void CommandDispatcher::addCmdLine(string line) {
int CRLNRidx = 0;
do {
CRLNRidx = line.find("\n");
string s;
if (CRLNRidx >=0) {
s = line.substr(0,CRLNRidx);
line = line.substr(CRLNRidx+1);
} else {
s = line;
}
if (line.compare("") != 0) {
int idx = cortexCmdJson.find("\"line\"");
if (idx >= 0)
cortexCmdJson += ", ";
string time = currentTimeToString();
cortexCmdJson += "{\"id\":" + int_to_string(cmdLineCounter++) +
", \"time\":\"" + htmlEncode(time) + "\"" +
", \"traj\":\"" + htmlEncode(oneTimeTrajectoryName) + "\"" +
", \"line\":\"" + htmlEncode(s) + "\"" +
"}";
oneTimeTrajectoryName = "";
}
}
while ((CRLNRidx >= 0));
}
void CommandDispatcher::addLogLine(string line) {
string time;
if ((line.length() > 24) && (line[13] == ':') && (line[16] == ':')) {
time = line.substr(11,12);
line = line.substr(24);
} else
time = currentTimeToString();
int idx = cortexLogJson.find("\"line\"");
if (idx >= 0)
cortexLogJson += ", ";
cortexLogJson += "{\"id\":" + int_to_string(logLineCounter++) +
", \"time\":\"" + htmlEncode(time) + "\"" +
", \"line\":\"" + htmlEncode(line) + "\"}";
// remove staff from beginning if log gets loo long to be displayed
while (cortexLogJson.length() > LOGVIEW_MAXSIZE) {
int idx = cortexLogJson.find("{\"id\"");
if (idx >= 0) {
idx = cortexLogJson.find("{\"id\"", idx+1);
if (idx>= 0) {
cortexLogJson = cortexLogJson.substr(idx);
}
}
}
}
void MainWindow::send()
{
bool ok = true;
QString horas = ui->hoursLineEdit->text();
int h = horas.toInt(&ok);
if(!ok || h < 1 || h > 24){
msgBox->setText("Invalid Hours field");
msgBox->setIcon(QMessageBox::Warning);
msgBox->setStandardButtons(QMessageBox::Ok);
msgBox->exec();
ui->hoursLineEdit->clear();
}else{
QString projectId = ui->projectBox->itemData(ui->projectBox->currentIndex()).toString();
QString description = ui->descriptionEdit->toPlainText();
htmlEncode(&description);
QString shortDescription = description;
if (description.length() > 30) {
shortDescription.truncate(30);
shortDescription += "...";
}
QString str = QString("Added %1 hours to %2 (%3)").arg(horas).arg(ui->projectBox->currentText()).arg(shortDescription);
ui->statusLog->setText(str);
acdp.send(projectId,horas,description);
}
}
void CommandDispatcher::addAlert(string line) {
int idx = alertJson.find("\"line\"");
if (idx >= 0)
alertJson += ", ";
alertJson += "{\"id\":" + int_to_string(alertCounter++) + ", \"line\":\"" + htmlEncode(line) + "\"}";
}
void hPrintEncodedNonBreak(char *s)
/* Print with htmlEncode and non-break */
{
char *encoded = htmlEncode(s);
hPrintNonBreak(encoded);
freeMem(encoded);
}
void bamMethods(struct track *track)
/* Methods for BAM alignment files. */
{
knetUdcInstall();
boolean isBamWig = cartUsualBooleanClosestToHome(cart, track->tdb, FALSE,
BAMWIG_MODE, (trackDbSettingClosestToHome(track->tdb, BAMWIG_MODE) != NULL));
if (isBamWig)
{
bamWigMethods(track, track->tdb, 0, NULL);
return;
}
track->canPack = TRUE;
boolean isPaired = cartUsualBooleanClosestToHome(cart, track->tdb, FALSE,
BAM_PAIR_ENDS_BY_NAME,
(trackDbSettingClosestToHome(track->tdb, BAM_PAIR_ENDS_BY_NAME) != NULL));
char *tdbShowNames = trackDbSetting(track->tdb, BAM_SHOW_NAMES);
boolean showNames = cartUsualBooleanClosestToHome(cart, track->tdb, FALSE,
