void doLabContacts(struct cart *theCart)
{
char *subId = cartString(theCart, "lab");
cartWebStart(cart, database, "ENCODE DCC: Contacts for submission: %s",subId);
struct sqlConnection *conn = sqlConnect(database);
char query[10 * 1024];
struct sqlResult *sr;
char **row;
printf("<a href=docIdView?db=%s> Return </a><BR>", database);
safef(query, sizeof query, "select user_id from %s where id = %s ", "projects",subId);
char *userId = sqlQuickString(conn, query);
safef(query, sizeof query, "select name,email,pi from %s where id = '%s' ", "users",userId);
sr = sqlGetResult(conn, query);
printf("<pre>");
while ((row = sqlNextRow(sr)) != NULL)
{
printf("Name: %s\nEmail: %s\nPI: %s", row[0], row[1], row[2]);
}
sqlFreeResult(&sr);
sqlDisconnect(&conn);
cartWebEnd();
}
void doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
cart = theCart;
char *db = cartUsualString(cart, "db", hDefaultDb());
cartWebStart(cart, db, "Public Sessions");
/* Not in a form; can't use cartSaveSession() to set up an hgsid input */
printf ("<script>var common = {hgsid:\"%s\"};</script>\n", cartSessionId(cart));
jsIncludeDataTablesLibs();
printf("<p>Sessions allow users to save snapshots of the Genome Browser "
"and its current configuration, including displayed tracks, position, "
"and custom track data. The Public Sessions tool allows users to easily "
"share those sessions that they deem interesting with the rest of the "
"world's researchers. You can add your own sessions to this list by "
"checking the appropriate box on the "
"<a href=\"../cgi-bin/hgSession?%s\">Session Management</a> page.</p>\n"
"<p>See the "
"<a href=\"../goldenPath/help/hgSessionHelp.html\">Sessions User's Guide</a> "
"for more information.\n</p>", cartSidUrlString(cart));
showGalleryTab();
cartWebEnd();
}
/* Mimic behaviour of doGoodReport do less stuff... */
void doGoodReportZoo(FILE *dummy, struct coordConvRep *ccr)
/** output the result of a successful conversion */
{
cartWebStart(cart, database, "Coordinate Conversion for %s %s:%d-%d",
ccr->from->date, ccr->from->chrom, ccr->from->chromStart, ccr->from->chromEnd);
printWebWarnings();
printf("<p><b>Success:</b> %s\n", ccr->msg);
printSucessWarningZoo();
printf("<ul><li><b>Original Coordinates:</b> %s %s:%d-%d ",
ccr->from->date ,ccr->from->chrom, ccr->from->chromStart, ccr->from->chromEnd);
printf("<a href=\"%s\">[browser]</a></li>\n",
makeBrowserUrl(ccr->from->version, ccr->from->chrom, ccr->from->chromStart, ccr->from->chromEnd));
printf("<li><b>Region of Original Coordinates Converted:</b> %s %s:%d-%d ",
ccr->from->date ,ccr->from->chrom, ccr->from->next->chromStart, ccr->from->next->chromEnd);
printf("<a href=\"%s\">[browser]</a></li>\n",
makeBrowserUrl(ccr->from->version, ccr->from->chrom, ccr->from->next->chromStart, ccr->from->next->chromEnd));
printf("<li><b>New Coordinates:</b> %s %s:%d-%d ",
ccr->to->date ,ccr->to->chrom, ccr->to->chromStart, ccr->to->chromEnd);
printf("<a href=\"%s\">[browser]</a></li></ul>\n",
makeBrowserUrl(ccr->to->version, ccr->to->chrom, ccr->to->chromStart, ccr->to->chromEnd));
/* Trouble shooting isn't applicable in this case yet... ccr doesn't contain proper info.. */
/* printTroubleShooting(ccr); */
cartWebEnd();
}
void doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
char *database = cgiOptionalString("db");
char *rtdbServer = cfgOption("rtdb.server");
char *rtdbPort = cfgOption("rtdb.port");
char *rtdbChoices = cfgOption("rtdb.databases");
struct slName *dbs = slNameListFromComma(rtdbChoices);
cart = theCart;
cartWebStart(cart, database, "MGC RTDB Update");
if (!rtdbServer)
errAbort("rtdb.update not defined in the hg.conf file. "
"Chances are this CGI isn't meant for this machine.");
if (!rtdbPort)
errAbort("rtdb.update not defined in the hg.conf file. "
"Chances are this CGI isn't meant for this machine.");
/* create HMTL form if button wasn't pressed. Otherwise, run the update */
if (!cgiVarExists("RTDBSubmit"))
makeForm(dbs);
else if ((database == NULL) || (!slNameInList(dbs, database)))
{
makeForm(dbs);
printf("<br>Error: Select one of databases listed.");
}
else
updateServer(rtdbServer, rtdbPort, database);
cartWebEnd();
slNameFreeList(&dbs);
}
void doMiddle(struct cart *theCart)
/* Set up pretty web display and save cart in global. */
{
char *key = NULL;
char *file = NULL;
cart = theCart;
key = cartOptionalString(cart, "key");
if (isValidKey(key))
{
file = cartOptionalString(cart, "file");
if(NULL == file)
{
printIndexFile();
}
else
{
printFile(file);
}
}
else
{
cartWebStart(theCart, database, "SECURE CGI \n");
cartRemove(cart, "key");
printf("INVALID KEY\n");
cartWebEnd();
}
}
void mainPage(struct sqlConnection *conn, int id, char *geneName)
/* Put up fancy main page - image, caption, and then a bunch of thumbnails. */
{
struct slInt *thumbList = NULL, *thumb;
cartWebStart(cart, NULL, "UCSC BioImage Browser on %s", geneName);
printf("<A HREF=\"");
printf("../cgi-bin/hgBioImage?%s=%d&%s=on", hgbiId, id, hgbiDoFullSize);
printf("\">");
printf("<IMG SRC=\"/%s\" BORDER=1></A><BR>\n", bioImageScreenSizePath(conn, id));
printf("\n");
printCaption(conn, id, geneName);
htmlHorizontalLine();
printf("Other images associated with gene. Click to view details.<BR>");
thumbList = bioImageOnSameGene(conn, id);
for (thumb = thumbList; thumb != NULL; thumb = thumb->next)
{
char *imageFile = bioImageThumbSizePath(conn, thumb->val);
printf("<A HREF=\"../cgi-bin/hgBioImage?%s=%d\">", hgbiId, thumb->val);
printf("<IMG SRC=\"/%s\" BORDER=1></A>\n", imageFile);
printf(" ");
}
cartWebEnd();
}
void doDocIdReport(struct cart *theCart)
{
char *docId = cartString(theCart, "docId");
cartWebStart(cart, database, "ENCODE DCC: Validation report for docId %s",docId);
struct sqlConnection *conn = sqlConnect(database);
char query[10 * 1024];
struct sqlResult *sr;
char **row;
boolean beenHere = FALSE;
printf("<a href=docIdView?db=%s> Return </a><BR>", database);
safef(query, sizeof query, "select * from %s where ix=%s", docIdTable,docId);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
if (beenHere)
errAbort("found more than one record with ix value %s in table %s",
docId, docIdTable);
beenHere = TRUE;
struct docIdSub *docIdSub = docIdSubLoad(row);
cgiDecode(docIdSub->valReport, docIdSub->valReport, strlen(docIdSub->valReport));
//printf("tempFile is %s\n<BR>", tempFile);
printf("<pre>%s", docIdSub->valReport);
}
cartWebEnd();
}
void doKgMethod()
/* display knownGene.html content (UCSC Known Genes
* Method, Credits, and Data Use Restrictions) */
{
cartWebStart(cart, database, "Methods, Credits, and Use Restrictions");
struct trackDb *tdb = hTrackDbForTrack(database, genomeSetting("knownGene"));
hPrintf("%s", tdb->html);
cartWebEnd();
}
void doMiddle(struct cart *theCart)
/* Write header and body of html page. */
{
cart = theCart;
dnaUtilOpen();
cartWebStart(cart, NULL, "UCSC In-Silico PCR");
dispatch();
cartWebEnd();
}
/* This is very similar to doForm except it's for Zoo species */
void doFormZoo(struct cart *lCart)
/** Print out the form for users */
{
char **genomeList = NULL;
int genomeCount = 0;
char *dbChoice = NULL;
int i = 0;
cart = lCart;
cartWebStart(cart, databases, "Converting Coordinates Between Species");
puts(
"<p>This page attempts to convert coordinates from one Zoo species' CFTR region\n"
"to another. The mechanism for doing this is to use the blastz alignments which have been\n"
