static void doBigSelectPage(char *db, char *table)
/* Put up big field selection page. Assumes html page open already*/
{
struct joiner *joiner = allJoiner;
struct dbTable *dtList, *dt;
char dbTableBuf[256];
cartSetString(cart, hgtaFieldSelectTable, getDbTable(db, table));
if (strchr(table, '.'))
htmlOpen("Select Fields from %s", table);
else
htmlOpen("Select Fields from %s.%s", db, table);
hPrintf("<FORM NAME=\"mainForm\" ACTION=\"%s\" METHOD=%s>\n", cgiScriptName(),
cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
cgiMakeHiddenVar(hgtaDatabase, db);
cgiMakeHiddenVar(hgtaTable, table);
dbOverrideFromTable(dbTableBuf, &db, &table);
showTableFields(db, table, TRUE);
dtList = extraTableList(selFieldLinkedTablePrefix());
showLinkedFields(dtList);
dt = dbTableNew(db, table);
slAddHead(&dtList, dt);
showLinkedTables(joiner, dtList, selFieldLinkedTablePrefix(),
hgtaDoSelectFieldsMore, "allow selection from checked tables");
/* clean up. */
hPrintf("</FORM>");
cgiDown(0.9);
htmlClose();
joinerFree(&joiner);
}
static void doBigFilterPage(struct sqlConnection *conn, char *db, char *table)
/* Put up filter page on given db.table. */
{
struct joiner *joiner = allJoiner;
struct dbTable *dtList, *dt;
char dbTableBuf[256];
if (strchr(table, '.'))
htmlOpen("Filter on Fields from %s", table);
else
htmlOpen("Filter on Fields from %s.%s", db, table);
jsIncludeFile("jquery.js", NULL);
jsIncludeFile("utils.js", NULL);
commonCssStyles();
hPrintf("<FORM ACTION=\"%s\" METHOD=%s>\n", cgiScriptName(),
cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
cgiMakeHiddenVar(hgtaDatabase, db);
cgiMakeHiddenVar(hgtaTable, table);
dbOverrideFromTable(dbTableBuf, &db, &table);
filterControlsForTable(db, table);
dtList = extraTableList(filterLinkedTablePrefix);
showLinkedFilters(dtList);
dt = dbTableNew(db, table);
slAddHead(&dtList, dt);
showLinkedTables(joiner, dtList, filterLinkedTablePrefix,
hgtaDoFilterMore, "allow filtering using fields in checked tables");
hPrintf("</FORM>\n");
cgiDown(0.9);
htmlClose();
}
void getBackgroundStatus(char *url)
/* fetch status as the latest complete html block available */
{
char *html = NULL;
if (fileSize(url)==0)
{
htmlOpen("Background Status");
errAbort("No output found. Expecting output in [%s].", url);
htmlClose();
return;
}
readInGulp(url, &html, NULL);
int numLines = chopString(html, "\n", NULL, 1000000);
char **lines = NULL;
AllocArray(lines, numLines);
chopString(html, "\n", lines, numLines);
int end;
for (end=numLines-1; end >= 0 && ! (endsWith(lines[end], "</html>") || endsWith(lines[end], "</HTML>")) ; --end)
/* do nothing */ ;
if (end < 0)
{
htmlOpen("Background Status");
errAbort("No complete html found");
htmlClose();
return;
}
int start;
for (start=end; start >= 0 && ! (startsWith("<html>", lines[start]) || startsWith("<HTML>", lines[start])) ; --start)
/* do nothing */ ;
if (start < 0)
{
htmlOpen("Background Status");
errAbort("No html start tag found");
htmlClose();
return;
}
puts("Content-Type: text/html\n");
int line;
boolean autoRefreshFound = FALSE;
boolean successfullyUploaded = FALSE;
for (line=start; line <= end; line++)
{
puts(lines[line]);
if (startsWith("setTimeout(\"location = location;", lines[line]))
autoRefreshFound = TRUE;
if (startsWith("Output has been successfully uploaded", lines[line]))
successfullyUploaded = TRUE;
}
// if it looks like the background is no longer running,
// include the .err stdout output for more informative problem message
char urlErr[512];
char *textErr = NULL;
safef(urlErr, sizeof urlErr, "%s.err", url);
if (!autoRefreshFound && !successfullyUploaded && (fileSize(urlErr) > 0))
{
readInGulp(urlErr, &textErr, NULL);
printf("%s", textErr);
}
}
void doSetUserRegions(struct sqlConnection *conn)
/* Respond to set regions button. */
{
char *oldPasted = cartUsualString(cart, hgtaEnteredUserRegions, "");
char *db = cartOptionalString(cart, hgtaUserRegionsDb);
if (db && !sameString(db, database))
oldPasted = "";
htmlOpen("Enter region definition\n");
hPrintf("<FORM ACTION=\"%s\" METHOD=POST "
" ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n", getScriptName());
cartSaveSession(cart);
hPrintf("<TABLE><TR><TD ALIGN=LEFT>\n");
hPrintf("Paste regions:");
hPrintf("</TD><TD ALIGN=RIGHT>");
hPrintf("Or upload file: <INPUT TYPE=FILE NAME=\"%s\"> <BR>\n",
hgtaEnteredUserRegionFile);
hPrintf("</TD></TR><TR><TD COLSPAN=2 ALIGN=LEFT>\n");
cgiMakeTextArea(hgtaEnteredUserRegions, oldPasted, 10, 70);
hPrintf("</TD></TR><TR><TD COLSPAN=2 ALIGN=LEFT>\n");
cgiMakeButton(hgtaDoSubmitUserRegions, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearSetUserRegionsText, "clear");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</TD></TR></TABLE>");
hPrintf("</FORM><BR>\n");
webIncludeHelpFile("hgTbUserRegionsHelp", FALSE);
htmlClose();
}
void genomicFormatPage(struct sqlConnection *conn)
/* Put up page asking for what sort of genomic sequence. */
{
struct hTableInfo *hti = getHti(database, curTable, conn);
htmlOpen("%s Genomic Sequence", curTableLabel());
if (doGalaxy())
startGalaxyForm();
else
hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
hgSeqOptionsHtiCart(hti, cart);
hPrintf("<BR>\n");
if (doGalaxy())
{
/* pass parameter to get sequence to Galaxy */
cgiMakeHiddenVar(hgtaDoGenomicDna, "get sequence");
printGalaxySubmitButtons();
}
else
{
cgiMakeButton(hgtaDoGenomicDna, "get sequence");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>");
}
cgiDown(0.9);
htmlClose();
}
void doOutPalOptions(struct sqlConnection *conn)
/* Output pal page. */
{
htmlOpen("Select multiple alignment and options for %s", curTrack->shortLabel);
palOptions(cart, conn, addOurButtons, hgtaDoPal);
htmlClose();
}
void doGetGreatOutput(void (*dispatch)())
{
struct tempName tn;
int saveStdout;
FILE *f;
trashDirFile(&tn, "great", cartSessionId(cart), ".bed");
f = fopen(tn.forCgi, "w");
/* We want to capture hgTables stdout output to a trash file
* which will later be fetched by Great via URL. */
/* Workaround because stdout stream is not assignable on some operating systems */
fflush(stdout);
saveStdout = dup(STDOUT_FILENO);
dup2(fileno(f),STDOUT_FILENO); /* closes STDOUT before setting it again */
fclose(f);
dispatch(); /* this writes to stdout */
/* restore stdout */
fflush(stdout);
dup2(saveStdout ,STDOUT_FILENO); /* closes STDOUT before setting it back to saved descriptor */
close(saveStdout);
cartRemove(cart, hgtaDoGreatOutput);
htmlOpen("Table Browser integration with GREAT");
doSubmitToGreat(tn.forCgi);
htmlClose();
}
void doUploadIdentifiers(struct sqlConnection *conn)
/* Respond to upload identifiers button. */
{
struct hTableInfo *hti = maybeGetHti(database, curTable, conn);
char *idField = getIdField(database, curTrack, curTable, hti);
htmlOpen("Upload Identifiers for %s", curTableLabel());
if (idField == NULL)
errAbort("Sorry, I can't tell which field of table %s to treat as the "