BAM_SHOW_NAMES, SETTING_IS_ON(tdbShowNames));
char *colorMode = cartOrTdbString(cart, track->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT);
char *userTag = cartOrTdbString(cart, track->tdb, BAM_COLOR_TAG, BAM_COLOR_TAG_DEFAULT);
if (sameString(colorMode, BAM_COLOR_MODE_TAG) && userTag != NULL)
{
if (! (isalpha(userTag[0]) && isalnum(userTag[1]) && userTag[2] == '\0'))
{
warn("%s: BAM tag '%s' is not valid -- must be a letter followed by a letter or number.",
track->tdb->shortLabel, htmlEncode(userTag));
cartRemoveVariableClosestToHome(cart, track->tdb, FALSE, BAM_COLOR_TAG);
}
}
addBamBaseAndIndelSettings(track->tdb);
if (isPaired)
{
linkedFeaturesSeriesMethods(track);
track->loadItems = bamPairedLoadItems;
track->drawItems = bamLinkedFeaturesSeriesDraw;
track->drawItemAt = bamPairedDrawAt;
}
else
{
linkedFeaturesMethods(track);
track->loadItems = bamLoadItems;
track->drawItems = bamLinkedFeaturesDraw;
track->drawItemAt = bamDrawAt;
}
if (!showNames)
{
track->drawName = TRUE; // ironic, but this is how to suppress item labels in pack mode.
track->drawLeftLabels = maybeDrawLeftLabels;
}
track->nextItemButtonable = track->nextExonButtonable = FALSE;
track->nextPrevItem = NULL;
track->nextPrevExon = NULL;
if (sameString(colorMode, BAM_COLOR_MODE_GRAY))
track->colorShades = shadesOfGray;
}
QString StringUtils::htmlEncode(
QString text, bool urlAsLinks, bool newlineAsBr) {
QString s;
QHash<int,int> linksIndexes; // start of link index -> length of link
if (urlAsLinks) {
QRegularExpressionMatchIterator it = linkRe.globalMatch(text);
while (it.hasNext()) {
QRegularExpressionMatch match = it.next();
linksIndexes.insert(match.capturedStart(0), match.capturedLength(0));
}
}
for (int i = 0; i < text.length(); ) {
if (urlAsLinks && linksIndexes.contains(i)) {
int l = linksIndexes.value(i);
QString html = htmlEncode(text.mid(i, l), false), href = html;
href.replace("\"", "%22");
s.append("<a href=\"").append(href).append("\">").append(html)
.append("</a>");
i += l;
} else {
const QChar c = text.at(i);
switch(c.toLatin1()) {
case '<':
s.append("<");
break;
case '>':
s.append(">");
break;
case '&':
s.append("&");
break;
case '"':
s.append(""");
break;
case '\'':
s.append("'");
break;
case '\n':
if (newlineAsBr)
s.append("<br/>\n");
else
s.append(c);
break;
default:
s.append(c);
}
++i;
}
}
return s;
}
char *bamGetTagString(const bam1_t *bam, char *tag, char *buf, size_t bufSize)
/* If bam's tags include the given 2-character tag, place the value into
* buf (zero-terminated, trunc'd if nec) and return a pointer to buf,
* or NULL if tag is not present. */
{
if (tag == NULL)
errAbort("NULL tag passed to bamGetTagString");
if (! (isalpha(tag[0]) && isalnum(tag[1]) && tag[2] == '\0'))
errAbort("bamGetTagString: invalid tag '%s'", htmlEncode(tag));
char *val = NULL;
// adapted from part of bam.c bam_format1:
uint8_t *s = bam1_aux(bam);
while (s < bam->data + bam->data_len)
{
uint8_t type, key[2];
key[0] = s[0]; key[1] = s[1];
s += 2; type = *s; ++s;
if (key[0] == tag[0] && key[1] == tag[1])
{
if (type == 'A') { snprintf(buf, bufSize, "%c", *s);}
else if (type == 'C') { snprintf(buf, bufSize, "%u", *s); }
else if (type == 'c') { snprintf(buf, bufSize, "%d", *s); }
