void loadRNAHybridization(struct track *tg)
/* Load the items in one custom track - just move beds in
* window... */
{
struct rnaHybridization *rnaHyb, *list = NULL;
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char **row;
int rowOffset;
int minlengthSetting = cartUsualInt(cart, "rnaHybridization.minlength", 20);
int maxlengthSetting = cartUsualInt(cart, "rnaHybridization.maxlength", 20);
double gcSetting = (double)cartUsualInt(cart, "rnaHybridization.gc", 50) / 100;
int hideTrnaSetting = cartUsualBoolean(cart, "rnaHybridization.hideTrna", FALSE);
int showKnownTargetsSetting = cartUsualBoolean(cart, "rnaHybridization.showKnownTargets", TRUE);
sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
rnaHyb = rnaHybridizationLoad(row);
if(rnaHyb->matchLength >= minlengthSetting
&& rnaHyb->matchLength <= maxlengthSetting
&& rnaHyb->gcContent >= gcSetting
&& !(hideTrnaSetting && strlen(rnaHyb->trnaTarget) > 0)
&& !(showKnownTargetsSetting && !rnaHyb->targetAnnotation))
slAddHead(&list, rnaHyb);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
slReverse(&list);
tg->items = list;
}
void dispatch()
/* Look at input variables and figure out which page to show. */
{
char *db, *organism;
int maxSize = 4000;
int minPerfect = 15;
int minGood = 15;
char *fPrimer = cartUsualString(cart, "wp_f", "");
char *rPrimer = cartUsualString(cart, "wp_r", "");
boolean flipReverse = cartUsualBoolean(cart, "wp_flipReverse", FALSE);
struct pcrServer *serverList = getServerList();
getDbAndGenome(cart, &db, &organism, oldVars);
/* Get variables. */
maxSize = cartUsualInt(cart, "wp_size", maxSize);
minPerfect = cartUsualInt(cart, "wp_perfect", minPerfect);
minGood = cartUsualInt(cart, "wp_good", minGood);
if (minPerfect < 15)
minPerfect = 15;
if (minGood < minPerfect)
minGood = minPerfect;
/* Decide based on transient variables what page to put up.
* By default put up get primer page. */
if (isNotEmpty(fPrimer) && isNotEmpty(rPrimer) &&
!cartVarExists(cart, "wp_showPage"))
{
struct pcrServer *server = NULL;
struct targetPcrServer *targetServer = NULL;
char *target = cartUsualString(cart, "wp_target", "genome");
if (isEmpty(target) || sameString(target, "genome"))
server = findServer(db, serverList);
else
{
targetServer = getTargetServerList(db, target);
if (targetServer == NULL)
errAbort("Can't find targetPcr server for db=%s, target=%s",
db, target);
}
fPrimer = gfPcrMakePrimer(fPrimer);
rPrimer = gfPcrMakePrimer(rPrimer);
if (doPcr(server, targetServer, fPrimer, rPrimer,
maxSize, minPerfect, minGood, flipReverse))
return;
}
doGetPrimers(db, organism, serverList,
fPrimer, rPrimer, maxSize, minPerfect, minGood, flipReverse);
}
void printSections(struct section *sectionList, struct sqlConnection *conn,
char *geneId)
/* Print each section in turn. */
{
struct section *section;
for (section = sectionList; section != NULL; section = section->next)
{
char *closeVarName = sectionCloseVar(section->name);
boolean isOpen = !(cartUsualInt(cart, closeVarName, 0));
char *otherState = (isOpen ? "1" : "0");
char *indicator = (isOpen ? "-" : "+");
char *indicatorImg = (isOpen ? "../images/remove.gif" : "../images/add.gif");
struct dyString *header = dyStringNew(0);
//keep the following line for future debugging need
//printf("<br>printing %s section\n", section->name);fflush(stdout);
dyStringPrintf(header, "<A NAME=\"%s\"></A>", section->name);
dyStringPrintf(header, "<A HREF=\"%s?%s&%s=%s#%s\" class=\"bigBlue\"><IMG src=\"%s\" alt=\"%s\" class=\"bigBlue\"></A> ",
geneCgi, cartSidUrlString(cart), closeVarName, otherState, section->name, indicatorImg, indicator);
dyStringAppend(header, section->longLabel);
webNewSection(header->string);
if (isOpen)
{
section->print(section, conn, geneId);
}
else
{
printf("Press \"+\" in the title bar above to open this section.");
}
dyStringFree(&header);
}
}
void oneTrackInit()
/* Set up global variables using cart settings and initialize libs. */
{
hPrintDisable();
database = cartUsualString(cart, "db", "ce4");
hSetDb(database);
organism = hOrganism(database);
withLeftLabels = FALSE; /* Left labels are not supported. */
withCenterLabels = cartUsualBoolean(cart, "centerLabels", FALSE);
withGuidelines = cartUsualBoolean(cart, "guidelines", FALSE);
revCmplDisp = cartUsualBooleanDb(cart, database, REV_CMPL_DISP, FALSE);
position = cartUsualString(cart, "position", "chrI:4001-5000");
