boolean maybeTouchFile(char *fileName)
/* If file exists, set its access and mod times to now. If it doesn't exist, create it.
* Return FALSE if we have a problem doing so (e.g. when qateam is gdb'ing and code tries
* to touch some file owned by www). */
{
if (fileExists(fileName))
{
struct utimbuf ut;
ut.actime = ut.modtime = clock1();
int ret = utime(fileName, &ut);
if (ret != 0)
{
warn("utime(%s) failed (ownership?)", fileName);
return FALSE;
}
}
else
{
FILE *f = fopen(fileName, "w");
if (f == NULL)
return FALSE;
else
carefulClose(&f);
}
return TRUE;
}
int main()
{
{ // code block, need it to testing memory leaks
ClockMessageSystem messageSystem;
Clock clock1(messageSystem, 200);
Clock clock2(messageSystem, 700);
{
Clock clock3(messageSystem, 900);
clock3.Post(mds::Message(0, new char(0)), 0);
}
clock1.Post(mds::Message(0, NULL), 0);
clock2.Post(mds::Message(0, NULL), 0);
messageSystem.Loop();
//messageSystem.ClearQueue();
}
{
ClockMessageSystem messageSystem;
TestSend testSend1(messageSystem);
TestSend testSend2(messageSystem);
testSend1.Post(mds::Message(0, NULL), 100);
testSend2.Post(mds::Message(0, NULL), 300);
messageSystem.Loop();
}
_CrtDumpMemoryLeaks();
return 0;
}
int getkey (int interval)
{
int message;
double rem, target;
// prevent strange behaviour due to programmer mistakes
if (interval < 0) interval = -1;
switch (interval)
{
case -1:
while (1)
{
message = getmessage (-1);
if (IS_KEY (message) && message > 0) break;
}
break;
case 0:
while (TRUE)
{
message = getmessage (0);
if (message == 0) break;
if (IS_KEY (message)) break;
}
break;
default:
target = clock1 () + ((double)interval)/1000.;
message = -1;
while (TRUE)
{
rem = target - clock1();
if (rem <= 0.) break;
message = getmessage ((int)(rem*1000.));
if (IS_KEY(message) && message > 0) break;
}
}
return message;
}
struct slName *getTableNames(struct sqlConnection *conn)
/* Return a list of names of tables that have not been excluded by
* command line options. */
{
char *query = hoursOld ? "NOSQLINJ show table status" : "NOSQLINJ show tables";
struct sqlResult *sr = sqlGetResult(conn, query);
struct slName *tableList = NULL;
char **row = NULL;
int startTime = clock1();
int ageThresh = hoursOld * 3600;
while((row = sqlNextRow(sr)) != NULL)
{
struct slName *tableName = NULL;
struct slName *pat = NULL;
boolean gotMatch = FALSE;
if (hoursOld)
{
if (row[11] != NULL)
{
int tableUpdateTime = sqlDateToUnixTime(row[11]);
int ageInSeconds = startTime - tableUpdateTime;
if (ageInSeconds > ageThresh)
continue;
}
else
{
verbose(2,
"Got NULL update time for table %s.%s with hoursOld=%d\n",
sqlGetDatabase(conn), row[0], hoursOld);
}
}
for (pat = excludePatterns; pat != NULL; pat=pat->next)
{
if (wildMatch(pat->name, row[0]))
{
gotMatch = TRUE;
break;
}
}
if (gotMatch)
continue;
if (verboseLevel() >= 3 || justList)
fprintf(stderr, "Adding %s\n", row[0]);
tableName = newSlName(row[0]);
slAddHead(&tableList, tableName);
}
sqlFreeResult(&sr);
if (justList)
exit(0);
slReverse(&tableList);
return tableList;
}
int main(int argc, char *argv[])
{
char *genoListName;
char *otherListName;
char *oocFileName;
char *typeName;
char *outName;
struct patSpace *patSpace;
long startTime, endTime;
char **genoList;
int genoListSize;
char *genoListBuf;
char **otherList;
int otherListSize;
char *otherListBuf;
char *genoName;
int i;
int blockCount = 0;
struct dnaSeq **seqListList = NULL, *seq = NULL;
char *outRoot;
struct sqlConnection *conn;
enum ffStringency stringency = ffCdna;
int seedSize = 10;
FILE *out;
boolean noHead = FALSE;
struct repeatTracker *rt;
struct hash *repeatHash = newHash(10);
hostName = getenv("HOST");
pushWarnHandler(warnHandler);
startTime = clock1();
cgiSpoof(&argc, argv);
minMatch = cgiOptionalInt("minMatch", minMatch);
maxBad = cgiOptionalInt("maxBad", maxBad);
minBases = cgiOptionalInt("minBases", minBases);
dnaUtilOpen();
#ifdef DEBUG
/* Hard wire command line input so don't have to type it in each
* time run the stupid Gnu debugger. */
genoListName = "pFoo/geno.lst";
otherListName = "pFoo/bacend.lst";
typeName = "genomic";
oocFileName = "/d/biodata/human/10.ooc";
outName = "pFoo/pFoo.psl";
#else
if (argc != 6 && argc != 7)
usage();
genoListName = argv[1];
otherListName = argv[2];
typeName = argv[3];
oocFileName = argv[4];
if (sameWord(oocFileName, "none"))
oocFileName = NULL;
outName = argv[5];
if (argc == 7)
{
if (sameWord("noHead", argv[6]))