else if (type == 'S') { snprintf(buf, bufSize, "%u", *(uint16_t*)s); }
else if (type == 's') { snprintf(buf, bufSize, "%d", *(int16_t*)s); }
else if (type == 'I') { snprintf(buf, bufSize, "%u", *(uint32_t*)s); }
else if (type == 'i') { snprintf(buf, bufSize, "%d", *(int32_t*)s); }
else if (type == 'f') { snprintf(buf, bufSize, "%g", *(float*)s); }
else if (type == 'd') { snprintf(buf, bufSize, "%lg", *(double*)s); }
else if (type == 'Z' || type == 'H') strncpy(buf, (char *)s, bufSize);
else buf[0] = '\0';
buf[bufSize-1] = '\0'; // TODO: is this nec?? see man pages
val = buf;
break;
}
else
{
if (type == 'A' || type == 'C' || type == 'c') { ++s; }
else if (type == 'S' || type == 's') { s += 2; }
else if (type == 'I' || type == 'i' || type == 'f') { s += 4; }
else if (type == 'd') { s += 8; }
else if (type == 'Z' || type == 'H')
{
while (*s++);
}
}
}
return val;
}
static void makeDisplayAlleles(struct vcfRecord *rec, boolean showLeftBase, char leftBase,
int endLength, boolean showLength, boolean encodeHtml,
char **displayAls)
/* If necessary, show the left base that we trimmed and/or abbreviate long sequences. */
{
struct dyString *dy = dyStringNew(128);
int i;
for (i = 0; i < rec->alleleCount; i++)
{
dyStringClear(dy);
if (showLeftBase)
dyStringPrintf(dy, "(%c)", leftBase);
abbreviateLongSeq(rec->alleles[i], endLength, showLength, dy);
if (encodeHtml)
displayAls[i] = htmlEncode(dy->string);
else
displayAls[i] = cloneString(dy->string);
}
}
static void printValueHistogram(char *db, char *table, char *field)
/* Print very simple-minded text histogram. */
{
double maxHist = 60;
double scale = -1.0;
struct sqlConnection *conn = hAllocConn(db);
struct sqlResult *sr;
char **row;
char query[256];
sqlSafef(query, sizeof(query),
"select %s, count(*) as count from %s group by %s order by count desc",
field, table, field);
sr = sqlGetResult(conn, query);
hTableStart();
hPrintf("<TR>");
hPrintf("<TH>value</TH>");
hPrintf("<TH>count</TH>");
hPrintf("<TH>graph</TH>");
hPrintf("</TR>");
while ((row = sqlNextRow(sr)) != NULL)
{
char *name = htmlEncode(row[0]);
int count = atoi(row[1]);
int starCount;
if (scale < 0)
scale = (maxHist)/count;
hPrintf("<TR><TD>%s</TD>", name);
hPrintf("<TD ALIGN=RIGHT>%d</TD>", count);
hPrintf("<TD>");
starCount = round(scale*count);
if (starCount > 0)
starOut(stdout, starCount);
else
hPrintf(" ");
hPrintf("</TD></TR>\n");
freeMem(name);
}
// hPrintf("</TABLE>");
hTableEnd();
hFreeConn(&conn);
}
static void printKeysWithDescriptions(struct vcfFile *vcff, int wordCount, char **words,
struct vcfInfoDef *infoDefs, boolean stripToSymbol)
/* Given an array of keys, print out a list of values with descriptions if descriptions are
* available. If stripToSymbol, when searching infoDefs, pick the actual key out of
* <>'s and other extraneous stuff (e.g. "(C)<DEL>" --> "DEL"). */
{
int i;
for (i = 0; i < wordCount; i++)
{
if (i > 0)
printf(", ");
char *displayKey = words[i];
char *descKey = displayKey;
if (stripToSymbol)
{
char *p = strchr(displayKey, '<');
if (p)
{
descKey = cloneString(p+1);
p = strchr(descKey, '>');
if (p)
*p = '\0';
}
}
char *description = NULL;
struct vcfInfoDef *def;
for (def = infoDefs; def != NULL; def = def->next)
