393c8a7bb0e4dc56856fcbe514a4aa65914f096b lrnassar Wed Feb 12 11:25:50 2020 -0800 Fixing linkout to GTF files on download server refs #24810 diff --git src/hg/hgTables/mainPage.c src/hg/hgTables/mainPage.c index 9ee309b..9988063 100644 --- src/hg/hgTables/mainPage.c +++ src/hg/hgTables/mainPage.c @@ -1,1037 +1,1037 @@ /* mainPage - stuff to put up the first table browser page. */ /* Copyright (C) 2014 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "htmshell.h" #include "cheapcgi.h" #include "cart.h" #include "cartTrackDb.h" #include "textOut.h" #include "jksql.h" #include "hdb.h" #include "web.h" #include "jsHelper.h" #include "hui.h" #include "hgColors.h" #include "trackDb.h" #include "grp.h" #include "hgTables.h" #include "joiner.h" #include "trackDb.h" #include "hubConnect.h" #include "trackHub.h" #include "hgConfig.h" static struct dyString *onChangeStart() /* Start up a javascript onChange command */ { struct dyString *dy = jsOnChangeStart(); jsDropDownCarryOver(dy, hgtaTrack); jsDropDownCarryOver(dy, hgtaGroup); jsTrackedVarCarryOver(dy, hgtaRegionType, "regionType"); jsTextCarryOver(dy, hgtaRange); jsDropDownCarryOver(dy, hgtaOutputType); jsTextCarryOver(dy, hgtaOutFileName); return dy; } static char *onChangeClade() /* Return javascript executed when they change clade. */ { struct dyString *dy = onChangeStart(); jsDropDownCarryOver(dy, "clade"); jsDropDownCarryOver(dy, hgtaTable); dyStringAppend(dy, " document.hiddenForm.org.value=0;"); dyStringAppend(dy, " document.hiddenForm.db.value=0;"); dyStringAppend(dy, " document.hiddenForm.position.value='';"); return jsOnChangeEnd(&dy); } static char *onChangeOrg() /* Return javascript executed when they change organism. */ { struct dyString *dy = onChangeStart(); jsDropDownCarryOver(dy, "clade"); jsDropDownCarryOver(dy, "org"); jsDropDownCarryOver(dy, hgtaTable); dyStringAppend(dy, " document.hiddenForm.db.value=0;"); dyStringAppend(dy, " document.hiddenForm.position.value='';"); return jsOnChangeEnd(&dy); } static char *onChangeDb() /* Return javascript executed when they change database. */ { struct dyString *dy = onChangeStart(); jsDropDownCarryOver(dy, "clade"); jsDropDownCarryOver(dy, "db"); jsDropDownCarryOver(dy, hgtaTable); dyStringAppend(dy, " document.hiddenForm.position.value='';"); return jsOnChangeEnd(&dy); } static char *onChangeGroupOrTrack() /* Return javascript executed when they change group. */ { struct dyString *dy = onChangeStart(); jsDropDownCarryOver(dy, "clade"); jsDropDownCarryOver(dy, "db"); jsDropDownCarryOver(dy, "org"); dyStringPrintf(dy, " document.hiddenForm.%s.value=0;", hgtaTable); return jsOnChangeEnd(&dy); } static char *onChangeTable() /* Return javascript executed when they change group. */ { struct dyString *dy = onChangeStart(); jsDropDownCarryOver(dy, "clade"); jsDropDownCarryOver(dy, "db"); jsDropDownCarryOver(dy, "org"); jsDropDownCarryOver(dy, hgtaTable); return jsOnChangeEnd(&dy); } void makeRegionButtonExtraHtml(char *val, char *selVal, char *extraHtml) /* Make region radio button including a little Javascript to save selection state * and optional extra html attributes. */ { jsMakeTrackingRadioButtonExtraHtml(hgtaRegionType, "regionType", val, selVal, extraHtml); } void makeRegionButton(char *val, char *selVal) /* Make region radio button including a little Javascript * to save selection state. */ { makeRegionButtonExtraHtml(val, selVal, NULL); } struct grp *showGroupField(char *groupVar, char *event, char *groupScript, struct sqlConnection *conn, boolean allTablesOk) /* Show group control. Returns selected group. */ { struct grp *group, *groupList = fullGroupList; struct grp *selGroup = findSelectedGroup(groupList, groupVar); hPrintf("<B>group:</B>\n"); hPrintf("<SELECT NAME=%s id='%s'>\n", groupVar, groupVar); jsOnEventById(event,groupVar,groupScript); for (group = groupList; group != NULL; group = group->next) { if (allTablesOk || differentString(group->name, "allTables")) hPrintf(" <OPTION VALUE=%s%s>%s\n", group->name, (group == selGroup ? " SELECTED" : ""), group->label); } hPrintf("</SELECT>\n"); return selGroup; } static void addIfExists(struct hash *hash, struct slName **pList, char *name) /* Add name to tail of list if it exists in hash. */ { if (hashLookup(hash, name)) slNameAddTail(pList, name); } struct slName *getDbListForGenome() /* Get list of selectable databases. */ { struct hash *hash = sqlHashOfDatabases(); struct slName *dbList = NULL; addIfExists(hash, &dbList, database); addIfExists(hash, &dbList, "uniProt"); addIfExists(hash, &dbList, "proteome"); addIfExists(hash, &dbList, "go"); addIfExists(hash, &dbList, "hgFixed"); addIfExists(hash, &dbList, "visiGene"); addIfExists(hash, &dbList, "ultra"); return dbList; } char *findSelDb() /* Find user selected database (as opposed to genome database). */ { struct slName *dbList = getDbListForGenome(); char *selDb = cartUsualString(cart, hgtaTrack, NULL); if (!slNameInList(dbList, selDb)) selDb = cloneString(dbList->name); slFreeList(&dbList); return selDb; } struct trackDb *showTrackField(struct grp *selGroup, char *trackVar, char *event, char *trackScript, boolean disableNoGenome) /* Show track control. Returns selected track. */ { struct trackDb *track, *selTrack = NULL; if (trackScript == NULL) trackScript = ""; if (sameString(selGroup->name, "allTables")) { char *selDb = findSelDb(); struct slName *dbList = getDbListForGenome(), *db; hPrintf("<B>database:</B>\n"); hPrintf("<SELECT NAME=\"%s\" id='%s'>\n", trackVar, trackVar); jsOnEventById(event, trackVar, trackScript); for (db = dbList; db != NULL; db = db->next) { hPrintf(" <OPTION VALUE=%s%s>%s\n", db->name, (sameString(db->name, selDb) ? " SELECTED" : ""), db->name); } hPrintf("</SELECT>\n"); } else { boolean allTracks = sameString(selGroup->name, "allTracks"); hPrintf("<B>track:</B>\n"); hPrintf("<SELECT NAME=\"%s\" id='%s'>\n", trackVar, trackVar); jsOnEventById(event, trackVar, trackScript); if (allTracks) { selTrack = findSelectedTrack(fullTrackList, NULL, trackVar); slSort(&fullTrackList, trackDbCmpShortLabel); } else { selTrack = findSelectedTrack(fullTrackList, selGroup, trackVar); } boolean selTrackIsDisabled = FALSE; struct trackDb *firstEnabled = NULL; for (track = fullTrackList; track != NULL; track = track->next) { if (allTracks || sameString(selGroup->name, track->grp)) { hPrintf(" <OPTION VALUE=\"%s\"", track->track); if (cartTrackDbIsNoGenome(database, track->table)) hPrintf(NO_GENOME_CLASS); if (disableNoGenome && isNoGenomeDisabled(database, track->table)) { hPrintf(" DISABLED"); if (track == selTrack) selTrackIsDisabled = TRUE; } else if (firstEnabled == NULL) firstEnabled = track; if (track == selTrack && !selTrackIsDisabled) hPrintf(" SELECTED"); hPrintf(">%s</OPTION>", track->shortLabel); } } if (selTrackIsDisabled) selTrack = firstEnabled; hPrintf("</SELECT>\n"); } hPrintf("\n"); return selTrack; } char *unsplitTableName(char *table) /* Convert chr*_name to name */ { if (startsWith("chr", table)) { char *s = strrchr(table, '_'); if (s != NULL) { table = s + 1; } } return table; } struct slName *tablesForDb(char *db) /* Find tables associated with database. */ { boolean isGenomeDb = sameString(db, database); struct sqlConnection *conn = hAllocConn(db); struct slName *raw, *rawList = sqlListTables(conn); struct slName *cooked, *cookedList = NULL; struct hash *uniqHash = newHash(0); hFreeConn(&conn); for (raw = rawList; raw != NULL; raw = raw->next) { if (cartTrackDbIsAccessDenied(db, raw->name)) continue; if (isGenomeDb) { /* Deal with tables split across chromosomes. */ char *root = unsplitTableName(raw->name); if (cartTrackDbIsAccessDenied(db, root)) continue; if (!hashLookup(uniqHash, root)) { hashAdd(uniqHash, root, NULL); cooked = slNameNew(root); slAddHead(&cookedList, cooked); } } else { char dbTable[256]; safef(dbTable, sizeof(dbTable), "%s.