf(h, "<li> files changed: %d</li>\n", totalFileCount);
fprintf(h, "</ul>\n");
}
fprintf(h, "</body>\n</html>\n");
fclose(h);
}
void doUserCommits(char *u, struct commit *commits, int *saveUlc, int *saveUfc)
/* process one user, commit-view */
{
char userPath[1024];
safef(userPath, sizeof(userPath), "%s/%s/%s/%s/index.html", outDir, outPrefix, "user", u);
FILE *h = mustOpen(userPath, "w");
fprintf(h, "<html>\n<head>\n<title>Commits for %s</title>\n</head>\n</body>\n", u);
fprintf(h, "<h1>Commits for %s</h1>\n", u);
fprintf(h, "switch to <A href=\"index-by-file.html\">files view</A>, <A href=\"../index.html\">user index</A>\n");
fprintf(h, "<h3>%s to %s (%s to %s) %s</h3>\n", startTag, endTag, startDate, endDate, title);
fprintf(h, "<ul>\n");
int userLinesChanged = 0;
int userFileCount = 0;
char *cDiff = NULL, *cHtml = NULL, *fDiff = NULL, *fHtml = NULL;
char *relativePath = NULL;
char *commonPath = NULL;
struct commit *c = NULL;
struct files *f = NULL;
for(c = commits; c; c = c->next)
{
if (sameString(c->author, u))
{
//fprintf(h, "%s\n", c->commitId);
//fprintf(h, "%s\n", c->date);
char *cc = htmlEncode(c->comment);
char *ccc = replaceChars(cc, "\n", "<br>\n");
fprintf(h, "<li>%s\n", ccc);
freeMem(cc);
freeMem(ccc);
makeDiffAndSplit(c, u, FALSE);
makeDiffAndSplit(c, u, TRUE);
for(f = c->files; f; f = f->next)
{
char path[1024];
// context unified
safef(path, sizeof(path), "%s/%s%s", "context", f->path, c->commitId);
relativePath = cloneString(path);
safef(path, sizeof(path), "%s/%s/%s/%s/%s", outDir, outPrefix, "user", u, relativePath);
commonPath = cloneString(path);
safef(path, sizeof(path), "%s.html", commonPath);
cHtml = cloneString(path);
safef(path, sizeof(path), "%s.diff", commonPath);
cDiff = cloneString(path);
// make context html page
f->linesChanged = makeHtml(cDiff, cHtml, f->path, c->commitId);
userLinesChanged += f->linesChanged;
++userFileCount;
freeMem(cDiff);
freeMem(cHtml);
safef(path, sizeof(path), "%s.html", relativePath);
cHtml = cloneString(path);
safef(path, sizeof(path), "%s.diff", relativePath);
cDiff = cloneString(path);
// full text (up to 10,000 lines)
freeMem(relativePath);
safef(path, sizeof(path), "%s/%s%s", "full", f->path, c->commitId);
relativePath = cloneString(path);
safef(path, sizeof(path), "%s/%s/%s/%s/%s", outDir, outPrefix, "user", u, relativePath);
freeMem(commonPath);
commonPath = cloneString(path);
safef(path, sizeof(path), "%s.html", commonPath);
fHtml = cloneString(path);
safef(path, sizeof(path), "%s.diff", commonPath);
fDiff = cloneString(path);
//git show --unified=10000 11a20b6cd113d75d84549eb642b7f2ac7a2594fe src/utils/qa/weeklybld/buildEnv.csh
// make full html page
makeHtml(fDiff, fHtml, f->path, c->commitId);
freeMem(fDiff);
freeMem(fHtml);
safef(path, sizeof(path), "%s.html", relativePath);
fHtml = cloneString(path);
safef(path, sizeof(path), "%s.diff", relativePath);
fDiff = cloneString(path);
// make file diff links
fprintf(h, "<ul><li> %s - lines changed %d, "
"context: <A href=\"%s\">html</A>, <A href=\"%s\">text</A>, "
"full: <A href=\"%s\">html</A>, <A href=\"%s\">text</A></li></ul>\n"
