static void hubConnectRemakeTrackHubVar(struct cart *cart)
/* Remake trackHub cart variable if need be from various check box vars. */
{
if (cartVarExists(cart, hgHubConnectRemakeTrackHub))
{
struct slPair *hubVarList = cartVarsWithPrefix(cart, hgHubConnectHubVarPrefix);
int prefixLength = strlen(hgHubConnectHubVarPrefix);
struct dyString *trackHubs = dyStringNew(0);
struct slPair *hubVar;
boolean firstOne = TRUE;
for (hubVar = hubVarList; hubVar != NULL; hubVar = hubVar->next)
{
if (cartBoolean(cart, hubVar->name))
{
if (firstOne)
firstOne = FALSE;
else
dyStringAppendC(trackHubs, ' ');
dyStringAppend(trackHubs, hubVar->name + prefixLength);
}
}
slPairFreeList(&hubVarList);
cartSetString(cart, hubConnectTrackHubsVarName, trackHubs->string);
dyStringFree(&trackHubs);
cartRemove(cart, hgHubConnectRemakeTrackHub);
}
}
char *fileFormatSelectHtml(char *name, char *selected, char *extraHtml)
// returns an allocated string of HTML for the fileType select drop down
{
struct slPair *fileTypes = fileFormatSearchWhiteList();
if (slCount(fileTypes) > 0)
{
char *dropDownHtml = cgiMakeSingleSelectDropList(name,fileTypes,selected,
ANYLABEL,NULL,extraHtml);
slPairFreeList(&fileTypes);
return dropDownHtml;
}
return NULL;
}
char *mdbSelectsHtmlRows(struct sqlConnection *conn,struct slPair *mdbSelects,
struct slPair *mdbVars,int cols,boolean fileSearch)
// genereates the html for the table rows containing mdb var and val selects.
// Assume tableSearch unless fileSearch
{
struct dyString *output = dyStringNew(1024);
dyStringPrintf(output,"<tr><td colspan='%d' align='right' class='lineOnTop' style='height:20px; "
"max-height:20px;'><em style='color:%s; width:200px;'>ENCODE terms</em>"
"</td></tr>\n", cols,COLOR_DARKGREY);
struct slPair *mdbSelect = mdbSelects;
int row = 0;
for (;mdbSelect != NULL; mdbSelect = mdbSelect->next)
{
char buf[256];
char *dropDownHtml = NULL;
#define PLUS_MINUS_BUTTON "<input type='button' id='%sButton%d' value='%c' " \
"style='font-size:.7em;' title='%s' " \
"onclick='findTracks.mdbSelectPlusMinus(this,%d)'>"
#define ADD_PM_BUTTON(type,num,value) \
dyStringPrintf(output,PLUS_MINUS_BUTTON, (type), (num), (value), \
((value) == '+' ? "add another row after":"delete"), (num))
dyStringAppend(output,"<tr valign='top' class='mdbSelect'><td nowrap>\n");
row++;
if (slCount(mdbSelects) > 2 || row > 2)
ADD_PM_BUTTON("minus", row, '-');
else
dyStringAppend(output," ");
ADD_PM_BUTTON("plus", row, '+');
dyStringAppend(output,"</td><td>and </td><td colspan=3 nowrap>\n");
safef(buf, sizeof(buf), "%s%i", METADATA_NAME_PREFIX, row);
// Left side select of vars
dropDownHtml = cgiMakeSingleSelectDropList(buf, mdbVars,mdbSelect->name, NULL,"mdbVar",
"style='font-size:.9em;' onchange='findTracks.mdbVarChanged(this);'");
if (dropDownHtml)
{
dyStringAppend(output,dropDownHtml);
freeMem(dropDownHtml);
}
// Right side select of vals
safef(buf, sizeof(buf), "%s%i", METADATA_VALUE_PREFIX, row);
enum cvSearchable searchBy = cvSearchMethod(mdbSelect->name);
if (searchBy == cvSearchBySingleSelect || searchBy == cvSearchByMultiSelect)
{
dyStringPrintf(output,"</td>\n<td align='right' id='isLike%i' style='width:10px; "
"white-space:nowrap;'>is%s</td>\n<td nowrap id='%s' "
"style='max-width:600px;'>\n",
row,(searchBy == cvSearchByMultiSelect?" among":""),buf);
struct slPair *pairs = mdbValLabelSearch(conn, mdbSelect->name, MDB_VAL_STD_TRUNCATION,
FALSE, !fileSearch, fileSearch);
// not tags, either a file or table search