%s", db, raw->name); cooked = slNameNew(dbTable); slAddHead(&cookedList, cooked); } } hashFree(&uniqHash); slFreeList(&rawList); slSort(&cookedList, slNameCmp); return cookedList; } char *showTableField(struct trackDb *track, char *varName, boolean useJoiner) /* Show table control and label. */ { struct slName *name, *nameList = NULL; char *selTable; if (track == NULL) nameList = tablesForDb(findSelDb()); else nameList = cartTrackDbTablesForTrack(database, track, useJoiner); /* Get currently selected table. If it isn't in our list * then revert to first in list. */ selTable = cartUsualString(cart, varName, nameList->name); if (!slNameInListUseCase(nameList, selTable)) selTable = nameList->name; /* Print out label and drop-down list. */ hPrintf("<B>table: </B>"); hPrintf("<SELECT NAME=\"%s\" id='%s'>\n", varName, varName); jsOnEventById("change", varName, onChangeTable()); struct trackDb *selTdb = NULL; for (name = nameList; name != NULL; name = name->next) { struct trackDb *tdb = NULL; if (track != NULL) tdb = findTdbForTable(database,track,name->name, ctLookupName); hPrintf("<OPTION VALUE=\"%s\"", name->name); // Disable options for related tables that are noGenome -- if a non-positional table // is selected then we output its entire contents. if (cartTrackDbIsNoGenome(database, name->name) && (track == NULL || differentString(track->table, name->name))) hPrintf(" DISABLED"NO_GENOME_CLASS); else if (sameString(selTable, name->name)) { hPrintf(" SELECTED"); selTdb = tdb; } if (tdb != NULL) if ((curTrack == NULL) || differentWord(tdb->shortLabel, curTrack->shortLabel)) hPrintf(">%s (%s)\n", tdb->shortLabel, name->name); else hPrintf(">%s\n", name->name); else hPrintf(">%s\n", name->name); } hPrintf("</SELECT>\n"); if (!trackHubDatabase(database)) { char *restrictDate = encodeRestrictionDateDisplay(database,selTdb); if (restrictDate) { hPrintf("<A HREF=\'%s\' TARGET=BLANK>restricted until:</A> %s", ENCODE_DATA_RELEASE_POLICY, restrictDate); freeMem(restrictDate); } } return selTable; } struct outputType /* Info on an output type. */ { struct outputType *next; char *name; /* Symbolic name of type. */ char *label; /* User visible label. */ }; static void showOutDropDown(struct outputType *otList, struct outputType *otDefault) /* Display output drop-down. */ { struct outputType *ot; char *outputType = cartUsualString(cart, hgtaOutputType, otList->name); if (otDefault != NULL && otDefault != otList) { boolean otInOtList = FALSE; for (ot = otList; ot != NULL; ot = ot->next) if (sameString(ot->name, outputType)) { otInOtList = TRUE; break; } if (! otInOtList) outputType = otDefault->name; } hPrintf("<SELECT id='outputTypeDropdown' NAME=\"%s\">", hgtaOutputType); for (ot = otList; ot != NULL; ot = ot->next) { hPrintf(" <OPTION VALUE=%s", ot->name); if (sameString(ot->name, outputType)) hPrintf(" SELECTED"); if (sameString(ot->name, outBed) || sameString(ot->name, outWigBed)) hPrintf(" id=\"outBed\""); hPrintf(">%s\n", ot->label); } hPrintf("</SELECT>\n"); hPrintf(" "); hPrintf("<DIV style='display:none; opacity:0.9; border: 1px solid #EEE; margin: 2px; padding: 4px' id='gffNote'>" "<b>Note:</b> Table Browser GTF files contain transcripts, but no gene identifiers or symbols.<br> " "If you are looking for fully formatted " "gene model files for use in genome analysis pipelines,<br>check the " - "<a href='https://hgdownload.soe.ucsc.edu/%s/bigZips/genes'>bigZips/genes</a> " + "<a href='https://hgdownload.soe.ucsc.edu/goldenPath/%s/bigZips/genes'>bigZips/genes</a> " "directory on our download server.