, f->path, f->linesChanged
, cHtml, cDiff, fHtml, fDiff);
freeMem(relativePath);
freeMem(commonPath);
freeMem(cDiff);
freeMem(cHtml);
freeMem(fDiff);
freeMem(fHtml);
}
fprintf(h, "</li>\n");
}
}
fprintf(h, "</ul>\n");
fprintf(h, "switch to <A href=\"index-by-file.html\">files view</A>, <A href=\"../index.html\">user index</A>\n");
fprintf(h, "</body>\n</html>\n");
fclose(h);
*saveUlc = userLinesChanged;
*saveUfc = userFileCount;
}
void hgTrackDb(char *org, char *database, char *trackDbName, char *sqlFile, char *hgRoot,
boolean strict)
/* hgTrackDb - Create trackDb table from text files. */
{
struct trackDb *td;
char tab[PATH_LEN];
safef(tab, sizeof(tab), "%s.tab", trackDbName);
struct trackDb *tdbList = buildTrackDb(org, database, hgRoot, strict);
tdbList = flatten(tdbList);
slSort(&tdbList, trackDbCmp);
verbose(1, "Loaded %d track descriptions total\n", slCount(tdbList));
/* Write to tab-separated file; hold off on html, since it must be encoded */
{
verbose(2, "Starting write of tabs to %s\n", tab);
FILE *f = mustOpen(tab, "w");
for (td = tdbList; td != NULL; td = td->next)
{
hVarSubstTrackDb(td, database);
char *hold = td->html;
td->html = "";
subChar(td->type, '\t', ' '); /* Tabs confuse things. */
subChar(td->shortLabel, '\t', ' '); /* Tabs confuse things. */
subChar(td->longLabel, '\t', ' '); /* Tabs confuse things. */
trackDbTabOut(td, f);
td->html = hold;
}
carefulClose(&f);
verbose(2, "Wrote tab representation to %s\n", tab);
}
/* Update database */
{
char *create, *end;
char query[256];
struct sqlConnection *conn = sqlConnect(database);
/* Load in table definition. */
readInGulp(sqlFile, &create, NULL);
create = trimSpaces(create);
create = substituteTrackName(create, trackDbName);
end = create + strlen(create)-1;
if (*end == ';') *end = 0;
sqlRemakeTable(conn, trackDbName, create);
/* Load in regular fields. */
sqlSafef(query, sizeof(query), "load data local infile '%s' into table %s", tab, trackDbName);
verbose(2, "sending mysql \"%s\"\n", query);
sqlUpdate(conn, query);
verbose(2, "done tab file load");
/* Load in html and settings fields. */
for (td = tdbList; td != NULL; td = td->next)
{
if (isEmpty(td->html))
{
if (strict && !trackDbLocalSetting(td, "parent") && !trackDbLocalSetting(td, "superTrack") &&
!sameString(td->track,"cytoBandIdeo"))
{
fprintf(stderr, "Warning: html missing for %s %s %s '%s'\n",org, database, td->track, td->shortLabel);
}
}
else
{
updateBigTextField(conn, trackDbName, "tableName", td->track, "html", td->html);
}
if (td->settingsHash != NULL)
{
char *settings = settingsFromHash(td->settingsHash);
updateBigTextField(conn, trackDbName, "tableName", td->track,
"settings", settings);
if (showSettings)
{
verbose(1, "%s: type='%s';", td->track, td->type);
if (isNotEmpty(settings))
{
char *oneLine = replaceChars(settings, "\n", "; ");
eraseTrailingSpaces(oneLine);
verbose(1, " %s", oneLine);
freeMem(oneLine);
}
verbose(1, "\n");
}
freeMem(settings);
}
}
sqlDisconnect(&conn);
verbose(1, "Loaded database %s\n", database);
}
}
void cleanTicketNumbers(LPFIELDSRESULTS lpFieldsResults) {