"identifier field.", curTable);
hPrintf("<FORM ACTION=\"%s\" METHOD=POST ENCTYPE=\"multipart/form-data\">\n",
getScriptName());
cartSaveSession(cart);
hPrintf("Please enter the name of a file from your computer that contains a ");
hPrintf("space, tab, or ");
hPrintf("line separated list of the items you want to include.\n");
explainIdentifiers(database, conn, idField);
hPrintf("<BR>\n");
hPrintf("<INPUT TYPE=FILE NAME=\"%s\"> ", hgtaPastedIdentifiers);
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoPastedIdentifiers, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>");
cgiDown(0.9);
htmlClose();
}
void doMainPage(struct sqlConnection *conn)
/* Put up the first page user sees. */
{
htmlOpen("Table Browser");
mainPageAfterOpen(conn);
htmlClose();
}
void doValueRange(char *field)
/* Put up value histogram. */
{
char *db = cartString(cart, hgtaDatabase);
char *table = cartString(cart, hgtaHistoTable);
boolean showItemRgb = FALSE;
showItemRgb=bedItemRgb(findTdbForTable(db, curTrack, table, ctLookupName));
// should we expect itemRgb instead of "reserved"
if (showItemRgb && sameWord(field, "reserved"))
htmlOpen("Value range for %s.%s.itemRgb", db, table);
else
htmlOpen("Value range for %s.%s.%s", db, table, field);
printValueRange(db, table, field);
htmlClose();
}
void doMainPage(struct sqlConnection *conn, boolean webStarted)
/* Put up the first page user sees. */
{
if (!webStarted)
htmlOpen("Table Browser");
mainPageAfterOpen(conn);
htmlClose();
}
void doValueHistogram(char *field)
/* Put up value histogram. */
{
char *db = cartString(cart, hgtaDatabase);
char *table = cartString(cart, hgtaHistoTable);
htmlOpen("Value histogram for %s.%s.%s", db, table, field);
printValueHistogram(db, table, field);
htmlClose();
}
void verifyGreatFormat(const char *output)
{
if (!sameString(output, outBed) && !sameString(output, outWigBed))
{
htmlOpen("Sorry!");
errAbort("GREAT requires that the output format be BED format.\n"
"Some tracks are not available in BED format and thus cannot be passed to GREAT.\n"
"Please go back and ensure that BED format is chosen.");
htmlClose();
}
}
static void genePredOptions(struct trackDb *track, char *type,
struct sqlConnection *conn)
/* Put up sequence type options for gene prediction tracks. */
{
char *predType = cartUsualString(cart, hgtaGeneSeqType, genePredMenu[0]);
char *dupType = cloneString(type);
char *typeWords[3];
int typeWordCount, typeIx;
/* Type field has 1-3 words which are in order:
* genePred pepTable mrnaTable */
typeWordCount = chopLine(dupType, typeWords);
/* TypeIx will be 0 (genomic) 1 (protein) 2(mrna). */
typeIx = stringArrayIx(predType, genePredMenu, typeWordCount);
if (typeIx < 0)
predType = genePredMenu[0];
htmlOpen("Select sequence type for %s", track->shortLabel);
hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
if (isRefGeneTrack(track->table))
{
/* RefGene covers all 3 types, but in it's own way. */
for (typeIx = 0; typeIx < 3; ++typeIx)
{
genePredTypeButton(genePredMenu[typeIx], predType);
hPrintf(" %s<BR>\n", genePredMenu[typeIx]);
}
}
else
{
/* Otherwise we always have genomic, and we have
* peptide/mrna only if there are corresponding table
* in the type field. */
for (typeIx = 0; typeIx < typeWordCount; ++typeIx)
{
if (typeIx == 0 || sqlTableExists(conn, typeWords[typeIx]))
{
genePredTypeButton(genePredMenu[typeIx], predType);
hPrintf(" %s<BR>\n", genePredMenu[typeIx]);
}
}
}
cgiMakeButton(hgtaDoGenePredSequence, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>\n");
cgiDown(0.9);
htmlClose();
freez(&dupType);
}
void doClearIdentifiers(struct sqlConnection *conn)
/* Respond to clear identifiers button. */
{
char *fileName;
htmlOpen("Table Browser (Cleared Identifiers)");
fileName = identifierFileName();
if (fileName != NULL)
remove(fileName);
cartRemove(cart, hgtaIdentifierFile);
cartRemove(cart, hgtaPastedIdentifiers);
mainPageAfterOpen(conn);
htmlClose();
}
void doGreatTopLevel()
/* intermediate page for formats printed directly from top form */
{
struct dyString *name = getRequestName();
htmlOpen("Send BED data to GREAT as %s", dyStringContents(name));
freeDyString(&name);
verifyGreatAssemblies();
startGreatForm();
cgiMakeHiddenVar(hgtaDoTopSubmit, "get output");
printGreatSubmitButtons();
hPrintf("<div style='height:.9em;'></div>\n");
htmlClose();
}
void doClearUserRegions(struct sqlConnection *conn)
/* Respond to clear user regions button. */
{
char *fileName = userRegionsFileName();
htmlOpen("Table Browser (Cleared Region List)");
if (fileName != NULL)
remove(fileName);
cartRemove(cart, hgtaEnteredUserRegions);
cartRemove(cart, hgtaEnteredUserRegionFile);
cartRemove(cart, hgtaUserRegionsFile);
cartRemove(cart, hgtaRegionType);
mainPageAfterOpen(conn);
htmlClose();
}
static void showMissingOutputFileForm()
/* User needs to specify the output file */
{
htmlOpen("GenomeSpace");
printf("Please specify the output file field for GenomeSpace Data Manager.");
printf("<br>");
printf("<br>");
// TODO handle filename with a path.
// ACTUALLY, this probably just works.
printf("Your output file name may contain a path.");
printf("<br>");
printf("<br>");
printf("<FORM ACTION=\"/cgi-bin/hgTables\" METHOD=GET>"
"<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"Back\" ></FORM>", hgtaDoMainPage);
htmlClose();
}
void doPasteIdentifiers(struct sqlConnection *conn)
/* Respond to paste identifiers button. */
{
struct sqlConnection *alternateConn = conn;
char *actualDb = database;
if (sameWord(curTable, WIKI_TRACK_TABLE))
{
alternateConn = wikiConnect();
actualDb = wikiDbName();
}
char *oldPasted = forCurTable() ?
cartUsualString(cart, hgtaPastedIdentifiers, "") : "";
struct hTableInfo *hti = maybeGetHti(actualDb, curTable, conn);
char *idField = getIdField(actualDb, curTrack, curTable, hti);
htmlOpen("Paste In Identifiers for %s", curTableLabel());
if (idField == NULL)
errAbort("Sorry, I can't tell which field of table %s to treat as the "
"identifier field.", curTable);
hPrintf("<FORM ACTION=\"%s\" METHOD=%s>\n", getScriptName(),
cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
hPrintf("Please paste in the identifiers you want to include.\n");
if (sqlDatabaseExists("hgTemp"))
explainIdentifiers(actualDb, alternateConn, idField);
else
warn("No hgTemp database found for temporary tables.<br>Please src/product/README.mysql.setup for more information.");
hPrintf("<BR>\n");
cgiMakeTextArea(hgtaPastedIdentifiers, oldPasted, 10, 70);
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoPastedIdentifiers, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearPasteIdentifierText, "clear");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>");
cgiDown(0.9);
htmlClose();
if (sameWord(curTable, WIKI_TRACK_TABLE))
wikiDisconnect(&alternateConn);
}
static void showGsLoginForm()
/* User needs to login to GS */
{
// TODO should this be a redirect?