noHead = TRUE;
else
usage();
}
#endif
if (sameWord(typeName, "mRNA") || sameWord(typeName, "cDNA"))
{
stringency = ffCdna;
}
else if (sameWord(typeName, "genomic"))
{
stringency = ffTight;
}
else if (sameWord(typeName, "g2g"))
{
stringency = ffTight;
veryTight = TRUE;
seedSize = 11;
}
else if (sameString(typeName, "asm"))
{
stringency = ffTight;
avoidSelfSelf = TRUE;
}
else
{
warn("Unrecognized otherType %s\n", typeName);
usage();
}
readAllWordsOrFa(genoListName, &genoList, &genoListSize, &genoListBuf);
filterMissingFiles(genoList, &genoListSize);
if (genoListSize <= 0)
errAbort("There are no files that exist in %s\n", genoListName);
readAllWordsOrFa(otherListName, &otherList, &otherListSize, &otherListBuf);
if (otherListSize <= 0)
errAbort("There are no files that exist in %s\n", otherListName);
filterMissingFiles(otherList, &otherListSize);
out = mustOpen(outName, "w");
if (!noHead)
pslWriteHead(out);
AllocArray(seqListList, genoListSize);
for (i=0; i<genoListSize; ++i)
{
genoName = genoList[i];
if (!startsWith("#", genoName) )
seqListList[i] = seq = faReadAllDna(genoName);
for (;seq != NULL; seq = seq->next)
{
int size = seq->size;
char *name = seq->name;
struct hashEl *hel;
AllocVar(rt);
AllocArray(rt->repBytes, size);
rt->seq = seq;
if ((hel = hashLookup(repeatHash, name)) != NULL)
errAbort("Duplicate %s in %s\n", name, genoName);
hashAdd(repeatHash, name, rt);
}
storeMasked(repeatHash, genoName);
}
patSpace = makePatSpace(seqListList, genoListSize, seedSize, oocFileName, minMatch, 2000);
endTime = clock1();
printf("Made index in %ld seconds\n", (endTime-startTime));
startTime = endTime;
for (i=0; i<otherListSize; ++i)
{
FILE *f;
char *otherName;
int c;
int dotCount = 0;
struct dnaSeq otherSeq;
ZeroVar(&otherSeq);
otherName = otherList[i];
if (startsWith("#", otherName) )
continue;
f = mustOpen(otherName, "r");
while ((c = fgetc(f)) != EOF)
if (c == '>')
break;
printf("%s\n", otherName);
fflush(stdout);
while (faFastReadNext(f, &otherSeq.dna, &otherSeq.size, &otherSeq.name))
{
aliSeqName = otherSeq.name;
oneStrand(patSpace, repeatHash, &otherSeq, FALSE, stringency, out);
reverseComplement(otherSeq.dna, otherSeq.size);
oneStrand(patSpace, repeatHash, &otherSeq, TRUE, stringency, out);
aliSeqName = NULL;
}
fclose(f);
}
freePatSpace(&patSpace);
endTime = clock1();
printf("Alignment time is %ld sec\n", (endTime-startTime));
startTime = endTime;
fclose(out);
return 0;
}
void doSearchTracks(struct group *groupList)
{
if (!advancedJavascriptFeaturesEnabled(cart))
{
warn("Requires advanced javascript features.");
return;
}
struct group *group;
char *groups[128];
char *labels[128];
int numGroups = 1;
groups[0] = ANYLABEL;
labels[0] = ANYLABEL;
char *currentTab = cartUsualString(cart, TRACK_SEARCH_CURRENT_TAB, "simpleTab");
char *nameSearch = cartOptionalString(cart, TRACK_SEARCH_ON_NAME);
#ifdef TRACK_SEARCH_ON_TYPE
char *typeSearch = cartOptionalString(cart, TRACK_SEARCH_ON_TYPE);
#else///ifndef TRACK_SEARCH_ON_TYPE
char *typeSearch = NULL;
#endif///def TRACK_SEARCH_ON_TYPE
char *descSearch;
char *groupSearch = cartOptionalString(cart, TRACK_SEARCH_ON_GROUP);
boolean doSearch = sameString(cartOptionalString(cart, TRACK_SEARCH), "Search") || cartUsualInt(cart, TRACK_SEARCH_PAGER, -1) >= 0;
struct sqlConnection *conn = hAllocConn(database);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
int numMetadataSelects, tracksFound = 0;
int numMetadataNonEmpty = 0;
char **mdbVar = NULL;
char **mdbVal = NULL;
#ifdef ONE_FUNC
struct hash *parents = newHash(4);
#endif///def ONE_FUNC
boolean simpleSearch;
struct trix *trix;
char trixFile[HDB_MAX_PATH_STRING];
char **descWords = NULL;
int descWordCount = 0;
boolean searchTermsExist = FALSE;
int cols;
char buf[512];
if(sameString(currentTab, "simpleTab"))
{
descSearch = cartOptionalString(cart, TRACK_SEARCH_SIMPLE);
simpleSearch = TRUE;
freez(&nameSearch);
#ifdef TRACK_SEARCH_ON_TYPE
freez(&typeSearch);
#endif///def TRACK_SEARCH_ON_TYPE
freez(&groupSearch);
}
else
{
descSearch = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR);
simpleSearch = FALSE;
}
if(descSearch)
stripChar(descSearch, '"');
trackList = getTrackList(&groupList, -2); // global
makeGlobalTrackHash(trackList);
// NOTE: This is necessary when container cfg by '*' results in vis changes
// This will handle composite/view override when subtrack specific vis exists, AND superTrack reshaping.