if (slCount(pairs) > 0)
{
char *dropDownHtml = cgiMakeSelectDropList((searchBy == cvSearchByMultiSelect),
buf, pairs,mdbSelect->val, ANYLABEL,"mdbVal",
"style='min-width:200px; font-size:.9em;' "
"onchange='findTracks.mdbValChanged(this);'");
if (dropDownHtml)
{
dyStringAppend(output,dropDownHtml);
freeMem(dropDownHtml);
}
slPairFreeList(&pairs);
}
}
else if (searchBy == cvSearchByFreeText)
{
dyStringPrintf(output,"</td><td align='right' id='isLike%i' style='width:10px; "
"white-space:nowrap;'>contains</td>\n<td nowrap id='%s' "
"style='max-width:600px;'>\n",row,buf);
dyStringPrintf(output,"<input type='text' name='%s' value='%s' class='mdbVal freeText' "
"style='max-width:310px; width:310px; font-size:.9em;' "
"onchange='findTracks.mdbVarChanged(true);'>\n",
buf,(mdbSelect->val ? (char *)mdbSelect->val: ""));
}
else if (searchBy == cvSearchByWildList)
{
dyStringPrintf(output,"</td><td align='right' id='isLike%i' style='width:10px; "
"white-space:nowrap;'>is among</td>\n<td nowrap id='%s' "
"style='max-width:600px;'>\n",row,buf);
dyStringPrintf(output,"<input type='text' name='%s' value='%s' class='mdbVal wildList' "
"title='enter comma separated list of values' "
"style='max-width:310px; width:310px; font-size:.9em;' "
"onchange='findTracks.mdbVarChanged(true);'>\n",
buf,(mdbSelect->val ? (char *)mdbSelect->val: ""));
}
//else if (searchBy == cvSearchByDateRange || searchBy == cvSearchByIntegerRange)
// {
// // TO BE IMPLEMENTED
// }
dyStringPrintf(output,"<span id='helpLink%i'> </span></td>\n", row);
dyStringPrintf(output,"</tr>\n");
}
dyStringPrintf(output,"<tr><td colspan='%d' align='right' style='height:10px; "
"max-height:10px;'> </td></tr>", cols);
return dyStringCannibalize(&output);
}
void hashElSlPairListFree(struct hashEl **pEl)
/* Free up the list in one of the hashEls. */
{
struct slPair **pList = (struct slPair **)pEl;
slPairFreeList(pList);
}
static void doFileSearch(char *db,char *organism,struct cart *cart,struct trackDb *tdbList)
{
struct sqlConnection *conn = hAllocConn(db);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
if (!sqlTableExists(conn, "metaDb"))
{
warn("Assembly %s %s does not support Downloadable Files search.", organism, hFreezeFromDb(db));
hFreeConn(&conn);
return;
}
char *nameSearch = cartOptionalString(cart, TRACK_SEARCH_ON_NAME);
char *descSearch=NULL;
char *fileTypeSearch = cartOptionalString(cart, FILE_SEARCH_ON_FILETYPE);
boolean doSearch = sameWord(cartUsualString(cart, FILE_SEARCH,"no"), "search");
#ifdef ONE_FUNC
struct hash *parents = newHash(4);
#endif///def ONE_FUNC
boolean searchTermsExist = FALSE; // FIXME: Why is this needed?
int cols;
#ifdef USE_TABS
enum searchTab selectedTab = simpleTab;
char *currentTab = cartUsualString(cart, FILE_SEARCH_CURRENT_TAB, "simpleTab");
if (sameString(currentTab, "simpleTab"))
{
selectedTab = simpleTab;
descSearch = cartOptionalString(cart, TRACK_SEARCH_SIMPLE);
freez(&nameSearch);
}
else if (sameString(currentTab, "filesTab"))
{
selectedTab = filesTab;
descSearch = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR);
}
#else///ifndef USE_TABS
enum searchTab selectedTab = filesTab;
descSearch = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR);
#endif///ndef USE_TABS
#ifdef USE_TABS
struct trix *trix;
char trixFile[HDB_MAX_PATH_STRING];
getSearchTrixFile(db, trixFile, sizeof(trixFile));
trix = trixOpen(trixFile);
#endif///def USE_TABS
printf("<div style='max-width:1080px;'>");
// FIXME: Do we need a form at all?