char *resultsStr = lpFieldsResults->result;
int numGr, i, k;
int iStart, iStop;
char strT[10];
int ret;
int numLines = 0;
int thGroups = 5;
int numChars;
int beginCut = 0;
resultTmp[0] = 0;
cand2Tmp[0] = 0;
// test every line
//printf("\n\n");
//printf(resultsStr);
//printf("\n\n");
// get number of lines
i = 0;
while(1){
if(getLine(resultsStr, i, &iStart, &iStop) < 0) break;
numLines++;
i++;
}
// test last lines
// printf("--- numLines= %d\n",numLines);
k = numLines-1;
while(k>0){
if(getLine(resultsStr, k, &iStart, &iStop) < 0) break;
if(testLineConf(lpFieldsResults, iStart, iStop) < 0)
numLines--;
else
break;
k--;
}
i = 0;
k = 0;
while(i < numLines){
if(getLine(resultsStr, i, &iStart, &iStop) < 0) break;
testLeftSideForLine(resultsStr, &iStart, iStop);
//printLine(resultsStr, iStart, iStop);
numGr = getNumberOfGroups(resultsStr, iStart, iStop);
beginCut = 0;
// printf("--- line i= %d; numGr= %d, iStart= %d, iStop= %d\n",i, numGr, iStart, iStop);
numChars = getNumChars(resultsStr, iStart, iStop);
//printf("--- line i= %d; numGr= %d, numChars= %d\n",i, numGr, numChars);
if(numGr == thGroups){
beginCut = testBeginCut(lpFieldsResults, iStart, iStop);
if(beginCut > 0)
numGr++;
}
// printLine(resultsStr, iStart, iStop);
// printf("--- line i= %d; numGr= %d, numChars= %d\n",i, numGr, numChars);
if(numGr > thGroups && strlen(resultsStr) > 15 && numChars < 20){
copyLine(lpFieldsResults, iStart, iStop);
// printLine(resultsStr, iStart, iStop);
// printfQuad();
// printf("--- line i= %d; %s\n",i, result);
if(beginCut > 0){
// printf("--- line i= %d; beginCut= %d\n",i, beginCut);
strT[0] = 'A'+k;
strT[1] = 32;
strT[2] = 0;
replaceChars(0, -1, strT);
}else{
getFirstCharFromNumLine(&iStart, &iStop);
// printfQuad();
// printf("--- getFirstCharFromNumLine i= %d; iStart= %d, iStop= %d\n",i, iStart, iStop);
if(numGr < 8 && iStart == 0 && iStop == 0 && result[1] != 32) {
strT[0] = 'A'+k;
strT[1] = 32;
strT[2] = 0;
replaceChars(0, -1, strT);
}else{
// printf("--- numGr= %d; iStart= %d, iStop= %d, result[1]= %d\n",numGr, iStart, iStop, result[1]);
strT[0] = 'A'+k;
strT[1] = 0;
replaceChars(iStart, iStop, strT);
}
}
iStop = -1;
ret = getFirstQPFromNumLine(&iStart, &iStop);
if(ret >= 0) {
replaceChars(iStart, iStop, "QP");
}
if( ret > 0 || numGr >6) {
if(getSecondQPFromNumLine(&iStart, &iStop) >=0){
replaceChars(iStart, iStop, "QP");
}
}
addLineToTmp();
k++;
//printTmp();
}
i++;
}
copyResultsBack(lpFieldsResults);
}
static void loadDatabase(char *database, char *track, int bedSize, struct bedStub *bedList)
/* Load database from bedList. */
{
struct sqlConnection *conn;
struct dyString *dy = newDyString(1024);
char *tab = (char *)NULL;
int loadOptions = (optionExists("onServer") ? SQL_TAB_FILE_ON_SERVER : 0);
if ( ! noLoad )
conn = sqlConnect(database);
if ((char *)NULL != tmpDir)
tab = cloneString(rTempName(tmpDir,"loadBed",".tab"));
else
tab = cloneString("bed.tab");
if (bedDetail && sqlTable == NULL)
errAbort("bedDetail format requires sqlTable option");
if (bedDetail && !strictTab)
errAbort("bedDetail format must be tab separated");
if (bedDetail && !noBin)