if (sameString(descKey, def->key))
{
description = def->description;
break;
}
char *htmlKey = htmlEncode(displayKey);
if (description)
printf("%s (%s)", htmlKey, description);
else
printf("%s", htmlKey);
}
printf("<BR>\n");
}
char *checkParams(char *database, char *prefix, char *type)
/* If we don't have valid CGI parameters, quit with a Bad Request HTTP response. */
{
pushWarnHandler(htmlVaBadRequestAbort);
pushAbortHandler(htmlVaBadRequestAbort);
if(prefix == NULL || database == NULL)
errAbort("%s", "Missing prefix and/or db CGI parameter");
if (! hDbIsActive(database))
errAbort("'%s' is not a valid, active database", htmlEncode(database));
if (isNotEmpty(type) && differentString(type, ALT_OR_PATCH))
errAbort("'%s' is not a valid type", type);
char *table = NULL;
if (! sameOk(type, ALT_OR_PATCH))
{
struct sqlConnection *conn = hAllocConn(database);
table = connGeneSuggestTable(conn);
hFreeConn(&conn);
if(table == NULL)
errAbort("gene autosuggest is not supported for db '%s'", database);
}
popWarnHandler();
popAbortHandler();
return table;
}
WString htmlEncode(const WString& text, WFlags<HtmlEncodingFlag> flags)
{
return WString::fromUTF8(htmlEncode(text.toUTF8(), flags));
}
TCHAR* SimpleHTMLEncoder::encodeText(TCHAR* originalText)
{
return htmlEncode(originalText);
}
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;
}
int makeHtml(char *diffPath, char *htmlPath, char *path, char *commitId)
/* Make a color-coded html diff
* Return the number of lines changed */
{
int linesChanged = 0;
FILE *h = mustOpen(htmlPath, "w");
struct lineFile *lf = lineFileOpen(diffPath, TRUE);
int lineSize;
char *line;
char *xline = NULL;
char fmtString[256];
boolean inBody = FALSE;
boolean inBlock = TRUE;
int blockP = 0, blockN = 0;
fprintf(h, "<html>\n<head>\n<title>%s %s</title>\n</head>\n</body>\n<pre>\n", path, commitId);
boolean hasMore = TRUE;
while (hasMore)
{
boolean checkEob = FALSE;
hasMore = lineFileNext(lf, &line, &lineSize);
if (hasMore)
{
char *color = NULL;
xline = htmlEncode(line);
if (line[0] == '-')
{
color = "#FF9999"; /* deleted text light red */
if (inBody)
{
inBlock = TRUE;
++blockN;
}
}
else if (line[0] == '+')
{
color = "#99FF99"; /* added text light green */
if (inBody)
{
inBlock = TRUE;
++blockP;
}
}
else
{
if (line[0] == '@')
color = "#FFFF99"; /* diff control text light yellow (red+green) */
checkEob = TRUE;
}
if (color)
safef(fmtString, sizeof(fmtString), "<span style=\"background-color:%s\">%%s</span>\n", color);
else
safef(fmtString, sizeof(fmtString), "%%s\n");
fprintf(h, fmtString, xline);
if (line[0] == '@')
inBody = TRUE;
freeMem(xline);
}
else
{
checkEob = TRUE;
}
if (checkEob && inBlock)
{
inBlock = FALSE;
if (blockP >= blockN)
linesChanged += blockP;
else
linesChanged += blockN;
blockP = 0;
blockN = 0;
}
}
lineFileClose(&lf);
fprintf(h, "</pre>\n</body>\n</html>\n");
fclose(h);
return linesChanged;
}
static struct hgPositions *genomePosCJ(struct jsonWrite *jw,
char *db, char *spec, char **retChromName,
int *retWinStart, int *retWinEnd, struct cart *cart)
/* Search for positions in genome that match user query.
* Return an hgp unless there is a problem. hgp->singlePos will be set if a single
* position matched.