"done between each Zoo species and use this to convert coordinates. In general these should\n"
"be reasonable conversions however the user is advised to not take the conversions as absolute \n"
"standards. Furthermore a given region from a given species is not necessarily alignable to any\n"
"region in a different species.\n"
);
/* Get all Zoo species since we are using blastz static alignments */
getIndexedGenomeDescriptionsZoo(&genomeList, &genomeCount,FALSE);
/* choose whether to use the db supplied by cgi or our default */
if(origDb != NULL && strstr(origDb, "zoo") == NULL)
errAbort("Sorry, this mode of the program only works between zoo species.");
dbChoice = chooseDb(origDb, genomeList[0]);
printf("<form action=\"../cgi-bin/hgCoordConv\" method=get>\n");
printf("<br><br>\n");
printf("<table><tr>\n");
printf("<b><td><table><tr><td>Original Species: </b>\n");
cgiMakeDropList("origGenome", genomeList, genomeCount, dbChoice);
printf("</td></tr></table></td>\n");
printf(" <b><td><table><tr><td>Original Position: </b>\n");
/* if someone has passed in a position fill it in for them */
if(position == NULL)
cgiMakeTextVar("position",defaultPos, 30);
else
cgiMakeTextVar("position",position, 30);
printf("</td></tr></table></td>\n");
printf("<b><td><table><tr><td>New Species: </b>\n");
freez(&genomeList);
genomeCount =0;
getIndexedGenomeDescriptionsZoo(&genomeList, &genomeCount, FALSE);
cgiMakeDropList("newGenome", genomeList, genomeCount, genomeList[genomeCount -1]);
printf("</td></tr></table></td></tr>\n");
printf("<tr><td colspan=6 align=right><br>\n");
cgiMakeButton("Submit","submit");
printf("</center></td></tr></table>\n");
cgiMakeHiddenVar("calledSelf", "on");
printf("</form>\n");
cartWebEnd();
}
void doBadReport(FILE *dummy, struct coordConvRep *ccr)
/** output the result of a flawed conversion */{
cartWebStart(cart, database, "Coordinate Conversion for %s %s:%d-%d",
ccr->from->date, ccr->from->chrom, ccr->from->chromStart, ccr->from->chromEnd);
printWebWarnings();
printf("<p><b>Conversion Not Successful:</B> %s\n", ccr->msg);
printf("<p><a href=\"%s\">View old Coordinates in %s browser.</a>\n",
makeBrowserUrl(ccr->from->version, ccr->from->chrom, ccr->from->chromStart, ccr->from->chromEnd),
ccr->from->date);
printTroubleShooting(ccr);
cartWebEnd();
}
void doForm(struct cart *lCart)
/** Print out the form for users */
{
char **genomeList = NULL;
int genomeCount = 0;
char *dbChoice = NULL;
int i = 0;
cart = lCart;
cartWebStart(cart, databases, "Converting Coordinates Between Drafts");
puts(
"<p>This page attempts to convert coordinates from one draft of the human genome\n"
"to another. The mechanism for doing this is to cut out and align pieces from the\n"
"old draft and align them to the new draft making sure that\n"
"they are in the same order and orientation. In general the smaller the sequence the better\n"
"the chances of successful conversion.\n"
);
getIndexedGenomeDescriptions(&genomeList, &genomeCount, TRUE);
/* choose whether to use the db supplied by cgi or our default */
if(origDb != NULL && strstr(origDb, "hg") == NULL)
errAbort("Sorry, currently the conversion program only works with human genomes.");
dbChoice = chooseDb(origDb, genomeList[0]);
printf("<form action=\"../cgi-bin/hgCoordConv\" method=get>\n");
printf("<br><br>\n");
printf("<table><tr>\n");
printf("<b><td><table><tr><td>Original Draft: </b>\n");
cgiMakeDropList("origGenome", genomeList, genomeCount, dbChoice);
printf("</td></tr></table></td>\n");
printf(" <b><td><table><tr><td>Original Position: </b>\n");
/* if someone has passed in a position fill it in for them */
if(position == NULL)
cgiMakeTextVar("position",defaultPos, 30);
else
cgiMakeTextVar("position",position, 30);
printf("</td></tr></table></td>\n");
printf("<b><td><table><tr><td>New Draft: </b>\n");
freez(&genomeList);
genomeCount =0;
getIndexedGenomeDescriptions(&genomeList, &genomeCount, TRUE);
cgiMakeDropList("newGenome", genomeList, genomeCount, genomeList[genomeCount -1]);
printf("</td></tr></table></td></tr>\n");
printf("<tr><td colspan=6 align=right><br>\n");
cgiMakeButton("Submit","submit");
printf("</center></td></tr></table>\n");
cgiMakeHiddenVar("calledSelf", "on");
printf("</form>\n");
cartWebEnd();
}
void doDocIdMeta(struct cart *theCart)
{
char *docId = cartString(theCart, "docId");
cartWebStart(cart, database, "ENCODE DCC: Metadata for docId %s",docId);
struct sqlConnection *conn = sqlConnect(database);
char query[10 * 1024];
struct sqlResult *sr;
char **row;
struct tempName tn;
trashDirFile(&tn, "docId", "meta", ".txt");
char *tempFile = tn.forCgi;
boolean beenHere = FALSE;
printf("<a href=docIdView?db=%s> Return </a><BR>", database);
safef(query, sizeof query, "select * from %s where ix=%s", docIdTable,docId);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
if (beenHere)
errAbort("found more than one record with ix value %s in table %s",
docId, docIdTable);
beenHere = TRUE;
struct docIdSub *docIdSub = docIdSubLoad(row);
cgiDecode(docIdSub->metaData, docIdSub->metaData, strlen(docIdSub->metaData));
//printf("tempFile is %s\n<BR>", tempFile);
FILE *f = mustOpen(tempFile, "w");
fwrite(docIdSub->metaData, strlen(docIdSub->metaData), 1, f);
fclose(f);
boolean validated;
struct mdbObj *mdbObj = mdbObjsLoadFromFormattedFile(tempFile, &validated);
unlink(tempFile);
if (mdbObj->next)
errAbort("got more than one metaObj from metaData");
for(; mdbObj; mdbObj = mdbObj->next)
{
printf("<BR>object: %s\n", mdbObj->obj);
struct mdbVar *vars = mdbObj->vars;
for(; vars; vars = vars->next)
{
printf("<BR>%s %s\n", vars->var, vars->val);
}
}
}
cartWebEnd();
}
void doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
char *db = NULL;
char *ignored;
struct trackDb *tracks;
struct trackRef *tr;
struct group *group, *groups = NULL;
cart = theCart;
cartWebStart(cart, NULL, "ENCODE Track Data Versions (%s)", db);
getDbAndGenome(cart, &db, &ignored, NULL);
tracks = hTrackDb(db);
groups = groupTracks(db, tracks);
for (group = groups; group != NULL; group = group->next)
{
if (group->tracks == NULL || !startsWith("encode", group->name))
continue;
hTableStart();
puts("<TR>");
puts("<TH align=LEFT colspan=3 BGCOLOR=#536ED3>");
printf("<B> %s</B> ", wrapWhiteFont(group->label));
printf(" ");
puts("</TH>\n");
puts("</TR>");
for (tr = group->tracks; tr != NULL; tr = tr->next)
{
char *version = trackDbSetting(tr->track, "dataVersion");
if (version)
stripString(version, "ENCODE ");
puts("<TR><TD>");
printf(" %s", tr->track->shortLabel);
puts("</TD><TD>");
printf(" %s", version ? version : " ");
puts("</TD><TD>");
printf(" %s", tr->track->longLabel);
puts("</TD></TR>");
}
/*
printf("\t%s\t%s\t%s\n", version,
tr->track->shortLabel, tr->track->longLabel);
*/
hTableEnd();
puts("<BR>");
}
cartWebEnd();
}
void doMiddle(struct cart *theCart)
/* Write header and body of html page. */
{
char *userSeq;
char *db, *organism;
boolean clearUserSeq = cgiBoolean("Clear");
cart = theCart;
dnaUtilOpen();
orgChange = sameOk(cgiOptionalString("changeInfo"),"orgChange");
if (orgChange)
{
cgiVarSet("db", hDefaultDbForGenome(cgiOptionalString("org")));
}
getDbAndGenome(cart, &db, &organism, oldVars);
char *oldDb = cloneString(db);
findClosestServer(&db, &organism);
/* Get sequence - from userSeq variable, or if
* that is empty from a file. */
if (clearUserSeq)