</DIV>", database); hPrintf(" "); jsInline("function checkGtfNote() {" "if (document.getElementById('outputTypeDropdown').value==='gff') " " document.getElementById('gffNote').style.display=''; " "else " " document.getElementById('gffNote').style.display='none'; " "}" "$(document).ready(checkGtfNote);\n" ); jsOnEventById("change", "outputTypeDropdown", "checkGtfNote()"); if (!cfgOptionBooleanDefault("hgta.disableSendOutput", FALSE)) { hPrintf(" Send output to "); struct dyString *dy = dyStringNew(256); dyStringAppend(dy, "document.getElementById('checkboxGreat').checked=false;"); if (isGenomeSpaceEnabled()) dyStringAppend(dy, "document.getElementById('checkboxGenomeSpace').checked=false;"); dyStringAppend(dy, "return true;"); cgiMakeCheckBoxWithId("sendToGalaxy", doGalaxy(), "checkboxGalaxy"); jsOnEventById("click", "checkboxGalaxy", dy->string); hPrintf("<A HREF=\""GALAXY_URL_BASE"\" target=_BLANK>Galaxy</A>\n"); nbSpaces(2); cgiMakeCheckBoxWithId("sendToGreat", doGreat(), "checkboxGreat"); jsOnEventById("click", "checkboxGreat", "return onSelectGreat();"); hPrintf(" <A HREF=\"http://great.stanford.edu\" target=_BLANK>GREAT</A>"); if (isGenomeSpaceEnabled()) { nbSpaces(2); cgiMakeCheckBoxWithId("sendToGenomeSpace", doGenomeSpace(), "checkboxGenomeSpace"); jsOnEventById("click", "checkboxGenomeSpace", "document.getElementById('checkboxGreat').checked=false;" "document.getElementById('checkboxGalaxy').checked=false; return true;"); hPrintf(" <A HREF=\"http://www.genomespace.org\" target=_BLANK>GenomeSpace</A>"); } } hPrintf("</TD></TR>\n"); } struct outputType otAllFields = { NULL, outPrimaryTable,"all fields from selected table", }; struct outputType otSelected = { NULL, outSelectedFields, "selected fields from primary and related tables", }; struct outputType otSequence = { NULL, outSequence, "sequence", }; struct outputType otPal = { NULL, outPalOptions, "CDS FASTA alignment from multiple alignment", }; struct outputType otGff = { NULL, outGff, "GTF - gene transfer format (limited)", }; struct outputType otBed = { NULL, outBed, "BED - browser extensible data", }; struct outputType otCustomTrack = { NULL, outCustomTrack, "custom track", }; struct outputType otHyperlinks = { NULL, outHyperlinks, "hyperlinks to Genome Browser", }; struct outputType otWigData = { NULL, outWigData, "data points", }; struct outputType otWigBed = { NULL, outWigBed, "bed format", }; struct outputType otMaf = { NULL, outMaf, "MAF - multiple alignment format", }; struct outputType otChromGraphData = { NULL, outChromGraphData, "data points", }; struct outputType otMicroarrayNames = { NULL, outMicroarrayNames, "microarray names", }; struct outputType otMicroarrayGroupings = { NULL, outMicroarrayGroupings, "microarray groupings", }; static void showOutputTypeRow(boolean isWig, boolean isBedGr, boolean isPositional, boolean isMaf, boolean isChromGraphCt, boolean isPal, boolean isMicroarray, boolean isHalSnake) /* Print output line. */ { struct outputType *otList = NULL, *otDefault = NULL; boolean bedifiedOnly = (anySubtrackMerge(database, curTable) || anyIntersection()); hPrintf("<TR><TD><B>output format:</B>\n"); if (isBedGr) { if (! bedifiedOnly) { slAddTail(&otList, &otAllFields); slAddTail(&otList, &otSelected); } slAddTail(&otList, &otWigData); slAddTail(&otList, &otWigBed); slAddTail(&otList, &otCustomTrack); slAddTail(&otList, &otHyperlinks); } else if (isWig) { slAddTail(&otList, &otWigData); slAddTail(&otList, &otWigBed); slAddTail(&otList, &otCustomTrack); // hyperlinks output works for db-wiggle but not for bigWig } else if (isHalSnake) { slAddTail(&otList, &otMaf); } else if (isMaf) { slAddTail(&otList, &otMaf); if (! bedifiedOnly) slAddTail(&otList, &otAllFields); } else if (isChromGraphCt) { slAddTail(&otList, &otChromGraphData); } else if (isMicroarray) { slAddTail(&otList, &otMicroarrayNames); slAddTail(&otList, &otAllFields); slAddTail(&otList, &otSelected); slAddTail(&otList, &otHyperlinks); } else