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/hgTracks/searchTracks.c src/hg/hgTracks/searchTracks.c
index 75915e0..5269f8d 100644
--- src/hg/hgTracks/searchTracks.c
+++ src/hg/hgTracks/searchTracks.c
@@ -1,808 +1,843 @@
/* Track search code used by hgTracks CGI */
/* Copyright (C) 2012 The Regents of the University of California
* See README in this or parent directory for licensing information. */
#include "common.h"
#include "search.h"
#include "hCommon.h"
#include "memalloc.h"
#include "obscure.h"
#include "dystring.h"
#include "hash.h"
#include "cheapcgi.h"
#include "hPrint.h"
#include "htmshell.h"
#include "cart.h"
#include "hgTracks.h"
#include "web.h"
#include "jksql.h"
#include "hdb.h"
#include "mdb.h"
#include "fileUi.h"
#include "trix.h"
#include "jsHelper.h"
#include "imageV2.h"
#define TRACK_SEARCH_FORM "trackSearch"
#define SEARCH_RESULTS_FORM "searchResults"
#define TRACK_SEARCH_CURRENT_TAB "tsCurTab"
#define TRACK_SEARCH_SIMPLE "tsSimple"
#define TRACK_SEARCH_ON_NAME "tsName"
#define TRACK_SEARCH_ON_TYPE "tsType"
#define TRACK_SEARCH_ON_GROUP "tsGroup"
#define TRACK_SEARCH_ON_DESCR "tsDescr"
#define TRACK_SEARCH_SORT "tsSort"
static int gCmpGroup(const void *va, const void *vb)
/* Compare groups based on label. */
{
const struct group *a = *((struct group **)va);
const struct group *b = *((struct group **)vb);
return strcmp(a->label, b->label);
}
// Would like to do a radio button choice ofsorts
enum sortBy
{
sbRelevance=0,
sbAbc =1,
sbHierarchy=2,
};
static int gCmpTrackHierarchy(const void *va, const void *vb)
/* Compare tracks based on longLabel. */
{
const struct slRef *aa = *((struct slRef **)va);
const struct slRef *bb = *((struct slRef **)vb);
const struct track *a = ((struct track *) aa->val);
const struct track *b = ((struct track *) bb->val);
if ( tdbIsFolder(a->tdb) && !tdbIsFolder(b->tdb))
return -1;
else if (!tdbIsFolder(a->tdb) && tdbIsFolder(b->tdb))
return 1;
if ( tdbIsContainer(a->tdb) && !tdbIsContainer(b->tdb))
return -1;
else if (!tdbIsContainer(a->tdb) && tdbIsContainer(b->tdb))
return 1;
if (!tdbIsContainerChild(a->tdb) && tdbIsContainerChild(b->tdb))
return -1;
else if ( tdbIsContainerChild(a->tdb) && !tdbIsContainerChild(b->tdb))
return 1;
return strcasecmp(a->longLabel, b->longLabel);
}
static int gCmpTrack(const void *va, const void *vb)
/* Compare tracks based on longLabel. */
{
const struct slRef *aa = *((struct slRef **)va);
const struct slRef *bb = *((struct slRef **)vb);
const struct track *a = ((struct track *) aa->val);
const struct track *b = ((struct track *) bb->val);
return strcasecmp(a->longLabel, b->longLabel);
}
static void findTracksSort(struct slRef **pTrack, enum sortBy sortBy)
{
if (sortBy == sbHierarchy)
slSort(pTrack, gCmpTrackHierarchy);
else if (sortBy == sbAbc)
slSort(pTrack, gCmpTrack);
else
slReverse(pTrack);
}
static int getFormatTypes(char ***pLabels, char ***pTypes)
{
char *crudeTypes[] = {
ANYLABEL,
"bam",
"psl",
"chain",
"netAlign",
"maf",
"bed",
"bigBed",
"ctgPos",
"expRatio",
"genePred",
"broadPeak",
"narrowPeak",
"rmsk",
"bedGraph",
"bigWig",
"wig",
"wigMaf"
};
// Non-standard:
// type altGraphX
// type axt
// type bed5FloatScore
// type bed5FloatScoreWithFdr
// type chromGraph
// type clonePos
// type coloredExon
// type encodeFiveC
// type factorSource
// type ld2
// type logo
// type maf
// type sample
// type wigMafProt 0.0 1.0
char *nicerTypes[] = {
ANYLABEL,
"Alignment binary (bam) - binary SAM",
"Alignment Blast (psl) - Blast output",
"Alignment Chains (chain) - Pairwise alignment",
"Alignment Nets (netAlign) - Net alignments",
"Alignments (maf) - multiple alignment format",
"bed - browser extensible data",
"bigBed - self index, often remote bed format",
"ctgPos - Contigs",
"expRatio - Expression ratios",
"Genes (genePred) - Gene prediction and annotation",
"Peaks Broad (broadPeak) - ENCODE large region peak format",
"Peaks Narrow (narrowPeak) - ENCODE small region peak format",
"Repeats (rmsk) - Repeat masking",
"Signal (bedGraph) - graphically represented bed data",
"Signal (bigWig) - self index, often remote wiggle format",
"Signal (wig) - wiggle format",
"Signal (wigMaf) - multiple alignment wiggle"
};
int ix = 0, count = sizeof(crudeTypes)/sizeof(char *);
char **labels;
char **values;
AllocArray(labels, count);
AllocArray(values, count);
for (ix=0;ix<count;ix++)
{
labels[ix] = cloneString(nicerTypes[ix]);
values[ix] = cloneString(crudeTypes[ix]);
}
*pLabels = labels;
*pTypes = values;
return count;
}
static struct slRef *simpleSearchForTracksstruct(char *simpleEntry)
// Performs the simple search and returns the found tracks.