{
cartSetString(cart, "userSeq", "");
cartSetString(cart, "seqFile", "");
}
userSeq = cartUsualString(cart, "userSeq", "");
if (isEmpty(userSeq))
{
userSeq = cartOptionalString(cart, "seqFile");
}
if (isEmpty(userSeq) || orgChange)
{
cartWebStart(theCart, db, "%s BLAT Search", trackHubSkipHubName(organism));
if (differentString(oldDb, db))
printf("<HR><P><EM><B>Note:</B> BLAT search is not available for %s %s; "
"defaulting to %s %s</EM></P><HR>\n",
hGenome(oldDb), hFreezeDate(oldDb), organism, hFreezeDate(db));
askForSeq(organism,db);
cartWebEnd();
}
else
{
blatSeq(skipLeadingSpaces(userSeq), organism);
}
}
void correlatePage(struct sqlConnection *conn)
/* Put up correlation page. */
{
cartWebStart(cart, database, "Correlations of all pairs of graphs");
hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\" METHOD=GET>\n");
cartSaveSession(cart);
struct slRef *ggRefList = ggAllVisible(conn);
struct slRef *aRef, *bRef;
hPrintf("<TABLE><TR><TD>");
webPrintLinkTableStart();
webPrintLabelCell("Graph A");
webPrintLabelCell("Graph B");
webPrintLabelCell("R");
webPrintLabelCell("R-Squared");
for (aRef = ggRefList; aRef != NULL; aRef = aRef->next)
{
for (bRef = aRef->next; bRef != NULL; bRef = bRef->next)
{
hPrintf("</TR><TR>");
correlateGraphs(aRef->val, bRef->val);
}
}
webPrintLinkTableEnd();
hPrintf("</TD><TD>");
hPrintf("<CENTER>");
cgiMakeButton("submit", "return to graphs");
hPrintf("</CENTER>");
hPrintf("</TD></TR></TABLE>");
hPrintf("<P>R, also known as Pearson's correlation coefficient, is a measure ");
hPrintf("of the extent that two graphs move together. The value of R ranges ");
hPrintf("between -1 and 1. A positive R indicates that the graphs tend to ");
hPrintf("move in the same direction, while a negative R indicates that they ");
hPrintf("tend to move in opposite directions.</P>\n");
hPrintf("<P>R-Squared (which is indeed just R*R) measures how much of the ");
hPrintf("variation in one graph can be explained by a linear dependence on ");
hPrintf("the other graph. R-Squared ranges between 0 when the two graphs are ");
hPrintf("independent to 1 when the graphs are completely dependent.</P>");
hPrintf("</FORM>");
cartWebEnd();
}
void doMiddle(struct cart *theCart)
/* Set up globals and make web plabel */
{
cart = theCart;
char *db = cartUsualString(cart, "db", hDefaultDb());
cartWebStart(cart, db, "Try and get some simple D3 things running inside of Genome Browser web framework.");
printf("<script src=\"//cdnjs.cloudflare.com/ajax/libs/d3/3.4.4/d3.min.js\"></script>");
printf("<script src=\"/js/d3pie.min.js\"></script>");
struct slPair *data= slPairNew("A","100");
slPairAdd(&data, "B", "10");
slPairAdd(&data, "C", "1");
slReverse(&data);
printf("<div id=\"pieChart1\">\n");
drawPrettyPieGraph(data, "pieChart1", "Title", "Subtitle");
printf("</div>\n");
slPairAdd(&data, "D", "10");
printf("<div id=\"pieChart2\">\n");
drawPrettyPieGraph(data, "pieChart1", "A new title", "cool subtitle!");
printf("</div>\n");
slPairAdd(&data, "W", "15");
printf("<div id=\"pieChart3\">\n");
drawPrettyPieGraph(data, "pieChart1", "Title", "Testing out what a much longer subtitle will look like... How many characters can I put here?");
printf("</div>\n");
slPairAdd(&data, "Z", "30");
printf("<div id=\"pieChart4\">\n");
drawPrettyPieGraph(data, "pieChart1", "How do much largers titles look?", "Subtitle");
printf("</div>\n");
printf("<style>\npieChart1{\n align:center;} </style>");
#ifdef SOON
drawPieGraph(data);
drawPieGraph(data);
slPairAdd(&data, "E", "15");
drawPieGraph(data);
slPairAdd(&data, "F", "25");
drawPieGraph(data);
slPairAdd(&data, "G", "50");
drawPieGraph(data);
#endif /* SOON */
cartWebEnd();
}
void configureOnePage()
/* Put up configuration for one graph. */
{
/* Figure out which graph we're configuring. */
char *graphName = cartString(cart, "g");
struct genoGraph *gg = hashFindVal(ggHash, graphName);
if (gg == NULL)
{
/* Warn/return rather than abort if have problems, so that
* cartRemovePrefix(hggDo) is executed to keep us from error
* loop forever... */
warn("Graph %s not found", graphName);
return;
}
/* Put up web page with controls */
cartWebStart(cart, database, "Configure %s", gg->shortLabel);
hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\" METHOD=GET>\n");
cartSaveSession(cart);
cgiMakeHiddenVar(hggConfigure, "on");
struct chromGraphSettings *cgs = gg->settings;
char varName[chromGraphVarNameMaxSize];
chromGraphVarName(gg->name, "minVal", varName);
hPrintf("display min value: ");
cartMakeIntVar(cart, varName, cgs->minVal, 5);
chromGraphVarName(gg->name, "maxVal", varName);
hPrintf(" max value: ");
cartMakeIntVar(cart, varName, cgs->maxVal, 5);
hPrintf("<BR>\n");
hPrintf("draw connecting lines between markers separated by up to ");
chromGraphVarName(gg->name, "maxGapToFill", varName);
cartMakeIntVar(cart, varName, cgs->maxGapToFill, 8);
hPrintf(" bases.");
hPrintf("<BR>\n");
cgiMakeButton("submit", "submit");
hPrintf("</FORM>\n");
cartWebEnd();
}
void submitUpload(struct sqlConnection *conn)
/* Called when they've submitted from uploads page */
{
char *urlText = cartUsualString(cart, hggUploadUrl, NULL);
char *fileText = cartUsualString(cart, hggUploadFile, NULL);
char *rawText = urlText;
if (isNotEmpty(fileText))
rawText = fileText;
int rawTextSize = strlen(rawText);
struct errCatch *errCatch = errCatchNew();
cartWebStart(cart, database, "Data Upload Complete (%d bytes)", rawTextSize);
hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\">");
cartSaveSession(cart);
if (errCatchStart(errCatch))
trySubmitUpload(conn, rawText);
errCatchFinish(&errCatch);
cartRemove(cart, hggUploadFile);
hPrintf("<CENTER>");
cgiMakeButton("submit", "OK");
hPrintf("</CENTER>");
hPrintf("</FORM>");
cartWebEnd();
}
void doGoodReport(FILE *dummy, struct coordConvRep *ccr)
/** output the result of a successful conversion */
{
cartWebStart(cart, database, "Coordinate Conversion for %s %s:%d-%d",
ccr->from->date, ccr->from->chrom, ccr->from->chromStart, ccr->from->chromEnd);
printWebWarnings();
printf("<p><b>Success:</b> %s\n", ccr->msg);
if(sameString(ccr->midPsl->strand, "-"))
{
printf(" It appears that the orientation of your coordinate range has been inverted.\n");
}
printSucessWarning();
printf("<ul><li><b>Old Coordinates:</b> %s %s:%d-%d ",
ccr->from->date ,ccr->from->chrom, ccr->from->chromStart, ccr->from->chromEnd);
printf("<a href=\"%s\">[browser]</a></li>\n",
makeBrowserUrl(ccr->from->version, ccr->from->chrom, ccr->from->chromStart, ccr->from->chromEnd));
printf("<li><b>New Coordinates:</b> %s %s:%d-%d ",
ccr->to->date ,ccr->to->chrom, ccr->to->chromStart, ccr->to->chromEnd);
printf("<a href=\"%s\">[browser]</a></li></ul>\n",
makeBrowserUrl(ccr->to->version, ccr->to->chrom, ccr->to->chromStart, ccr->to->chromEnd));
printTroubleShooting(ccr);
cartWebEnd();
}
void cartMain(struct cart *theCart)
/* We got the persistent/CGI variable cart. Now
* set up the globals and make a web page. */
{
hgBotDelay();
cart = theCart;
getDbAndGenome(cart, &database, &genome, oldVars);
initGenbankTableNames(database);
getGenomeSettings();
if (cartVarExists(cart, hggDoKgMethod))
doKgMethod();
else if (cartVarExists(cart, hggDoTxInfoDescription))
doTxInfoDescription();
else
{
struct sqlConnection *conn = NULL;
char *geneName = cartUsualString(cart, hggGene, NULL);
if (isEmpty(geneName))
{
// Silly googlebots.