if (isPositional) { if (! bedifiedOnly) { slAddTail(&otList, &otAllFields); slAddTail(&otList, &otSelected); } else otDefault = &otBed; slAddTail(&otList, &otSequence); slAddTail(&otList, &otGff); if (isPal) slAddTail(&otList, &otPal); slAddTail(&otList, &otBed); slAddTail(&otList, &otCustomTrack); slAddTail(&otList, &otHyperlinks); } else { slAddTail(&otList, &otAllFields); slAddTail(&otList, &otSelected); } showOutDropDown(otList, otDefault); } void nbSpaces(int count) /* Print some non-breaking spaces. */ { int i; for (i=0; i<count; ++i) hPrintf(" "); } void showMainControlTable(struct sqlConnection *conn) /* Put up table with main controls for main page. */ { struct grp *selGroup; boolean isWig = FALSE, isPositional = FALSE, isMaf = FALSE, isBedGr = FALSE, isChromGraphCt = FALSE, isPal = FALSE, isArray = FALSE, isBam = FALSE, isVcf = FALSE, isHalSnake = FALSE, isLongTabix = FALSE, isHic = FALSE; boolean gotClade = hGotClade(); struct hTableInfo *hti = NULL; hPrintf("<TABLE BORDER=0>\n"); /* Print clade, genome and assembly line. */ { if (gotClade) { hPrintf("<TR><TD><B>clade:</B>\n"); printCladeListHtml(hGenome(database), "change", onChangeClade()); nbSpaces(3); hPrintf("<B>genome:</B>\n"); printGenomeListForCladeHtml(database, "change", onChangeOrg()); } else { hPrintf("<TR><TD><B>genome:</B>\n"); printGenomeListHtml(database, "change", onChangeOrg()); } nbSpaces(3); hPrintf("<B>assembly:</B>\n"); printAssemblyListHtml(database, "change", onChangeDb()); hPrintf("</TD></TR>\n"); } /* Print group and track line. */ { hPrintf("<TR><TD>"); selGroup = showGroupField(hgtaGroup, "change", onChangeGroupOrTrack(), conn, hAllowAllTables()); nbSpaces(3); curTrack = showTrackField(selGroup, hgtaTrack, "change", onChangeGroupOrTrack(), FALSE); nbSpaces(3); boolean hasCustomTracks = FALSE; struct trackDb *t; for (t = fullTrackList; t != NULL; t = t->next) { if (isCustomTrack(t->table)) { hasCustomTracks = TRUE; break; } } hOnClickButton("showMainCtlTbl_Ct", "document.customTrackForm.submit();return false;", hasCustomTracks ? CT_MANAGE_BUTTON_LABEL : CT_ADD_BUTTON_LABEL); hPrintf(" "); if (hubConnectTableExists()) hOnClickButton("showMainCtlTbl_Hub", "document.trackHubForm.submit();return false;", "track hubs"); hPrintf("</TD></TR>\n"); } /* Print table line. */ { hPrintf("<TR><TD>"); curTable = showTableField(curTrack, hgtaTable, TRUE); if (isHubTrack(curTable) || (strchr(curTable, '.') == NULL)) /* In same database */ { hti = getHti(database, curTable, conn); isPositional = htiIsPositional(hti); } isLongTabix = isLongTabixTable( curTable); isBam = isBamTable(curTable); isHic = isHicTable(curTable); isVcf = isVcfTable(curTable, NULL); isWig = isWiggle(database, curTable); if (isBigWigTable(curTable)) { isPositional = TRUE; isWig = TRUE; } isHalSnake = isHalTable( curTable); isMaf = isMafTable(database, curTrack, curTable); isBedGr = isBedGraph(curTable); isArray = isMicroarray(curTrack, curTable); struct trackDb *tdb = findTdbForTable(database, curTrack, curTable, ctLookupName); isPal = isPalCompatible(conn, tdb, curTable); nbSpaces(1); if (isCustomTrack(curTable)) { isChromGraphCt = isChromGraph(tdb); } cgiMakeButton(hgtaDoSchema, "describe table schema"); hPrintf("</TD></TR>\n"); } if (curTrack == NULL) { struct trackDb *tdb = hTrackDbForTrack(database, curTable); struct trackDb *cTdb = hCompositeTrackDbForSubtrack(database, tdb); if (cTdb) curTrack = cTdb; else curTrack = tdb; isMaf = isMafTable(database, curTrack, curTable); } /* Table-specific options */ if (isHicTable(curTable)) hicMainPageConfig(cart, hTrackDbForTrack(database,curTable)); /* Region line */ { char *regionType; if (cartVarExists(cart, "hgFind.matches")) // coming back from a search regionType = cartUsualString(cart, hgtaRegionType, hgtaRegionTypeRange); else