printf("<form action='../cgi-bin/hgFileSearch' name='%s' id='%s' method='get'>\n\n",
FILE_SEARCH_FORM,FILE_SEARCH_FORM);
cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo
printf("<input type='hidden' name='db' value='%s'>\n", db);
printf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_DEL_ROW);
printf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_ADD_ROW);
#ifdef USE_TABS
printf("<input type='hidden' name='%s' id='currentTab' value='%s'>\n",
FILE_SEARCH_CURRENT_TAB, currentTab);
printf("<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='#filesTab'><B style='font-size:.9em;font-family: arial, Geneva, "
"Helvetica, san-serif;'>Files</B></a></li>\n"
"</ul>\n",cgiBrowser()==btIE?"width:1060px;":"max-width:inherit;");
// Files tab
printf("<div id='simpleTab' style='max-width:inherit;'>\n");
printf("<table id='simpleTable' style='width:100%%; font-size:.9em;'><tr><td colspan='2'>");
printf("<input type='text' name='%s' id='simpleSearch' class='submitOnEnter' value='%s' "
"style='max-width:1000px; width:100%%;' onkeyup='findTracks.searchButtonsEnable(true);'>\n",
TRACK_SEARCH_SIMPLE,descSearch == NULL ? "" : descSearch);
if (selectedTab==simpleTab && descSearch)
searchTermsExist = TRUE;
printf("</td></tr><td style='max-height:4px;'></td></tr></table>");
printf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n",
FILE_SEARCH);
printf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' "
"onclick='findTracks.clear();'>\n");
printf("<input type='submit' name='submit' value='cancel' class='cancel' "
"style='font-size:.8em;'>\n");
printf("</div>\n");
#endif///def USE_TABS
// Files tab
printf("<div id='filesTab' style='width:inherit;'>\n"
"<table id='filesTable' cellSpacing=0 style='width:inherit; font-size:.9em;'>\n");
cols = 8;
// Track Name contains
printf("<tr><td colspan=3></td>");
printf("<td nowrap><b style='max-width:100px;'>Track Name:</b></td>");
printf("<td align='right'>contains</td>\n");
printf("<td colspan='%d'>", cols - 4);
printf("<input type='text' name='%s' id='nameSearch' class='submitOnEnter' value='%s' "
"onkeyup='findTracks.searchButtonsEnable(true);' style='min-width:326px; font-size:.9em;'>",
TRACK_SEARCH_ON_NAME, nameSearch == NULL ? "" : nameSearch);
printf("</td></tr>\n");
// Description contains
printf("<tr><td colspan=2></td><td align='right'>and </td>");
printf("<td><b style='max-width:100px;'>Description:</b></td>");
printf("<td align='right'>contains</td>\n");
printf("<td colspan='%d'>", cols - 4);
printf("<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);
printf("</td></tr>\n");
if (selectedTab==filesTab && descSearch)
searchTermsExist = TRUE;
// Set up Group dropdown
struct grp *grps = hLoadGrps(db);
grps = groupsFilterForTdbList(&grps,tdbList);
int numGroups = slCount(grps) + 1; // Add Any
char **groups = needMem(sizeof(char *) * numGroups);
char **labels = needMem(sizeof(char *) * numGroups);
groups[0] = ANYLABEL;
labels[0] = ANYLABEL;
int ix=1;
struct grp *grp = grps;
for (; grp != NULL; grp = grp->next,ix++)
{
groups[ix] = cloneString(grp->name);