{
struct slRef *tracks = NULL;
// Prepare for trix search
if (!isEmpty(simpleEntry))
{
int trixWordCount = 0;
char *tmp = cloneString(simpleEntry);
char *val = nextWord(&tmp);
struct slName *el, *trixList = NULL;
while (val != NULL)
{
slNameAddTail(&trixList, val);
trixWordCount++;
val = nextWord(&tmp);
}
if (trixWordCount > 0)
{
// Unfortunately trixSearch can't handle the slName list
int i;
char **trixWords = needMem(sizeof(char *) * trixWordCount);
for (i = 0, el = trixList; el != NULL; i++, el = el->next)
trixWords[i] = strLower(el->name);
// Now open the trix file
char trixFile[HDB_MAX_PATH_STRING];
getSearchTrixFile(database, trixFile, sizeof(trixFile));
struct trix *trix = trixOpen(trixFile);
struct trixSearchResult *tsList = trixSearch(trix, trixWordCount, trixWords, tsmExpand);
for ( ; tsList != NULL; tsList = tsList->next)
{
struct track *track = (struct track *) hashFindVal(trackHash, tsList->itemId);
if (track != NULL) // It is expected that this is NULL
{ // (e.g. when trix references trackDb tracks which have no tables)
refAdd(&tracks, track);
}
}
//trixClose(trix); // don't bother (this is a CGI that is about to end)
}
}
return tracks;
}
static struct slRef *advancedSearchForTracks(struct sqlConnection *conn,struct group *groupList,
char *nameSearch, char *typeSearch, char *descSearch,
char *groupSearch, struct slPair *mdbPairs)
// Performs the advanced search and returns the found tracks.
{
int tracksFound = 0;
struct slRef *tracks = NULL;
int numMetadataNonEmpty = 0;
struct slPair *pair = mdbPairs;
for (; pair!= NULL;pair=pair->next)
{
if (!isEmpty((char *)(pair->val)))
numMetadataNonEmpty++;
}
if (!isEmpty(groupSearch) && sameString(groupSearch,ANYLABEL))
groupSearch = NULL;
if (!isEmpty(typeSearch) && sameString(typeSearch,ANYLABEL))
typeSearch = NULL;
if (isEmpty(nameSearch) && isEmpty(typeSearch) && isEmpty(descSearch)
&& isEmpty(groupSearch) && numMetadataNonEmpty == 0)
return NULL;
// First do the metaDb searches, which can be done quickly for all tracks with db queries.
struct hash *matchingTracks = NULL;
if (numMetadataNonEmpty)
{
struct mdbObj *mdbObj, *mdbObjs = mdbObjRepeatedSearch(conn,mdbPairs,TRUE,FALSE);
if (mdbObjs)
{
for (mdbObj = mdbObjs; mdbObj != NULL; mdbObj = mdbObj->next)
{
if (matchingTracks == NULL)
matchingTracks = newHash(0);
hashAddInt(matchingTracks, mdbObj->obj, 1);
}
mdbObjsFree(&mdbObjs);
}
if (matchingTracks == NULL)
return NULL;
}
// Set the word lists up once
struct slName *nameList = NULL;
if (!isEmpty(nameSearch))
nameList = slNameListOfUniqueWords(cloneString(nameSearch),TRUE); // TRUE means respect quotes
struct slName *descList = NULL;
if (!isEmpty(descSearch))
descList = slNameListOfUniqueWords(cloneString(descSearch),TRUE);
struct group *group;
for (group = groupList; group != NULL; group = group->next)
{
if (isEmpty(groupSearch) || sameString(group->name, groupSearch))
{
if (group->trackList == NULL)
continue;
struct trackRef *tr;
for (tr = group->trackList; tr != NULL; tr = tr->next)
{
struct track *track = tr->track;
char *trackType = cloneFirstWord(track->tdb->type); // will be spilled
if ((matchingTracks == NULL || hashLookup(matchingTracks, track->track) != NULL)
&& ( isEmpty(typeSearch)
|| (sameWord(typeSearch, trackType) && !tdbIsComposite(track->tdb)))
&& (isEmpty(nameSearch) || searchNameMatches(track->tdb, nameList))
&& (isEmpty(descSearch) || searchDescriptionMatches(track->tdb, descList)))
{
if (track != NULL)
{
tracksFound++;
refAdd(&tracks, track);
}
else
warn("found group track is NULL.");
}
if (track->subtracks != NULL)
{
struct track *subTrack;