// TODO should it require https? - note our apache virtual hosts are not set up to work with it yet?
// GS Login Page
htmlOpen("GenomeSpace");
printf("Please login to GenomeSpace.");
printf("<br>");
printf("<br>");
printf("<FORM ACTION=\"/cgi-bin/hgTables\" METHOD=POST>");
printf("<table>");
printf("<tr><td align=right><B>User:</B></td><td><INPUT TYPE=TEXT NAME=\"%s\" SIZE=20 VALUE=\"\"></td></tr>", hgtaGsUser);
printf("<tr><td><B>Password:</B></td><td><INPUT TYPE=PASSWORD NAME=\"%s\" SIZE=20 VALUE=\"\"></td></tr>", hgtaGsPassword);
printf("<tr><td> </td><td><INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"Login to GenomeSpace\"></td></tr>", hgtaDoGsLogin);
printf("</form>");
printf("<tr><td> </td><td><FORM ACTION=\"/cgi-bin/hgTables\" METHOD=GET>"
"<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"Cancel\" ></FORM></td></tr>", hgtaDoMainPage);
printf("</table>");
htmlClose();
}
void doSubtrackMergeMore(struct sqlConnection *conn)
/* Respond to subtrack merge create/edit button */
{
char *dbTable = getDbTable(database, curTable);
htmlOpen("Merge subtracks of %s (%s)",
curTrack->table, curTrack->longLabel);
hPrintf("<FORM ACTION=\"../cgi-bin/hgTables\" NAME=\"mainForm\" METHOD=%s>\n",
cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
/* Currently selected subtrack table will be the primary subtrack in the
* merge. */
cgiMakeHiddenVar(hgtaNextSubtrackMergePrimary, dbTable);
hPrintf("<H3>Select a subset of subtracks to merge:</H3>\n");
hCompositeUi(database, cart, curTrack, curTable, hgtaDoSubtrackMergePage, "mainForm",
fullTrackHash);
hPrintf("<H3>Select a merge operation:</H3>\n");
struct trackDb *primary = subTdbFind(curTrack,curTable);
if (isWiggle(database, curTable) || isBedGraph(curTable) || isBigWigTable(curTable))
showWiggleMergeOptions(primary->longLabel);
else
showBedMergeOptions();
hPrintf("If a filter is specified on the main Table Browser page, it will "
"be applied only to %s, not to any other selected subtrack. ",
primary->longLabel);
hPrintf("If an intersection is specified on the main page, it will be applied "
"to the result of this merge.<P>\n");
hPrintf("<P>\n");
cgiMakeButton(hgtaDoSubtrackMergeSubmit, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>\n");
htmlClose();
}
void doSummaryStatsBed(struct sqlConnection *conn)
/* Put up page showing summary stats for track that is in database
* or that is bed-format custom. */
{
struct bed *bedList = NULL;
struct region *regionList = getRegions(), *region;
char *regionName = getRegionName();
long long regionSize = 0, gapTotal = 0, realSize = 0;
long startTime, midTime, endTime;
long loadTime = 0, calcTime = 0, freeTime = 0;
struct covStats *itemCovList = NULL, *blockCovList = NULL, *cov;
int itemCount = 0;
struct hTableInfo *hti = getHti(database, curTable, conn);
int minScore = BIGNUM, maxScore = -BIGNUM;
long long sumScores = 0;
boolean hasBlocks = hti->hasBlocks;
boolean hasScore = (hti->scoreField[0] != 0);
int fieldCount;
htmlOpen("%s (%s) Summary Statistics", curTableLabel(), curTable);
for (region = regionList; region != NULL; region = region->next)
{
struct lm *lm = lmInit(64*1024);
startTime = clock1000();
bedList = cookedBedList(conn, curTable, region, lm, &fieldCount);
if (fieldCount < 12)
hasBlocks = FALSE;
if (fieldCount < 5)
hasScore = FALSE;
midTime = clock1000();
loadTime += midTime - startTime;
if (bedList != NULL)
{
itemCount += slCount(bedList);
regionSize += region->end - region->start;
cov = calcSpanOverRegion(region, bedList);
slAddHead(&itemCovList, cov);
if (hasBlocks)
{
cov = calcBlocksOverRegion(region, bedList);
slAddHead(&blockCovList, cov);
}
if (hti->scoreField[0] != 0)
{
struct bed *bed;
for (bed = bedList; bed != NULL; bed = bed->next)
{
int score = bed->score;
if (score < minScore) minScore = score;
if (score > maxScore) maxScore = score;
sumScores += score;
}
}
}
endTime = clock1000();
calcTime += endTime - midTime;
lmCleanup(&lm);
bedList = NULL;
freeTime += clock1000() - endTime;
}
regionSize = basesInRegion(regionList, 0);
gapTotal = gapsInRegion(conn, regionList, 0);
realSize = regionSize - gapTotal;
hTableStart();
startTime = clock1000();
numberStatRow("item count", itemCount);
if (itemCount > 0)
{
cov = covStatsSum(itemCovList);
percentStatRow("item bases", cov->basesCovered, realSize);
percentStatRow("item total", cov->sumBases, realSize);
numberStatRow("smallest item", cov->minBases);
numberStatRow("average item", round((double)cov->sumBases/cov->itemCount));
numberStatRow("biggest item", cov->maxBases);
}
if (hasBlocks && itemCount > 0)
{
cov = covStatsSum(blockCovList);
hPrintf("<TR><TD>block count</TD><TD ALIGN=RIGHT>");
printLongWithCommas(stdout, cov->itemCount);
hPrintf("</TD></TR>\n");
percentStatRow("block bases", cov->basesCovered, realSize);
percentStatRow("block total", cov->sumBases, realSize);
numberStatRow("smallest block", cov->minBases);
numberStatRow("average block", round((double)cov->sumBases/cov->itemCount));
numberStatRow("biggest block", cov->maxBases);
}
if (hasScore != 0 && itemCount > 0 && sumScores != 0)
{
numberStatRow("smallest score", minScore);
numberStatRow("average score", round((double)sumScores/itemCount));
numberStatRow("biggest score", maxScore);
}
hTableEnd();
/* Show region and time stats part of stats page. */
webNewSection("Region and Timing Statistics");
hTableStart();
stringStatRow("region", regionName);
numberStatRow("bases in region", regionSize);
numberStatRow("bases in gaps", gapTotal);
floatStatRow("load time", 0.001*loadTime);
floatStatRow("calculation time", 0.001*calcTime);
floatStatRow("free memory time", 0.001*freeTime);
stringStatRow("filter", (anyFilter() ? "on" : "off"));
stringStatRow("intersection", (anyIntersection() ? "on" : "off"));
hTableEnd();
covStatsFreeList(&itemCovList);
covStatsFreeList(&blockCovList);
htmlClose();
}
void doIntersectMore(struct sqlConnection *conn)
/* Continue working in intersect page. */
{
struct trackDb *iTrack;
char *name = curTableLabel();
char *iName, *iTable;
char *onChange = onChangeEither();
char *op, *setting;
boolean wigOptions = (isWiggle(database, curTable) || isBedGraph(curTable));
// Note - bigWig is purposely left out of wigOptions. It supports more intersection options
// than wig does.