parentChildCartCleanup(trackList,cart,oldVars); // Subtrack settings must be removed when composite/view settings are updated
getSearchTrixFile(database, trixFile, sizeof(trixFile));
trix = trixOpen(trixFile);
slSort(&groupList, gCmpGroup);
for (group = groupList; group != NULL; group = group->next)
{
groupTrackListAddSuper(cart, group);
if (group->trackList != NULL)
{
groups[numGroups] = cloneString(group->name);
labels[numGroups] = cloneString(group->label);
numGroups++;
if (numGroups >= ArraySize(groups))
internalErr();
}
}
safef(buf, sizeof(buf),"Search for Tracks in the %s %s Assembly", organism, hFreezeFromDb(database));
webStartWrapperDetailedNoArgs(cart, database, "", buf, FALSE, FALSE, FALSE, FALSE);
hPrintf("<div style='max-width:1080px;'>");
hPrintf("<form action='%s' name='%s' id='%s' method='get'>\n\n", hgTracksName(),TRACK_SEARCH_FORM,TRACK_SEARCH_FORM);
cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo
safef(buf, sizeof(buf), "%lu", clock1());
cgiMakeHiddenVar("hgt_", buf); // timestamps page to avoid browser cache
hPrintf("<input type='hidden' name='db' value='%s'>\n", database);
hPrintf("<input type='hidden' name='%s' id='currentTab' value='%s'>\n", TRACK_SEARCH_CURRENT_TAB, currentTab);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_DEL_ROW);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_ADD_ROW);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_PAGER);
hPrintf("<div id='tabs' style='display:none; %s'>\n"
"<ul>\n"
"<li><a href='#simpleTab'><B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Search</B></a></li>\n"
"<li><a href='#advancedTab'><B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Advanced</B></a></li>\n"
"</ul>\n"
"<div id='simpleTab' style='max-width:inherit;'>\n",cgiBrowser()==btIE?"width:1060px;":"max-width:inherit;");
hPrintf("<table style='width:100%%; font-size:.9em;'><tr><td colspan='2'>");
hPrintf("<input type='text' name='%s' id='simpleSearch' class='submitOnEnter' value='%s' style='max-width:1000px; width:100%%;' onkeyup='findTracksSearchButtonsEnable(true);'>\n",
TRACK_SEARCH_SIMPLE,descSearch == NULL ? "" : descSearch);
if (simpleSearch && descSearch)
searchTermsExist = TRUE;
hPrintf("</td></tr><td style='max-height:4px;'></td></tr></table>");
//hPrintf("</td></tr></table>");
hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", TRACK_SEARCH);
hPrintf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' onclick='findTracksClear();'>\n");
hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' style='font-size:.8em;'>\n");
hPrintf("</div>\n");
// Advanced tab
hPrintf("<div id='advancedTab' style='width:inherit;'>\n"
"<table cellSpacing=0 style='width:inherit; font-size:.9em;'>\n");
cols = 8;
// Track Name contains
hPrintf("<tr><td colspan=3></td>");
hPrintf("<td nowrap><b style='max-width:100px;'>Track Name:</b></td>");
hPrintf("<td align='right'>contains</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
hPrintf("<input type='text' name='%s' id='nameSearch' class='submitOnEnter' value='%s' onkeyup='findTracksSearchButtonsEnable(true);' style='min-width:326px; font-size:.9em;'>",
TRACK_SEARCH_ON_NAME, nameSearch == NULL ? "" : nameSearch);
hPrintf("</td></tr>\n");
// Description contains
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>");
hPrintf("<td><b style='max-width:100px;'>Description:</b></td>");
hPrintf("<td align='right'>contains</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
hPrintf("<input type='text' name='%s' id='descSearch' value='%s' class='submitOnEnter' onkeyup='findTracksSearchButtonsEnable(true);' style='max-width:536px; width:536px; font-size:.9em;'>",
TRACK_SEARCH_ON_DESCR, descSearch == NULL ? "" : descSearch);
hPrintf("</td></tr>\n");
if (!simpleSearch && descSearch)
searchTermsExist = TRUE;
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n");