hUserAbort("Error: the hgg_gene parameter is missing from the cart and the CGI params.");
}
/* if kgProtMap2 table exists, this means we are doing KG III */
if (hTableExists(database, "kgProtMap2")) kgVersion = KG_III;
conn = hAllocConn(database);
curGeneId = findGeneId(conn, geneName);
getGenePosition(conn);
curGenePred = getCurGenePred(conn);
curGeneName = getGeneName(curGeneId, conn);
spConn = hAllocConn(UNIPROT_DB_NAME);
swissProtAcc = getSwissProtAcc(conn, spConn, curGeneId);
if (isRgdGene(conn)) swissProtAcc=getRgdGeneUniProtAcc(curGeneId, conn);
/* Check command variables, and do the ones that
* don't want to put up the hot link bar etc. */
if (cartVarExists(cart, hggDoGetMrnaSeq))
doGetMrnaSeq(conn, curGeneId, curGeneName);
else if (cartVarExists(cart, hggDoWikiTrack))
doWikiTrack(conn);
else if (cartVarExists(cart, hggDoGetProteinSeq))
doGetProteinSeq(conn, curGeneId, curGeneName);
else if (cartVarExists(cart, hggDoRnaFoldDisplay))
doRnaFoldDisplay(conn, curGeneId, curGeneName);
else if (cartVarExists(cart, hggDoOtherProteinSeq))
doOtherProteinSeq(conn, curGeneName);
else if (cartVarExists(cart, hggDoOtherProteinAli))
doOtherProteinAli(conn, curGeneId, curGeneName);
else
{
/* Default case - start fancy web page. */
measureTiming = isNotEmpty(cartOptionalString(cart, "measureTiming"));
struct trackDb *tdb = hTrackDbForTrack(database, genomeSetting("knownGene"));
isGencode = trackDbSettingOn(tdb, "isGencode");
isGencode2 = trackDbSettingOn(tdb, "isGencode2");
cartWebStart(cart, database, "%s Gene %s (%s) Description and Page Index",
genome, curGeneName, isGencode2 ? curGeneId : curAlignId);
webMain(conn, tdb);
cartWebEnd();
}
hFreeConn(&spConn);
hFreeConn(&conn);
}
cartRemovePrefix(cart, hggDoPrefix);
}
void doMiddle(struct cart *theCart)
/* Write header and body of html page. */
{
boolean gotDisconnect = FALSE;
cart = theCart;
if (cartVarExists(cart, hgHubDoClear))
{
doClearHub(cart);
cartWebEnd();
return;
}
if (cartVarExists(cart, hgHubDoDisconnect))
{
gotDisconnect = TRUE;
doDisconnectHub(cart);
// now rebuild the cart variable ("trackHubs") that has which lists which
// hubs are on.
hubConnectHubsInCart(cart);
}
if (cartVarExists(cart, hgHubDoReset))
{
doResetHub(cart);
}
cartWebStart(cart, NULL, "%s", pageTitle);
jsIncludeFile("jquery.js", NULL);
jsIncludeFile("utils.js", NULL);
jsIncludeFile("jquery-ui.js", NULL);
webIncludeResourceFile("jquery-ui.css");
jsIncludeFile("ajax.js", NULL);
jsIncludeFile("hgHubConnect.js", NULL);
jsIncludeFile("jquery.cookie.js", NULL);
printf("<div id=\"hgHubConnectUI\"> <div id=\"description\"> \n");
printf(
"<P>Track data hubs are collections of tracks from outside of UCSC that "
"can be imported into the Genome Browser. To import a public hub check "
"the box in the list below. "
"After import the hub will show up as a group of tracks with its own blue "
"bar and label underneath the main browser graphic, and in the "
"configure page. For more information, see the "
"<A HREF=\"../goldenPath/help/hgTrackHubHelp.html\" TARGET=_blank>"
"User's Guide</A>.</P>\n"
"<P><B>NOTE: Because Track Hubs are created and maintained by external sources,"
" UCSC is not responsible for their content.</B></P>"
);
printf("</div>\n");
getDbAndGenome(cart, &database, &organism, oldVars);
char *survey = cfgOptionEnv("HGDB_HUB_SURVEY", "hubSurvey");
char *surveyLabel = cfgOptionEnv("HGDB_HUB_SURVEY_LABEL", "hubSurveyLabel");
if (survey && differentWord(survey, "off"))
hPrintf("<span style='background-color:yellow;'><A HREF='%s' TARGET=_BLANK><EM><B>%s</EM></B></A></span>\n", survey, surveyLabel ? surveyLabel : "Take survey");
hPutc('\n');
// check to see if we have any new hubs
hubCheckForNew(cart);
// grab all the hubs that are listed in the cart
struct hubConnectStatus *hubList = hubConnectStatusListFromCartAll(cart);
checkTrackDbs(hubList);
// here's a little form for the add new hub button
printf("<FORM ACTION=\"%s\" NAME=\"addHubForm\">\n", "../cgi-bin/hgHubConnect");
cgiMakeHiddenVar("hubUrl", "");
cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
puts("</FORM>");
// this the form for the disconnect hub button
printf("<FORM ACTION=\"%s\" NAME=\"disconnectHubForm\">\n", "../cgi-bin/hgHubConnect");
cgiMakeHiddenVar("hubId", "");
cgiMakeHiddenVar(hgHubDoDisconnect, "on");
cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
puts("</FORM>");
// this the form for the reset hub button
printf("<FORM ACTION=\"%s\" NAME=\"resetHubForm\">\n", "../cgi-bin/hgHubConnect");
cgiMakeHiddenVar("hubUrl", "");
cgiMakeHiddenVar(hgHubDoReset, "on");
cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
puts("</FORM>");
// ... and now the main form
if (cartVarExists(cart, hgHubConnectCgiDestUrl))
destUrl = cartOptionalString(cart, hgHubConnectCgiDestUrl);
printf("<FORM ACTION=\"%s\" METHOD=\"POST\" NAME=\"mainForm\">\n", destUrl);
cartSaveSession(cart);
// we have two tabs for the public and unlisted hubs
printf("<div id=\"tabs\">"
"<ul> <li><a href=\"#publicHubs\">Public Hubs</a></li>"
"<li><a href=\"#unlistedHubs\">My Hubs</a></li> "
"</ul> ");
struct hash *publicHash = hgHubConnectPublic();
hgHubConnectUnlisted(hubList, publicHash);
printf("</div>");
printf("<div class=\"tabFooter\">");
cgiMakeButton("Submit", "Use Selected Hubs");
char *emailAddress = cfgOptionDefault("hub.emailAddress","*****@*****.**");
printf("<span class=\"small\">"
"Contact <A HREF=\"mailto:%s\">%s</A> to add a public hub."