for (subTrack = track->subtracks; subTrack != NULL; subTrack = subTrack->next)
{
trackType = cloneFirstWord(subTrack->tdb->type); // will be spilled
if ( (matchingTracks == NULL
|| hashLookup(matchingTracks, subTrack->track) != NULL)
&& (isEmpty(typeSearch) || sameWord(typeSearch, trackType))
&& (isEmpty(nameSearch) || searchNameMatches(subTrack->tdb, nameList))
&& (isEmpty(descSearch) // subtracks inherit description
|| searchDescriptionMatches(subTrack->tdb, descList)
|| (tdbIsCompositeChild(subTrack->tdb) && subTrack->parent
&& searchDescriptionMatches(subTrack->parent->tdb, descList))))
{
if (track != NULL)
{
tracksFound++;
refAdd(&tracks, subTrack);
}
else
warn("found subtrack is NULL.");
}
}
}
}
}
}
return tracks;
}
#define MAX_FOUND_TRACKS 100
static void findTracksPageLinks(int tracksFound, int startFrom)
{
if (tracksFound <= MAX_FOUND_TRACKS)
return;
// Opener
int willStartAt = 0;
int curPage = (startFrom/MAX_FOUND_TRACKS) + 1;
int endAt = startFrom+MAX_FOUND_TRACKS;
if (endAt > tracksFound)
endAt = tracksFound;
hPrintf("<span><em style='font-size:.9em;'>Listing %d - %d of %d tracks</em> ",
startFrom+1,endAt,tracksFound);
+char javascript[1024];
// << and <
if (startFrom >= MAX_FOUND_TRACKS)
{
- hPrintf("<a href='../cgi-bin/hgTracks?%s=Search&%s=0' title='First page of found tracks' "
- "onclick='return findTracks.page(\"%s\",0);'>«</a> ",
- TRACK_SEARCH,TRACK_SEARCH_PAGER,TRACK_SEARCH_PAGER);
+ hPrintf("<a href='../cgi-bin/hgTracks?%s=Search&%s=0' id='ftpl1' title='First page of found tracks'"
+ ">«</a> ",
+ TRACK_SEARCH,TRACK_SEARCH_PAGER);
+ safef(javascript, sizeof javascript, "return findTracks.page(\"%s\",0);", TRACK_SEARCH_PAGER);
+ jsOnEventById("click", "ftpl1", javascript);
+
willStartAt = startFrom - MAX_FOUND_TRACKS;
- hPrintf(" <a href='../cgi-bin/hgTracks?%s=Search&%s=%d' title='Previous page of found "
- "tracks' onclick='return findTracks.page(\"%s\",%d);'>‹</a> ",
- TRACK_SEARCH,TRACK_SEARCH_PAGER,willStartAt,TRACK_SEARCH_PAGER,willStartAt);
+ hPrintf(" <a href='../cgi-bin/hgTracks?%s=Search&%s=%d' id='ftpl2' "
+ "title='Previous page of found tracks'>‹</a> ",
+ TRACK_SEARCH,TRACK_SEARCH_PAGER,willStartAt);
+ safef(javascript, sizeof javascript, "return findTracks.page(\"%s\",%d);", TRACK_SEARCH_PAGER,willStartAt);
+ jsOnEventById("click", "ftpl2", javascript);
}
// page number links
int lastPage = (tracksFound/MAX_FOUND_TRACKS);
if ((tracksFound % MAX_FOUND_TRACKS) > 0)
lastPage++;
int thisPage = curPage - 3; // Window of 3 pages above and below
if (thisPage < 1)
thisPage = 1;
for (;thisPage <= lastPage && thisPage <= curPage + 3; thisPage++)
{
if (thisPage != curPage)
{
willStartAt = ((thisPage - 1) * MAX_FOUND_TRACKS);
endAt = willStartAt+ MAX_FOUND_TRACKS;
if (endAt > tracksFound)
endAt = tracksFound;
- hPrintf(" <a href='../cgi-bin/hgTracks?%s=Search&%s=%d' title='Page %d (%d - %d) "
- "tracks' onclick='return findTracks.page(\"%s\",%d);'>%d</a> ",
- TRACK_SEARCH,TRACK_SEARCH_PAGER,willStartAt,thisPage,willStartAt+1,endAt,
- TRACK_SEARCH_PAGER,willStartAt,thisPage);
+ hPrintf(" <a href='../cgi-bin/hgTracks?%s=Search&%s=%d' id='ftpl3' "
+ "title='Page %d (%d - %d) tracks'>%d</a> ",
+ TRACK_SEARCH,TRACK_SEARCH_PAGER,willStartAt,thisPage,willStartAt+1,endAt,thisPage);
+ safef(javascript, sizeof javascript, "return findTracks.page(\"%s\",%d);",TRACK_SEARCH_PAGER,willStartAt);
+ jsOnEventById("click", "ftpl3", javascript);
}
else
hPrintf(" <em style='color:%s;'>%d</em> ",COLOR_DARKGREY,thisPage);
}
// > and >>
if ((startFrom + MAX_FOUND_TRACKS) < tracksFound)
{
willStartAt = startFrom + MAX_FOUND_TRACKS;