struct hTableInfo *hti1 = maybeGetHti(database, curTable, conn), *hti2 = NULL;
htmlOpen("Intersect with %s", name);
hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
hPrintf("<TABLE BORDER=0>\n");
/* Print group and track line. */
hPrintf("Select a group, track and table to intersect with:\n");
iTrack = showGroupTrackRow(hgtaNextIntersectGroup, onChange,
hgtaNextIntersectTrack, onChange, conn);
iName = iTrack->shortLabel;
hPrintf("<TR><TD>\n");
iTable = showTableField(iTrack, hgtaNextIntersectTable, FALSE);
hti2 = maybeGetHti(database, iTable, conn);
hPrintf("</TD></TR>\n");
hPrintf("</TABLE>\n");
if (!wigOptions)
{
if (hti1 && hti1->hasBlocks)
hPrintf("<BR>Note: %s has gene/alignment structure. "
"Only the exons/blocks will be considered.\n", name);
if (hti2 && hti2->hasBlocks)
hPrintf("<BR>Note: %s has gene/alignment structure. "
"Only the bases covered by its exons/blocks will be "
"considered.\n", iName);
hPrintf("<H4>Intersect %s items with bases covered by %s:</H4>\n",
name, iName);
hPrintf("These combinations will maintain the names and "
"gene/alignment structure (if any) of %s: <P>\n",
name);
}
else
hPrintf("<P>\n");
op = cartUsualString(cart, hgtaNextIntersectOp, "any");
jsTrackingVar("op", op);
makeOpButton("any", op);
printf("All %s records that have any overlap with %s <BR>\n",
name, iName);
makeOpButton("none", op);
printf("All %s records that have no overlap with %s <BR>\n",
name, iName);
if (!wigOptions)
{
makeOpButton("more", op);
printf("All %s records that have at least ",
name);
setting = cartCgiUsualString(cart, hgtaNextMoreThreshold, "80");
cgiMakeTextVar(hgtaNextMoreThreshold, setting, 3);
printf(" %% overlap with %s <BR>\n", iName);
makeOpButton("less", op);
printf("All %s records that have at most ",
name);
setting = cartCgiUsualString(cart, hgtaNextLessThreshold, "80");
cgiMakeTextVar(hgtaNextLessThreshold, setting, 3);
printf(" %% overlap with %s <P>\n", iName);
}
else
{
/* keep javaScript onClick happy */
hPrintf("<input TYPE=HIDDEN NAME=\"hgta_nextMoreThreshold\" VALUE=80>\n");
hPrintf("<input TYPE=HIDDEN NAME=\"hgta_nextLessThreshold\" VALUE=80>\n");
hPrintf(" <P>\n");
}
if (!wigOptions)
{
boolean bigWig = isBigWigTable(curTable);
hPrintf("<H4>Intersect bases covered by %s and/or %s:</H4>\n",
name, iName);
if (!bigWig)
hPrintf("These combinations will discard the names and "
"gene/alignment structure (if any) of %s and produce a simple "
"list of position ranges.<P>\n",
name);
makeOpButton("and", op);
printf("Base-pair-wise intersection (AND) of %s and %s <BR>\n",
name, iName);
makeOpButton("or", op);
printf("Base-pair-wise union (OR) of %s and %s <P>\n",
name, iName);
hPrintf("Check the following boxes to complement one or both tables. "
"To complement a table means to include a base pair in the "
"intersection/union if it is <I>not</I> included in the table."
"<P>\n");
if (!bigWig)
{
jsMakeTrackingCheckBox(cart, hgtaNextInvertTable, "invertTable", FALSE);
printf("Complement %s before base-pair-wise intersection/union <BR>\n",
name);
}
jsMakeTrackingCheckBox(cart, hgtaNextInvertTable2, "invertTable2", FALSE);
printf("Complement %s before base-pair-wise intersection/union <P>\n",
iName);
}
else
{
/* keep javaScript onClick happy */
jsTrackingVar("op", op);
hPrintf("<SCRIPT>\n");
hPrintf("var invertTable=0;\n");
hPrintf("var invertTable2=0;\n");
hPrintf("</SCRIPT>\n");
hPrintf("(data track %s is not composed of gene records. Specialized intersection operations are not available.)<P>\n", name);
}
cgiMakeButton(hgtaDoIntersectSubmit, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>\n");
/* Hidden form - for benefit of javascript. */
{
static char *saveVars[32];
int varCount = ArraySize(nextVars);
memcpy(saveVars, nextVars, varCount * sizeof(saveVars[0]));
saveVars[varCount] = hgtaDoIntersectMore;
jsCreateHiddenForm(cart, getScriptName(), saveVars, varCount+1);
}
htmlClose();
}
void doSummaryStatsBigWig(struct sqlConnection *conn)
/* Put up page showing summary stats for bigWig track. */
{
struct trackDb *track = curTrack;
char *table = curTable;
char *shortLabel = (track == NULL ? table : track->shortLabel);
char *fileName = bigWigFileName(table, conn);
long startTime = clock1000();
htmlOpen("%s (%s) Big Wig Summary Statistics", shortLabel, table);
if (anySubtrackMerge(database, curTable))
hPrintf("<P><EM><B>Note:</B> subtrack merge is currently ignored on this "
"page (not implemented yet). Statistics shown here are only for "
"the primary table %s (%s).</EM>", shortLabel, table);
struct bbiFile *bwf = bigWigFileOpen(fileName);
struct region *region, *regionList = getRegions();
double sumData = 0, sumSquares = 0, minVal = 0, maxVal = 0;
bits64 validCount = 0;
if (!anyFilter() && !anyIntersection())
{
for (region = regionList; region != NULL; region = region->next)
{
struct bbiSummaryElement sum;
if (bbiSummaryArrayExtended(bwf, region->chrom, region->start, region->end,
bigWigIntervalQuery, 1, &sum))
{
if (validCount == 0)
{
minVal = sum.minVal;
maxVal = sum.maxVal;
}
else
{
if (sum.minVal < minVal)
minVal = sum.minVal;
if (sum.maxVal > maxVal)
maxVal = sum.maxVal;
}
sumData += sum.sumData;
sumSquares += sum.sumSquares;
validCount += sum.validCount;
}
}
}
else
{
double ll, ul;
enum wigCompare cmp;
getWigFilter(database, curTable, &cmp, &ll, &ul);
for (region = regionList; region != NULL; region = region->next)
{
struct lm *lm = lmInit(0);
struct bbiInterval *iv, *ivList;
ivList = intersectedFilteredBbiIntervalsOnRegion(conn, bwf, region, cmp, ll, ul, lm);
for (iv = ivList; iv != NULL; iv = iv->next)
{
double val = iv->val;
double size = iv->end - iv->start;
if (validCount == 0)
minVal = maxVal = val;
else
{
if (val < minVal)
minVal = val;
if (val > maxVal)
maxVal = val;
}
sumData += size*val;
sumSquares += size*val*val;
validCount += size;
}
lmCleanup(&lm);
}
}
hTableStart();
floatStatRow("mean", sumData/validCount);
floatStatRow("min", minVal);
floatStatRow("max", maxVal);
floatStatRow("standard deviation", calcStdFromSums(sumData, sumSquares, validCount));
numberStatRow("bases with data", validCount);
long long regionSize = basesInRegion(regionList,0);
long long gapTotal = gapsInRegion(conn, regionList,0);
numberStatRow("bases with sequence", regionSize - gapTotal);
numberStatRow("bases in region", regionSize);
wigFilterStatRow(conn);
stringStatRow("intersection", cartUsualString(cart, hgtaIntersectTable, "off"));
long wigFetchTime = clock1000() - startTime;
floatStatRow("load and calc time", 0.001*wigFetchTime);
hTableEnd();
bbiFileClose(&bwf);
htmlClose();
}
char *gsS3Upload(char *s3UploadUrl, char *inputFileName, off_t contentLength, char *base64Md5, char *hexMd5, char *contentType, boolean progress, char *fileName)
/* call s3 upload */
{
// S3 UPLOAD to Amazon Storage
struct dyString *reqExtra = newDyString(256);
dyStringPrintf(reqExtra, "Content-Length: %lld\r\n", (long long)contentLength);
dyStringPrintf(reqExtra, "Content-MD5: %s\r\n", base64Md5);
dyStringPrintf(reqExtra, "Content-Type: %s\r\n", contentType);
int sd = netOpenHttpExt(s3UploadUrl, "PUT", reqExtra->string);
if (sd < 0)
errAbort("failed to open socket for [%s]", s3UploadUrl);
unsigned char buffer[S3UPBUFSIZE];
int bufRead = 0;
FILE *f = mustOpen(inputFileName,"rb");
off_t totalUploaded = 0;
int lastPctUploaded = -1;
// upload the file contents
while ((bufRead = fread(&buffer, 1, S3UPBUFSIZE, f)) > 0)
{
int bufWrite = 0;
while (bufWrite < bufRead)
{
int socketWrite = write(sd, buffer + bufWrite, bufRead - bufWrite);
if (socketWrite == -1)
{
if (errno == 32) // broken pipe often happens when the ssh connection shuts down or has errors.