labels[ix] = cloneString(grp->label);
}
printf("<tr><td colspan=2></td><td align='right'>and </td>\n");
printf("<td><b style='max-width:100px;'>Group:</b></td>");
printf("<td align='right'>is</td>\n");
printf("<td colspan='%d'>", cols - 4);
char *groupSearch = cartOptionalString(cart, TRACK_SEARCH_ON_GROUP);
cgiMakeDropListFull(TRACK_SEARCH_ON_GROUP, labels, groups, numGroups, groupSearch,
"class='groupSearch' style='min-width:40%; font-size:.9em;'");
printf("</td></tr>\n");
if (selectedTab==filesTab && groupSearch)
searchTermsExist = TRUE;
// Track Type is (drop down)
printf("<tr><td colspan=2></td><td align='right'>and </td>\n");
printf("<td nowrap><b style='max-width:100px;'>Data Format:</b></td>");
printf("<td align='right'>is</td>\n");
printf("<td colspan='%d'>", cols - 4);
char *dropDownHtml = fileFormatSelectHtml(FILE_SEARCH_ON_FILETYPE,fileTypeSearch,
"style='min-width:40%; font-size:.9em;'");
if (dropDownHtml)
{
puts(dropDownHtml);
freeMem(dropDownHtml);
}
printf("</td></tr>\n");
if (selectedTab==filesTab && fileTypeSearch)
searchTermsExist = TRUE;
// mdb selects
struct slPair *mdbSelects = NULL;
if (metaDbExists)
{
struct slPair *mdbVars = mdbVarsSearchable(conn,FALSE,TRUE); // Not tables, just files
mdbSelects = mdbSelectPairs(cart, mdbVars);
char *output = mdbSelectsHtmlRows(conn,mdbSelects,mdbVars,cols,TRUE); // just for fileSearch
if (output)
{
puts(output);
freeMem(output);
}
slPairFreeList(&mdbVars);
}
printf("</table>\n");
printf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n",
FILE_SEARCH);
printf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' "
"onclick='findTracks.clear();'>\n");
printf("<input type='submit' name='submit' value='cancel' class='cancel' "
"style='font-size:.8em;'>\n");
printf("</div>\n");
#ifdef USE_TABS
printf("</div>\n"); // End tabs div
#endif///def USE_TABS
if (nameSearch != NULL && !strlen(nameSearch))
nameSearch = NULL;
if (descSearch != NULL && !strlen(descSearch))
descSearch = NULL;
if (groupSearch != NULL && sameString(groupSearch, ANYLABEL))
groupSearch = NULL;
printf("</form>\n");
printf("</div>"); // Restricts to max-width:1000px;
cgiDown(0.8);
if (measureTiming)
uglyTime("Generated search controls");
#ifdef USE_TABS
if (doSearch && selectedTab==simpleTab && isEmpty(descSearch))
doSearch = FALSE;
#endif///def USE_TABS
if (doSearch)
{
// Now search
#ifdef USE_TABS
struct slRef *foundTdbs = NULL;
if (selectedTab==simpleTab)
{
foundTdbs = simpleSearchForTdbs(trix,descWords,descWordCount);
// What to do now?
if (measureTiming)
uglyTime("Searched for tracks");
// Sort and Print results
if (selectedTab!=filesTab)
{
enum sortBy sortBy = cartUsualInt(cart,TRACK_SEARCH_SORT,sbRelevance);
int tracksFound = slCount(foundTdbs);
if (tracksFound > 1)
findTracksSort(&tracks,sortBy);
displayFoundTracks(cart,tracks,tracksFound,sortBy);
if (measureTiming)
uglyTime("Displayed found files");
}
}
else if (selectedTab==filesTab && mdbPairs != NULL)
#endif ///def USE_TABS
{
if (nameSearch || descSearch || groupSearch)
{ // Use nameSearch, descSearch and groupSearch to narrow down the list of composites.