hPrintf("<td><b style='max-width:100px;'>Group:</b></td>");
hPrintf("<td align='right'>is</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
cgiMakeDropListFull(TRACK_SEARCH_ON_GROUP, labels, groups, numGroups, groupSearch, "class='groupSearch' style='min-width:40%; font-size:.9em;'");
hPrintf("</td></tr>\n");
if (!simpleSearch && groupSearch)
searchTermsExist = TRUE;
#ifdef TRACK_SEARCH_ON_TYPE
// Track Type is (drop down)
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n");
hPrintf("<td nowrap><b style='max-width:100px;'>Data Format:</b></td>");
hPrintf("<td align='right'>is</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
char **formatTypes = NULL;
char **formatLabels = NULL;
int formatCount = getFormatTypes(&formatLabels, &formatTypes);
cgiMakeDropListFull(TRACK_SEARCH_ON_TYPE, formatLabels, formatTypes, formatCount, typeSearch, "class='typeSearch' style='min-width:40%; font-size:.9em;'");
hPrintf("</td></tr>\n");
if (!simpleSearch && typeSearch)
searchTermsExist = TRUE;
#endif///def TRACK_SEARCH_ON_TYPE
// Metadata selects require careful accounting
if(metaDbExists)
numMetadataSelects = printMdbSelects(conn, cart, simpleSearch, &mdbVar, &mdbVal, &numMetadataNonEmpty, cols);
else
numMetadataSelects = 0;
hPrintf("</table>\n");
hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", TRACK_SEARCH);
hPrintf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' onclick='findTracksClear();'>\n");
hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' style='font-size:.8em;'>\n");
//hPrintf("<a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a>\n");
hPrintf("</div>\n</div>\n");
hPrintf("</form>\n");
hPrintf("</div>"); // Restricts to max-width:1000px;
if(descSearch != NULL && !strlen(descSearch))
descSearch = NULL;
if(groupSearch != NULL && sameString(groupSearch, ANYLABEL))
groupSearch = NULL;
if(typeSearch != NULL && sameString(typeSearch, ANYLABEL))
typeSearch = NULL;
if(!isEmpty(descSearch))
{
char *tmp = cloneString(descSearch);
char *val = nextWord(&tmp);
struct slName *el, *descList = NULL;
int i;
while (val != NULL)
{
slNameAddTail(&descList, val);
descWordCount++;
val = nextWord(&tmp);
}
descWords = needMem(sizeof(char *) * descWordCount);
for(i = 0, el = descList; el != NULL; i++, el = el->next)
descWords[i] = strLower(el->name);
}
if (doSearch && simpleSearch && descWordCount <= 0)
doSearch = FALSE;
if(doSearch)
{
// Now search
struct slRef *tracks = NULL;
if(simpleSearch)
tracks = simpleSearchForTracksstruct(trix,descWords,descWordCount);
else
tracks = advancedSearchForTracks(conn,groupList,descWords,descWordCount,nameSearch,typeSearch,descSearch,groupSearch,numMetadataNonEmpty,numMetadataSelects,mdbVar,mdbVal);
// Sort and Print results
enum sortBy sortBy = cartUsualInt(cart,TRACK_SEARCH_SORT,sbRelevance);
tracksFound = slCount(tracks);
if(tracksFound > 1)
findTracksSort(&tracks,simpleSearch,sortBy);
displayFoundTracks(cart,tracks,tracksFound,sortBy);
}
hFreeConn(&conn);
webNewSection("About Track Search");
if(metaDbExists)
hPrintf("<p>Search for terms in track names, descriptions, groups, and ENCODE "
"metadata. If multiple terms are entered, only tracks with all terms "
"will be part of the results.");
else
hPrintf("<p>Search for terms in track descriptions, groups, and names. "
"If multiple terms are entered, only tracks with all terms "
"will be part of the results.");
hPrintf("<BR><a target='_blank' href='../goldenPath/help/trackSearch.html'>more help</a></p>\n");
webEndSectionTables();
}
int main (int argc, char *argv[])
{
int res;
char **list, buffer[8192];
double t1;
fastlist_t *fl;
/* fast_catlist_t *cl; */
if (argc != 2) error1 ("usage: %s exclude-file\n", argv[0]);
warning1 ("reading ruleset\n");
list = read_list (argv[1]);
if (list == NULL) error1 ("failed to load pattern list from %s\n", argv[1]);