{
warn("broken pipe, S3 server closed the ssh connection.");
break;
}
errnoAbort("error writing to socket for GenomeSpace upload");
}
bufWrite += socketWrite;
}
if (errno == 32)
break;
totalUploaded += bufRead;
int pctUploaded = 100.0*totalUploaded/contentLength;
if (progress && (pctUploaded != lastPctUploaded))
{
char nicenumber[1024]="";
sprintWithGreekByte(nicenumber, sizeof(nicenumber), contentLength);
// Various global flags must be reset to draw a fresh html output page.
webHeadAlreadyOutputed = FALSE;
webInTextMode = FALSE;
includedResourceFiles = NULL;
htmlWarnBoxSetUpAlready=FALSE;
htmlOpen("Uploading Output to GenomeSpace");
printf("Name: %s<br>\n", fileName);
printf("Size: %s<br>\n", nicenumber);
printf("Progress: %0d%%<br>\n", pctUploaded);
printf("<br>\n");
printf("<FORM ACTION=\"/cgi-bin/hgTables\" METHOD=GET>\n"
"<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"Back\" >"
"<INPUT TYPE=SUBMIT NAME=\"Refresh\" VALUE=\"Refresh\" onclick='window.location=window.location;return false;' >"
"</FORM>\n"
, hgtaDoMainPage);
puts("<script type=\"text/javascript\">");
puts("<!--");
puts("setTimeout(\"location = location;\",5000);");
puts("-->");
puts("</script>");
htmlClose();
fflush(stdout);
lastPctUploaded = pctUploaded;
}
}
carefulClose(&f);
char *responseCode = NULL;
char *s3UploadResponse = parseResponse(sd, &responseCode);
if (!sameString(responseCode, "200 OK"))
errAbort("Amazon S3 Response: %s", responseCode);
dyStringFree(&reqExtra);
return s3UploadResponse;
}
void gsSendToDM()
/* upload the generated file to DM */
{
// This is now run via fork/exec as a separate background process.
char *trashFileName = cartUsualString(cart, "gsTemp", "");
char *fileName = cartUsualString(cart, hgtaOutFileName, "");
// adjust upload name based on compression and existing extension
char *compressType = cartUsualString(cart, hgtaCompressType, textOutCompressNone);
if (!(isEmpty(compressType) || sameWord(compressType, textOutCompressNone)))
{
char *suffix = getCompressSuffix(compressType);
if (!endsWith(fileName, suffix))
fileName = addSuffix(fileName, suffix);
}
off_t fSize = fileSize(trashFileName);
char *gsToken = cartUsualString(cart, "gsToken", NULL);
char *contentType = "text/plain"; // some examples show applicaton/octet-stream
char *persDir = getGsPersonalDirectory(gsToken);
char *user = strrchr(persDir,'/');
++user;
char nicenumber[1024]="";
sprintWithGreekByte(nicenumber, sizeof(nicenumber), fSize);
htmlOpen("Uploading Output to GenomeSpace");
printf("Name: %s<br>\n", fileName);
printf("Size: %s<br>\n", nicenumber);
printf("Progress: 0%%<br>\n");
printf("You can remain on this page and monitor upload progress.<br>\n");
printf("Otherwise, feel free to continue working, and your output will appear in GenomeSpace when the upload is complete.<br>\n");
printf("<br>\n");
printf("<FORM ACTION=\"/cgi-bin/hgTables\" METHOD=GET>\n"
"<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"Back\" >\n"
"<INPUT TYPE=SUBMIT NAME=\"Refresh\" VALUE=\"Refresh\" onclick='window.location=window.location;return false;' >"
"</FORM>\n"
, hgtaDoMainPage);
puts("<script type=\"text/JavaScript\">");
puts("<!--");
puts("setTimeout(\"location = location;\",5000);");
puts("-->");
puts("</script>");
htmlClose();
fflush(stdout);
// MD5 COMPUTE
unsigned char md5[16]; /* Keep the md5 checksum here. */
md5ForFile(trashFileName,md5);
char *hexMd5 = md5ToHex(md5);
char *base64Md5 = base64Encode((char*)md5, 16);
char *s3UploadUrl = gsUploadUrl(gsToken, user, fileName, fSize, base64Md5, contentType);
char *s3Response = gsS3Upload(s3UploadUrl, trashFileName, fSize, base64Md5, hexMd5, contentType, TRUE, fileName);
if (sameString(s3Response,""))
{
// Reset global flags before drawing brand new page
webHeadAlreadyOutputed = FALSE;
webInTextMode = FALSE;
includedResourceFiles = NULL;
htmlWarnBoxSetUpAlready=FALSE;
htmlOpen("Uploaded Output to GenomeSpace");
printf("Name: %s<br>\n", fileName);
printf("Size: %s<br>\n", nicenumber);
printf("Output has been successfully uploaded.<br>\n");
printf("<br>");
printf("<FORM ACTION=\"/cgi-bin/hgTables\" METHOD=GET>\n"
"<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"Back\" ></FORM>\n"
, hgtaDoMainPage);
htmlClose();
fflush(stdout);
}
//printf("s3UploadUrl [%s]", s3UploadUrl);
//printf("<br>");
//printf("s3Response [%s]", s3Response);
//printf("<br>");
exit(0); // CANNOT RETURN
}
void doSummaryStatsWiggle(struct sqlConnection *conn)
/* Put up page showing summary stats for wiggle track. */
{
// grab the right trackDb for the current table. The curTrack variable
// has the composite trackDb in it
struct trackDb *track = hTrackDbForTrack(database, curTable);
char *table = curTable;
struct region *region, *regionList = getRegions();
char *regionName = getRegionName();
long long regionSize = 0;
long long gapTotal = 0;
long startTime = 0, wigFetchTime = 0;
char splitTableOrFileName[HDB_MAX_TABLE_STRING];
struct customTrack *ct = NULL;
boolean isCustom = FALSE;
struct wiggleDataStream *wds = NULL;
unsigned long long valuesMatched = 0;
int regionCount = 0;
int regionsDone = 0;
unsigned span = 0;
char *dataConstraint;
double ll = 0.0;
double ul = 0.0;
boolean hasConstraint = FALSE;
char *table2 = NULL;
boolean fullGenome = FALSE;
boolean statsHeaderDone = FALSE;
boolean gotSome = FALSE;
char *shortLabel = table;
long long statsItemCount = 0; /* global accumulators for overall */
int statsSpan = 0; /* stats summary on a multiple region */
double statsSumData = 0.0; /* output */
double statsSumSquares = 0.0; /* " " */
double lowerLimit = INFINITY; /* " " */
double upperLimit = -1.0 * INFINITY; /* " " */
startTime = clock1000();
if (track != NULL)
shortLabel = track->shortLabel;
/* Count the regions, when only one, we can do more stats */
for (region = regionList; region != NULL; region = region->next)
++regionCount;
htmlOpen("%s (%s) Wiggle Summary Statistics", shortLabel, table);
if (anySubtrackMerge(database, curTable))
hPrintf("<P><EM><B>Note:</B> subtrack merge is currently ignored on this "
"page (not implemented yet). Statistics shown here are only for "
"the primary table %s (%s).</EM>", shortLabel, table);
fullGenome = fullGenomeRegion();
WIG_INIT; /* ct, isCustom, hasConstraint, wds and table2 are set here */
for (region = regionList; region != NULL; region = region->next)
{
struct bed *intersectBedList = NULL;
int operations;
++regionsDone;
if (table2)
intersectBedList = bedTable2(conn, region, table2);
operations = wigFetchStats;
#if defined(NOT)
/* can't do the histogram now, that operation times out */
if (1 == regionCount)
operations |= wigFetchAscii;
#endif
wds->setChromConstraint(wds, region->chrom);
if (fullGenome)
wds->setPositionConstraint(wds, 0, 0);
else
wds->setPositionConstraint(wds, region->start, region->end);
if (hasConstraint)
wds->setDataConstraint(wds, dataConstraint, ll, ul);
/* depending on what is coming in on regionList, we may need to be
* smart about how often we call getData for these custom tracks
* since that is potentially a large file read each time.