noBin = TRUE;
/* First make table definition. */
if (sqlTable != NULL && !oldTable)
{
/* Read from file. */
char *sql, *s;
readInGulp(sqlTable, &sql, NULL);
/* Chop off end-of-statement semicolon if need be. */
s = strchr(sql, ';');
if (s != NULL) *s = 0;
if ( !noLoad )
{
if (renameSqlTable)
{
char *pos = stringIn("CREATE TABLE ", sql);
if (pos == NULL)
errAbort("Can't find CREATE TABLE in %s\n", sqlTable);
char *oldSql = cloneString(sql);
nextWord(&pos); nextWord(&pos);
char *tableName = nextWord(&pos);
sql = replaceChars(oldSql, tableName, track);
}
verbose(1, "Creating table definition for %s\n", track);
sqlRemakeTable(conn, track, sql);
if (!noBin)
addBinToEmptyTable(conn, track);
adjustSqlTableColumns(conn, track, bedSize);
}
freez(&sql);
}
else if (!oldTable)
{
int minLength;
if (noLoad)
minLength=6;
else if (maxChromNameLength)
minLength = maxChromNameLength;
else
minLength = hGetMinIndexLength(database);
verbose(2, "INDEX chrom length: %d\n", minLength);
/* Create definition statement. */
verbose(1, "Creating table definition for %s\n", track);
dyStringPrintf(dy, "CREATE TABLE %s (\n", track);
if (!noBin)
dyStringAppend(dy, " bin smallint unsigned not null,\n");
dyStringAppend(dy, " chrom varchar(255) not null,\n");
dyStringAppend(dy, " chromStart int unsigned not null,\n");
dyStringAppend(dy, " chromEnd int unsigned not null,\n");
if (bedSize >= 4)
maybeBedGraph(4, dy, " name varchar(255) not null,\n");
if (bedSize >= 5)
{
if (allowNegativeScores)
maybeBedGraph(5, dy, " score int not null,\n");
else
maybeBedGraph(5, dy, " score int unsigned not null,\n");
}
if (bedSize >= 6)
maybeBedGraph(6, dy, " strand char(1) not null,\n");
if (bedSize >= 7)
maybeBedGraph(7, dy, " thickStart int unsigned not null,\n");
if (bedSize >= 8)
maybeBedGraph(8, dy, " thickEnd int unsigned not null,\n");
/* As of 2004-11-22 the reserved field is used as itemRgb in code */
if (bedSize >= 9)
maybeBedGraph(9, dy, " reserved int unsigned not null,\n");
if (bedSize >= 10)
maybeBedGraph(10, dy, " blockCount int unsigned not null,\n");
if (bedSize >= 11)
maybeBedGraph(11, dy, " blockSizes longblob not null,\n");
if (bedSize >= 12)
maybeBedGraph(12, dy, " chromStarts longblob not null,\n");
if (bedSize >= 13)
maybeBedGraph(13, dy, " expCount int unsigned not null,\n");
if (bedSize >= 14)
maybeBedGraph(14, dy, " expIds longblob not null,\n");
if (bedSize >= 15)
maybeBedGraph(15, dy, " expScores longblob not null,\n");
dyStringAppend(dy, "#Indices\n");
if (nameIx && (bedSize >= 4) && (0 == bedGraph))
dyStringAppend(dy, " INDEX(name(16)),\n");
if (noBin)
{
dyStringPrintf(dy, " INDEX(chrom(%d),chromStart)\n", minLength);
}
else
{
dyStringPrintf(dy, " INDEX(chrom(%d),bin)\n", minLength);
}
dyStringAppend(dy, ")\n");
if (noLoad)
verbose(2,"%s", dy->string);
else
sqlRemakeTable(conn, track, dy->string);
}
verbose(1, "Saving %s\n", tab);
writeBedTab(tab, bedList, bedSize);
if ( ! noLoad )
{
verbose(1, "Loading %s\n", database);
if (customTrackLoader)
sqlLoadTabFile(conn, tab, track, loadOptions|SQL_TAB_FILE_WARN_ON_WARN);
else
sqlLoadTabFile(conn, tab, track, loadOptions);