fl = prepare_fastlist (list);
/*
printf ("shortest simple rule: %d\n", fl->shortest);
for (i=0; i<fl->n_simple; i++)
{
printf ("%d %d %s\n",
fl->rules[fl->simple[i]].type,
fl->rules[fl->simple[i]].category,
fl->rules[fl->simple[i]].rule);
}
*/
/*
for (i=0; i<fl->n; i++)
{
printf ("%d %d %s\n", fl->rules[i].type, fl->rules[i].category,
fl->rules[i].rule);
}
*/
/* for (i=0; i<fl->n_simple; i++) printf ("SIMPLE: %s\n", fl->simple[i]); */
/* for (i=0; i<fl->n_complex; i++) printf ("COMPLEX: %s\n", fl->complex[i]); */
/* cl = prepare_catlist (list); */
/*
for (i=0; i<cl->n_simple; i++)
printf ("SIMPLE: %d.%s\n", cl->simple[i].category, cl->simple[i].rule);
for (i=0; i<cl->n_coll; i++)
{
printf ("COMPLEX: %d (%d rules)\n",
cl->colls[i].coll_id, cl->colls[i].nrules);
for (j=0; j<cl->colls[i].nrules; j++)
{
printf (" %s\n", cl->colls[i].rules[j]);
}
}
*/
/*
printf ("slow:\n");
t1 = clock1 ();
res = check_list (list, argv[2]);
t1 = clock1 () - t1;
if (res)
printf ("%s is included (%.3f sec)\n", argv[2], t1);
else
printf ("%s is excluded (%.3f sec)\n", argv[2], t1);
*/
while ((fgets (buffer, sizeof(buffer), stdin) != NULL))
{
str_strip (buffer, " \r\n");
if (normalize_url2 (buffer) < 0)
{
printf ("bad url: %s\n", buffer);
continue;
}
t1 = clock1 ();
res = check_fastlist (fl, buffer);
t1 = clock1 () - t1;
if (res)
printf ("%s is included (%.3f sec)\n", buffer, t1);
else
printf ("%s is excluded (%.3f sec)\n", buffer, t1);
}
return 0;
}
static void phoneHome()
{
static boolean beenHere = FALSE;
if (beenHere) /* one at a time please */
return;
beenHere = TRUE;
char *expireTime = cfgOptionDefault("browser.cgiExpireMinutes", "20");
unsigned expireMinutes = sqlUnsigned(expireTime);
expireSeconds = expireMinutes * 60;
char trashFile[PATH_LEN];
safef(trashFile, sizeof(trashFile), "%s/registration.txt", trashDir());
/* trashFile does not exist during command line execution */
if(fileExists(trashFile)) /* update access time for trashFile */
{
struct utimbuf ut;
struct stat mystat;
ZeroVar(&mystat);
if (stat(trashFile,&mystat)==0)
{
ut.actime = clock1();
ut.modtime = mystat.st_mtime;
}
else
{
ut.actime = ut.modtime = clock1();
}
(void) utime(trashFile, &ut);
if (expireSeconds > 0)
{
(void) signal(SIGALRM, cgiApoptosis);
(void) alarm(expireSeconds); /* CGI timeout */
}
return;
}
char *scriptName = cgiScriptName();
char *ip = getenv("SERVER_ADDR");
if (scriptName && ip) /* will not be true from command line execution */
{
FILE *f = fopen(trashFile, "w");
if (f) /* rigamarole only if we can get a trash file */
{
time_t now = time(NULL);
char *localTime;
extern char *tzname[2];
struct tm *tm = localtime(&now);
localTime = sqlUnixTimeToDate(&now,FALSE); /* FALSE == localtime */
fprintf(f, "%s, %s, %s %s, %s\n", scriptName, ip, localTime,
tm->tm_isdst ? tzname[1] : tzname[0], trashFile);
fclose(f);
chmod(trashFile, 0666);
pid_t pid0 = fork();
if (0 == pid0) /* in child */
{
close(STDOUT_FILENO); /* do not hang up Apache finish for parent */
expireSeconds = 0; /* no error message from this exit */
(void) signal(SIGALRM, cgiApoptosis);
(void) alarm(6); /* timeout here in 6 seconds */
#include "versionInfo.h"
char url[1024];
safef(url, sizeof(url), "%s%s%s%s%s%s", "http://",
"genomewiki.", "ucsc.edu/", "cgi-bin/useCount?", "version=browser.v",
CGI_VERSION);
/* 6 second alarm will exit this page fetch if it does not work */
(void) htmlPageGetWithCookies(url, NULL); /* ignore return */
exit(0);
} /* child of fork has done exit(0) normally or via alarm */
} /* trash file open OK */
if (expireSeconds > 0)
{
(void) signal(SIGALRM, cgiApoptosis);
(void) alarm(expireSeconds); /* CGI timeout */
}
} /* an actual CGI binary */
} /* phoneHome() */
int
sc_main(int argc, char *argv[])
{
sc_signal<pkt> pkt_in0;
sc_signal<pkt> pkt_in1;
sc_signal<pkt> pkt_in2;
sc_signal<pkt> pkt_in3;