regionType = cartUsualString(cart, hgtaRegionType, hgtaRegionTypeGenome); char *range = cartUsualString(cart, hgtaRange, ""); if (isPositional) { boolean doEncode = FALSE; if (!trackHubDatabase(database)) doEncode = sqlTableExists(conn, "encodeRegions"); hPrintf("<TR><TD><B>region:</B>\n"); /* If regionType not allowed force it to "genome". */ if ((sameString(regionType, hgtaRegionTypeUserRegions) && userRegionsFileName() == NULL) || (sameString(regionType, hgtaRegionTypeEncode) && !doEncode)) regionType = hgtaRegionTypeGenome; // Is "genome" is not allowed because of tdb 'tableBrowser noGenome'? boolean disableGenome = ((curTrack && cartTrackDbIsNoGenome(database, curTrack->table)) || (curTable && cartTrackDbIsNoGenome(database, curTable))); // If "genome" is selected but not allowed, force it to "range": if (sameString(regionType, hgtaRegionTypeGenome) && disableGenome) regionType = hgtaRegionTypeRange; jsTrackingVar("regionType", regionType); if (disableGenome) { makeRegionButtonExtraHtml(hgtaRegionTypeGenome, regionType, "DISABLED"); hPrintf(" <span"NO_GENOME_CLASS">genome (unavailable for selected track)</span>" " "); } else { makeRegionButton(hgtaRegionTypeGenome, regionType); hPrintf(" genome "); } if (doEncode) { makeRegionButton(hgtaRegionTypeEncode, regionType); hPrintf(" ENCODE Pilot regions "); } makeRegionButton(hgtaRegionTypeRange, regionType); hPrintf(" position "); hPrintf("<INPUT TYPE=TEXT NAME=\"%s\" id='%s' SIZE=26 VALUE=\"%s\">\n", hgtaRange, hgtaRange, range); jsOnEventById("focus", hgtaRange, jsRadioUpdate(hgtaRegionType, "regionType", "range")); cgiMakeButton(hgtaDoLookupPosition, "lookup"); hPrintf(" "); if (userRegionsFileName() != NULL) { makeRegionButton(hgtaRegionTypeUserRegions, regionType); hPrintf(" defined regions "); cgiMakeButton(hgtaDoSetUserRegions, "change"); hPrintf(" "); cgiMakeButton(hgtaDoClearUserRegions, "clear"); } else cgiMakeButton(hgtaDoSetUserRegions, "define regions"); hPrintf("</TD></TR>\n"); } else { /* Need to put at least stubs of cgi variables in for JavaScript to work. */ jsTrackingVar("regionType", regionType); cgiMakeHiddenVar(hgtaRange, range); cgiMakeHiddenVar(hgtaRegionType, regionType); } /* Select identifiers line (if applicable). */ if (!isWig && getIdField(database, curTrack, curTable, hti) != NULL) { hPrintf("<TR><TD><B>identifiers (names/accessions):</B>\n"); cgiMakeButton(hgtaDoPasteIdentifiers, "paste list"); hPrintf(" "); cgiMakeButton(hgtaDoUploadIdentifiers, "upload list"); if (identifierFileName() != NULL) { hPrintf(" "); cgiMakeButton(hgtaDoClearIdentifiers, "clear list"); } hPrintf("</TD></TR>\n"); } } /* microarray options */ /* button for option page here (median/log-ratio, etc) */ /* Filter line. */ { hPrintf("<TR><TD><B>filter:</B>\n"); if (anyFilter()) { cgiMakeButton(hgtaDoFilterPage, "edit"); hPrintf(" "); cgiMakeButton(hgtaDoClearFilter, "clear"); if (isWig || isBedGr) wigShowFilter(conn); } else { cgiMakeButton(hgtaDoFilterPage, "create"); } hPrintf("</TD></TR>\n"); } /* Composite track subtrack merge line. */ boolean canSubtrackMerge = (curTrack && tdbIsComposite(curTrack) && !isBam && !isVcf && !isLongTabix && !isHic); if (canSubtrackMerge) { hPrintf("<TR><TD><B>subtrack merge:</B>\n"); if (anySubtrackMerge(database, curTable)) { cgiMakeButton(hgtaDoSubtrackMergePage, "edit"); hPrintf(" "); cgiMakeButton(hgtaDoClearSubtrackMerge, "clear"); } else { cgiMakeButton(hgtaDoSubtrackMergePage, "create"); } hPrintf("</TD></TR>\n"); } /* Intersection line. */ if (isPositional) { if (anyIntersection()) { hPrintf("<TR><TD><B>intersection with %s:</B>\n", cartString(cart, hgtaIntersectTable)); cgiMakeButton(hgtaDoIntersectPage, "edit"); hPrintf(" "); cgiMakeButton(hgtaDoClearIntersect, "clear"); hPrintf("</TD></TR>\n"); } else if (canIntersect(database, curTable)) { hPrintf("<TR><TD><B>intersection:</B>\n"); cgiMakeButton(hgtaDoIntersectPage, "create"); hPrintf("</TD></TR>\n"); } } /* Correlation line. */ struct trackDb *tdb = findTdbForTable(database, curTrack, curTable, ctLookupName); if (correlateTrackTableOK(tdb, curTable)) { char *table2 = cartUsualString(cart, hgtaCorrelateTable, "none"); hPrintf("<TR><TD><B>correlation:</B>\n"); if (differentWord(table2, "none") && strlen(table2) && ! isNoGenomeDisabled(database, table2)) { struct grp *groupList = fullGroupList; struct grp *selGroup = findSelectedGroup(groupList, hgtaCorrelateGroup); struct trackDb *tdb2 = findSelectedTrack(fullTrackList, selGroup,hgtaCorrelateTrack); if (tdbIsComposite(tdb2)) { struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(tdb2->subtracks); struct slRef *tdbRef; for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next) { struct trackDb *subTdb = tdbRef->val; if (sameString(table2, subTdb->table)) { tdb2 = subTdb; break; } } slFreeList(&tdbRefList); } cgiMakeButton(hgtaDoCorrelatePage, "calculate"); cgiMakeButton(hgtaDoClearCorrelate, "clear"); if (tdb2 && tdb2->shortLabel) hPrintf(" (with: %s)", tdb2->shortLabel); #ifdef NOT_YET /* debugging dbg vvvvv */ if (curTrack && curTrack->type) /* dbg */ { hPrintf("<BR> (debug: '%s', '%s(%s)')", curTrack->type, tdb2->type, table2); } /* debugging debug ^^^^^ */ #endif } else cgiMakeButton(hgtaDoCorrelatePage, "create"); hPrintf("</TD></TR>\n"); } /* Print output type line. */ showOutputTypeRow(isWig, isBedGr, isPositional, isMaf, isChromGraphCt, isPal, isArray, isHalSnake); /* Print output destination line. */ { char *compressType = cartUsualString(cart, hgtaCompressType, textOutCompressNone); char *fileName = cartUsualString(cart, hgtaOutFileName, ""); hPrintf("<TR><TD>\n"); hPrintf("<B>output file:</B> "); cgiMakeTextVar(hgtaOutFileName, fileName, 29); hPrintf(" (leave blank to keep output in browser)</TD></TR>\n"); hPrintf("<TR><TD>\n"); hPrintf("<B>file type returned: </B>"); cgiMakeRadioButton(hgtaCompressType, textOutCompressNone, sameWord(textOutCompressNone, compressType)); hPrintf(" plain text  "); cgiMakeRadioButton(hgtaCompressType, textOutCompressGzip, sameWord(textOutCompressGzip, compressType)); hPrintf(" gzip compressed"); hPrintf("</TD></TR>\n"); } hPrintf("</TABLE>\n"); /* Submit buttons. */ { hPrintf("<BR>\n"); if (isWig || isBam || isVcf || isLongTabix || isHic) { char *name; extern char *maxOutMenu[]; char *maxOutput = maxOutMenu[0]; if (isCustomTrack(curTable)) name=filterFieldVarName("ct", curTable, "_", filterMaxOutputVar); else name=filterFieldVarName(database,curTable, "_",filterMaxOutputVar); maxOutput = cartUsualString(cart, name, maxOutMenu[0]); if (isWig) hPrintf( "<I>Note: to return more than %s lines, change the filter setting" " (above). The entire data set may be available for download as" " a very large file that contains the original data values (not" " compressed into the wiggle format) -- see the Downloads page." "</I><BR>", maxOutput); else if (isBam || isVcf || isLongTabix || isHic) hPrintf( "<I>Note: to return more than %s lines, change the filter setting" " (above). Please consider downloading the entire data from our Download pages." "</I><BR>", maxOutput); } else if (anySubtrackMerge(database, curTable) || anyIntersection()) { hPrintf("<I>Note: The all fields and selected fields output formats " "are not available when a%s has been specified.</I><BR>", canSubtrackMerge ? " subtrack merge or intersection" : "n intersection"); } cgiMakeButton(hgtaDoTopSubmit, "get output"); hPrintf(" "); if (isPositional || isWig) { cgiMakeButton(hgtaDoSummaryStats, "summary/statistics"); hPrintf(" "); } #ifdef SOMETIMES hPrintf(" "); cgiMakeButton(hgtaDoTest, "test"); #endif /* SOMETIMES */ } hPrintf("<P>" "To reset <B>all</B> user cart settings (including custom tracks), \n" "<A HREF=\"/cgi-bin/cartReset?destination=%s\">click here</A>.