hgParseChromRange(position, &chromName, &winStart, &winEnd);
insideX = 0; /* Left labels are not supported. */
insideWidth = cartUsualInt(cart, "pix", 640);
leftLabelX = 0;
leftLabelWidth = 0; /* Left labels are not supported. */
winBaseCount = winEnd - winStart;
basesPerPixel = ((float)winBaseCount) / ((float)insideWidth);
zoomedToCdsColorLevel = (winBaseCount <= insideWidth*3);
seqBaseCount = hChromSize(database, chromName);
initTl();
zoomedToBaseLevel = (winBaseCount <= insideWidth / tl.mWidth);
zoomedToCodonLevel = (ceil(winBaseCount/3) * tl.mWidth) <= insideWidth;
createHgFindMatchHash();
}
void cartMain(struct cart *theCart)
/* We got the persistent/CGI variable cart. Now
* set up the globals and make a web page. */
{
cart = theCart;
/* Break out new block after have set cart */
{
int id = cartUsualInt(cart, hgbiId, 1);
struct sqlConnection *conn = sqlConnect("bioImage");
char *geneName = bioImageGeneName(conn, id);
if (cartVarExists(cart, hgbiDoFullSize))
{
htmStart(stdout, "BioImage Full Sized Image");
printf("<IMG SRC=\"/%s\"><BR>\n", bioImageFullSizePath(conn, id));
printCaption(conn, id, geneName);
htmlEnd();
}
else /* Default case - start fancy web page. */
{
mainPage(conn, id, geneName);
}
cartRemovePrefix(cart, hgbiDoPrefix);
sqlDisconnect(&conn);
}
}
char *identifierWhereClause(char *idField, struct hash *idHash)
/* If the number of pasted IDs is reasonably low, return a where-clause component for the IDs. */
{
if (idHash == NULL || idField == NULL)
return NULL;
int numIds = hashNumEntries(idHash);
int maxIdsInWhere = cartUsualInt(cart, "hgt_maxIdsInWhere", DEFAULT_MAX_IDS_IN_WHERE);
if (numIds > 0 && numIds <= maxIdsInWhere)
{
struct dyString *dy = dyStringNew(16 * numIds);
dyStringPrintf(dy, "%s in (", idField);
struct hashCookie hc = hashFirst(idHash);
boolean first = TRUE;
char *id;
while ((id = hashNextName(&hc)) != NULL)
{
if (first)
first = FALSE;
else
dyStringAppend(dy, ", ");
dyStringPrintf(dy, "'%s'", id);
}
dyStringAppend(dy, ")");
return dyStringCannibalize(&dy);
}
return NULL;
}
boolean sectionIsOpen(struct section *section)
/* Check cart and ra to see if section is open(-) or closed(+) */
{
char *closeVarName = sectionCloseVar(section->name);
char *vis = sectionSetting(section, "visibility");
int defaultClosed = (vis && sameString(vis, "hide")) ? 1 : 0;
return !(cartUsualInt(cart, closeVarName, defaultClosed));
}
void webFilteredSqlTable(struct cart *cart, struct sqlConnection *conn,
char *fields, char *from, char *initialWhere,
char *returnUrl, char *varPrefix, int maxFieldWidth,
struct hash *tagOutWrappers, void *wrapperContext,
boolean withFilters, char *itemPlural, int pageSize, struct hash *suggestHash, void (*addFunc)(void) )
/* Given a query to the database in conn that is basically a select query broken into
* separate clauses, construct and display an HTML table around results. This HTML table has
* column names that will sort the table, and optionally (if withFilters is set)
* it will also allow field-by-field wildcard queries on a set of controls it draws above
* the labels.
* Much of the functionality rests on the call to webFilteredFieldedTable. This function
* does the work needed to bring in sections of potentially huge results sets into
* the fieldedTable. */
{
struct dyString *query;
struct dyString *where;
webTableBuildQuery(cart, from, initialWhere, varPrefix, fields, withFilters, &query, &where);
/* Figure out size of query result */
struct dyString *countQuery = dyStringNew(0);
sqlDyStringPrintf(countQuery, "%s", ""); // TODO check with Galt on how to get reasonable checking back.
dyStringPrintf(countQuery, "select count(*) from %s", from);
dyStringAppend(countQuery, where->string);
int resultsSize = sqlQuickNum(conn, countQuery->string);
dyStringFree(&countQuery);
char pageVar[64];
safef(pageVar, sizeof(pageVar), "%s_page", varPrefix);
int page = 0;
struct fieldedTableSegment context = { .tableSize=resultsSize};
if (resultsSize > pageSize)
{
page = cartUsualInt(cart, pageVar, 0) - 1;
if (page < 0)
page = 0;
int lastPage = (resultsSize-1)/pageSize;
if (page > lastPage)
page = lastPage;
context.tableOffset = page * pageSize;
dyStringPrintf(query, " limit %d offset %d", pageSize, context.tableOffset);
}
struct fieldedTable *table = fieldedTableFromDbQuery(conn, query->string);