if (isNotEmpty(nameSearch) || isNotEmpty(descSearch) || isNotEmpty(groupSearch))
{
struct trackDb *tdbList = hTrackDb(db);
struct trackDb *tdbsMatch = tdbFilterBy(&tdbList, nameSearch, descSearch,
groupSearch);
// Now we have a list of tracks, so we need a unique list of composites to add
doSearch = mdbSelectsAddFoundComposites(&mdbSelects,tdbsMatch);
}
}
if (doSearch && mdbSelects != NULL && isNotEmpty(fileTypeSearch))
fileSearchResults(db, conn, cart, mdbSelects, fileTypeSearch);
else
printf("<DIV id='filesFound'><BR>No files found.<BR></DIV><BR>\n");
if (measureTiming)
uglyTime("Searched for files");
}
slPairFreeList(&mdbSelects);
}
hFreeConn(&conn);
webNewSection("About " FILE_SEARCH_NAME);
printf("Search for downloadable ENCODE files by entering search terms in "
"the Track name or Description fields and/or by making selections with "
"the group, data format, and/or ENCODE metadata drop-downs.");
printf("<BR><a target='_blank' href='../goldenPath/help/fileSearch.html'>more help</a>\n");
}
int main(int argc, char *argv[])
{
long enteredMainTime = clock1000();
struct dyString *output = newDyString(10000);
setUdcCacheDir();
cgiSpoof(&argc, argv);
pushWarnHandler(htmlVaBadRequestAbort);
pushAbortHandler(htmlVaBadRequestAbort);
char *database = cgiString("db");
char *cmd = cgiString("cmd");
char *jsonp = cgiOptionalString("jsonp");
if (!hDbExists(database))
errAbort("Invalid database '%s'", database);
if (!strcmp(cmd, "defaultPos"))
{
dyStringPrintf(output, "{\"pos\": \"%s\"}", hDefaultPos(database));
}
else if (!strcmp(cmd, "metaDb"))
{
// Return list of values for given metaDb var
// e.g. http://genome.ucsc.edu/hgApi?db=hg18&cmd=metaDb&var=cell
struct sqlConnection *conn = hAllocConn(database);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
if (metaDbExists)
{
char *var = cgiOptionalString("var");
if (!var)
errAbort("Missing var parameter");
boolean fileSearch = (cgiOptionalInt("fileSearch",0) == 1);
struct slPair *pairs = mdbValLabelSearch(conn, var, MDB_VAL_STD_TRUNCATION, FALSE,
!fileSearch, fileSearch);
struct slPair *pair;
dyStringPrintf(output, "[\n");
for (pair = pairs; pair != NULL; pair = pair->next)
{
if (pair != pairs)
dyStringPrintf(output, ",\n");
dyStringPrintf(output, "['%s','%s']", javaScriptLiteralEncode(mdbPairLabel(pair)),
javaScriptLiteralEncode(mdbPairVal(pair)));
}
dyStringPrintf(output, "\n]\n");
}
else
errAbort("Assembly does not support metaDb");
}
// TODO: move to lib since hgTracks and hgApi share
#define METADATA_VALUE_PREFIX "hgt_mdbVal"
else if (startsWith(METADATA_VALUE_PREFIX, cmd))
{
// Returns metaDb value control: drop down or free text, with or without help link.
// e.g. http://genome.ucsc.edu/hgApi?db=hg18&cmd=hgt_mdbVal3&var=cell
// TODO: Move guts to lib, so that hgTracks::searchTracks.c and hgApi.c can share
struct sqlConnection *conn = hAllocConn(database);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
if (metaDbExists)
{
char *var = cgiOptionalString("var");
if (!var)
errAbort("Missing var parameter");
int ix = atoi(cmd+strlen(METADATA_VALUE_PREFIX)); // 1 based index
if (ix == 0) //
errAbort("Unsupported 'cmd' parameter");
enum cvSearchable searchBy = cvSearchMethod(var);
char name[128];
safef(name,sizeof name,"%s%i",METADATA_VALUE_PREFIX,ix);
if (searchBy == cvSearchBySingleSelect || searchBy == cvSearchByMultiSelect)
{
boolean fileSearch = (cgiOptionalInt("fileSearch",0) == 1);
struct slPair *pairs = mdbValLabelSearch(conn, var, MDB_VAL_STD_TRUNCATION, FALSE,
!fileSearch, fileSearch);
if (slCount(pairs) > 0)
{
char *dropDownHtml =
cgiMakeSelectDropList((searchBy == cvSearchByMultiSelect),
name, pairs, NULL, ANYLABEL, "mdbVal",
"style='min-width: 200px; font-size: .9em;' "
"onchange='findTracksMdbValChanged(this);'");
if (dropDownHtml)
{
dyStringAppend(output,dropDownHtml);
freeMem(dropDownHtml);
}
slPairFreeList(&pairs);
}
}
else if (searchBy == cvSearchByFreeText)
{