- hPrintf(" <a href='../cgi-bin/hgTracks?%s=Search&%s=%d' title='Next page of found tracks' "
- "onclick='return findTracks.page(\"%s\",%d);'>›</a> ",
- TRACK_SEARCH,TRACK_SEARCH_PAGER,willStartAt,TRACK_SEARCH_PAGER,willStartAt);
+ hPrintf(" <a href='../cgi-bin/hgTracks?%s=Search&%s=%d' id='ftpl4' "
+ "title='Next page of found tracks'>›</a> ",
+ TRACK_SEARCH,TRACK_SEARCH_PAGER,willStartAt);
+ safef(javascript, sizeof javascript, "return findTracks.page(\"%s\",%d);",TRACK_SEARCH_PAGER,willStartAt);
+ jsOnEventById("click", "ftpl4", javascript);
+
willStartAt = tracksFound - (tracksFound % MAX_FOUND_TRACKS);
if (willStartAt == tracksFound)
willStartAt -= MAX_FOUND_TRACKS;
- hPrintf(" <a href='../cgi-bin/hgTracks?%s=Search&%s=%d' title='Last page of found tracks' "
- "onclick='return findTracks.page(\"%s\",%d);'>»</a></span>\n",
- TRACK_SEARCH,TRACK_SEARCH_PAGER,willStartAt,TRACK_SEARCH_PAGER,willStartAt);
+ hPrintf(" <a href='../cgi-bin/hgTracks?%s=Search&%s=%d' id='ftpl5' title='Last page of found tracks' "
+ ">»</a></span>\n",
+ TRACK_SEARCH,TRACK_SEARCH_PAGER,willStartAt);
+ safef(javascript, sizeof javascript, "return findTracks.page(\"%s\",%d);",TRACK_SEARCH_PAGER,willStartAt);
+ jsOnEventById("click", "ftpl5", javascript);
}
}
static void displayFoundTracks(struct cart *cart, struct slRef *tracks, int tracksFound,
enum sortBy sortBy)
// Routine for displaying found tracks
{
+char id[256];
+char javascript[1024];
hPrintf("<div id='found' style='display:none;'>\n"); // This div is emptied with 'clear' button
if (tracksFound < 1)
{
hPrintf("<p>No tracks found</p>\n");
}
else
{
hPrintf("<form action='%s' name='%s' id='%s' method='post'>\n\n",
hgTracksName(),SEARCH_RESULTS_FORM,SEARCH_RESULTS_FORM);
cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo
int startFrom = 0;
hPrintf("<table id='foundTracks'>\n");
// Opening view in browser button and foundTracks count
#define ENOUGH_FOUND_TRACKS 10
if (tracksFound >= ENOUGH_FOUND_TRACKS)
{
hPrintf("<tr><td nowrap colspan=3>\n");
hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='return to browser' class='viewBtn' "
"style='font-size:.8em;'>");
hPrintf(" <span class='selCbCount'></span>\n");
startFrom = cartUsualInt(cart,TRACK_SEARCH_PAGER,0);
if (startFrom > 0 && startFrom < tracksFound)
{
int countUp = 0;
for (countUp=0; countUp < startFrom;countUp++)
{
if (slPopHead(&tracks) == NULL) // memory waste
break;
}
}
hPrintf("</td><td align='right' valign='bottom'>\n");
findTracksPageLinks(tracksFound,startFrom);
hPrintf("</td></tr>\n");
}
// Begin foundTracks table
//hPrintf("<table id='foundTracks'><tr><td colspan='2'>\n");
hPrintf("<tr><td colspan='2'>\n");
hPrintf("</td><td align='right'>\n");
hPrintf("</td></tr><tr bgcolor='#%s'><td>",HG_COL_HEADER);
#define PM_BUTTON \
- "<IMG height=18 width=18 onclick=\"return findTracks.checkAllWithWait(%s);\" " \
+ "<IMG height=18 width=18 " \
"id='btn_%s' src='../images/%s' title='%s all found tracks'>"
- hPrintf(PM_BUTTON,"true", "plus_all", "add_sm.gif", "Select");
- hPrintf(PM_BUTTON,"false","minus_all","remove_sm.gif","Unselect");
+ hPrintf(PM_BUTTON,"plus_all", "add_sm.gif", "Select");
+ hPrintf(PM_BUTTON,"minus_all","remove_sm.gif","Unselect");
+ safef(javascript, sizeof javascript, "return findTracks.checkAllWithWait(true);");
+ jsOnEventById("click", "btn_plus_all", javascript);
+ safef(javascript, sizeof javascript, "return findTracks.checkAllWithWait(false);");
+ jsOnEventById("click", "btn_minus_all", javascript);
hPrintf("</td><td><b>Visibility</b></td><td colspan=2> <b>Track Name</b>\n");
// Sort options?