webFilteredFieldedTable(cart, table, returnUrl, varPrefix, maxFieldWidth,
tagOutWrappers, wrapperContext, withFilters, itemPlural, pageSize, &context, suggestHash, addFunc);
fieldedTableFree(&table);
dyStringFree(&query);
dyStringFree(&where);
}
struct genoLay *ggLayout(struct sqlConnection *conn,
int graphRows, int graphCols)
/* Figure out how to lay out image. */
{
int i,j;
struct genoLayChrom *chromList;
int oneRowHeight;
int minLeftLabelWidth = 0, minRightLabelWidth = 0;
/* Figure out basic dimensions of image. */
trackLayoutInit(&tl, cart);
tl.picWidth = cartUsualInt(cart, hggImageWidth, hgDefaultPixWidth);
/* Refine all graphs actually used, and calculate label
* widths if need be. */
for (i=0; i<graphRows; ++i)
{
for (j=0; j<graphCols; ++j)
{
char *source = graphSourceAt(i,j);
if (source != NULL)
{
struct genoGraph *gg = hashFindVal(ggHash, source);
if (gg != NULL)
{
ggRefineUsed(gg);
if (withLabels)
{
int labelWidth;
labelWidth = ggLabelWidth(gg, tl.font);
if (j == 0 && labelWidth > minLeftLabelWidth)
minLeftLabelWidth = labelWidth;
if (j == 1 && labelWidth > minRightLabelWidth)
minRightLabelWidth = labelWidth;
}
}
}
}
}
/* Get list of chromosomes and lay them out. */
chromList = genoLayDbChroms(conn, FALSE);
oneRowHeight = graphHeight()+betweenRowPad;
return genoLayNew(chromList, tl.font, tl.picWidth, graphRows*oneRowHeight,
minLeftLabelWidth, minRightLabelWidth, chromLayout());
}
void integerFilterWithLimits(char *db, char *table, char *field, char *label,
int min,int max,char *logOp)
/* Print out a filter constraint for an integer within a range. */
{
char *name;
hPrintf("<TR VALIGN=BOTTOM align='left'><TD> %s is</TD><TD colspan=2>\n", label);
name = filterFieldVarName(db, table, field, filterCmpVar);
cgiMakeDropListClassWithStyle(name, cmpOpMenu, cmpOpMenuSize,
cartUsualString(cart, name, cmpOpMenu[0]),"normalText","width: 76px");
puts("</TD><TD>\n");
name = filterPatternVarName(db, table, field);
int val = cartUsualInt(cart, name, 0);
cgiMakeIntVarWithLimits(name,val,label,140,min,max);
if (logOp == NULL)
logOp = "";
hPrintf(" %s</TD></TR>\n", logOp);
}
static void getUiState(struct cartJson *cj, struct hash *paramHash)
/* Write out JSON for hgGateway.js's uiState object using current cart settings. */
{
char *db = cartUsualString(cj->cart, "db", hDefaultDb());
char *position = cartUsualString(cart, "position", hDefaultPos(db));
char *hubUrl = NULL;
if (trackHubDatabase(db))
{
struct trackHub *hub = hubConnectGetHubForDb(db);
hubUrl = hub->url;
}
writeFindPositionInfo(cj->jw, db, hTaxId(db), hubUrl, position);
// If cart already has a pix setting, pass that along; otherwise the JS will
// set pix according to web browser window width.
int pix = cartUsualInt(cj->cart, "pix", 0);
if (pix)
jsonWriteNumber(cj->jw, "pix", pix);
}
void doSearchTracks(struct group *groupList)
{
if (!advancedJavascriptFeaturesEnabled(cart))
{
warn("Requires advanced javascript features.");
return;
}
struct group *group;
char *groups[128];
char *labels[128];
int numGroups = 1;
groups[0] = ANYLABEL;
labels[0] = ANYLABEL;
char *currentTab = cartUsualString(cart, TRACK_SEARCH_CURRENT_TAB, "simpleTab");
char *nameSearch = cartOptionalString(cart, TRACK_SEARCH_ON_NAME);
#ifdef TRACK_SEARCH_ON_TYPE
char *typeSearch = cartOptionalString(cart, TRACK_SEARCH_ON_TYPE);
#else///ifndef TRACK_SEARCH_ON_TYPE
char *typeSearch = NULL;
#endif///def TRACK_SEARCH_ON_TYPE
char *descSearch;
char *groupSearch = cartOptionalString(cart, TRACK_SEARCH_ON_GROUP);
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 numMetadataSelects, tracksFound = 0;
int numMetadataNonEmpty = 0;
char **mdbVar = NULL;
char **mdbVal = NULL;
#ifdef ONE_FUNC
struct hash *parents = newHash(4);
#endif///def ONE_FUNC
boolean simpleSearch;
struct trix *trix;
char trixFile[HDB_MAX_PATH_STRING];
char **descWords = NULL;
int descWordCount = 0;
boolean searchTermsExist = FALSE;
int cols;
char buf[512];
if(sameString(currentTab, "simpleTab"))
{
descSearch = cartOptionalString(cart, TRACK_SEARCH_SIMPLE);
simpleSearch = TRUE;
freez(&nameSearch);
#ifdef TRACK_SEARCH_ON_TYPE
freez(&typeSearch);
#endif///def TRACK_SEARCH_ON_TYPE
freez(&groupSearch);
}
else
{
descSearch = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR);
simpleSearch = FALSE;
}
if(descSearch)
stripChar(descSearch, '"');
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.