"</span>\n", emailAddress,emailAddress);
printf("</div>");
cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
printf("</div>\n");
puts("</FORM>");
cartWebEnd();
}
void blatSeq(char *userSeq, char *organism)
/* Blat sequence user pasted in. */
{
FILE *f;
struct dnaSeq *seqList = NULL, *seq;
struct tempName pslTn, faTn;
int maxSingleSize, maxTotalSize, maxSeqCount;
int minSingleSize = minMatchShown;
char *genome, *db;
char *type = cgiString("type");
char *seqLetters = cloneString(userSeq);
struct serverTable *serve;
int conn;
int oneSize, totalSize = 0, seqCount = 0;
boolean isTx = FALSE;
boolean isTxTx = FALSE;
boolean txTxBoth = FALSE;
struct gfOutput *gvo;
boolean qIsProt = FALSE;
enum gfType qType, tType;
struct hash *tFileCache = gfFileCacheNew();
boolean feelingLucky = cgiBoolean("Lucky");
getDbAndGenome(cart, &db, &genome, oldVars);
if(!feelingLucky)
cartWebStart(cart, db, "%s BLAT Results", trackHubSkipHubName(organism));
/* Load user sequence and figure out if it is DNA or protein. */
if (sameWord(type, "DNA"))
{
seqList = faSeqListFromMemText(seqLetters, TRUE);
uToT(seqList);
isTx = FALSE;
}
else if (sameWord(type, "translated RNA") || sameWord(type, "translated DNA"))
{
seqList = faSeqListFromMemText(seqLetters, TRUE);
uToT(seqList);
isTx = TRUE;
isTxTx = TRUE;
txTxBoth = sameWord(type, "translated DNA");
}
else if (sameWord(type, "protein"))
{
seqList = faSeqListFromMemText(seqLetters, FALSE);
isTx = TRUE;
qIsProt = TRUE;
}
else
{
seqList = faSeqListFromMemTextRaw(seqLetters);
isTx = !seqIsDna(seqList);
if (!isTx)
{
for (seq = seqList; seq != NULL; seq = seq->next)
{
seq->size = dnaFilteredSize(seq->dna);
dnaFilter(seq->dna, seq->dna);
toLowerN(seq->dna, seq->size);
subChar(seq->dna, 'u', 't');
}
}
else
{
for (seq = seqList; seq != NULL; seq = seq->next)
{
seq->size = aaFilteredSize(seq->dna);
aaFilter(seq->dna, seq->dna);
toUpperN(seq->dna, seq->size);
}
qIsProt = TRUE;
}
}
if (seqList != NULL && seqList->name[0] == 0)
{
freeMem(seqList->name);
seqList->name = cloneString("YourSeq");
}
trimUniq(seqList);
/* If feeling lucky only do the first on. */
if(feelingLucky && seqList != NULL)
{
seqList->next = NULL;
}
/* Figure out size allowed. */
maxSingleSize = (isTx ? 10000 : 75000);
maxTotalSize = maxSingleSize * 2.5;
#ifdef LOWELAB
maxSeqCount = 200;
#else
maxSeqCount = 25;
#endif
/* Create temporary file to store sequence. */
trashDirFile(&faTn, "hgSs", "hgSs", ".fa");
faWriteAll(faTn.forCgi, seqList);
/* Create a temporary .psl file with the alignments against genome. */
trashDirFile(&pslTn, "hgSs", "hgSs", ".pslx");
f = mustOpen(pslTn.forCgi, "w");
gvo = gfOutputPsl(0, qIsProt, FALSE, f, FALSE, TRUE);
serve = findServer(db, isTx);
/* Write header for extended (possibly protein) psl file. */
if (isTx)
{
if (isTxTx)
{
qType = gftDnaX;
tType = gftDnaX;
}
else
{
qType = gftProt;
tType = gftDnaX;
}
}
else
{
qType = gftDna;
tType = gftDna;
}
pslxWriteHead(f, qType, tType);
if (qType == gftProt)
{
minSingleSize = 14;
}
else if (qType == gftDnaX)
{
minSingleSize = 36;
}
/* Loop through each sequence. */
for (seq = seqList; seq != NULL; seq = seq->next)
{
printf(" "); fflush(stdout); /* prevent apache cgi timeout by outputting something */
oneSize = realSeqSize(seq, !isTx);
if ((seqCount&1) == 0) // Call bot delay every 2nd time starting with first time
hgBotDelay();
if (++seqCount > maxSeqCount)
{
warn("More than 25 input sequences, stopping at %s.",
seq->name);
break;
}
if (oneSize > maxSingleSize)
{
warn("Sequence %s is %d letters long (max is %d), skipping",
seq->name, oneSize, maxSingleSize);
continue;
}
if (oneSize < minSingleSize)
{
warn("Warning: Sequence %s is only %d letters long (%d is the recommended minimum)",
seq->name, oneSize, minSingleSize);
// we could use "continue;" here to actually enforce skipping,
// but let's give the short sequence a chance, it might work.
// minimum possible length = tileSize+stepSize, so mpl=16 for dna stepSize=5, mpl=10 for protein.
if (qIsProt && oneSize < 1) // protein does not tolerate oneSize==0
continue;
}
totalSize += oneSize;
if (totalSize > maxTotalSize)
{
warn("Sequence %s would take us over the %d letter limit, stopping here.",
seq->name, maxTotalSize);
break;
}
conn = gfConnect(serve->host, serve->port);
if (isTx)
{
gvo->reportTargetStrand = TRUE;
if (isTxTx)
{
gfAlignTransTrans(&conn, serve->nibDir, seq, FALSE, 5,
tFileCache, gvo, !txTxBoth);
if (txTxBoth)
{
reverseComplement(seq->dna, seq->size);
conn = gfConnect(serve->host, serve->port);
gfAlignTransTrans(&conn, serve->nibDir, seq, TRUE, 5,
tFileCache, gvo, FALSE);
}
}
else
{
gfAlignTrans(&conn, serve->nibDir, seq, 5, tFileCache, gvo);
}
}
else
{
gfAlignStrand(&conn, serve->nibDir, seq, FALSE, minMatchShown, tFileCache, gvo);
reverseComplement(seq->dna, seq->size);
conn = gfConnect(serve->host, serve->port);
gfAlignStrand(&conn, serve->nibDir, seq, TRUE, minMatchShown, tFileCache, gvo);
}
gfOutputQuery(gvo, f);
}
carefulClose(&f);
showAliPlaces(pslTn.forCgi, faTn.forCgi, serve->db, qType, tType,
organism, feelingLucky);
if(!feelingLucky)
cartWebEnd();
gfFileCacheFree(&tFileCache);
}
void showAliPlaces(char *pslName, char *faName, char *database,
enum gfType qType, enum gfType tType,
char *organism, boolean feelingLucky)
/* Show all the places that align. */
{
struct lineFile *lf = pslFileOpen(pslName);
struct psl *pslList = NULL, *psl;
char *browserUrl = hgTracksName();
char *hgcUrl = hgcName();
char uiState[64];
char *vis;
char unhideTrack[64];
char *sort = cartUsualString(cart, "sort", sortList[0]);
char *output = cartUsualString(cart, "output", outputList[0]);
boolean pslOut = startsWith("psl", output);
boolean isStraightNuc = (qType == gftRna || qType == gftDna);
int minThreshold = (isStraightNuc ? minMatchShown : 0);
sprintf(uiState, "%s=%s", cartSessionVarName(), cartSessionId(cart));
/* If user has hidden BLAT track, add a setting that will unhide the
track if user clicks on a browser link. */
vis = cartOptionalString(cart, "hgUserPsl");
if (vis != NULL && sameString(vis, "hide"))
snprintf(unhideTrack, sizeof(unhideTrack), "&hgUserPsl=dense");
else
unhideTrack[0] = 0;
while ((psl = pslNext(lf)) != NULL)
{