sc_signal<pkt> pkt_out0;
sc_signal<pkt> pkt_out1;
sc_signal<pkt> pkt_out2;
sc_signal<pkt> pkt_out3;
sc_signal<sc_int<4> > id0, id1, id2, id3;
sc_signal<bool> switch_cntrl;
sc_clock clock1("CLOCK1", 75, SC_NS, 0.5, 0.0, SC_NS);
sc_clock clock2("CLOCK2", 30, SC_NS, 0.5, 10.0, SC_NS);
// Module instiatiations follow
// Note that modules can be connected by hooking up ports
// to signals by name or by using a positional notation
sender sender0("SENDER0");
// hooking up signals to ports by name
sender0.pkt_out(pkt_in0);
sender0.source_id(id0);
sender0.CLK(clock1);
sender sender1("SENDER1");
// hooking up signals to ports by position
sender1(pkt_in1, id1, clock1);
sender sender2("SENDER2");
// hooking up signals to ports by name
sender2.pkt_out(pkt_in2);
sender2.source_id(id2);
sender2.CLK(clock1);
sender sender3("SENDER3");
// hooking up signals to ports by position
sender3( pkt_in3, id3, clock1 );
switch_clk switch_clk1("SWITCH_CLK");
// hooking up signals to ports by name
switch_clk1.switch_cntrl(switch_cntrl);
switch_clk1.CLK(clock2);
mcast_pkt_switch switch1("SWITCH");
// hooking up signals to ports by name
switch1.switch_cntrl(switch_cntrl);
switch1.in0(pkt_in0);
switch1.in1(pkt_in1);
switch1.in2(pkt_in2);
switch1.in3(pkt_in3);
switch1.out0(pkt_out0);
switch1.out1(pkt_out1);
switch1.out2(pkt_out2);
switch1.out3(pkt_out3);
receiver receiver0("RECEIVER0");
// hooking up signals to ports by name
receiver0.pkt_in(pkt_out0);
receiver0.sink_id(id0);
receiver receiver1("RECEIVER1");
// hooking up signals to ports by position
receiver1( pkt_out1, id1 );
receiver receiver2("RECEIVER2");
// hooking up signals to ports by name
receiver2.pkt_in(pkt_out2);
receiver2.sink_id(id2);
receiver receiver3("RECEIVER3");
// hooking up signals to ports by position
receiver3( pkt_out3, id3 );
sc_start(0, SC_NS);
#if !defined(__SUNPRO_CC)
id0.write(0);
id1.write(1);
id2.write(2);
id3.write(3);
#else
// you cannot do that with SC5.0
// since it doesn't support member templates
id0.write(sc_int<4>(0));
id0.write(sc_int<4>(1));
id0.write(sc_int<4>(2));
id0.write(sc_int<4>(3));
#endif
sc_start();
return 0;
}
void doSearchTracks(struct group *groupList)
{
webIncludeResourceFile("ui.dropdownchecklist.css");
jsIncludeFile("ui.dropdownchecklist.js",NULL);
// This line is needed to get the multi-selects initialized
jsIncludeFile("ddcl.js",NULL);
struct group *group;
char *groups[128];
char *labels[128];
int numGroups = 1;
groups[0] = ANYLABEL;
labels[0] = ANYLABEL;
char *nameSearch = cartOptionalString(cart, TRACK_SEARCH_ON_NAME);
char *typeSearch = cartUsualString( cart, TRACK_SEARCH_ON_TYPE,ANYLABEL);
char *simpleEntry = cartOptionalString(cart, TRACK_SEARCH_SIMPLE);
char *descSearch = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR);
char *groupSearch = cartUsualString( cart, TRACK_SEARCH_ON_GROUP,ANYLABEL);
boolean doSearch = sameString(cartOptionalString(cart, TRACK_SEARCH), "Search")
|| cartUsualInt(cart, TRACK_SEARCH_PAGER, -1) >= 0;
struct sqlConnection *conn = hAllocConn(database);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
int tracksFound = 0;
boolean searchTermsExist = FALSE;
int cols;
char buf[512];
char *currentTab = cartUsualString(cart, TRACK_SEARCH_CURRENT_TAB, "simpleTab");
enum searchTab selectedTab = (sameString(currentTab, "advancedTab") ? advancedTab : simpleTab);
// NOTE: could support quotes in simple tab by detecting quotes and choosing
// to use doesNameMatch() || doesDescriptionMatch()
if (selectedTab == simpleTab && !isEmpty(simpleEntry))
stripChar(simpleEntry, '"');
trackList = getTrackList(&groupList, -2); // global
makeGlobalTrackHash(trackList);
// NOTE: This is necessary when container cfg by '*' results in vis changes
// This will handle composite/view override when subtrack specific vis exists,
// AND superTrack reshaping.