parentChildCartCleanup(trackList,cart,oldVars); // Subtrack settings must be removed when composite/view settings are updated
getSearchTrixFile(database, trixFile, sizeof(trixFile));
trix = trixOpen(trixFile);
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 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='findTracksSearchButtonsEnable(true);'>\n",
TRACK_SEARCH_SIMPLE,descSearch == NULL ? "" : descSearch);
if (simpleSearch && descSearch)
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='findTracksClear();'>\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 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='findTracksSearchButtonsEnable(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='findTracksSearchButtonsEnable(true);' style='max-width:536px; width:536px; font-size:.9em;'>",
TRACK_SEARCH_ON_DESCR, descSearch == NULL ? "" : descSearch);
hPrintf("</td></tr>\n");
if (!simpleSearch && 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 (!simpleSearch && groupSearch)
searchTermsExist = TRUE;
#ifdef TRACK_SEARCH_ON_TYPE
// 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 (!simpleSearch && typeSearch)
searchTermsExist = TRUE;
#endif///def TRACK_SEARCH_ON_TYPE
// Metadata selects require careful accounting
if(metaDbExists)
numMetadataSelects = printMdbSelects(conn, cart, simpleSearch, &mdbVar, &mdbVal, &numMetadataNonEmpty, cols);
else
numMetadataSelects = 0;
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='findTracksClear();'>\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</div>\n");
hPrintf("</form>\n");
hPrintf("</div>"); // Restricts to max-width:1000px;
if(descSearch != NULL && !strlen(descSearch))
descSearch = NULL;
if(groupSearch != NULL && sameString(groupSearch, ANYLABEL))
groupSearch = NULL;
if(typeSearch != NULL && sameString(typeSearch, ANYLABEL))
typeSearch = NULL;
if(!isEmpty(descSearch))
{
char *tmp = cloneString(descSearch);
char *val = nextWord(&tmp);
struct slName *el, *descList = NULL;
int i;
while (val != NULL)
{
slNameAddTail(&descList, val);
descWordCount++;
val = nextWord(&tmp);
}
descWords = needMem(sizeof(char *) * descWordCount);
for(i = 0, el = descList; el != NULL; i++, el = el->next)
descWords[i] = strLower(el->name);
}
if (doSearch && simpleSearch && descWordCount <= 0)
doSearch = FALSE;
if(doSearch)
{
// Now search
struct slRef *tracks = NULL;
if(simpleSearch)
tracks = simpleSearchForTracksstruct(trix,descWords,descWordCount);
else
tracks = advancedSearchForTracks(conn,groupList,descWords,descWordCount,nameSearch,typeSearch,descSearch,groupSearch,numMetadataNonEmpty,numMetadataSelects,mdbVar,mdbVal);
// Sort and Print results
enum sortBy sortBy = cartUsualInt(cart,TRACK_SEARCH_SORT,sbRelevance);
tracksFound = slCount(tracks);
if(tracksFound > 1)
findTracksSort(&tracks,simpleSearch,sortBy);
displayFoundTracks(cart,tracks,tracksFound,sortBy);
}
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();
}
static int printMdbSelects(struct sqlConnection *conn,struct cart *cart,boolean simpleSearch,char ***pMdbVar,char ***pMdbVal,int *numMetadataNonEmpty,int cols)
// Prints a table of mdb selects if appropriate and returns number of them
{
// figure out how many metadata selects are visible.
int delSearchSelect = cartUsualInt(cart, TRACK_SEARCH_DEL_ROW, 0); // 1-based row to delete
int addSearchSelect = cartUsualInt(cart, TRACK_SEARCH_ADD_ROW, 0); // 1-based row to insert after
int numMetadataSelects = 0;
char **mdbVar = NULL;
char **mdbVal = NULL;
char **mdbVars = NULL;
char **mdbVarLabels = NULL;
int i, count = metaDbVars(conn, &mdbVars, &mdbVarLabels);
for(;;)
{
char buf[256];
safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, numMetadataSelects + 1);
char *str = cartOptionalString(cart, buf);
if(isEmpty(str))
break;
else
numMetadataSelects++;
}
if(delSearchSelect)
numMetadataSelects--;
if(addSearchSelect)
numMetadataSelects++;
if(numMetadataSelects)
{
mdbVar = needMem(sizeof(char *) * numMetadataSelects);
mdbVal = needMem(sizeof(char *) * numMetadataSelects);
*pMdbVar = mdbVar;
*pMdbVal = mdbVal;
int i;
for(i = 0; i < numMetadataSelects; i++)
{
char buf[256];
int offset; // used to handle additions/deletions
if(addSearchSelect > 0 && i >= addSearchSelect)
offset = 0; // do nothing to offset (i.e. copy data from previous row)
else if(delSearchSelect > 0 && i + 1 >= delSearchSelect)
offset = 2;
else
offset = 1;
safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, i + offset);
mdbVar[i] = cloneString(cartOptionalString(cart, buf));
if(!simpleSearch)
{
int j;
boolean found = FALSE;
// We need to make sure mdbVar[i] is valid in this assembly; if it isn't, reset it to "cell".
for(j = 0; j < count && !found; j++)
if(sameString(mdbVars[j], mdbVar[i]))
found = TRUE;
if(found)
{
safef(buf, sizeof(buf), "%s%d", METADATA_VALUE_PREFIX, i + offset);
mdbVal[i] = cloneString(cartOptionalString(cart, buf));
if(sameString(mdbVal[i], ANYLABEL))
mdbVal[i] = NULL;
}
else
{
mdbVar[i] = cloneString("cell");
mdbVal[i] = NULL;
}
if(!isEmpty(mdbVal[i]))
(*numMetadataNonEmpty)++;
}
}
if(delSearchSelect > 0)
{
char buf[255];
safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, numMetadataSelects + 1);
cartRemove(cart, buf);
safef(buf, sizeof(buf), "%s%d", METADATA_VALUE_PREFIX, numMetadataSelects + 1);
cartRemove(cart, buf);
}
}
else
{
// create defaults
numMetadataSelects = 2;
mdbVar = needMem(sizeof(char *) * numMetadataSelects);
mdbVal = needMem(sizeof(char *) * numMetadataSelects);
mdbVar[0] = "cell";
mdbVar[1] = "antibody";