if (! noHistory)
{
char comment[256];
/* add a comment to the history table and finish up connection */
safef(comment, sizeof(comment),
"Add %d element(s) from bed list to %s table",
slCount(bedList), track);
hgHistoryComment(conn, comment);
}
if(fillInScoreColumn != NULL)
{
char query[500];
char buf[500];
struct sqlResult *sr;
safef(query, sizeof(query), "select sum(score) from %s", track);
if(sqlQuickQuery(conn, query, buf, sizeof(buf)))
{
unsigned sum = sqlUnsigned(buf);
if (!sum)
{
safef(query, sizeof(query), "select min(%s), max(%s) from %s", fillInScoreColumn, fillInScoreColumn, track);
if ((sr = sqlGetResult(conn, query)) != NULL)
{
char **row = sqlNextRow(sr);
if(row != NULL)
{
float min = sqlFloat(row[0]);
float max = sqlFloat(row[1]);
if ( !(max == -1 && min == -1)) // if score is -1 then ignore, as if it werent present
{
if (max == min || sameString(row[0],row[1])) // this will lead to 'inf' score value in SQL update causing an error
errAbort("Could not set score in table %s max(%s)=min(%s)=%s\n", track, fillInScoreColumn, fillInScoreColumn, row[0]);
sqlFreeResult(&sr);
// Calculate a, b s/t f(x) = ax + b maps min-max => minScore-1000
float a = (1000-minScore) / (max - min);
float b = 1000 - ((1000-minScore) * max) / (max - min);
safef(query, sizeof(query), "update %s set score = round((%f * %s) + %f)", track, a, fillInScoreColumn, b);
int changed = sqlUpdateRows(conn, query, NULL);
verbose(2, "update query: %s; changed: %d\n", query, changed);
}
else
{
sqlFreeResult(&sr);
verbose(2, "score not updated; all values for column %s are -1\n", fillInScoreColumn);
}
}
}
}
}
}
sqlDisconnect(&conn);
/* if temp dir specified, unlink file to make it disappear */
if ((char *)NULL != tmpDir)
unlink(tab);
}
else
verbose(1, "No load option selected, see file: %s\n", tab);
} /* static void loadDatabase() */
void galleryDisplay(struct galleryEntry *galList)
/* Print a table containing the gallery data from galList */
{
struct galleryEntry *thisSession = galList;
/* Hide the orderable columns and disable ordering on the visible columns
* https://datatables.net/reference/option/columnDefs for more info.
* Then set up the ordering drop-down menu */
printf ("<script type=\"text/javascript\">");
printf("$(document).ready(function () {\n"
" $('#sessionTable').DataTable({\"columnDefs\": [{\"visible\":false, \"targets\":[2,3]},\n"
" {\"orderable\":false, \"targets\":[0,1]}\n"
" ],\n"
" \"dom\":\"lftip\",\n"
" \"stateSave\":true,\n"
" \"stateSaveCallback\": %s,\n"
" \"stateLoadCallback\": %s,\n"
" });\n"
/* Recover previous sorting choice from the cart settings, if available */
" var startOrder = $('#sessionTable').DataTable().order();\n"
" if (startOrder[0][0] == 3) {\n"
" if (startOrder[0][1] == \"asc\") {\n"
" $('#sortMethod').val(\"useAsc\");\n"
" } else {\n"
" $('#sortMethod').val(\"useDesc\");\n"
" }\n"
" } else {\n"
" if (startOrder[0][0] == 2) {\n"
" if (startOrder[0][1] == \"asc\") {\n"
" $('#sortMethod').val(\"dateAsc\");\n"
" } else {\n"
" $('#sortMethod').val(\"dateDesc\");\n"
" }\n"
" } else {\n"