if (tracksFound >= ENOUGH_FOUND_TRACKS)
{
hPrintf("<span style='float:right;'>Sort:");
- cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "0", (sortBy == sbRelevance),
- "onclick=\"findTracks.sortNow(this);\"");
+ cgiMakeOnEventRadioButtonWithClass(TRACK_SEARCH_SORT, "0", (sortBy == sbRelevance),
+ NULL,"click", "findTracks.sortNow(this);");
hPrintf("by Relevance");
- cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "1", (sortBy == sbAbc),
- "onclick=\"findTracks.sortNow(this);\"");
+ cgiMakeOnEventRadioButtonWithClass(TRACK_SEARCH_SORT, "1", (sortBy == sbAbc),
+ NULL,"click", "findTracks.sortNow(this);");
hPrintf("Alphabetically");
- cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "2",(sortBy == sbHierarchy),
- "onclick=\"findTracks.sortNow(this);\"");
+ cgiMakeOnEventRadioButtonWithClass(TRACK_SEARCH_SORT, "2", (sortBy == sbHierarchy),
+ NULL,"click", "findTracks.sortNow(this);");
hPrintf("by Hierarchy </span>\n");
}
hPrintf("</td></tr>\n");
// Set up json for js functionality
struct jsonElement *jsonTdbVars = newJsonObject(newHash(8));
int trackCount=0;
boolean containerTrackCount = 0;
struct slRef *ptr;
while((ptr = slPopHead(&tracks)))
{
if (++trackCount > MAX_FOUND_TRACKS)
break;
struct track *track = (struct track *) ptr->val;
jsonTdbSettingsBuild(jsonTdbVars, track, FALSE); // FALSE: No config from track search
if (tdbIsFolder(track->tdb)) // supertrack
hPrintf("<tr class='bgLevel4' valign='top' class='found'>\n");
else if (tdbIsContainer(track->tdb))
hPrintf("<tr class='bgLevel3' valign='top' class='found'>\n");
else
hPrintf("<tr class='bgLevel2' valign='top' class='found'>\n");
hPrintf("<td align='center'>\n");
// Determine visibility and checked state
track->visibility = tdbVisLimitedByAncestors(cart, track->tdb, TRUE, TRUE);
boolean checked = ( track->visibility != tvHide );
if (tdbIsContainerChild(track->tdb))
{
// Don't need all 4 states here. Visible=checked&&enabled
checked = fourStateVisible(subtrackFourStateChecked(track->tdb,cart));
// Checked is only if subtrack level vis is also set!
checked = (checked && ( track->visibility != tvHide ));
}
// Setup the check box
#define CB_HIDDEN_VAR "<INPUT TYPE=HIDDEN disabled=true NAME='%s_sel' VALUE='%s'>"
// subtracks and folder children get "_sel" var. ("_sel" var is temp on folder children)
if (tdbIsContainerChild(track->tdb) || tdbIsFolderContent(track->tdb))
hPrintf(CB_HIDDEN_VAR,track->track,checked?"1":CART_VAR_EMPTY);
- #define CB_SEEN "<INPUT TYPE=CHECKBOX id='%s_sel_id' VALUE='on' class='selCb' " \
- "onclick='findTracks.clickedOne(this,true);'%s>"
+ #define CB_SEEN "<INPUT TYPE=CHECKBOX id='%s_sel_id' VALUE='on' class='selCb' %s>"
hPrintf(CB_SEEN,track->track,(checked ? " CHECKED" : ""));
+ safef(id, sizeof id, "%s_sel_id", track->track); // XSS Filter?
+ safef(javascript, sizeof javascript, "findTracks.clickedOne(this,true);");
+ jsOnEventById("click", id, javascript);
hPrintf("</td><td>\n");
// Setup the visibility drop down
#define VIS_HIDDEN_VAR "<INPUT TYPE=HIDDEN disabled=true NAME='%s' VALUE='%s'>"
hPrintf(VIS_HIDDEN_VAR,track->track,CART_VAR_EMPTY); // All tracks get vis hidden var
- char extra[512];
if (tdbIsFolder(track->tdb))
{
- safef(extra,sizeof(extra),"id='%s_id' onchange='findTracks.changeVis(this)'",
- track->track);
+ safef(javascript, sizeof javascript, "findTracks.changeVis(this);");
+ struct slPair *event = slPairNew("change", cloneString(javascript));
hideShowDropDownWithClassAndExtra(track->track, (track->visibility != tvHide),
- "normalText visDD",extra);
+ "normalText visDD", event);
}
else
{
- safef(extra,sizeof(extra),"id='%s_id' onchange='findTracks.changeVis(this)'",
- track->track);
+ safef(javascript, sizeof javascript, "findTracks.changeVis(this);");
+ struct slPair *event = slPairNew("change", cloneString(javascript));
hTvDropDownClassWithJavascript(NULL, track->visibility,track->canPack,
- "normalText seenVis",extra);
+ "normalText seenVis",event);
}
// If this is a container track, allow configuring...
