void dyOutTest()
// Tests of dyOut functions
{
printf("Plain printf\n");
dyOutPrintf("1 dyOutPrintf unopened\n");
int token1 = dyOutOpen(0);
dyOutPrintf("2 dyOutOpen:1\n");
dyOutFlush(token1);
dyOutPrintf("3^10 1:%d after flush\n",dyOutStackDepth());
int token2 = dyOutOpen(256);
dyOutPrintf("4 dsOpen:2 len1:%d len2:%d lenAll:%d\n",
dyOutSize(token1),dyOutSize(token2),dyOutSizeAll());
dyOutRegisterAltStream(stderr);
dyOutFlush(token2);
dyOutUnregisterAltStream(stderr);
dyOutPrintf("5 2:%d After flush len1:%d len2:%d lenAll:%d\n",
dyOutStackDepth(),dyOutSize(token1),dyOutSize(token2),dyOutSizeAll());
dyOutFlushAndClose(token2);
dyOutPrintf("6 1:%d After flushAndClose:2 len1:%d\n",dyOutStackDepth(),dyOutSize(token1));
token2 = dyOutOpen(256);
dyOutPrintf("7 dyOutOpen:2 reopen:2 WILL ABANDON CONTENT\n");
char *content = cloneString(dyOutContent(token2));
dyOutAbandonContent(token2);
dyOutPrintf("8x7 2:%d len1:%d len2:%d lenAll:%d isEmpty2:%s\n",
dyOutStackDepth(),dyOutSize(token1),dyOutSize(token2),dyOutSizeAll(),
(dyOutIsEmpty(token2) ? "EMPTY":"NOT_EMPTY"));
strSwapChar(content,'\n','~'); // Replace newline before printing.
dyOutPrintf("9 2:%d No flush yet len1:%d len2:%d lenAll:%d prev7:[%s]\n",
dyOutStackDepth(),dyOutSize(token1),dyOutSize(token2),dyOutSizeAll(),content);
freez(&content);
int token3 = dyOutOpen(256);
dyOutPuts("10 Open:3 Line doubled and out of turn due to dyOutPrintDirectly()");
dyOutPrintDirectly(token3,stdout);
dyOutPrintf("11 3:%d Just prior to closing all. len1:%d len2:%d len3:%d lenAll:%d",
dyOutStackDepth(),
dyOutSize(token1),dyOutSize(token2),dyOutSize(token3),dyOutSizeAll());
int token4 = dyOutOpen(256);
dyOutPrintf("12 Open:4 Opened stack:%d WILL ABANDON\n",dyOutStackDepth());
dyOutAbandon(token4);
dyOutPutc('\n');
dyOutPuts("13 Puts: Added last '\\n' with dsPutc(), this with dsPuts().");
dyOutPrintf("14 3:%d Last line! Expect 7 & 12 missing, 10 dupped. lenAll:%d Bye.\n",
dyOutStackDepth(),dyOutSizeAll());
dyOutFlushAndCloseAll();
assert(dyOutStack == NULL);
int ix = 0;
for (;ix<20;ix++) // tested to 1000
{
dyOutOpen(32); // Don't even care about tokens!
if (ix == 0)
dyOutPrintf("CannibalizeAndCloseAll():");
dyOutPrintf(" %d",dyOutStackDepth());
}
content = dyOutCannibalizeAndCloseAll();
printf("\n[%s]\n",content);
freez(&content);
}
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);
}
int trackHubCrawl(char *hubUrl)
/* Crawl a track data hub and output strings useful in a search */
{
struct errCatch *errCatch = errCatchNew();
struct trackHub *hub = NULL;
int retVal = 0;
if (errCatchStart(errCatch))
{
hub = trackHubOpen(hubUrl, "hub_0");
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
retVal = 1;
fprintf(stderr, "%s\n", errCatch->message->string);
}
errCatchFree(&errCatch);
if (hub == NULL)
return 1;
FILE *searchFp =stdout;
struct trackHubGenome *genomeList = hub->genomeList;
for(; genomeList ; genomeList = genomeList->next)
fprintf(searchFp, "%s\t%s\n",hub->url, trackHubSkipHubName(genomeList->name));
fprintf(searchFp, "%s\t%s\t%s\n",hub->url, hub->shortLabel, hub->longLabel);
if (hub->descriptionUrl != NULL)
{
char *html = netReadTextFileIfExists(hub->descriptionUrl);
char *stripHtml =htmlTextStripTags(html);
strSwapChar(stripHtml, '\n', ' ');
strSwapChar(stripHtml, '\t', ' ');
strSwapChar(stripHtml, '\015', ' ');
strSwapChar(stripHtml, ')', ' ');
strSwapChar(stripHtml, '(', ' ');
strSwapChar(stripHtml, '[', ' ');
strSwapChar(stripHtml, ']', ' ');
fprintf(searchFp, "%s\t%s\n",hub->url, stripHtml);
}
trackHubClose(&hub);
return retVal;
}
boolean searchDescriptionMatches(struct trackDb *tdb, struct slName *wordList)
// returns TRUE if all words in preparsed list matches html description page.
// A "word" can be "multiple words" (parsed from quoteed string).