if (psl->match >= minThreshold)
slAddHead(&pslList, psl);
}
lineFileClose(&lf);
if (pslList == NULL)
{
puts("<table><tr><td><hr>Sorry, no matches found<hr><td></tr></table>");
return;
}
if (sameString(sort, "query,start"))
{
slSort(&pslList, pslCmpQuery);
}
else if (sameString(sort, "query,score"))
{
slSort(&pslList, pslCmpQueryScore);
}
else if (sameString(sort, "score"))
{
slSort(&pslList, pslCmpScore);
}
else if (sameString(sort, "chrom,start"))
{
slSort(&pslList, pslCmpTargetStart);
}
else if (sameString(sort, "chrom,score"))
{
slSort(&pslList, pslCmpTargetScore);
}
else
{
slSort(&pslList, pslCmpQueryScore);
}
if(feelingLucky)
{
/* If we found something jump browser to there. */
if(slCount(pslList) > 0)
printLuckyRedirect(browserUrl, pslList, database, pslName, faName, uiState, unhideTrack);
/* Otherwise call ourselves again not feeling lucky to print empty
results. */
else
{
cartWebStart(cart, database, "%s BLAT Results", trackHubSkipHubName(organism));
showAliPlaces(pslName, faName, database, qType, tType, organism, FALSE);
cartWebEnd();
}
}
else if (pslOut)
{
printf("<TT><PRE>");
if (!sameString(output, "psl no header"))
pslxWriteHead(stdout, qType, tType);
for (psl = pslList; psl != NULL; psl = psl->next)
pslTabOut(psl, stdout);
printf("</PRE></TT>");
}
else
{
printf("<H2>BLAT Search Results</H2>");
printf("<TT><PRE>");
printf(" ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN\n");
printf("---------------------------------------------------------------------------------------------------\n");
for (psl = pslList; psl != NULL; psl = psl->next)
{
printf("<A HREF=\"%s?position=%s:%d-%d&db=%s&ss=%s+%s&%s%s\">",
browserUrl, psl->tName, psl->tStart + 1, psl->tEnd, database,
pslName, faName, uiState, unhideTrack);
printf("browser</A> ");
printf("<A HREF=\"%s?o=%d&g=htcUserAli&i=%s+%s+%s&c=%s&l=%d&r=%d&db=%s&%s\">",
hgcUrl, psl->tStart, pslName, cgiEncode(faName), psl->qName, psl->tName,
psl->tStart, psl->tEnd, database, uiState);
printf("details</A> ");
printf("%-14s %5d %5d %5d %5d %5.1f%% %4s %2s %9d %9d %6d\n",
psl->qName, pslScore(psl), psl->qStart+1, psl->qEnd, psl->qSize,
100.0 - pslCalcMilliBad(psl, TRUE) * 0.1,
skipChr(psl->tName), psl->strand, psl->tStart+1, psl->tEnd,
psl->tEnd - psl->tStart);
}
printf("</PRE></TT>");
}
pslFreeList(&pslList);
}
void uploadPage()
/* Put up initial upload page. */
{
char *oldFileName = cartUsualString(cart, hggUploadFile "__filename", "");
cartWebStart(cart, database, "Upload Data to Genome Graphs");
hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\" METHOD=\"POST\" ENCTYPE=\"multipart/form-data\">");
cartSaveSession(cart);
hPrintf("name of data set: ");
cartMakeTextVar(cart, hggDataSetName, "", 16);
hPrintf("<BR>");
hPrintf("description: ");
cartMakeTextVar(cart, hggDataSetDescription, "", 64);
hPrintf("<BR>\n");
hPrintf("file format: ");
cgiMakeDropList(hggFormatType, formatNames, ArraySize(formatNames),
cartUsualString(cart, hggFormatType, formatNames[0]));
hPrintf("<BR>\n");
hPrintf(" markers are: ");
cgiMakeDropList(hggMarkerType, markerNames, ArraySize(markerNames),
cartUsualString(cart, hggMarkerType, markerNames[0]));
hPrintf("<BR>\n");
hPrintf(" column labels: ");
cgiMakeDropList(hggColumnLabels, colLabelNames, ArraySize(colLabelNames),
cartUsualString(cart, hggColumnLabels, colLabelNames[0]));
hPrintf("<BR>\n");
hPrintf("display min value: ");
cartMakeTextVar(cart, hggMinVal, "", 5);
hPrintf(" max value: ");
cartMakeTextVar(cart, hggMaxVal, "", 5);
hPrintf("<BR>\n");
hPrintf("label values: ");
cartMakeTextVar(cart, hggLabelVals, "", 32);
hPrintf("<BR>\n");
hPrintf("draw connecting lines between markers separated by up to ");
cartMakeIntVar(cart, hggMaxGapToFill, 25000000, 8);
hPrintf(" bases.<BR>");
hPrintf("<BR>\n");
hPrintf("file name: <INPUT TYPE=FILE NAME=\"%s\" VALUE=\"%s\">", hggUploadFile,
oldFileName);
hPrintf("<BR>\n");
hPrintf(" or<BR>\n");
hPrintf("Paste URLs or data:<br>");
cgiMakeTextArea(hggUploadUrl, "", 7, 73);
hPrintf("<BR>\n");
hPrintf("<BR>\n");
cgiMakeButton(hggSubmitUpload, "submit");
hPrintf("</FORM>\n");
hPrintf("<i>Note: If you are uploading more than one data set please give them ");
hPrintf("different names. Only the most recent data set of a given name is ");
hPrintf("kept. Otherwise data sets will be kept for at least 48 hours from ");
hPrintf("last use. After that time you may have to upload them again.</i>");
/* Put up section that describes file formats. */
webNewSection("Upload file formats");
hPrintf("%s",
"<P>The upload file is a table in some format. In all formats there is "
"a single line for each marker. "
"Each line starts with information on the marker, and ends with "
"the numerical values associated with that marker. The exact format "
"of the line depends on what is selected from the markers drop "
"down menu. If this is <i>chromosome base</i> then the line will "
"contain the tab or space-separated fields: chromosome, position, "
"and value(s). The first base in a chromosome is considered position 0. "
"An example <i>chromosome base</i> type line is:<PRE><TT>\n"
"chrX 100000 1.23\n"
"</TT></PRE>The lines for other marker types contain two fields: "
"marker and value(s). For dbSNP rsID's an example is:<PRE><TT>\n"
"rs10218492 0.384\n"
"</TT></PRE>"
"</P><P>"
"The file can contain multiple value fields. In this case a "
"separate graph will be available for each value column in the input "
"table. It's a "
"good idea to set the display min/max values above if you want the "
"graphs to share the same scale."
"</P>"
);
webNewSection("Using the upload page");
hPrintf(
"To upload a file in any of the supported formats, "
"locate the file on your computer using the controls next to <B>file name</B>, "
"or supply a <B>URL</B> to the data, "
"and then submit. The other controls on this form are optional, though "
"filling them out will sometimes enhance the display. In general "
"the controls that default to <i>best guess</i> can be left alone, "
"since the guess is almost always correct. The controls for display min and "
"max values and connecting lines can be set later via the configuration "
"page as well. Here is a description of each control."