if (tdbIsContainer(track->tdb) || tdbIsFolder(track->tdb))
{
containerTrackCount++; // Using onclick ensures return to search tracks on submit
hPrintf(" <IMG SRC='../images/folderWrench.png' style='cursor:pointer;' "
- "title='Configure this track container...' "
- "onclick='findTracks.configSet(\"%s\");'> ", track->track);
+ "id='%s_confSet' title='Configure this track container...' "
+ "> ", track->track);
+ safef(id, sizeof id, "%s_confSet", track->track); // XSS Filter?
+ safef(javascript, sizeof javascript, "findTracks.configSet(\"%s\");", track->track);
+ jsOnEventById("click", id, javascript);
}
//#define SHOW_PARENT_FOLDER
#ifdef SHOW_PARENT_FOLDER
else if (tdbIsContainerChild(track->tdb) || tdbIsFolderContent(track->tdb))
{
struct trackDb *parentTdb =
tdbIsContainerChild(track->tdb) ? tdbGetContainer(track->tdb)
: tdbGetImmediateFolder(track->tdb);
if (parentTdb != NULL) // Using href will not return to search tracks on submit
hPrintf(" <A HREF='../cgi-bin/hgTrackUi?g=%s'><IMG SRC='../images/folderC.png'"
" title='Navigate to parent container...'></A> ", parentTdb->track);
}
#endif///def SHOW_PARENT_FOLDER
hPrintf("</td>\n");
// shortLabel has description popup and longLabel has "..." metadata
- hPrintf("<td><a target='_top' onclick=\"popUp.hgTrackUi('%s',true); return false;\" "
+ hPrintf("<td><a target='_top' id='%s_dispFndTrk' "
"href='%s' title='Display track details'>%s</a></td>\n",
track->track, trackUrl(track->track, NULL), track->shortLabel);
+ safef(id, sizeof id, "%s_dispFndTrk", track->track);
+ safef(javascript, sizeof javascript, "popUp.hgTrackUi('%s',true); return false;", track->track);
+ jsOnEventById("click", id, javascript);
hPrintf("<td>%s", track->longLabel);
compositeMetadataToggle(database, track->tdb, NULL, TRUE, FALSE);
hPrintf("</td></tr>\n");
}
//hPrintf("</table>\n");
// Closing view in browser button and foundTracks count
hPrintf("<tr><td nowrap colspan=3>");
hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='Return to Browser' class='viewBtn' "
"style='font-size:.8em;'>");
hPrintf(" <span class='selCbCount'></span>");
if (tracksFound >= ENOUGH_FOUND_TRACKS)
{
hPrintf("</td><td align='right' valign='top'>\n");
findTracksPageLinks(tracksFound,startFrom);
hPrintf("</td></tr>\n");
}
hPrintf("</table>\n");
if (containerTrackCount > 0)
hPrintf("<BR><IMG SRC='../images/folderWrench.png'> Tracks so marked are containers "
"which group related data tracks. Containers may need additional configuration "
"(by clicking on the <IMG SRC='../images/folderWrench.png'> icon) before they can "
"be viewed in the browser.<BR>\n");
//hPrintf("* Tracks so marked are containers which group related data tracks. These may "
// "not be visible unless further configuration is done. Click on the * to "
// "configure these.<BR><BR>\n");
hPrintf("\n</form>\n");
// be done with json
jsonTdbSettingsUse(jsonTdbVars);
}
hPrintf("</div>"); // This div allows the clear button to empty it
}
void doSearchTracks(struct group *groupList)
{
+char javascript[1024];
webIncludeResourceFile("ui.dropdownchecklist.css");
jsIncludeFile("ui.dropdownchecklist.js",NULL);
// This line is needed to get the multi-selects initialized
jsIncludeFile("ddcl.js",NULL);
struct group *group;
char *groups[128];
char *labels[128];
int numGroups = 1;
groups[0] = ANYLABEL;
labels[0] = ANYLABEL;
char *nameSearch = cartOptionalString(cart, TRACK_SEARCH_ON_NAME);
char *typeSearch = cartUsualString( cart, TRACK_SEARCH_ON_TYPE,ANYLABEL);
char *simpleEntry = cartOptionalString(cart, TRACK_SEARCH_SIMPLE);
char *descSearch = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR);
char *groupSearch = cartUsualString( cart, TRACK_SEARCH_ON_GROUP,ANYLABEL);
boolean doSearch = sameString(cartOptionalString(cart, TRACK_SEARCH), "Search")
|| cartUsualInt(cart, TRACK_SEARCH_PAGER, -1) >= 0;
struct sqlConnection *conn = hAllocConn(database);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
int tracksFound = 0;
int cols;
char buf[512];
char *currentTab = cartUsualString(cart, TRACK_SEARCH_CURRENT_TAB, "simpleTab");
enum searchTab selectedTab = (sameString(currentTab, "advancedTab") ? advancedTab : simpleTab);
// NOTE: could support quotes in simple tab by detecting quotes and choosing
// to use doesNameMatch() || doesDescriptionMatch()
if (selectedTab == simpleTab && !isEmpty(simpleEntry))
stripChar(simpleEntry, '"');
trackList = getTrackList(&groupList, -2); // global
makeGlobalTrackHash(trackList);
// NOTE: This is necessary when container cfg by '*' results in vis changes
// This will handle composite/view override when subtrack specific vis exists,
// AND superTrack reshaping.