mdbVal[0] = ANYLABEL;
mdbVal[1] = ANYLABEL;
}
hPrintf("<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>", cols,COLOR_DARKGREY);
for(i = 0; i < numMetadataSelects; i++)
{
char **terms = NULL, **labels = NULL;
char buf[256];
int len;
#define PRINT_BUTTON(name,value,msg,js) printf("<input type='submit' name='%s' value='%s' style='font-size:.7em;' title='%s' onclick='%s'>", (name), (value), (msg), (js));
hPrintf("<tr><td>\n");
if(numMetadataSelects > 2 || i >= 2)
{
safef(buf, sizeof(buf), "return delSearchSelect(this, %d);", i + 1);
PRINT_BUTTON(TRACK_SEARCH, "-", "delete this row", buf);
}
else
hPrintf(" ");
hPrintf("</td><td>\n");
safef(buf, sizeof(buf), "return addSearchSelect(this, %d);", i + 1);
PRINT_BUTTON(TRACK_SEARCH, "+", "add another row after this row", buf);
hPrintf("</td><td>and </td><td colspan=3 nowrap>\n");
safef(buf, sizeof(buf), "%s%i", METADATA_NAME_PREFIX, i + 1);
#ifdef CV_SEARCH_SUPPORTS_FREETEXT
cgiDropDownWithTextValsAndExtra(buf, mdbVarLabels, mdbVars,count,mdbVar[i],"class='mdbVar' style='font-size:.9em;' onchange='findTracksMdbVarChanged2(this);'");
// TODO: move to lib since hgTracks and hgApi share
enum mdbCvSearchable searchBy = mdbCvSearchMethod(mdbVar[i]);
if (searchBy == cvsSearchByMultiSelect)
{
// TO BE IMPLEMENTED
}
else if (searchBy == cvsSearchBySingleSelect)
{
safef(buf, sizeof(buf), "%s%i", METADATA_VALUE_PREFIX, i + 1);
hPrintf("</td><td align='right' id='isLike%d' style='width:10px;'>is</td><td nowrap id='%s' style='max-width:600px;'>\n",i + 1,buf);
len = getTermArray(conn, &labels, &terms, mdbVar[i]);
cgiMakeDropListFull(buf, labels, terms, len, mdbVal[i], "class='mdbVal single' style='min-width:200px; font-size:.9em;' onchange='findTracksSearchButtonsEnable(true);'");
}
else if (searchBy == cvsSearchByFreeText)
{
safef(buf, sizeof(buf), "%s%i", METADATA_VALUE_PREFIX, i + 1);
hPrintf("</td><td align='right' id='isLike%d' style='width:10px;'>contains</td><td nowrap id='%s' style='max-width:600px;'>\n",i + 1,buf);
hPrintf("<input type='text' name='%s' value='%s' class='mdbVal freeText' onkeyup='findTracksSearchButtonsEnable(true);' style='max-width:310px; width:310px; font-size:.9em;'>",
buf,(mdbVal[i] ? mdbVal[i]: ""));
}
else if (searchBy == cvsSearchByDateRange || searchBy == cvsSearchByIntegerRange)
{
// TO BE IMPLEMENTED
}
#else//ifndef CV_SEARCH_SUPPORTS_FREETEXT
cgiDropDownWithTextValsAndExtra(buf, mdbVarLabels, mdbVars,count,mdbVar[i],"class='mdbVar' style='font-size:.9em;' onchange='findTracksMdbVarChanged(this);'");
hPrintf("</td><td align='right' style='width:10px;'>is</td><td nowrap style='max-width:600px;'>is\n");
len = getTermArray(conn, &labels, &terms, mdbVar[i]);
safef(buf, sizeof(buf), "%s%i", METADATA_VALUE_PREFIX, i + 1);
cgiMakeDropListFull(buf, labels, terms, len, mdbVal[i], "class='mdbVal' style='min-width:200px; font-size:.9em;' onchange='findTracksSearchButtonsEnable(true);'");
#endif///ndef CV_SEARCH_SUPPORTS_FREETEXT
hPrintf("<span id='helpLink%d'>help</span></td>\n", i + 1);
hPrintf("</tr>\n");
}
hPrintf("<tr><td colspan='%d' align='right' style='height:10px; max-height:10px;'> </td></tr>", cols);
//hPrintf("<tr><td colspan='%d' align='right' class='lineOnTop' style='height:20px; max-height:20px;'> </td></tr>", cols);
return numMetadataSelects;
}
static void displayFoundTracks(struct cart *cart, struct slRef *tracks, int tracksFound,enum sortBy sortBy)
// Routine for displaying found tracks
{
hPrintf("<div id='found' style='display:none;'>\n"); // This div allows the clear button to empty it
if(tracksFound < 1)
{
hPrintf("<p>No tracks found</p>\n");
}
else
{
struct hash *tdbHash = makeTrackHash(database, chromName);
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(" <FONT class='selCbCount'></font>\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");
#define PM_BUTTON "<IMG height=18 width=18 onclick=\"return findTracksCheckAllWithWait(%s);\" id='btn_%s' src='../images/%s' title='%s all found tracks'>"
hPrintf("</td></tr><tr bgcolor='#%s'><td>",HG_COL_HEADER);
hPrintf(PM_BUTTON,"true", "plus_all", "add_sm.gif", "Select");
hPrintf(PM_BUTTON,"false","minus_all","remove_sm.gif","Unselect");
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),"onchange=\"findTracksSortNow(this);\"");
hPrintf("by Relevance");
cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "1", (sortBy == sbAbc), "onchange=\"findTracksSortNow(this);\"");
hPrintf("Alphabetically");
cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "2",(sortBy == sbHierarchy), "onchange=\"findTracksSortNow(this);\"");
hPrintf("by Hierarchy </span>\n");
}
hPrintf("</td></tr>\n");
// Set up json for js functionality
struct dyString *jsonTdbVars = NULL;
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 configuration from track search
if (tdbIsFolder(track->tdb)) // supertrack
hPrintf("<tr bgcolor='%s' valign='top' class='found'>\n","#EED5B7");//"#DEB887");//"#E6B426");//#FCECC0//COLOR_LTGREY);//COLOR_LTGREEN);//COLOR_TRACKLIST_LEVEL1);
else if (tdbIsContainer(track->tdb))
hPrintf("<tr bgcolor='%s' valign='top' class='found'>\n",COLOR_TRACKLIST_LEVEL3);
else
hPrintf("<tr bgcolor='%s' valign='top' class='found'>\n",COLOR_TRACKLIST_LEVEL2);
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))
{
checked = fourStateVisible(subtrackFourStateChecked(track->tdb,cart)); // Don't need all 4 states here. Visible=checked&&enabled
checked = (checked && ( track->visibility != tvHide )); // Checked is only if subtrack level vis is also set!
