a53b9958fa734f73aeffb9ddfe2fbad1ca65f90c galt Mon Jan 30 16:18:41 2017 -0800 Check-in of CSP2 Content-Security-Policy work. All C-language CGIs should now support CSP2 in browser to stop major forms of XSS javascript injection. Javascript on pages is gathered together, and then emitted in a single script block at the end with a nonce that tells the browser, this is js that we generated instead of being injected by a hacker. Both inline script from script blocks and inline js event handlers had to be pulled out and separated. You will not see js sprinkled through-out the page now. Older browsers that support CSP1 or that do not understand CSP at all will still work, just without protection. External js libraries loaded at runtime need to be added to the CSP policy header in src/lib/htmshell.c. diff --git src/hg/hgTables/mainPage.c src/hg/hgTables/mainPage.c index a41bcc9..77573c1 100644 --- src/hg/hgTables/mainPage.c +++ src/hg/hgTables/mainPage.c @@ -1,1003 +1,1015 @@ /* 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 *groupScript, +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 %s>\n", groupVar, groupScript); +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 *trackScript, +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 %s>\n", trackVar, trackScript); + 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\" %s>\n", trackVar, trackScript); + 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\" %s>\n", varName, onChangeTable()); +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 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(" "); if (!cfgOptionBooleanDefault("hgta.disableSendOutput", FALSE)) { hPrintf(" Send output to "); struct dyString *dy = dyStringNew(256); dyStringAppend(dy, - "onclick=\"document.getElementById('checkboxGreat').checked=false;"); + "document.getElementById('checkboxGreat').checked=false;"); if (isGenomeSpaceEnabled()) dyStringAppend(dy, "document.getElementById('checkboxGenomeSpace').checked=false;"); dyStringAppend(dy, - "return true;\""); - cgiMakeCheckBoxIdAndJS("sendToGalaxy", doGalaxy(), - "checkboxGalaxy", dy->string); + "return true;"); + cgiMakeCheckBoxWithId("sendToGalaxy", doGalaxy(), "checkboxGalaxy"); + jsOnEventById("click", "checkboxGalaxy", dy->string); hPrintf("<A HREF=\""GALAXY_URL_BASE"\" target=_BLANK>Galaxy</A>\n"); nbSpaces(2); - cgiMakeCheckBoxIdAndJS("sendToGreat", doGreat(), - "checkboxGreat", - "onclick=\"return onSelectGreat();\""); + cgiMakeCheckBoxWithId("sendToGreat", doGreat(), "checkboxGreat"); + jsOnEventById("click", "checkboxGreat", "return onSelectGreat();"); hPrintf(" <A HREF=\"http://great.stanford.edu\" target=_BLANK>GREAT</A>"); if (isGenomeSpaceEnabled()) { nbSpaces(2); - cgiMakeCheckBoxIdAndJS("sendToGenomeSpace", doGenomeSpace(), - "checkboxGenomeSpace", - "onclick=\"document.getElementById('checkboxGreat').checked=false;" - "document.getElementById('checkboxGalaxy').checked=false; return true;\""); + 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", }; 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; 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), onChangeClade()); + printCladeListHtml(hGenome(database), "change", onChangeClade()); nbSpaces(3); hPrintf("<B>genome:</B>\n"); - printGenomeListForCladeHtml(database, onChangeOrg()); + printGenomeListForCladeHtml(database, "change", onChangeOrg()); } else { hPrintf("<TR><TD><B>genome:</B>\n"); - printGenomeListHtml(database, onChangeOrg()); + printGenomeListHtml(database, "change", onChangeOrg()); } nbSpaces(3); hPrintf("<B>assembly:</B>\n"); - printAssemblyListHtml(database, onChangeDb()); + printAssemblyListHtml(database, "change", onChangeDb()); hPrintf("</TD></TR>\n"); } /* Print group and track line. */ { hPrintf("<TR><TD>"); - selGroup = showGroupField(hgtaGroup, onChangeGroupOrTrack(), conn, hAllowAllTables()); + selGroup = showGroupField(hgtaGroup, "change", onChangeGroupOrTrack(), conn, hAllowAllTables()); nbSpaces(3); - curTrack = showTrackField(selGroup, hgtaTrack, onChangeGroupOrTrack(), FALSE); + 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("document.customTrackForm.submit();return false;", + hOnClickButton("showMainCtlTbl_Ct", "document.customTrackForm.submit();return false;", hasCustomTracks ? CT_MANAGE_BUTTON_LABEL : CT_ADD_BUTTON_LABEL); hPrintf(" "); if (hubConnectTableExists()) - hOnClickButton("document.trackHubForm.submit();return false;", "track hubs"); + 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); 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); } /* Region line */ { char *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\" SIZE=26 VALUE=\"%s\" onFocus=\"%s\">\n", - hgtaRange, range, jsRadioUpdate(hgtaRegionType, "regionType", "range")); + 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); 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) { 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) 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, the " "<A HREF=\"../goldenPath/help/hgTablesHelp.html\">User's Guide</A> for " "general information and sample queries, and the OpenHelix Table Browser " "<A HREF=\"http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28\" " "TARGET=_blank>tutorial</A> for a narrated presentation of the software " "features and usage. " "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.cse.ucsc.edu/downloads.html\"" ">Sequence and Annotation Downloads</A> page." , getGenomeSpaceText() ); -hPrintf("<script type=\"text/javascript\">\n"); // When GREAT is selected, disable the other checkboxes and force output to BED -hPrintf("function onSelectGreat() {\n"); -hPrintf("document.getElementById('checkboxGalaxy').checked=false;\n"); +struct dyString *js = dyStringNew(1024); +dyStringPrintf(js, + "function onSelectGreat() {\n" + " document.getElementById('checkboxGalaxy').checked=false;\n"); if (isGenomeSpaceEnabled()) - hPrintf("document.getElementById('checkboxGenomeSpace').checked=false;\n"); -hPrintf("document.getElementById('outBed').selected=true;\n"); -hPrintf("return true;\n"); -hPrintf("}\n"); + dyStringPrintf(js, + " document.getElementById('checkboxGenomeSpace').checked=false;\n"); +dyStringPrintf(js, + " document.getElementById('outBed').selected=true;\n" + " return true;\n" + "}\n"); +jsInline(js->string); + // Disable/enable noGenome tracks depending on whether region is genome. -hPrintf("function maybeDisableNoGenome() {\n" +dyStringClear(js); +dyStringPrintf(js, + "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" - "</script>\n"); + "});\n"); +jsInline(js->string); /* 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(); }