// Subtrack settings must be removed when composite/view settings are updated
parentChildCartCleanup(trackList,cart,oldVars);
slSort(&groupList, gCmpGroup);
for (group = groupList; group != NULL; group = group->next)
{
groupTrackListAddSuper(cart, group);
if (group->trackList != NULL)
{
groups[numGroups] = cloneString(group->name);
labels[numGroups] = cloneString(group->label);
numGroups++;
if (numGroups >= ArraySize(groups))
internalErr();
}
}
safef(buf, sizeof(buf),"Search for Tracks in the %s %s Assembly",
organism, hFreezeFromDb(database));
webStartWrapperDetailedNoArgs(cart, database, "", buf, FALSE, FALSE, FALSE, FALSE);
hPrintf("<div style='max-width:1080px;'>");
hPrintf("<form action='%s' name='%s' id='%s' method='get'>\n\n",
hgTracksName(),TRACK_SEARCH_FORM,TRACK_SEARCH_FORM);
cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo
safef(buf, sizeof(buf), "%lu", clock1());
cgiMakeHiddenVar("hgt_", buf); // timestamps page to avoid browser cache
hPrintf("<input type='hidden' name='db' value='%s'>\n", database);
hPrintf("<input type='hidden' name='%s' id='currentTab' value='%s'>\n",
TRACK_SEARCH_CURRENT_TAB, currentTab);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_DEL_ROW);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_ADD_ROW);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_PAGER);
hPrintf("<div id='tabs' style='display:none; %s'>\n<ul>\n<li><a href='#simpleTab'>"
"<B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Search</B>"
"</a></li>\n<li><a href='#advancedTab'>"
"<B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Advanced</B>"
"</a></li>\n</ul>\n<div id='simpleTab' style='max-width:inherit;'>\n",
cgiBrowser()==btIE?"width:1060px;":"max-width:inherit;");
hPrintf("<table id='simpleTable' style='width:100%%; font-size:.9em;'><tr><td colspan='2'>");
hPrintf("<input type='text' name='%s' id='simpleSearch' class='submitOnEnter' value='%s' "
- "style='max-width:1000px; width:100%%;' onkeyup='findTracks.searchButtonsEnable(true);'>\n",
+ "style='max-width:1000px; width:100%%;'>\n",
TRACK_SEARCH_SIMPLE,simpleEntry == NULL ? "" : simpleEntry);
+safef(javascript, sizeof javascript, "findTracks.searchButtonsEnable(true);");
+jsOnEventById("keyup", "simpleSearch", javascript);
hPrintf("</td></tr><td style='max-height:4px;'></td></tr></table>");
//hPrintf("</td></tr></table>");
hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' "
"style='font-size:.8em;'>\n", TRACK_SEARCH);
-hPrintf("<input type='button' name='clear' value='clear' class='clear' "
- "style='font-size:.8em;' onclick='findTracks.clear();'>\n");
+hPrintf("<input type='button'id='doSTClear1' name='clear' value='clear' class='clear' "
+ "style='font-size:.8em;'>\n");
+safef(javascript, sizeof javascript, "findTracks.clear();");
+jsOnEventById("click", "doSTClear1", javascript);
hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' "
"style='font-size:.8em;'>\n");
hPrintf("</div>\n");
// Advanced tab
hPrintf("<div id='advancedTab' style='width:inherit;'>\n"
"<table id='advancedTable' cellSpacing=0 style='width:inherit; font-size:.9em;'>\n");
cols = 8;
// Track Name contains
hPrintf("<tr><td colspan=3></td>");
hPrintf("<td nowrap><b style='max-width:100px;'>Track Name:</b></td>");
hPrintf("<td align='right'>contains</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
hPrintf("<input type='text' name='%s' id='nameSearch' class='submitOnEnter' value='%s' "
- "onkeyup='findTracks.searchButtonsEnable(true);' style='min-width:326px; font-size:.9em;'>",
+ "style='min-width:326px; font-size:.9em;'>",
TRACK_SEARCH_ON_NAME, nameSearch == NULL ? "" : nameSearch);
+safef(javascript, sizeof javascript, "findTracks.searchButtonsEnable(true);");
+jsOnEventById("keyup", "nameSearch", javascript);
hPrintf("</td></tr>\n");
// Description contains
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>");
hPrintf("<td><b style='max-width:100px;'>Description:</b></td>");
hPrintf("<td align='right'>contains</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
hPrintf("<input type='text' name='%s' id='descSearch' value='%s' class='submitOnEnter' "