}
// Setup the check box
#define CB_HIDDEN_VAR "<INPUT TYPE=HIDDEN disabled=true NAME='%s_sel' VALUE='%s'>"
if (tdbIsContainerChild(track->tdb) || tdbIsFolderContent(track->tdb)) // subtracks and folder children get "_sel" var. ("_sel" var is temporary on folder children)
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='findTracksClickedOne(this,true);'%s>"
hPrintf(CB_SEEN,track->track,(checked?" CHECKED":""));
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='findTracksChangeVis(this)'",track->track);
hideShowDropDownWithClassAndExtra(track->track, (track->visibility != tvHide), "normalText visDD",extra);
}
else
{
safef(extra,sizeof(extra),"id='%s_id' onchange='findTracksChangeVis(this)'",track->track);
hTvDropDownClassWithJavascript(NULL, track->visibility,track->canPack,"normalText seenVis",extra);
}
// If this is a container track, allow configuring...
if (tdbIsContainer(track->tdb) || tdbIsFolder(track->tdb))
{
containerTrackCount++;
hPrintf(" <a href='hgTrackUi?db=%s&g=%s&%s=Search' title='Configure this container track...'><IMG SRC='../images/folderWrench.png'></a> ",database,track->track,TRACK_SEARCH);
}
hPrintf("</td>\n");
// shortLabel has description popup and longLabel has "..." metadata
hPrintf("<td><a target='_top' onclick=\"hgTrackUiPopUp('%s',true); return false;\" href='%s' title='Display track details'>%s</a></td>\n", track->track, trackUrl(track->track, NULL), track->shortLabel);
hPrintf("<td>%s", track->longLabel);
compositeMetadataToggle(database, track->tdb, "...", TRUE, FALSE, tdbHash);
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(" <FONT class='selCbCount'></font>");
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
hWrites(jsonTdbSettingsUse(&jsonTdbVars));
}
#ifdef OMIT
if(!doSearch)
{
hPrintf("<p><b>Recently Done</b><ul>\n"
"<li>Can now page through found tracks 100 at a time.</li>"
"<li>Added <IMG SRC='../images/folderWrench.png'> icon for contqainers with a configuration link. Is this okay?</li>"
"<li>SuperTracks can now be found.</li>"
"<li>Configuration of superTrack children's vis should result in proper superTrack reshaping. (This is really an hgTrackUi feature.)</li>"
"<li>Added sort toggle: Relevance, Alphabetically or by Hierarchy.</li>"
"<li>Composite/view visibilites in hgTrackUi get reshaped to reflect found/selected subtracks. (In demo1: only default state composites; demo2: all composites.)</li>"
"<li>Non-data 'container' tracks (composites and supertracks) have '*' to mark them, and can be configured before displaying. Better suggestions?</li>"
"</ul></p>"
"<p><b>Suggested improvments:</b><ul>\n"
"<li>The metadata values will not be white-listed, but it would be nice to have more descriptive text for them. A short label added to cv.ra?</li>"
"<li>Look and feel of found track list (here) and composite subtrack list (hgTrackUi) should converge. Jim suggests look and feel of hgTracks 'Configure Tracks...' list instead.</li>"
"<li>Drop-down list of terms (cells, antibodies, etc.) should be multi-select with checkBoxes as seen in filterComposites. Perhaps saved for v2.0.</li>"
"</ul></p>\n");
}
#endif///def OMIT
hPrintf("</div>"); // This div allows the clear button to empty it
}
void configMultiRegionPage()
/* Do multi-region config page after setting track visibility. If vis is -2, then visibility
* is unchanged. If -1 then set visibility to default, otherwise it should
* be tvHide, tvDense, etc. */
{
char *groupTarget;
struct track *trackList;
struct track *ideoTrack;
struct group *groupList;
int vis = -2;
configInitTrackList(vis, &groupTarget, &trackList, &ideoTrack, &groupList);
hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n", hgTracksName(),
cartUsualString(cart, "formMethod", "POST"));
webStartWrapperDetailedNoArgs(cart, database, "", "", FALSE, FALSE, FALSE, FALSE);
cartSaveSession(cart);
hPrintf("<BR>\n");
hTableStart();
virtModeType = cartUsualString(cart, "virtModeType", virtModeType);
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "default", sameWord("default", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Exit multi-region mode");
hPrintf("</TD></TR>\n");
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database)) // no db conn for assembly hubs
conn = hAllocConn(database);
// Do we have a gene table for exonMostly?