*/
if (isCustom)
{
if (ct->dbTrack)
{
struct sqlConnection *trashConn = hAllocConn(CUSTOM_TRASH);
struct trackDb *tdb = findTdbForTable(database, curTrack, table, ctLookupName);
span = minSpan(trashConn, splitTableOrFileName, region->chrom,
region->start, region->end, cart, tdb);
wds->setSpanConstraint(wds, span);
valuesMatched = getWigglePossibleIntersection(wds, region,
CUSTOM_TRASH, table2, &intersectBedList,
splitTableOrFileName, operations);
hFreeConn(&trashConn);
}
else
{
valuesMatched = getWigglePossibleIntersection(wds, region, NULL,
table2, &intersectBedList, splitTableOrFileName, operations);
/* XXX We need to properly get the smallest span for custom tracks */
/* This is not necessarily the correct answer here */
if (wds->stats)
span = wds->stats->span;
else
span = 1;
}
}
else
{
if (hFindSplitTable(database, region->chrom, table, splitTableOrFileName, sizeof splitTableOrFileName, NULL))
{
span = minSpan(conn, splitTableOrFileName, region->chrom,
region->start, region->end, cart, track);
wds->setSpanConstraint(wds, span);
valuesMatched = getWigglePossibleIntersection(wds, region,
database, table2, &intersectBedList, splitTableOrFileName,
operations);
if (intersectBedList)
span = 1;
}
}
/* when doing multiple regions, we need to print out each result as
* it happens to keep the connection open to the browser and
* prevent any timeout since this could take a while.
* (worst case test is quality track on panTro1)
*/
if (wds->stats)
statsItemCount += wds->stats->count;
if (wds->stats && (regionCount > 1) && (valuesMatched > 0))
{
double sumData = wds->stats->mean * wds->stats->count;
double sumSquares;
if (wds->stats->count > 1)
sumSquares = (wds->stats->variance * (wds->stats->count - 1)) +
((sumData * sumData)/wds->stats->count);
else
sumSquares = sumData * sumData;
/* global accumulators for overall summary */
statsSpan = wds->stats->span;
statsSumData += sumData;
statsSumSquares += sumSquares;
if (wds->stats->lowerLimit < lowerLimit)
lowerLimit = wds->stats->lowerLimit;
if ((wds->stats->lowerLimit + wds->stats->dataRange) > upperLimit)
upperLimit = wds->stats->lowerLimit + wds->stats->dataRange;
if (statsHeaderDone)
wds->statsOut(wds, database, "stdout", TRUE, TRUE, FALSE, TRUE);
else
{
wds->statsOut(wds, database, "stdout", TRUE, TRUE, TRUE, TRUE);
statsHeaderDone = TRUE;
}
wds->freeStats(wds);
gotSome = TRUE;
}
if ((regionCount > MAX_REGION_DISPLAY) &&
(regionsDone >= MAX_REGION_DISPLAY))
{
hPrintf("<TR><TH ALIGN=CENTER COLSPAN=12> Can not display more "
"than %d regions, <BR> would take too much time </TH></TR>\n",
MAX_REGION_DISPLAY);
break; /* exit this for loop */
}
} /*for (region = regionList; region != NULL; region = region->next) */
if (hasConstraint)
freeMem(dataConstraint); /* been cloned into wds */
if (1 == regionCount)
{
statsPreamble(wds, regionList->chrom, regionList->start, regionList->end,
span, valuesMatched, table2);
/* 3 X TRUE = sort results, html table output, with header,
* the FALSE means close the table after printing, no more rows to
* come. The case in the if() statement was already taken care of
* in the statsPreamble() printout. No need to do that again.
*/
if ( ! ((valuesMatched == 0) && table2) )
wds->statsOut(wds, database, "stdout", TRUE, TRUE, TRUE, FALSE);
regionSize = basesInRegion(regionList,0);
gapTotal = gapsInRegion(conn, regionList,0);
}
else
{ /* this is a bit of a kludge here since these printouts are done in the
* library source wigDataStream.c statsOut() function and
* this is a clean up of that. That function should be
* pulled out of there and made independent and more
* versatile.