// Subtrack settings must be removed when composite/view settings are updated
parentChildCartCleanup(trackList,cart,oldVars);
slSort(&groupList, gCmpGroup);
for (group = groupList; group != NULL; group = group->next)
{
groupTrackListAddSuper(cart, group);
if (group->trackList != NULL)
{
groups[numGroups] = cloneString(group->name);
labels[numGroups] = cloneString(group->label);
numGroups++;
if (numGroups >= ArraySize(groups))
internalErr();
}
}
safef(buf, sizeof(buf),"Search for Tracks in the %s %s Assembly",
organism, hFreezeFromDb(database));
webStartWrapperDetailedNoArgs(cart, database, "", buf, FALSE, FALSE, FALSE, FALSE);
hPrintf("<div style='max-width:1080px;'>");
hPrintf("<form action='%s' name='%s' id='%s' method='get'>\n\n",
hgTracksName(),TRACK_SEARCH_FORM,TRACK_SEARCH_FORM);
cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo
safef(buf, sizeof(buf), "%lu", clock1());
cgiMakeHiddenVar("hgt_", buf); // timestamps page to avoid browser cache
hPrintf("<input type='hidden' name='db' value='%s'>\n", database);
hPrintf("<input type='hidden' name='%s' id='currentTab' value='%s'>\n",
TRACK_SEARCH_CURRENT_TAB, currentTab);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_DEL_ROW);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_ADD_ROW);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_PAGER);
hPrintf("<div id='tabs' style='display:none; %s'>\n<ul>\n<li><a href='#simpleTab'>"
"<B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Search</B>"
"</a></li>\n<li><a href='#advancedTab'>"
"<B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Advanced</B>"
"</a></li>\n</ul>\n<div id='simpleTab' style='max-width:inherit;'>\n",
cgiBrowser()==btIE?"width:1060px;":"max-width:inherit;");
hPrintf("<table id='simpleTable' style='width:100%%; font-size:.9em;'><tr><td colspan='2'>");
hPrintf("<input type='text' name='%s' id='simpleSearch' class='submitOnEnter' value='%s' "
"style='max-width:1000px; width:100%%;' onkeyup='findTracks.searchButtonsEnable(true);'>\n",
TRACK_SEARCH_SIMPLE,simpleEntry == NULL ? "" : simpleEntry);
if (selectedTab==simpleTab && simpleEntry)
searchTermsExist = TRUE;
hPrintf("</td></tr><td style='max-height:4px;'></td></tr></table>");
//hPrintf("</td></tr></table>");
hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' "
"style='font-size:.8em;'>\n", TRACK_SEARCH);
hPrintf("<input type='button' name='clear' value='clear' class='clear' "
"style='font-size:.8em;' onclick='findTracks.clear();'>\n");
hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' "
"style='font-size:.8em;'>\n");
hPrintf("</div>\n");
// Advanced tab
hPrintf("<div id='advancedTab' style='width:inherit;'>\n"
"<table id='advancedTable' cellSpacing=0 style='width:inherit; font-size:.9em;'>\n");
cols = 8;
// Track Name contains
hPrintf("<tr><td colspan=3></td>");
hPrintf("<td nowrap><b style='max-width:100px;'>Track Name:</b></td>");
hPrintf("<td align='right'>contains</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
hPrintf("<input type='text' name='%s' id='nameSearch' class='submitOnEnter' value='%s' "
"onkeyup='findTracks.searchButtonsEnable(true);' style='min-width:326px; font-size:.9em;'>",
TRACK_SEARCH_ON_NAME, nameSearch == NULL ? "" : nameSearch);
hPrintf("</td></tr>\n");
// Description contains
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>");
hPrintf("<td><b style='max-width:100px;'>Description:</b></td>");
hPrintf("<td align='right'>contains</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
hPrintf("<input type='text' name='%s' id='descSearch' value='%s' class='submitOnEnter' "
"onkeyup='findTracks.searchButtonsEnable(true);' "
"style='max-width:536px; width:536px; font-size:.9em;'>",
TRACK_SEARCH_ON_DESCR, descSearch == NULL ? "" : descSearch);
hPrintf("</td></tr>\n");
if (selectedTab==advancedTab && !isEmpty(descSearch))
searchTermsExist = TRUE;
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n");
hPrintf("<td><b style='max-width:100px;'>Group:</b></td>");
hPrintf("<td align='right'>is</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
cgiMakeDropListFull(TRACK_SEARCH_ON_GROUP, labels, groups, numGroups, groupSearch,
"class='groupSearch' style='min-width:40%; font-size:.9em;'");
hPrintf("</td></tr>\n");
if (selectedTab==advancedTab && !isEmpty(groupSearch) && !sameString(groupSearch,ANYLABEL))
searchTermsExist = TRUE;
// Track Type is (drop down)
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n");