* Otherwise display list of positions, put # of positions in retWinStart,
* and return NULL. */
{
char *hgAppName = "cartJson";
struct hgPositions *hgp = NULL;
char *chrom = NULL;
int start = BIGNUM;
int end = 0;
char *terms[16];
int termCount = chopByChar(cloneString(spec), ';', terms, ArraySize(terms));
boolean multiTerm = (termCount > 1);
int i = 0;
for (i = 0; i < termCount; i++)
{
trimSpaces(terms[i]);
if (isEmpty(terms[i]))
continue;
hgp = hgPositionsFind(db, terms[i], "", hgAppName, cart, multiTerm);
if (hgp == NULL || hgp->posCount == 0)
{
jsonWriteStringf(jw, "error",
"Sorry, couldn't locate %s in genome database", htmlEncode(terms[i]));
if (multiTerm)
jsonWriteStringf(jw, "error",
"%s not uniquely determined -- can't do multi-position search.",
terms[i]);
*retWinStart = 0;
return NULL;
}
if (hgp->singlePos != NULL)
{
if (chrom != NULL && !sameString(chrom, hgp->singlePos->chrom))
{
jsonWriteStringf(jw, "error",
"Sites occur on different chromosomes: %s, %s.",
chrom, hgp->singlePos->chrom);
return NULL;
}
chrom = hgp->singlePos->chrom;
if (hgp->singlePos->chromStart < start)
start = hgp->singlePos->chromStart;
if (hgp->singlePos->chromEnd > end)
end = hgp->singlePos->chromEnd;
}
else
{
hgPositionsJson(jw, db, hgp, cart);
if (multiTerm && hgp->posCount != 1)
{
jsonWriteStringf(jw, "error",
"%s not uniquely determined (%d locations) -- "
"can't do multi-position search.",
terms[i], hgp->posCount);
return NULL;
}
break;
}
}
if (hgp != NULL)
{
*retChromName = chrom;
*retWinStart = start;
*retWinEnd = end;
}
return hgp;
}
QString MainWindow::formatChange(int index,QString c){
c="\n"+c+"\n";
QVector<QString> lines = c.split("\n").toVector();
QString formatted = "";
QString tmp;
QString tmp2;
QString tmp3;
QString afterName = "";
for(int i=1;i<lines.size()-1;i++){
tmp = lines.at(i);
tmp2 = lines.at(i+1);
tmp3 = lines.at(i-1);
if(tmp.startsWith("---") && tmp3.startsWith("index")){
if(tmp.startsWith("--- a/") && tmp2.startsWith("+++ b/")){
bool a = false;
if(tmp.indexOf("\"")>0){
a = true;
tmp.replace("\"","");
}
tmp = tmp.mid(6);
tmp = (a?"\"":"") + path + "/" + htmlEncode(tmp) + (a?"\"":"");
tmp="<hr><p style='line-height:16px;color:#921AFF'>修改文件 : "+tmp+"</p>\n";
formatted.append(tmp);
}else if(tmp == "--- /dev/null"){
bool a = false;
if(tmp2.indexOf("\"")>0){
a = true;
tmp2.replace("\"","");
}
tmp2=tmp2.mid(6);
tmp2 = (a?"\"":"") + path + "/" + htmlEncode(tmp2) + (a?"\"":"");
tmp="<hr><p style='line-height:16px;color:#921AFF'>新建文件 : "+tmp2+"</p>\n";
formatted.append(tmp);
}else if(tmp2 == "+++ /dev/null"){
bool a = false;
if(tmp.indexOf("\"")>0){
a = true;
tmp.replace("\"","");
}
tmp = tmp.mid(6);
tmp = (a?"\"":"") + path + "/" + htmlEncode(tmp) + (a?"\"":"");
tmp="<hr><p style='line-height:16px;color:#921AFF'>删除文件 : "+tmp+"</p>\n";
formatted.append(tmp);
}else{
tmp="<hr><p style='line-height:16px;color:#FF8000'>"+htmlEncode(tmp)+"</p>\n";
formatted.append(tmp);
tmp2="<hr><p style='line-height:16px;color:#2828FF'>"+htmlEncode(tmp2)+"</p>\n";
formatted.append(tmp);
}
tmp="<p style='line-height:16px'><font style='color:#2828FF'>"+mList.at(index).at(0)+"</font> 对比于 <font style='color:#FF8000'>"+mList.at(index+1).at(0)+"</font> 的差异</p>\n";