findBestEMGeneTable(trackList);
if (emGeneTable)
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "exonMostly", sameWord("exonMostly", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Show exons using %s. Use padding of: ", emGeneTrack->shortLabel);
hIntVar("emPadding", cartUsualInt(cart, "emPadding", emPadding), 3);
hPrintf(" bases.");
hPrintf("</TD></TR>\n");
}
if (emGeneTable)
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "geneMostly", sameWord("geneMostly", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Show genes using %s. Use padding of: ", emGeneTrack->shortLabel);
hIntVar("gmPadding", cartUsualInt(cart, "gmPadding", gmPadding), 3);
hPrintf(" bases.");
hPrintf("</TD></TR>\n");
}
/* obsolete
if (conn && sqlTableExists(conn,"knownCanonical"))
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "kcGenes", sameWord("kcGenes", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Show gene regions genome-wide.");
hPrintf("</TD></TR>\n");
}
*/
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "customUrl", sameWord("customUrl", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Enter Custom regions as BED, or a URL to them:<br>");
multiRegionsBedUrl = cartUsualString(cart, "multiRegionsBedUrl", multiRegionsBedUrl);
struct dyString *dyMultiRegionsBedInput = dyStringNew(256);
if (strstr(multiRegionsBedUrl,"://"))
{
dyStringAppend(dyMultiRegionsBedInput, multiRegionsBedUrl);
}
else
{
if (fileExists(multiRegionsBedUrl))
{
struct lineFile *lf = lineFileMayOpen(multiRegionsBedUrl, TRUE);
char *line;
int lineSize;
while (lineFileNext(lf, &line, &lineSize))
{
dyStringPrintf(dyMultiRegionsBedInput, "%s\n", line);
}
lineFileClose(&lf);
}
}
hPrintf("<TEXTAREA NAME='multiRegionsBedInput' ID='multiRegionsBedInput' rows='4' cols='58' style='white-space: pre;'>%s</TEXTAREA>",
dyMultiRegionsBedInput->string);
hPrintf("</TD></TR>\n");
/* The AllChroms option will be released in future
if (emGeneTable && sqlTableExists(conn, emGeneTable))
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "singleTrans", sameWord("singleTrans", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Show only one transcript using an ID from %s : ", emGeneTrack->shortLabel);
char *trans = cartUsualString(cart, "singleTransId", singleTransId);
char sql[1024];
sqlSafef(sql, sizeof sql, "select name from %s where name='%s'", emGeneTable, trans);
char *result = sqlQuickString(conn, sql);
if (!result)
{
sqlSafef(sql, sizeof sql, "select name from %s limit 1", emGeneTable);
trans = sqlQuickString(conn, sql);
}
hTextVar("singleTransId", trans, 20);
hPrintf("</TD></TR>\n");
}
*/
if (conn)
{
boolean altLocExists = sqlTableExists(conn, "altLocations");
boolean fixLocExists = sqlTableExists(conn, "fixLocations");
if (altLocExists || fixLocExists)
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "singleAltHaplo",
sameWord("singleAltHaplo", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Show one alternate haplotype");
if (fixLocExists)
hPrintf(" or fix patch");
hPrintf(", placed on its chromosome, using ID: ");
char *haplo = cartUsualString(cart, "singleAltHaploId", singleAltHaploId);
char *foundHaplo = NULL;
char sql[1024];
if (altLocExists)
{
sqlSafef(sql, sizeof sql,
"select name from altLocations where name rlike '^%s(:[0-9-]+)?'", haplo);
foundHaplo = sqlQuickString(conn, sql);
}
if (!foundHaplo && fixLocExists)
{
sqlSafef(sql, sizeof sql,
"select name from fixLocations where name rlike '^%s(:[0-9-]+)?'", haplo);
foundHaplo = sqlQuickString(conn, sql);
}
if (!foundHaplo)
{
if (altLocExists)
sqlSafef(sql, sizeof sql, "select name from altLocations limit 1");
else
sqlSafef(sql, sizeof sql, "select name from fixLocations limit 1");
haplo = sqlQuickString(conn, sql);
chopSuffixAt(haplo, ':');
}
hTextVar("singleAltHaploId", haplo, 60);
hPrintf("</TD></TR>\n");
}
}
/* disable demo for now
if (sameString(database,"hg19") || sameString(database, "hg38"))
{
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo1", sameWord("demo1", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo1 two windows on two chroms (default pos on chr21, and same loc on chr22)");
hPrintf("</TD></TR>\n");
}
*/
/* Disabled for now
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo2", sameWord("demo2", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo2 multiple ");
hIntVar("demo2NumWindows", cartUsualInt(cart, "demo2NumWindows", demo2NumWindows), 3);
hPrintf(" windows on one chrom chr21 def posn, window size ");
hIntVar("demo2WindowSize", cartUsualInt(cart, "demo2WindowSize", demo2WindowSize), 3);
hPrintf(" and step size ");
hIntVar("demo2StepSize", cartUsualInt(cart, "demo2StepSize", demo2StepSize), 3);
hPrintf(" exon-like");
hPrintf("</TD></TR>\n");
*/
/* The AllChroms option will be released in future
if (conn) // requires chromInfo from database.
{ // TODO allow it to use assembly hubs via trackHubAllChromInfo() ?