dyStringPrintf(output,"<input type='text' name='%s' value='' class='mdbVal freeText' "
"onchange='findTracksMdbValChanged(this);' style='max-width:310px; "
"width:310px; font-size:.9em;'>", name);
}
else if (searchBy == cvSearchByWildList)
{
dyStringPrintf(output,"<input type='text' name='%s' value='' class='mdbVal wildList' "
"title='enter comma separated list of values' "
"onchange='findTracksMdbValChanged(this);' style='max-width:310px; "
"width:310px; font-size:.9em;'>", name);
}
else if (searchBy == cvSearchByDateRange || searchBy == cvSearchByIntegerRange)
{
// TO BE IMPLEMENTED
}
else
errAbort("Metadata variable not searchable");
dyStringPrintf(output,"<span id='helpLink%i'> </span>",ix);
}
else
errAbort("Assembly does not support metaDb");
}
else if (!strcmp(cmd, "tableMetadata"))
{ // returns an html table with metadata for a given track
char *trackName = cgiOptionalString("track");
boolean showLonglabel = (NULL != cgiOptionalString("showLonglabel"));
boolean showShortLabel = (NULL != cgiOptionalString("showShortLabel"));
if (trackName != NULL)
{
// hTrackDbForTrackAndAncestors avoids overhead of getting whole track list!
struct trackDb *tdb = hTrackDbForTrackAndAncestors(database, trackName);
if (tdb != NULL)
{
char * html = metadataAsHtmlTable(database,tdb,showLonglabel,showShortLabel);
if (html)
{
dyStringAppend(output,html);
freeMem(html);
}
else
dyStringPrintf(output,"No metadata found for track %s.",trackName);
}
else
dyStringPrintf(output,"Track %s not found",trackName);
}
else
dyStringAppend(output,"No track variable found");
}
else if (sameString(cmd, "codonToPos") || sameString(cmd, "exonToPos"))
{
char query[256];
struct sqlResult *sr;
char **row;
struct genePred *gp;
char *name = cgiString("name");
char *table = cgiString("table");
int num = cgiInt("num");
struct sqlConnection *conn = hAllocConn(database);
sqlSafef(query, sizeof(query), "select name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds from %s where name = '%s'", table, name);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
gp = genePredLoad(row);
boolean found;
int start, end;
if (sameString(cmd, "codonToPos"))
found = codonToPos(gp, num, &start, &end);
else
found = exonToPos(gp, num, &start, &end);
if (found)
dyStringPrintf(output, "{\"pos\": \"%s:%d-%d\"}", gp->chrom, start + 1, end);
else
dyStringPrintf(output, "{\"error\": \"%d is an invalid %s for this gene\"}", num, sameString(cmd, "codonToPos") ? "codon" : "exon");
}
else
dyStringPrintf(output, "{\"error\": \"Couldn't find item: %s\"}", name);
sqlFreeResult(&sr);
hFreeConn(&conn);
}
else
{
warn("unknown cmd: %s",cmd);
errAbort("Unsupported 'cmd' parameter");
}
apiOut(dyStringContents(output), jsonp);
cgiExitTime("hgApi", enteredMainTime);
return 0;
}
void doSearchTracks(struct group *groupList)
{
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;
boolean searchTermsExist = FALSE;
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",
TRACK_SEARCH_SIMPLE,simpleEntry == NULL ? "" : simpleEntry);
if (selectedTab==simpleTab && simpleEntry)
searchTermsExist = TRUE;
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='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;'>",
TRACK_SEARCH_ON_NAME, nameSearch == NULL ? "" : nameSearch);
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);
hPrintf("</td></tr>\n");
if (selectedTab==advancedTab && !isEmpty(descSearch))
searchTermsExist = TRUE;
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;'");
hPrintf("</td></tr>\n");
if (selectedTab==advancedTab && !isEmpty(groupSearch) && !sameString(groupSearch,ANYLABEL))
searchTermsExist = TRUE;
// 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;'");
hPrintf("</td></tr>\n");
if (selectedTab==advancedTab && !isEmpty(typeSearch) && !sameString(typeSearch,ANYLABEL))
searchTermsExist = TRUE;
// 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='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();
}