// Because description contains html, quoted string match has limits.
// DANGER: this will alter html of tdb struct (replacing \n with ' ',
// so the html should not be displayed after.
{
if (tdb->html == NULL)
return (wordList != NULL);
if (strchr(tdb->html,'\n')) // DANGER: don't own memory.
strSwapChar(tdb->html,'\n',' '); // However, this CGI will use html for no other purpose
struct slName *word = wordList;
for (; word != NULL; word = word->next)
{
if (!searchMatchToken(tdb->html,word->name))
return FALSE;
}
return TRUE;
}
int documentLink(struct hash *ra, char *term, char *docTerm,char *dir,
char *title,boolean genericDoc)
// Compare controlled vocab based on term value
{
boolean docsPrinted = 0;
char *s;
if (title == NULL)
title = docTerm;
//can use hg.conf to direct links back to main UCSC server if a mirror doesn't
//want all the PDFs
char *baseUrl = cfgOptionDefault("hgEncodeVocabDocBaseUrl", "");
// add links to protocol doc if it exists
char docUrl[PATH_LEN];
char docFile[PATH_LEN];
// parse setting
s = hashFindVal(ra,docTerm);
if (s != NULL)
{
if (sameWord(s,"missing"))
printf(" <em>missing</em>\n");
else
{
char *docSetting = cloneString(s);
char *settings=docSetting;
int count=0;
while ((s = nextWord(&settings)) != NULL)
{
char *docTitle = NULL;
char *fileName = NULL;
if (strchr(s,':')) // lab Specific setting
{
docTitle = strSwapChar(s,':',0);
fileName = docTitle + strlen(docTitle) + 1;
}
else
{
docTitle = title;
fileName = s;
}
if (count>0)
printf("<BR>");
count++;
docTitle = htmlEncode(strSwapChar(docTitle,'_',' '));
if (sameWord(fileName,"missing"))
printf("%s<em>missing</em>\n",docTitle);
else
{
safef(docUrl, sizeof(docUrl), "%s%s%s", baseUrl, dir, fileName);
safef(docFile, sizeof(docFile), "%s%s", hDocumentRoot(), docUrl);
printf(" <A TARGET=_BLANK HREF=%s>%s</A>\n", docUrl,docTitle);
docsPrinted++;
}
freeMem(docTitle);
}
freeMem(docSetting);
}
}
else if (genericDoc)
{ // generate a standard name
safef(docUrl, sizeof(docUrl), "%s%s%s_protocol.pdf", baseUrl, dir, term);
safef(docFile, sizeof(docFile), "%s%s", hDocumentRoot(), docUrl);
if (fileExists(docFile))
{
printf(" <A TARGET=_BLANK HREF=%s>%s</A>\n", docUrl,title);
docsPrinted++;
}
}
return docsPrinted;
}
boolean doCellRow(struct hash *ra, char *org)
// print one cell row
{
char *s;
s = hashFindVal(ra, ORGANISM);
if (s != NULL)
{
char *cellOrg = cloneString(s);
strLower(cellOrg);
if (differentString(cellOrg, org))
return FALSE;
}
// pathBuffer for new protocols not in human
char pathBuffer[PATH_LEN];
safef(pathBuffer, sizeof(pathBuffer), "/ENCODE/protocols/cell/%s/",org);
if (sameWord(org, ORG_HUMAN))
{
if (cgiOptionalInt("tier",0))
{
if (hashFindVal(ra,"tier") == NULL)
return FALSE;
if (atoi(hashFindVal(ra,"tier"))!=cgiOptionalInt("tier",0))
return FALSE;
}
if (cgiOptionalString("tiers"))
{
if (hashFindVal(ra,"tier") == NULL)
return FALSE;
boolean found=FALSE;
char *tiers=cloneString(cgiOptionalString("tiers"));
char *tier;
(void)strSwapChar(tiers,',',' ');
while ((tier=nextWord(&tiers)))
{
if (atoi(hashFindVal(ra,"tier"))==atoi(tier))
{
found=TRUE;
break;
}
}
if (!found)
return FALSE;
}
puts("<TR>");
char *term = printTerm(ra);
printSetting(ra, "tier");
printDescription(ra,NULL,-1);
printSetting(ra,"lineage");
printSetting(ra,"tissue");
printSetting(ra,"karyotype");
printSetting(ra,"sex");
printDocumentLink(ra,term,"protocol",pathBuffer,NULL,TRUE);
printSettingsWithUrls(ra,"orderUrl","vendorName","vendorId");
printSettingsWithUrls(ra,"termUrl","termId",NULL);
printLabel(ra,term);
puts("</TR>");
}
else // non-human cell type
{
puts("<TR>");
char *term = printTerm(ra);
printDescription(ra,NULL,8);
printSetting(ra,"category");
printSetting(ra,"tissue");
printSetting(ra,"sex");
//printSetting(ra,"karyotype");
printDocumentLink(ra,term,"protocol",pathBuffer,NULL,TRUE);
printSettingsWithUrls(ra,"orderUrl","vendorName","vendorId");
printSettingsWithUrls(ra,"termUrl","termId",NULL);
printLabel(ra,term);
puts("</TR>");
}
return TRUE;
}