"<UL>"
"<LI><B>name of data set:</B> Displayed in graph drop-down in Genome Graphs "
" and as trackname in Genome Browser. Only the first 16 characters are "
" visible in some contexts. For data sets with multiple graphs, this is the "
" first part of the name, shared with all members of the data set.</LI>"
"<LI><B>description:</B> A short sentence describing the data set. Displayed in "
"the Genome Graphs and Genome Browser configuration pages, and as the center "
"label in the Genome Browser.</LI>"
"<LI><B>file format:</B> Controls whether the upload file is a tab-separated, "
" comma-separated, or space separated table.</LI>"
"<LI><B>markers are:</B> Describes how to map the data to chromosomes. The choices "
" are either the first column of the file is an ID of some sort, or the first column "
" is a chromosome and the next a base. The IDs can be SNP rs numbers, STS marker names "
" or ID's from any of the supported genotyping platforms.</LI>"
"<LI><B>column labels:</B> Controls whether the first row of the upload file is "
" interpreted as labels rather than data. If the first row contains text in the "
" numerical fields, or if the mapping fields are empty, it is interpreted by "
" \"best guess\" as labels. This is generally correct, but you can override this "
" interpretation by explicitly setting the control. </LI>"
"<LI><B>display min value/max value:</B> Set the range of the data set that will "
" be plotted. If left blank, the range will be taken from the min/max values in the "
" data set itself. For all data sets to share the same scale usually you'll need "
" to set this.</LI>"
"<LI><B>label values:</B> A comma-separated list of numbers for the vertical axis. "
" If left blank the axis will be labeled at the 1/3 and 2/3 point. </LI>"
"<LI><B>draw connecting lines:</B> Lines connecting data points separated by "
" no more than this number of bases are drawn. </LI>"
"<LI><B>file name, or Paste URLs or data:</B> Specify the uploaded data --"
" enter either a file on your local computer; or a URL at which the data file can be"
" found; or simply paste-in the data. If entries are made in both fields, the file name will take"
" precedence. </LI>");
cartWebEnd();
}
void doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
/* struct liftOverChain *chainList = NULL, *chain; */
char *userData;
/* char *dataFile; */
char *dataFormat;
char *organism;
char *db;
float minBlocks, minMatch;
boolean multiple, fudgeThick;
int minSizeQ, minSizeT;
boolean refreshOnly = FALSE;
/* char *err = NULL; */
struct liftOverChain *chainList = NULL, *choice;
cart = theCart;
if (cgiOptionalString(HGLFT_ERRORHELP_VAR))
{
puts("<PRE>");
puts(liftOverErrHelp());
//system("/usr/bin/cal");
puts("</PRE>");
return;
}
/* Get data to convert - from userData variable, or if
* that is empty from a file. */
if (cartOptionalString(cart, "SubmitFile"))
userData = cartOptionalString(cart, HGLFT_DATAFILE_VAR);
else
userData = cartOptionalString(cart, HGLFT_USERDATA_VAR);
dataFormat = cartCgiUsualString(cart, HGLFT_DATAFORMAT_VAR, DEFAULT_FORMAT);
cartWebStart(cart, NULL, "Lift Genome Annotations");
getDbAndGenome(cart, &db, &organism, oldVars);
chainList = liftOverChainListFiltered();
choice = defaultChoices(chainList, db);
if (choice == NULL)
errAbort("Sorry, no conversions available from this assembly\n");
minSizeQ = cartCgiUsualInt(cart, HGLFT_MINSIZEQ, choice->minSizeQ);
minSizeT = cartCgiUsualInt(cart, HGLFT_MINSIZET, choice->minSizeT);
minBlocks = cartCgiUsualDouble(cart, HGLFT_MINBLOCKS, choice->minBlocks);
minMatch = cartCgiUsualDouble(cart, HGLFT_MINMATCH, choice->minMatch);
fudgeThick = cartCgiUsualBoolean(cart, HGLFT_FUDGETHICK, (choice->fudgeThick[0]=='Y') ? TRUE : FALSE);
multiple = cartCgiUsualBoolean(cart, HGLFT_MULTIPLE, (choice->multiple[0]=='Y') ? TRUE : FALSE);
refreshOnly = cartCgiUsualInt(cart, HGLFT_REFRESHONLY_VAR, 0);
webMain(choice, dataFormat, multiple);
liftOverChainFreeList(&chainList);
if (!refreshOnly && userData != NULL && userData[0] != '\0')
{
struct hash *chainHash = newHash(0);
char *chainFile;
struct tempName oldTn, mappedTn, unmappedTn;
FILE *old, *mapped, *unmapped;
char *line;
int lineSize;
char *fromDb, *toDb;
int ct = 0, errCt = 0;
/* read in user data and save to file */
makeTempName(&oldTn, HGLFT, ".user");
old = mustOpen(oldTn.forCgi, "w");
fputs(userData, old);
fputs("\n", old); /* in case user doesn't end last line */
carefulClose(&old);
chmod(oldTn.forCgi, 0666);
/* setup output files -- one for converted lines, the other
* for lines that could not be mapped */
makeTempName(&mappedTn, HGLFT, ".bed");
makeTempName(&unmappedTn, HGLFT, ".err");
mapped = mustOpen(mappedTn.forCgi, "w");
chmod(mappedTn.forCgi, 0666);
unmapped = mustOpen(unmappedTn.forCgi, "w");
chmod(unmappedTn.forCgi, 0666);
fromDb = cgiString(HGLFT_FROMDB_VAR);
toDb = cgiString(HGLFT_TODB_VAR);
chainFile = liftOverChainFile(fromDb, toDb);
if (chainFile == NULL)
errAbort("ERROR: Can't convert from %s to %s: no chain file loaded",
fromDb, toDb);
readLiftOverMap(chainFile, chainHash);
if (sameString(dataFormat, WIGGLE_FORMAT))
/* TODO: implement Wiggle */
{}
else if (sameString(dataFormat, POSITION_FORMAT))
{
/* minSizeT here and in liftOverChain.c/h has been renamed minChainT in liftOver.c */
/* ignore multiple, it must be false when position is used */
ct = liftOverPositions(oldTn.forCgi, chainHash,
minMatch, minBlocks, 0, minSizeQ,
minSizeT, 0,
fudgeThick, mapped, unmapped, FALSE, NULL, &errCt);
}
else if (sameString(dataFormat, BED_FORMAT))
{
/* minSizeT here and in liftOverChain.c/h has been renamed minChainT in liftOver.c */
ct = liftOverBed(oldTn.forCgi, chainHash,
minMatch, minBlocks, 0, minSizeQ,
minSizeT, 0,
fudgeThick, mapped, unmapped, multiple, NULL, &errCt);
}
else
/* programming error */
errAbort("ERROR: Unsupported data format: %s\n", dataFormat);
webNewSection("Results");
if (ct)
{
/* some records succesfully converted */
cgiParagraph("");
printf("Successfully converted %d record", ct);
printf("%s: ", ct > 1 ? "s" : "");
printf("<A HREF=%s TARGET=_blank>View Conversions</A>\n", mappedTn.forCgi);
}
if (errCt)
{
/* some records not converted */
cgiParagraph("");
printf("Conversion failed on %d record", errCt);
printf("%s. ", errCt > 1 ? "s" : "");
printf("<A HREF=%s TARGET=_blank>Display failure file</A> \n",
unmappedTn.forCgi);
printf("<A HREF=\"../cgi-bin/hgLiftOver?%s=1\" TARGET=_blank>Explain failure messages</A>\n", HGLFT_ERRORHELP_VAR);
puts("<P>Failed input regions:\n");
struct lineFile *errFile = lineFileOpen(unmappedTn.forCgi, TRUE);
puts("<BLOCKQUOTE><PRE>\n");
while (lineFileNext(errFile, &line, &lineSize))
puts(line);
lineFileClose(&errFile);
puts("</PRE></BLOCKQUOTE>\n");
}
if (sameString(dataFormat, POSITION_FORMAT) && multiple)
{
puts("<BLOCKQUOTE><PRE>\n");
puts("Note: multiple checkbox ignored since it is not supported for position format.");
puts("</PRE></BLOCKQUOTE>\n");
}
carefulClose(&unmapped);
}
webDataFormats();
webDownloads();
cartWebEnd();
}
void doMiddle(struct cart *theCart)
/* Set up pretty web display. */
{
struct sqlConnection *conn, *conn2;
struct sqlConnection *connCentral = hConnectCentral();
char query[256], query2[256];
struct sqlResult *sr, *sr2;
char **row, **row2;
char buf[128];
char *answer;
char *database;
char *genome, *genomeDesc;