*/
long long realSize;
double variance;
double stddev;
/* Too expensive to lookup the numbers for thousands of regions */
regionSize = basesInRegion(regionList,MAX_REGION_DISPLAY);
gapTotal = gapsInRegion(conn, regionList,MAX_REGION_DISPLAY);
realSize = regionSize - gapTotal;
/* close the table which was left open in the loop above */
if (!gotSome)
hPrintf("<TR><TH ALIGN=CENTER COLSPAN=12> No data found matching this request </TH></TR>\n");
hPrintf("<TR><TH ALIGN=LEFT> SUMMARY: </TH>\n");
hPrintf("\t<TD> </TD>\n"); /* chromStart */
hPrintf("\t<TD> </TD>\n"); /* chromEnd */
hPrintf("\t<TD ALIGN=RIGHT> ");
printLongWithCommas(stdout, statsItemCount);
hPrintf(" </TD>\n" );
hPrintf("\t<TD ALIGN=RIGHT> %d </TD>\n", statsSpan);
hPrintf("\t<TD ALIGN=RIGHT> ");
printLongWithCommas(stdout, statsItemCount*statsSpan);
hPrintf(" (%.2f%%) </TD>\n",
100.0*(double)(statsItemCount*statsSpan)/(double)realSize);
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", lowerLimit);
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", upperLimit);
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", upperLimit - lowerLimit);
if (statsItemCount > 0)
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", statsSumData/statsItemCount);
else
hPrintf("\t<TD ALIGN=RIGHT> 0.0 </TD>\n");
stddev = 0.0;
variance = 0.0;
if (statsItemCount > 1)
{
variance = (statsSumSquares -
((statsSumData * statsSumData)/(double) statsItemCount)) /
(double) (statsItemCount - 1);
if (variance > 0.0)
stddev = sqrt(variance);
}
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", variance);
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", stddev);
hPrintf("</TR>\n");
wigStatsTableHeading(stdout, TRUE);
hPrintf("</TABLE></TD></TR></TABLE></P>\n");
}
#if defined(NOT)
/* can't do the histogram now, that operation times out */
/* Single region, we can do the histogram */
if ((valuesMatched > 1) && (1 == regionCount))
{
float *valuesArray = NULL;
size_t valueCount = 0;
struct histoResult *histoGramResult;
/* convert the ascii data listings to one giant float array */
valuesArray = wds->asciiToDataArray(wds, valuesMatched, &valueCount);
/* histoGram() may return NULL if it doesn't work */
histoGramResult = histoGram(valuesArray, valueCount,
NAN, (unsigned) 0, NAN, (float) wds->stats->lowerLimit,
(float) (wds->stats->lowerLimit + wds->stats->dataRange),
(struct histoResult *)NULL);
printHistoGram(histoGramResult, TRUE); /* TRUE == html output */
freeHistoGram(&histoGramResult);
wds->freeAscii(wds);
wds->freeArray(wds);
}
#endif
wds->freeStats(wds);
wiggleDataStreamFree(&wds);
wigFetchTime = clock1000() - startTime;
webNewSection("Region and Timing Statistics");
hTableStart();
stringStatRow("region", regionName);
numberStatRow("bases in region", regionSize);
numberStatRow("bases in gaps", gapTotal);
floatStatRow("load and calc time", 0.001*wigFetchTime);
wigFilterStatRow(conn);
stringStatRow("intersection", cartUsualString(cart, hgtaIntersectTable, "off"));
hTableEnd();
htmlClose();
} /* void doSummaryStatsWiggle(struct sqlConnection *conn) */
void doPastedIdentifiers(struct sqlConnection *conn)
/* Process submit in paste identifiers page. */
{
char *idText = trimSpaces(cartString(cart, hgtaPastedIdentifiers));
htmlOpen("Table Browser (Input Identifiers)");
if (isNotEmpty(idText))
{
/* Write terms to temp file, checking whether they have matches, and
* save temp file name. */
boolean saveIdText = (strlen(idText) < MAX_IDTEXT);
char *idTextForLf = saveIdText ? cloneString(idText) : idText;
struct lineFile *lf = lineFileOnString("idText", TRUE, idTextForLf);
char *line, *word;
struct tempName tn;
FILE *f;
int totalTerms = 0, foundTerms = 0;
struct slName* missingTerms = NULL;
struct dyString *exampleMissingIds = dyStringNew(256);
char *actualDb = database;
if (sameWord(curTable, WIKI_TRACK_TABLE))
actualDb = wikiDbName();
struct hTableInfo *hti = maybeGetHti(actualDb, curTable, conn);
char *idField = getIdField(actualDb, curTrack, curTable, hti);
if (idField == NULL)
{
warn("Sorry, I can't tell which field of table %s to treat as the "
"identifier field.", curTable);
webNewSection("Table Browser");
cartRemove(cart, hgtaIdentifierDb);
cartRemove(cart, hgtaIdentifierTable);
cartRemove(cart, hgtaIdentifierFile);
mainPageAfterOpen(conn);
htmlClose();
return;
}
struct slName *allTerms = NULL, *term;
while (lineFileNext(lf, &line, NULL))
{
while ((word = nextWord(&line)) != NULL)
{
term = slNameNew(word);
slAddHead(&allTerms, term);
totalTerms++;
}
}
slReverse(&allTerms);
lineFileClose(&lf);
char *extraWhere = NULL;
int maxIdsInWhere = cartUsualInt(cart, "hgt_maxIdsInWhere", DEFAULT_MAX_IDS_IN_WHERE);
if (totalTerms > 0 && totalTerms <= maxIdsInWhere)
extraWhere = slNameToInExpression(idField, allTerms);
struct lm *lm = lmInit(0);
struct hash *matchHash = getAllPossibleIds(conn, lm, idField, extraWhere);
trashDirFile(&tn, "hgtData", "identifiers", ".key");
f = mustOpen(tn.forCgi, "w");
for (term = allTerms; term != NULL; term = term->next)
{
struct slName *matchList = NULL, *match;
if (matchHash == NULL)
{
matchList = slNameNew(term->name);
}
else
{
/* Support multiple alias->id mappings: */
char upcased[1024];
safecpy(upcased, sizeof(upcased), term->name);
touppers(upcased);
struct hashEl *hel = hashLookup(matchHash, upcased);
if (hel != NULL)
{
matchList = slNameNew((char *)hel->val);
while ((hel = hashLookupNext(hel)) != NULL)
{
match = slNameNew((char *)hel->val);
slAddHead(&matchList, match);
}
}
}
if (matchList != NULL)
{
foundTerms++;
for (match = matchList; match != NULL; match = match->next)
{
mustWrite(f, match->name, strlen(match->name));
mustWrite(f, "\n", 1);
}
}
else
{
slAddHead(&missingTerms, slNameNew(term->name));
}
}
slReverse(&missingTerms);
carefulClose(&f);
cartSetString(cart, hgtaIdentifierDb, database);
cartSetString(cart, hgtaIdentifierTable, curTable);
cartSetString(cart, hgtaIdentifierFile, tn.forCgi);
if (saveIdText)
freez(&idTextForLf);
else
cartRemove(cart, hgtaPastedIdentifiers);
int missingCount = totalTerms - foundTerms;
if (missingCount > 0)
{
char *xrefTable, *aliasField;
getXrefInfo(conn, &xrefTable, NULL, &aliasField);
boolean xrefIsSame = xrefTable && sameString(curTable, xrefTable);
struct tempName tn;
trashDirFile(&tn, "hgt/missingIds", cartSessionId(cart), ".tmp");
FILE *f = mustOpen(tn.forCgi, "w");
int exampleCount = 0;
for (term = missingTerms; term != NULL; term = term->next)
{
if (exampleCount < 10)
{
++exampleCount;
dyStringPrintf(exampleMissingIds, "%s\n", term->name);
}
fprintf(f, "%s\n", term->name);
}
carefulClose(&f);
dyStringPrintf(exampleMissingIds, "\n<a href=%s>Complete list of missing identifiers<a>\n", tn.forHtml);
warn("Note: %d of the %d given identifiers have no match in "
"table %s, field %s%s%s%s%s. "
"Try the \"describe table schema\" button for more "
"information about the table and field.\n"
"%d %smissing identifier(s):\n"
"%s\n",