hPrintf("<td nowrap><b style='max-width:100px;'>Data Format:</b></td>");
hPrintf("<td align='right'>is</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
char **formatTypes = NULL;
char **formatLabels = NULL;
int formatCount = getFormatTypes(&formatLabels, &formatTypes);
cgiMakeDropListFull(TRACK_SEARCH_ON_TYPE, formatLabels, formatTypes, formatCount, typeSearch,
"class='typeSearch' style='min-width:40%; font-size:.9em;'");
hPrintf("</td></tr>\n");
if (selectedTab==advancedTab && !isEmpty(typeSearch) && !sameString(typeSearch,ANYLABEL))
searchTermsExist = TRUE;
// mdb selects
struct slPair *mdbSelects = NULL;
if (metaDbExists)
{
struct slPair *mdbVars = mdbVarsSearchable(conn,TRUE,FALSE); // Tables but not file only objects
mdbSelects = mdbSelectPairs(cart, mdbVars);
char *output = mdbSelectsHtmlRows(conn,mdbSelects,mdbVars,cols,FALSE); // not a fileSearch
if (output)
{
puts(output);
freeMem(output);
}
slPairFreeList(&mdbVars);
}
hPrintf("</table>\n");
hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' "
"style='font-size:.8em;'>\n", TRACK_SEARCH);
hPrintf("<input type='button' name='clear' value='clear' class='clear' "
"style='font-size:.8em;' onclick='findTracks.clear();'>\n");
hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' "
"style='font-size:.8em;'>\n");
//hPrintf("<a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a>\n");
hPrintf("</div>\n");
hPrintf("</div>\n");
hPrintf("</form>\n");
hPrintf("</div>"); // Restricts to max-width:1000px;
cgiDown(0.8);
if (measureTiming)
measureTime("Rendered tabs");
if (doSearch)
{
// Now search
struct slRef *tracks = NULL;
if (selectedTab==simpleTab && !isEmpty(simpleEntry))
tracks = simpleSearchForTracksstruct(simpleEntry);
else if (selectedTab==advancedTab)
tracks = advancedSearchForTracks(conn,groupList,nameSearch,typeSearch,descSearch,
groupSearch,mdbSelects);
if (measureTiming)
measureTime("Searched for tracks");
// Sort and Print results
if (selectedTab!=filesTab)
{
enum sortBy sortBy = cartUsualInt(cart,TRACK_SEARCH_SORT,sbRelevance);
tracksFound = slCount(tracks);
if (tracksFound > 1)
findTracksSort(&tracks,sortBy);
displayFoundTracks(cart,tracks,tracksFound,sortBy);
if (measureTiming)
measureTime("Displayed found tracks");
}
slPairFreeList(&mdbSelects);
}
hFreeConn(&conn);
webNewSection("About Track Search");
if (metaDbExists)
hPrintf("<p>Search for terms in track names, descriptions, groups, and ENCODE "
"metadata. If multiple terms are entered, only tracks with all terms "
"will be part of the results.");
else
hPrintf("<p>Search for terms in track descriptions, groups, and names. "
"If multiple terms are entered, only tracks with all terms "
"will be part of the results.");
hPrintf("<BR><a target='_blank' href='../goldenPath/help/trackSearch.html'>more help</a></p>\n");
webEndSectionTables();
}
/* connect to IPv4 address/port */
int ConnectIP (unsigned long IP, int port)
{
struct sockaddr_in conn;
int s, rc;
int rc1;
struct timeval timeout;
fd_set wrfds;
double target;
#if defined(__MINGW32__)
unsigned long blk;
#endif
/* create socket */
s = socket (AF_INET, SOCK_STREAM, 0);
if (s < 0)
{
/* warning1 ("cannot create socket\n"); */
return -2;
}
memset (&conn, 0, sizeof (conn));
conn.sin_family = AF_INET;
conn.sin_port = htons (port);
conn.sin_addr.s_addr = IP;
/* set nonblocking mode */
#if !defined(__MINGW32__)
fcntl (s, F_SETFL, O_NONBLOCK);
#else
blk = 1;
ioctlsocket (s, FIONBIO, &blk);
#endif
rc = connect (s, (struct sockaddr *)&conn, sizeof (struct sockaddr_in));
if (rc < 0)
{
if (errno != EINPROGRESS && errno != EAGAIN)
{
Close (s);
return -3;
}
target = clock1 () + timelimit;
do
{
timeout.tv_sec = 0;
timeout.tv_usec = 100000;
errno = 0;
FD_ZERO (&wrfds);
FD_SET (s, &wrfds);
rc1 = select (FD_SETSIZE, NULL, &wrfds, NULL, &timeout);
if (rc1 == 1)
{
#if !defined(__MINGW32__)
int rc2;
/* see if we really got a connection */
rc2 = connect (s, (struct sockaddr *)&conn, sizeof (struct sockaddr_in));
if (rc2 < 0 && errno == EISCONN) goto success; /* good! */
if (rc2 == 0) goto success; /* good for OpenBSD? */
if (rc2 < 0 && errno != EAGAIN)
{
Close (s);
return -3;
}
#else
goto success;
#endif
}
if (rc1 < 0 && errno == EINTR) continue; /* suspended */
}
while (clock1() < target);
Close (s);
return -4;
}
success:
/* reset nonblocking mode */
#if !defined(__MINGW32__)
fcntl (s, F_SETFL, 0);
#else
blk = 0;
ioctlsocket (s, FIONBIO, &blk);
#endif
return s;
}