char *kgID, *chrom, *txStart, *txEnd;
int iCnt = 1;
cart = theCart;
cartWebStart(theCart, database, "UCSC Known Genes List \n");
getDbAndGenome(cart, &database, &genome, oldVars);
if (!hTableExistsDb(database, "knownGene"))
{
printf("<br>Database %s currently does not have UCSC Known Genes.", database);
cartWebEnd();
return;
}
sprintf(query, "select description from dbDb where name = '%s'", database);
genomeDesc = strdup(sqlQuickQuery(connCentral, query, buf, sizeof(buf)));
hDisconnectCentral(&connCentral);
printf("<H2>%s Genome (%s Assembly)</H2>\n", genome, genomeDesc);
conn = hAllocConn(database);
conn2= hAllocConn(database);
sprintf(query2,"select kgID from %s.kgXref order by geneSymbol;",
database);
/* use the following for quck testing */
/*sprintf(query2,"select kgID, geneSymbol, description, spID, refseq from %s.kgXref order by geneSymbol limit 10;", database);
*/
sr2 = sqlMustGetResult(conn2, query2);
row2 = sqlNextRow(sr2);
while (row2 != NULL)
{
kgID = row2[0];
sprintf(query,"select chrom, txSTart, txEnd from %s.knownGene where name='%s'", database, kgID);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
chrom = row[0];
txStart = row[1];
txEnd = row[2];
printf("<A href=\"/cgi-bin/hgGene?db=%s&hgg_gene=%s",
database, kgID);
printf("&hgg_chrom=%s&hgg_start=%s&hgg_end=%s\">", chrom, txStart, txEnd);
printf("%d</A><BR>\n", iCnt);
iCnt++;
if ((iCnt % 1000) == 0) fflush(stdout);
sqlFreeResult(&sr);
row2 = sqlNextRow(sr2);
}
sqlFreeResult(&sr2);
cartWebEnd();
}
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();
}
void doStandard(struct cart *theCart)
{
cart = theCart;
cartWebStart(cart, database, "ENCODE DCC Submissions");
struct sqlConnection *conn = sqlConnect(database);
struct docIdSub *docIdSub;
char query[10 * 1024];
struct sqlResult *sr;
char **row;
struct tempName tn;
trashDirFile(&tn, "docId", "meta", ".txt");
char *tempFile = tn.forCgi;
//printf("tempFile is %s\n<BR>", tempFile);
// <Data type> <Cell Type> <Key Metadata> <View>
printf("<table border=1><tr>");
printf("<th>dataType</th>");
printf("<th>cell type</th>");
printf("<th>metadata</th>");
printf("<th>view</th>");
printf("<th>fileType</th>");
printf("<th>file</th>");
printf("<th>lab</th>");
printf("<th>assembly</th>");
printf("<th>subId</th>");
printf("<th>val-report</th>");
printf("</tr>\n");
safef(query, sizeof query, "select * from %s", docIdTable);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
docIdSub = docIdSubLoad(row);
verbose(2, "ix %d\n", docIdSub->ix);
verbose(2, "submitDate %s\n", docIdSub->submitDate);
verbose(2, "md5sum %s\n", docIdSub->md5sum);
verbose(2, "valReport %s\n", docIdSub->valReport);
verbose(2, "metaData %s\n", docIdSub->metaData);
verbose(2, "submitPath %s\n", docIdSub->submitPath);
verbose(2, "submitter %s\n", docIdSub->submitter);
cgiDecode(docIdSub->metaData, docIdSub->metaData, strlen(docIdSub->metaData));
//printf("tempFile %s\n", tempFile);
FILE *f = mustOpen(tempFile, "w");
fwrite(docIdSub->metaData, strlen(docIdSub->metaData), 1, f);
fclose(f);
boolean validated;
struct mdbObj *mdbObj = mdbObjsLoadFromFormattedFile(tempFile, &validated);
unlink(tempFile);
// <Data type> <Cell Type> <Key Metadata> <View>
char *docIdType = mdbObjFindValue(mdbObj, "type");
char *docIdComposite = mdbObjFindValue(mdbObj, "composite");
char buffer[10 * 1024];
safef(buffer, sizeof buffer, "%d", docIdSub->ix);
if (sameString(database, "encpipeline_beta"))
docIdDir = docIdDirBeta;
printf("<tr>");
printf("<td>%s</td> ", mdbObjFindValue(mdbObj, "dataType"));
printf("<td>%s</td> ", mdbObjFindValue(mdbObj, "cell"));
struct dyString *str = newDyString(100);
addValue(str, mdbObjFindValue(mdbObj, "antibody"));
addValue(str, mdbObjFindValue(mdbObj, "treatment"));
addValue(str, mdbObjFindValue(mdbObj, "rnaExtract"));
addValue(str, mdbObjFindValue(mdbObj, "localization"));
printf("<td>%s<a href=docIdView?docId=%s&db=%s&meta=\"\"> ...</a></td>", str->string,buffer, database);
freeDyString(&str);
printf("<td>%s</td> ", mdbObjFindValue(mdbObj, "view"));
printf("<td>%s</td> ", mdbObjFindValue(mdbObj, "type"));
printf("<td><a href=%s> %s</a></td>",
docIdGetPath(buffer, docIdDir, docIdType, NULL) ,
docIdDecorate(docIdComposite,docIdSub->ix));
char *lab = mdbObjFindValue(mdbObj, "lab");
char *subId = mdbObjFindValue(mdbObj, "subId");
printf("<td><a href=docIdView?docId=%s&db=%s&lab=\"%s\"> %s</a></td>",buffer, database, subId, lab);
printf("<td>%s</td> ", mdbObjFindValue(mdbObj, "assembly"));
printf("<td>%s</td> ", subId);
printf("<td><a href=docIdView?docId=%s&db=%s&report=\"\"> report</a></td>", buffer, database);
printf("</tr>\n");
}
printf("</table>");
sqlFreeResult(&sr);
sqlDisconnect(&conn);
cartWebEnd();
}
void configurePage()
/* Put up configuration page. */
{
cartWebStart(cart, database, "Configure Genome Graphs");
hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\" METHOD=GET>\n");
cartSaveSession(cart);
hPrintf("<TABLE>\n");
hPrintf("<TR>\n");
hPrintf("<TD>\n");
hPrintf("image width: ");
cgiMakeIntVar(hggImageWidth, cartUsualInt(cart, hggImageWidth, hgDefaultPixWidth), 4);
hPrintf("</TD>\n");
hPrintf("<TD>\n");
hPrintf("graph height: ");
cgiMakeIntVar(hggGraphHeight, graphHeight(), 3);
hPrintf("</TD>\n");
hPrintf("<TD>\n");
hPrintf(" graphs per line: ");
makeNumMenu(hggGraphsPerLine, minGraphsPerLine, maxGraphsPerLine,
graphsPerLine());
hPrintf("</TD>\n");
hPrintf("<TD>\n");
hPrintf(" lines of graphs: ");
makeNumMenu(hggLinesOfGraphs, minLinesOfGraphs, maxLinesOfGraphs,
linesOfGraphs());
hPrintf("</TD>\n");
hPrintf("</TR>\n");
hPrintf("</TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
hPrintf("chromosome layout: ");
cgiMakeDropList(hggChromLayout, chromLayouts, ArraySize(chromLayouts),
chromLayout());
hPrintf("</TD></TR></TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
hPrintf("numerical labels: ");
cartMakeCheckBox(cart, hggLabels, TRUE);
hPrintf(" <I>Label axis on left for first graph and on right for last graph</I>");
hPrintf("</TD></TR></TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
hPrintf("highlight missing: ");
cartMakeCheckBox(cart, hggYellowMissing, FALSE);
hPrintf(" <I>Highlight background in yellow/gray if there is missing data in first graph</I>");
hPrintf("</TD></TR></TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
hPrintf("region padding: ");
cgiMakeIntVar(hggRegionPad, regionPad(), 6);
hPrintf(" <I>Number of bases to add to either side of regions over threshold</I>");
hPrintf("</TD></TR></TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
cgiMakeButton("submit", "submit");
hPrintf("</TD></TR></TABLE>\n");
hPrintf("</TD>\n");
hPrintf("</FORM>\n");
webNewSection("Configure Graphs");
hPrintf("Click on the hyperlink by the graph name to configure it.");
hTableStart();
hPrintf("<TR><TH>name</TH>");
hPrintf("<TH>description</TH></TR>");
struct slRef *ref;
for (ref = ggList; ref != NULL; ref = ref->next)
{
struct genoGraph *gg = ref->val;
/* Only show custom graphs, stand-alone DB graphs, and composite */
/* graphs. Don't show subGraphs part of a composite. */
if (gg->isSubGraph == FALSE)
{
char *tmp = cgiEncode(gg->name);
hPrintf("<TR><TD><A HREF=\"../cgi-bin/hgGenome?%s&%s=on&g=%s\">",
cartSidUrlString(cart), hggConfigureOne, tmp);
freeMem(tmp);
hPrintf("%s</A></TD>", gg->shortLabel);
hPrintf("<TD>%s</TD></TR>\n", gg->longLabel);
}
}
hTableEnd();
cartWebEnd();
}