(totalTerms - foundTerms), totalTerms,
curTable, idField,
(xrefTable ? (xrefIsSame ? "" : " or in alias table ") : ""),
(xrefTable ? (xrefIsSame ? "" : xrefTable) : ""),
(xrefTable ? (xrefIsSame ? " or in field " : ", field ") : ""),
(xrefTable ? aliasField : ""),
exampleCount,
exampleCount < missingCount ? "example " : "",
exampleMissingIds->string
);
webNewSection("Table Browser");
}
lmCleanup(&lm);
hashFree(&matchHash);
}
else
{
cartRemove(cart, hgtaIdentifierFile);
}
mainPageAfterOpen(conn);
htmlClose();
}
void doBedOrCtOptions(char *table, struct sqlConnection *conn,
boolean doCt)
/* Put up form to get options on BED or custom track output. */
/* (Taken from hgText.c/doBedCtOptions) */
{
char *table2 = NULL; /* For now... */
struct hTableInfo *hti = getHti(database, table, conn);
char buf[256];
char *setting;
htmlOpen("Output %s as %s", table, (doCt ? "Custom Track" : "BED"));
if (doGalaxy())
startGalaxyForm();
else if (doGreat())
{
verifyGreatAssemblies();
startGreatForm();
}
else
hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
if (!doGreat())
{
hPrintf("%s\n", "<TABLE><TR><TD>");
if (doCt)
{
hPrintf("%s\n", "</TD><TD>"
"<A HREF=\"../goldenPath/help/customTrack.html\" TARGET=_blank>"
"Custom track</A> header: </B>");
}
else
{
cgiMakeCheckBox(hgtaPrintCustomTrackHeaders,
cartCgiUsualBoolean(cart, hgtaPrintCustomTrackHeaders, FALSE));
hPrintf("%s\n", "</TD><TD> <B> Include "
"<A HREF=\"../goldenPath/help/customTrack.html\" TARGET=_blank>"
"custom track</A> header: </B>");
}
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>name=");
safef(buf, sizeof(buf), "tb_%s", hti->rootName);
setting = cgiUsualString(hgtaCtName, buf);
cgiMakeTextVar(hgtaCtName, setting, 16);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>description=");
safef(buf, sizeof(buf), "table browser query on %s%s%s",
table, (table2 ? ", " : ""), (table2 ? table2 : ""));
setting = cgiUsualString(hgtaCtDesc, buf);
cgiMakeTextVar(hgtaCtDesc, setting, 50);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>visibility=");
if (isWiggle(database, table) || isBigWigTable(table))
{
setting = cartCgiUsualString(cart, hgtaCtVis, ctVisWigMenu[2]);
cgiMakeDropList(hgtaCtVis, ctVisWigMenu, ctVisWigMenuSize, setting);
}
else
{
setting = cartCgiUsualString(cart, hgtaCtVis, ctVisMenu[3]);
cgiMakeDropList(hgtaCtVis, ctVisMenu, ctVisMenuSize, setting);
}
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>url=");
setting = cartCgiUsualString(cart, hgtaCtUrl, "");
cgiMakeTextVar(hgtaCtUrl, setting, 50);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>");
hPrintf("%s\n", "</TD></TR></TABLE>");
}
if (isWiggle(database, table) || isBedGraph(table) || isBigWigTable(table) )
{
char *setting = NULL;
hPrintf("<P> <B> Select type of data output: </B> <BR>\n");
setting = cartCgiUsualString(cart, hgtaCtWigOutType, outWigData);
cgiMakeRadioButton(hgtaCtWigOutType, outWigBed, sameString(setting, outWigBed));
hPrintf("BED format (no data value information, only position)<BR>\n");
cgiMakeRadioButton(hgtaCtWigOutType, outWigData, sameString(setting, outWigData));
hPrintf("DATA VALUE format (position and real valued data)</P>\n");
}
else
{
cgiDown(0.9);
hPrintf("<B> Create one BED record per: </B>\n");
if ((anyIntersection() && intersectionIsBpWise()) ||
(anySubtrackMerge(database, table) && subtrackMergeIsBpWise()))
{
/* The original table may have blocks/CDS, described in hti, but
* that info will be lost after base pair-wise operations. So make
* a temporary copy of hti with its flags tweaked: */
struct hTableInfo simplifiedHti;
memcpy(&simplifiedHti, hti, sizeof(simplifiedHti));
simplifiedHti.hasBlocks = FALSE;
simplifiedHti.hasCDS = FALSE;
fbOptionsHtiCart(&simplifiedHti, cart);
}
else
fbOptionsHtiCart(hti, cart);
}
if (doCt)
{
if (doGalaxy())
{
/* send the action parameter with the form as well */
cgiMakeHiddenVar(hgtaDoGetCustomTrackFile, "get custom track in file");
printGalaxySubmitButtons();
}
else
{
cgiMakeButton(hgtaDoGetCustomTrackTb, "get custom track in table browser");
hPrintf(" ");
cgiMakeButton(hgtaDoGetCustomTrackFile, "get custom track in file");
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoGetCustomTrackGb, "get custom track in genome browser");
}
}
else
{
if (doGalaxy())
{
cgiMakeHiddenVar(hgtaDoGetBed, "get BED");
printGalaxySubmitButtons();
}
else if (doGreat())
{
cgiMakeHiddenVar(hgtaDoGetBed, "get BED");
printGreatSubmitButtons();
}
else
cgiMakeButton(hgtaDoGetBed, "get BED");
}
if (!doGalaxy() && !doGreat())
{
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>\n");
}
cgiDown(0.9);
htmlClose();
}
void doSubmitUserRegions(struct sqlConnection *conn)
/* Process submit in set regions page. */
{
char *idText = trimSpaces(cartString(cart, hgtaEnteredUserRegions));
char *userRegionFile = trimSpaces(cartString(cart, hgtaEnteredUserRegionFile));
boolean hasData = (idText != NULL && idText[0] != 0) ||
(userRegionFile != NULL && userRegionFile[0] != 0);
/* beware, the string pointers from cartString() point to strings in the
* cart hash. If they are manipulated and changed, they will get saved
* back to the cart in their changed form. You don't want to be
* altering them like that. Thus, the idText is duplicated below with
* the cloneString(idText)
*/
htmlOpen("Table Browser (Region definitions)");
/* presence of fileName text overrides previously existing text area
* contents
*/
if (userRegionFile != NULL && userRegionFile[0] != 0)
{
idText = cloneString(userRegionFile);
cartRemove(cart, hgtaEnteredUserRegions);
cartRemove(cart, hgtaUserRegionsFile);
cartSetString(cart, hgtaEnteredUserRegions, idText);
}
else
idText = cloneString(idText);
char *lineLimitText = limitText(idText);
if ( (strlen(lineLimitText) > 0) && (strlen(lineLimitText) != strlen(idText)) )
{
freeMem(idText);
idText = lineLimitText;
cartSetString(cart, hgtaEnteredUserRegions, lineLimitText);
}
else
freeMem(lineLimitText);
if (hasData)
{
struct tempName tn;
FILE *f;
struct bed *bedEl;
struct bed *bedList = parseRegionInput(idText);
if (NULL == bedList)
errAbort("no valid data points found in input");
trashDirFile(&tn, "hgtData", "user", ".region");
f = mustOpen(tn.forCgi, "w");
for (bedEl = bedList; bedEl; bedEl = bedEl->next )
{
if (bedEl->name)
fprintf(f, "%s\t%d\t%d\t%s\n",
bedEl->chrom, bedEl->chromStart, bedEl->chromEnd, bedEl->name);
else
fprintf(f, "%s\t%d\t%d\n",
bedEl->chrom, bedEl->chromStart, bedEl->chromEnd);
}
carefulClose(&f);
cartSetString(cart, hgtaUserRegionsDb, database);
cartSetString(cart, hgtaUserRegionsTable, curTable);
cartSetString(cart, hgtaUserRegionsFile, tn.forCgi);
cartSetString(cart, hgtaRegionType, hgtaRegionTypeUserRegions);
if (strlen(idText) > 64 * 1024)
cartRemove(cart, hgtaEnteredUserRegions);
}
else
{
cartRemove(cart, hgtaUserRegionsFile);
cartRemove(cart, hgtaEnteredUserRegionFile);
cartRemove(cart, hgtaRegionType);
}
mainPageAfterOpen(conn);
htmlClose();
}