\n", getScriptName()); } static char *getGenomeSpaceText() /* fetch GenomeSpace text if enabled */ { if (isGenomeSpaceEnabled()) { return "Send data to " "<A HREF=\"http://www.genomespace.org\" target=_BLANK>GenomeSpace</A> for use with diverse computational tools. "; } else { return ""; } } void mainPageAfterOpen(struct sqlConnection *conn) /* Put up main page assuming htmlOpen()/htmlClose() * will happen in calling routine. */ { hPrintf( "Use this program to retrieve the data associated with a track in text " "format, to calculate intersections between tracks, and to retrieve " "DNA sequence covered by a track. For help in using this application " "see <A HREF=\"#Help\">Using the Table Browser</A> for a description " "of the controls in this form, and the " "<A HREF=\"../goldenPath/help/hgTablesHelp.html\">User's Guide</A> for " "general information and sample queries. " "For more complex queries, you may want to use " "<A HREF=\""GALAXY_URL_BASE"\" target=_BLANK>Galaxy</A> or " "our <A HREF=\"../goldenPath/help/mysql.html\">public " "MySQL server</A>. " "To examine the biological function of your set through annotation " "enrichments, send the data to " "<A HREF=\"http://great.stanford.edu\" target=_BLANK>GREAT</A>. " "%s" "Refer to the " "<A HREF=\"../goldenPath/credits.html\">Credits</A> page for the list of " "contributors and usage restrictions associated with these data. " "All tables can be downloaded in their entirety from the " "<A HREF=\"http://hgdownload.soe.ucsc.edu/downloads.html\"" ">Sequence and Annotation Downloads</A> page." , getGenomeSpaceText() ); // When GREAT is selected, disable the other checkboxes and force output to BED jsInline( "function onSelectGreat() {\n" " document.getElementById('checkboxGalaxy').checked=false;\n"); if (isGenomeSpaceEnabled()) jsInline( " document.getElementById('checkboxGenomeSpace').checked=false;\n"); jsInline( " document.getElementById('outBed').selected=true;\n" " return true;\n" "}\n"); // Disable/enable noGenome tracks depending on whether region is genome. jsInline( "function maybeDisableNoGenome() {\n" " var regionTypeSelected = $('input[name=\"hgta_regionType\"]:checked').val();\n" " var regionIsGenome = (regionTypeSelected === 'genome');\n" " var $noGenomeOptions = $('select[name=\"hgta_track\"] option.hgtaNoGenome');\n" " $noGenomeOptions.attr('disabled', regionIsGenome)\n" " .css('color', regionIsGenome ? '' : 'black');\n" "}\n" "$(document).ready(function() {\n" // once when the page loads, and every time the user changes the region type: " maybeDisableNoGenome();\n" " $('input[name=\"hgta_regionType\"]').change(maybeDisableNoGenome);\n" "});\n"); /* Main form. */ hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n", getScriptName(), cartUsualString(cart, "formMethod", "POST")); cartSaveSession(cart); jsInit(); showMainControlTable(conn); hPrintf("</FORM>\n"); /* Hidden form - for benefit of javascript. */ { static char *saveVars[] = { "clade", "org", "db", hgtaGroup, hgtaTrack, hgtaTable, hgtaRegionType, hgtaRange, hgtaOutputType, hgtaOutFileName}; jsCreateHiddenForm(cart, getScriptName(), saveVars, ArraySize(saveVars)); } /* Hidden form for jumping to custom tracks CGI. */ hPrintf("<FORM ACTION='%s' NAME='customTrackForm'>", hgCustomName()); cartSaveSession(cart); hPrintf("</FORM>\n"); /* Hidden form for jumping to track hub manager CGI. */ hPrintf("<FORM ACTION='%s' NAME='trackHubForm'>", hgHubConnectName()); cartSaveSession(cart); hPrintf("</FORM>\n"); webNewSection("<A NAME=\"Help\"></A>Using the Table Browser\n"); printMainHelp(); cartFlushHubWarnings(); } void doMainPage(struct sqlConnection *conn) /* Put up the first page user sees. */ { htmlOpen("Table Browser"); mainPageAfterOpen(conn); htmlClose(); }