formatted.append(tmp);
if(afterName!=""){
formatted.append(afterName);
}
afterName="";
}else if(tmp.startsWith("new file mode ")){
tmp = tmp.mid(14);
afterName="<p style='line-height:16px'>新建的文件权限 : <font style='color:#00EC00'>"+tmp+"</font></p>\n";
}else if(tmp.startsWith("old mode ")){
tmp = tmp.mid(9);
tmp2 = tmp2.mid(9);
afterName="<p style='line-height:16px'>新权限 : <font style='color:#00EC00'>"+tmp2+"</font> 旧权限 : <font style='color:#FF9797'>"+tmp+"</font></p>\n";
}else if(tmp.startsWith("deleted file mode ")){
tmp = tmp.mid(18);
afterName="<p style='line-height:16px'>删除的文件权限 : <font style='color:#FF9797'>"+tmp+"</font></p>\n";
}else if(tmp.startsWith("+++")){
continue;
}else if(tmp.startsWith("+")){
tmp="<p style='line-height:16px;color:#00BB00'>"+htmlEncode(tmp)+"</p>\n";
formatted.append(tmp);
}else if(tmp.startsWith("-")){
tmp="<p style='line-height:16px;color:#FF2D2D'>"+htmlEncode(tmp)+"</p>\n";
formatted.append(tmp);
}else if(tmp.startsWith("@@")){
if(tmp.endsWith("@@")){
tmp="<p style='line-height:16px;color:#4A4AFF'>"+htmlEncode(tmp)+"</p>";
formatted.append(tmp+"\n");
}else{
tmp2 = tmp.left(tmp.lastIndexOf("@@")+2);
tmp2="<p style='line-height:16px;color:#4A4AFF'>"+htmlEncode(tmp2)+"</p>";
formatted.append(tmp2+"\n");
tmp2 = tmp.mid(tmp.lastIndexOf("@@")+2);
tmp2="<p style='line-height:16px;color:#4A4AFF'>"+htmlEncode(tmp2)+"</p>";
formatted.append(tmp2+"\n");
}
}else if(tmp.startsWith(" ")){
tmp="<p style='line-height:16px;color:#000000'>"+htmlEncode(tmp)+"</p>";
formatted.append(tmp+"\n");
}
}
return "<body style='font-family:Droid Sans Mono;'>"+formatted+"</body>";
}
struct linkedFeatures *bamToLf(const bam1_t *bam, void *data)
/* Translate a BAM record into a linkedFeatures item. */
{
struct bamTrackData *btd = (struct bamTrackData *)data;
const bam1_core_t *core = &bam->core;
struct linkedFeatures *lf;
struct psl *original = pslFromBam(bam);
if (original == NULL)
return NULL;
AllocVar(lf);
lf->score = core->qual;
lf->name = cloneString(bam1_qname(bam));
lf->orientation = (core->flag & BAM_FREVERSE) ? -1 : 1;
int length;
lf->components = sfFromNumericCigar(bam, &length);
lf->start = lf->tallStart = core->pos;
lf->end = lf->tallEnd = core->pos + length;
lf->extra = bamGetQuerySequence(bam, FALSE); // cds.c reverses if psl != NULL
lf->original = original;
int clippedQLen;
bamGetSoftClipping(bam, NULL, NULL, &clippedQLen);
if (sameString(btd->colorMode, BAM_COLOR_MODE_GRAY) &&
sameString(btd->grayMode, BAM_GRAY_MODE_ALI_QUAL))
{
lf->grayIx = shadeTransform(btd->aliQualShadeMin, btd->aliQualShadeMax, core->qual);
}
else if (sameString(btd->colorMode, BAM_COLOR_MODE_GRAY) &&
sameString(btd->grayMode, BAM_GRAY_MODE_BASE_QUAL))
{
UBYTE *quals = bamGetQueryQuals(bam, TRUE);
lf->components = expandSfQuals(lf->components, quals, lf->orientation, clippedQLen,
btd->baseQualShadeMin, btd->baseQualShadeMax);
lf->grayIx = maxShade - 3;
}
else if (sameString(btd->colorMode, BAM_COLOR_MODE_TAG) && isNotEmpty(btd->userTag))
{
char buf[16];
char *rgb = bamGetTagString(bam, btd->userTag, buf, sizeof(buf));
if (rgb != NULL)
{
// We don't have access to hvg at loadtime, so can't allocate color here.