" $('#sessionTable').DataTable().order([3,'desc']).draw();\n"
" $('#sortMethod').val(\"useDesc\");\n"
" }\n"
" }\n"
"});\n",
jsDataTableStateSave(hgPublicSessionsPrefix), jsDataTableStateLoad(hgPublicSessionsPrefix, cart));
printf ("function changeSort() {\n"
" var newSort = document.getElementById('sortMethod').value;\n"
" var theTable = $('#sessionTable').DataTable();\n"
" if (newSort == \"useDesc\") {theTable.order([3,'desc']).draw(); }\n"
" if (newSort == \"useAsc\") {theTable.order([3,'asc']).draw(); }\n"
" if (newSort == \"dateDesc\") {theTable.order([2,'desc']).draw(); }\n"
" if (newSort == \"dateAsc\") {theTable.order([2,'asc']).draw(); }\n"
"}\n");
printf("</script>\n");
printf ("<p>\n");
printf ("<b>Sort by:</b> <select id=\"sortMethod\" onchange=\"changeSort()\">\n");
printf ("\t\t<option value=\"useDesc\">Popularity (descending)</option>\n");
printf ("\t\t<option value=\"useAsc\">Popularity (ascending)</option>\n");
printf ("\t\t<option value=\"dateDesc\">Creation (newest first)</option>\n");
printf ("\t\t<option value=\"dateAsc\">Creation (oldest first)</option>\n");
printf ("</select></p>\n");
printf ("<table id=\"sessionTable\" class=\"sessionTable stripe hover row-border compact\" width=\"100%%\">\n"
" <thead>"
" <tr>"
" <th>Screenshot</th>\n"
" <th>Session Properties</th>\n"
" <th>Creation Date</th>\n"
" <th>Use Count</th>\n"
" </tr>\n"
" </thead>\n");
printf ("<tbody>\n");
while (thisSession != NULL)
{
char *settingString = NULL;
printf ("\t<tr>\n");
if (isNotEmpty(thisSession->imgUri))
{
printf ("\t\t<td><a href=\"../cgi-bin/hgTracks?%s\">",
dyStringContents(thisSession->sessionUrl));
printf ("<img src=\"%s\" class=\"sessionThumbnail\"></a></td>\n", thisSession->imgUri);
}
else
{
printf ("\t\t<td><center><nobr>Screenshot not available</nobr><br>\n");
printf ("\t\t<a href=\"../cgi-bin/hgTracks?%s\">Click Here</a> to view</center></td>\n",
dyStringContents(thisSession->sessionUrl));
}
struct hash *settingsHash = raFromString(thisSession->settings);
settingString = (char*) hashFindVal(settingsHash, "description");
if (settingString == NULL)
settingString = "";
else
{
settingString = replaceChars(settingString, "\\\\", "\\__ESC__");
settingString = replaceChars(settingString, "\\r", "\r");
settingString = replaceChars(settingString, "\\n", "\n");
settingString = replaceChars(settingString, "\\__ESC__", "\\");
}
printf ("\t\t<td><b>Description:</b> %s<br>\n", settingString);
printf ("\t\t<b>Author:</b> %s<br>\n", thisSession->userName);
printf ("\t\t<b>Session Name:</b> %s<br>\n", thisSession->sessionName);
printf ("\t\t<b>Genome Assembly:</b> %s<br>\n", thisSession->db);
printf ("\t\t<b>Creation Date:</b> %s<br>\n", thisSession->firstUse);
printf ("\t\t<b>Views:</b> %ld\n", thisSession->useCount);
printf ("\t\t</td>\n");
struct tm creationDate;
strptime(thisSession->firstUse, "%Y-%m-%d", &creationDate);
/* Hidden columns */
printf ("\t\t<td>%ld</td>\n", mktime(&creationDate));
printf ("\t\t<td>%ld</td>\n", thisSession->useCount);
printf ("\t</tr>\n");
thisSession = thisSession->next;
}
printf ("</tbody>\n");
printf ("</table>\n");
}