- "onkeyup='findTracks.searchButtonsEnable(true);' "
"style='max-width:536px; width:536px; font-size:.9em;'>",
TRACK_SEARCH_ON_DESCR, descSearch == NULL ? "" : descSearch);
+safef(javascript, sizeof javascript, "findTracks.searchButtonsEnable(true);");
+jsOnEventById("keyup", "descSearch", javascript);
hPrintf("</td></tr>\n");
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n");
hPrintf("<td><b style='max-width:100px;'>Group:</b></td>");
hPrintf("<td align='right'>is</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
-cgiMakeDropListFull(TRACK_SEARCH_ON_GROUP, labels, groups, numGroups, groupSearch,
- "class='groupSearch' style='min-width:40%; font-size:.9em;'");
+cgiMakeDropListFullExt(TRACK_SEARCH_ON_GROUP, labels, groups, numGroups, groupSearch,
+ NULL, NULL, "min-width:40%; font-size:.9em;", "groupSearch");
hPrintf("</td></tr>\n");
// Track Type is (drop down)
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n");
hPrintf("<td nowrap><b style='max-width:100px;'>Data Format:</b></td>");
hPrintf("<td align='right'>is</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
char **formatTypes = NULL;
char **formatLabels = NULL;
int formatCount = getFormatTypes(&formatLabels, &formatTypes);
-cgiMakeDropListFull(TRACK_SEARCH_ON_TYPE, formatLabels, formatTypes, formatCount, typeSearch,
- "class='typeSearch' style='min-width:40%; font-size:.9em;'");
+cgiMakeDropListFullExt(TRACK_SEARCH_ON_TYPE, formatLabels, formatTypes, formatCount, typeSearch,
+ NULL, NULL, "'min-width:40%; font-size:.9em;", "typeSearch");
hPrintf("</td></tr>\n");
// mdb selects
struct slPair *mdbSelects = NULL;
if (metaDbExists)
{
struct slPair *mdbVars = mdbVarsSearchable(conn,TRUE,FALSE); // Tables but not file only objects
mdbSelects = mdbSelectPairs(cart, mdbVars);
char *output = mdbSelectsHtmlRows(conn,mdbSelects,mdbVars,cols,FALSE); // not a fileSearch
if (output)
{
puts(output);
freeMem(output);
}
slPairFreeList(&mdbVars);
}
hPrintf("</table>\n");
hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' "
"style='font-size:.8em;'>\n", TRACK_SEARCH);
-hPrintf("<input type='button' name='clear' value='clear' class='clear' "
- "style='font-size:.8em;' onclick='findTracks.clear();'>\n");
+hPrintf("<input type='button' id='doSTClear2' name='clear' value='clear' class='clear' "
+ "style='font-size:.8em;'>\n");
+safef(javascript, sizeof javascript, "findTracks.clear();");
+jsOnEventById("click", "doSTClear2", javascript);
hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' "
"style='font-size:.8em;'>\n");
//hPrintf("<a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a>\n");
hPrintf("</div>\n");
hPrintf("</div>\n");
hPrintf("</form>\n");
hPrintf("</div>"); // Restricts to max-width:1000px;
cgiDown(0.8);
if (measureTiming)
measureTime("Rendered tabs");
if (doSearch)
{
// Now search
struct slRef *tracks = NULL;
if (selectedTab==simpleTab && !isEmpty(simpleEntry))
tracks = simpleSearchForTracksstruct(simpleEntry);
else if (selectedTab==advancedTab)
tracks = advancedSearchForTracks(conn,groupList,nameSearch,typeSearch,descSearch,
groupSearch,mdbSelects);
if (measureTiming)
measureTime("Searched for tracks");
// Sort and Print results
if (selectedTab!=filesTab)
{
enum sortBy sortBy = cartUsualInt(cart,TRACK_SEARCH_SORT,sbRelevance);
tracksFound = slCount(tracks);
if (tracksFound > 1)
findTracksSort(&tracks,sortBy);
displayFoundTracks(cart,tracks,tracksFound,sortBy);
if (measureTiming)
measureTime("Displayed found tracks");
}
slPairFreeList(&mdbSelects);
}
hFreeConn(&conn);
webNewSection("About Track Search");
if (metaDbExists)
hPrintf("<p>Search for terms in track names, descriptions, groups, and ENCODE "
"metadata. If multiple terms are entered, only tracks with all terms "
"will be part of the results.");
else
hPrintf("<p>Search for terms in track descriptions, groups, and names. "
"If multiple terms are entered, only tracks with all terms "
"will be part of the results.");
hPrintf("<BR><a target='_blank' href='../goldenPath/help/trackSearch.html'>more help</a></p>\n");
webEndSectionTables();
}