// Instead, pack RGB values into lf->filterColor which fortunately is an int.
unsigned char r, g, b;
if (parseRgb(rgb, &r, &g, &b))
lf->filterColor = MAKECOLOR_32(r,g,b);
else
{
static boolean already = FALSE;
if (! already)
{
warn("%s: At least one BAM tag value for %s (%s) is not in the expected "
"RGB format: N,N,N where each N is from 0 to 255.",
btd->tg->tdb->shortLabel, btd->userTag, htmlEncode(rgb));
already = TRUE;
btd->userTag = NULL;
}
}
}
else
lf->grayIx = maxShade;
}
else
lf->grayIx = maxShade;
return lf;
}
String SimpleHTMLEncoder::encodeText(const String& originalText)
{
return htmlEncode(originalText);
}
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;
}
void doGvf(struct trackDb *tdb, char *item)
/* Show details for variants represented as GVF, stored in a bed8Attrs table */
{
struct sqlConnection *conn = hAllocConn(database);
int start = cartInt(cart, "o");
char query[1024];
sqlSafef(query, sizeof(query),
"select * from %s where name = '%s' and chrom = '%s' and chromStart = %d",
tdb->table, item, seqName, start);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
if ((row = sqlNextRow(sr)) == NULL)
errAbort("doGvfDetails: can't find item '%s' in %s at %s:%d", item, database, seqName, start);
int rowOffset = hOffsetPastBin(database, seqName, tdb->table);
struct bed8Attrs *ba = bed8AttrsLoad(row+rowOffset);
bedPrintPos((struct bed *)ba, 3, tdb);
int i = 0;
// Note: this loop modifies ba->attrVals[i], assuming we won't use them again:
for (i = 0; i < ba->attrCount; i++)
{
// The ID is the bed8Attrs name and has already been displayed:
if (sameString(ba->attrTags[i], "ID"))
continue;
cgiDecode(ba->attrVals[i], ba->attrVals[i], strlen(ba->attrVals[i]));
char *tag = ba->attrTags[i];
// User-defined keywords used in dbVar's GVF:
if (sameString(tag, "var_type")) // This one isn't anymore, but I add it back (hg18.txt).
tag = "Variant type";
else if (sameString(tag, "clinical_int"))
tag = "Clinical interpretation";
else if (sameString(tag, "var_origin"))
tag = "Variant origin";
else if (islower(tag[0]))
// Uppercase for nice display, assuming user doesn't care which keywords are
// user-defined vs. GVF standard:
tag[0] = toupper(tag[0]);
// GVF standard Start_range and End_range tags (1-based coords):
if (sameString(tag, "Start_range") || sameString(tag, "End_range"))
{
char *copy = cloneString(ba->attrVals[i]);
char *words[3];
int wordCount = chopCommas(copy, words);
if (wordCount == 2 &&
(sameString(".", words[0]) || isInteger(words[0])) &&
(sameString(".", words[1]) || isInteger(words[1])))
{
boolean isStartRange = sameString(tag, "Start_range");
char *rangeStart = words[0], *rangeEnd = words[1];
if (sameString(".", rangeStart))
rangeStart = "unknown";
if (sameString(".", rangeEnd))
rangeEnd = "unknown";
if (isStartRange)
printf("<B>Start range</B>: outer start %s, inner start %s<BR>\n",
rangeStart, rangeEnd);
else
printf("<B>End range</B>: inner end %s, outer end %s<BR>\n",
rangeStart, rangeEnd);
}
else
// not formatted as expected, just print as-is:
printf("<B>%s</B>: %s<BR>\n", tag, htmlEncode(ba->attrVals[i]));
}
// Parent sounds like mom or dad (as in var_origin)... tweak it too:
else if (sameString(tag, "Parent"))
{
printf("<B>Variant region:</B> "
"<A HREF=\"http://www.ncbi.nlm.nih.gov/dbvar/variants/%s/\" "
"TARGET=_BLANK>%s</A><BR>\n", ba->attrVals[i], htmlEncode(ba->attrVals[i]));
}
else if (sameString(tag, "Name"))
{
char *url = trackDbSetting(tdb, "url");
// Show the Name only if it hasn't already appeared in the URL:
if (url == NULL || !stringIn("$$", url))
printf("<B>%s</B>: %s<BR>\n", tag, htmlEncode(ba->attrVals[i]));
}
else if (sameWord(tag, "Phenotype_id") && startsWith("HPO:HP:", ba->attrVals[i]))
{
subChar(tag, '_', ' ');
printf("<B>%s</B>: <A HREF=\"http://www.berkeleybop.org/obo/%s\" "
"TARGET=_BLANK>%s</A><BR>\n", tag, ba->attrVals[i]+strlen("HPO:"),
htmlEncode(ba->attrVals[i]));
}
else
{
subChar(tag, '_', ' ');
printf("<B>%s</B>: %s<BR>\n", tag, htmlEncode(ba->attrVals[i]));
}
}
sqlFreeResult(&sr);
hFreeConn(&conn);
/* printTrackHtml is done in genericClickHandlerPlus. */
}
static void explainIdentifiers(char *db, struct sqlConnection *conn, char *idField)
/* Tell the user what field(s) they may paste/upload values for, and give
* some examples. */
{
char *xrefTable = NULL, *xrefIdField = NULL, *aliasField = NULL;
getXrefInfo(conn, &xrefTable, &xrefIdField, &aliasField);
hPrintf("The items must be values of the <B>%s</B> field of the currently "
"selected table, <B>%s</B>",
idField, curTable);
if (aliasField != NULL)
{
if (sameString(curTable, xrefTable))
{
if (!sameString(idField, aliasField))
hPrintf(", or the <B>%s</B> field.\n", aliasField);
else
hPrintf(".\n");
}
else
hPrintf(", or the <B>%s</B> field of the alias table <B>%s</B>.\n",
aliasField, xrefTable);
}
else
hPrintf(".\n");
hPrintf("(The \"describe table schema\" button shows more information about "
"the table fields.)\n");
// on a browserbox, db is on the UCSC server, so cannot select into db, even if temporary
if (!isCustomTrack(curTable) && !hIsBrowserbox() && sqlCanCreateTemp(conn))
{
struct slName *exampleList = NULL, *ex;
hPrintf("Some example values:<BR>\n");
exampleList = getExamples(db, conn, curTable, idField,
aliasField != NULL ? 3 : 5);
for (ex = exampleList; ex != NULL; ex = ex->next)
{
char *tmp = htmlEncode(ex->name);
hPrintf("<TT>%s</TT><BR>\n", tmp);
freeMem(tmp);
}
if (aliasField != NULL)
{
char tmpTable[512];
char query[2048];
// do not use any db. prefix on curTable for name
char *plainCurTable = strrchr(curTable, '.');
if (plainCurTable)
plainCurTable++;
else
plainCurTable = curTable;
safef(tmpTable, sizeof(tmpTable), "hgTemp.tmp%s%s", plainCurTable, xrefTable);
if (differentString(xrefTable, curTable))
sqlSafef(query, sizeof(query),
"create temporary table %s select %s.%s as %s from %s,%s "
"where %s.%s = %s.%s and %s.%s != %s.%s limit 100000",
tmpTable, xrefTable, aliasField, aliasField, xrefTable, curTable,
xrefTable, xrefIdField, curTable, idField,
xrefTable, xrefIdField, xrefTable, aliasField);
else
sqlSafef(query, sizeof(query),
"create temporary table %s select %s from %s "
"where %s != %s limit 100000",
tmpTable, aliasField, xrefTable, aliasField, xrefIdField);
sqlUpdate(conn, query);
exampleList = getExamples(db, conn, tmpTable, aliasField, 3);
for (ex = exampleList; ex != NULL; ex = ex->next)
hPrintf("<TT>%s</TT><BR>\n", ex->name);
}
hPrintf("\n");
}
}