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "allChroms", sameWord("allChroms", virtModeType));
hPrintf("</TD><TD>");
hPrintf("<br>Show all chromosomes.<br><span style='color:red'>Warning:</span> Turn off all tracks except bigBed, bigWig, and very sparse tracks.<br>Press Hide All to hide all tracks.");
hPrintf("</TD></TR>\n");
}
*/
/* Disabled for now
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo4", sameWord("demo4", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo4 multiple (311) windows showing exons from TITIN gene uc031rqd.1.");
hPrintf("</TD></TR>\n");
*/
/* Disabled for now
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo5", sameWord("demo5", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo5 alt locus on hg38. Shows alt chrom surrounded by regions of same size from reference genome.");
hPrintf("</TD></TR>\n");
*/
/* Disabled for now
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo6", sameWord("demo6", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo6 shows zoomed in exon-exon junction from SOD1 gene, between exon1 and exon2.");
hPrintf("</TD></TR>\n");
*/
hTableEnd();
hPrintf("<BR>\n");
hPrintf("<TABLE style=\"border:0px; \">\n");
hPrintf("<TR><TD>");
hCheckBox("emAltHighlight", cartUsualBoolean(cart, "emAltHighlight", FALSE));
hPrintf("</TD><TD>");
hPrintf("Highlight alternating regions in multi-region view");
hPrintf("</TD></TR>\n");
hPrintf("</TABLE>\n");
hPrintf("<BR>\n");
hPrintf("<TABLE style=\"border:0px;width:650px \">\n");
hPrintf("<TR><TD>");
cgiMakeButton("topSubmit", "submit");
hPrintf("</TD><TD align=right>");
hPrintf("<A HREF=\"../goldenPath/help/multiRegionHelp.html\" target=_blank>Help</A>\n");
hPrintf("</TD></TR>\n");
hPrintf("</TABLE>\n");
hFreeConn(&conn);
cgiDown(0.9);
freez(&groupTarget);
webEndSectionTables();
hPrintf("</FORM>");
}
struct slPair *mdbSelectPairs(struct cart *cart, struct slPair *mdbVars)
// Returns the current mdb vars and vals in the table of drop down selects
{
// figure out how many metadata selects are visible.
int numMetadataSelects = 0;
struct slPair *mdbSelectPairs = NULL;
if (mdbVars == NULL)
return 0;
// Get the current number of rows in the table of mdb selects
for (;;)
{
char buf[256];
safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, numMetadataSelects + 1);
char *str = cartOptionalString(cart, buf);
if (isEmpty(str))
break;
else
numMetadataSelects++;
}
// Requesting to add or delete any?
int delSearchSelect = cartUsualInt(cart, TRACK_SEARCH_DEL_ROW, 0); // 1-based row to delete
int addSearchSelect = cartUsualInt(cart, TRACK_SEARCH_ADD_ROW, 0); // 1-based row to insert after
if (delSearchSelect)
numMetadataSelects--;
if (addSearchSelect)
numMetadataSelects++;
if (numMetadataSelects)
{
int ix;
char buf[256];
for (ix = 0; ix < numMetadataSelects; ix++)
{
int offset; // used to handle additions/deletions
if (addSearchSelect > 0 && ix >= addSearchSelect)
offset = 0; // do nothing to offset (i.e. copy data from previous row)
else if (delSearchSelect > 0 && ix + 1 >= delSearchSelect)
offset = 2;
else
offset = 1;
safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, ix + offset);
char *var = cartOptionalString(cart, buf);
char *val = NULL;
// We need to make sure var is valid in this assembly; if it isn't, reset it to "cell".
if (slPairFindVal(mdbVars,var) == NULL)
var = "cell";
else
{
safef(buf, sizeof(buf), "%s%d", METADATA_VALUE_PREFIX, ix + offset);
enum cvSearchable searchBy = cvSearchMethod(var);
if (searchBy == cvSearchByMultiSelect)
{
// Multi-selects as comma delimited list of values
struct slName *vals = cartOptionalSlNameList(cart,buf);
if (vals)
{
val = slNameListToString(vals,','); // A comma delimited list of values
slNameFreeList(&vals);
}
}
else if (searchBy == cvSearchBySingleSelect
|| searchBy == cvSearchByFreeText
|| searchBy == cvSearchByWildList)
val = cloneString(cartUsualString(cart, buf,ANYLABEL));
//else if (searchBy == cvSearchByDateRange || searchBy == cvSearchByIntegerRange)
// {
// // TO BE IMPLEMENTED
// }
if (val != NULL && sameString(val, ANYLABEL))
val = NULL;
}
slPairAdd(&mdbSelectPairs,var,val); // val already cloned
}
if (delSearchSelect > 0)
{
safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, numMetadataSelects + 1);
cartRemove(cart, buf);
safef(buf, sizeof(buf), "%s%d", METADATA_VALUE_PREFIX, numMetadataSelects + 1);
cartRemove(cart, buf);
}
}
else
{
// create defaults
slPairAdd(&mdbSelectPairs,"cell", NULL);
slPairAdd(&mdbSelectPairs,"antibody",NULL);
}
slReverse(&mdbSelectPairs);
return mdbSelectPairs;
}
void doImage(struct sqlConnection *conn)
/* Put up image page. */
{
int imageId = cartUsualInt(cart, hgpId, 0);
char *sidUrl = cartSidUrlString(cart);
char buf[1024];
char url[1024];
char *p = NULL;
char dir[256];
char name[128];
char extension[64];
int w = 0, h = 0;
htmlSetBgColor(0xE0E0E0);
htmStart(stdout, "do image");
puts(
"<script type=\"text/JavaScript\">"
"document.getElementsByTagName('html')[0].style.height=\"100%\";"
"document.getElementsByTagName('body')[0].style.height=\"100%\";"
"</script>"
);
if (!visiGeneImageSize(conn, imageId, &w, &h))
imageId = 0;
if (imageId != 0)
{
printf("<B>");
smallCaption(conn, imageId);
printf(".</B> Click image to zoom in, drag or arrow keys to move. "
"Caption is below.<BR>\n");
p=visiGeneFullSizePath(conn, imageId);
splitPath(p, dir, name, extension);
#ifdef DEBUG
safef(buf,sizeof(buf),"../bigImageTest.html?url=%s%s/%s&w=%d&h=%d",
dir,name,name,w,h);
#else
safef(buf,sizeof(buf),"../bigImage.html?url=%s%s/%s&w=%d&h=%d",
dir,name,name,w,h);
#endif
printf("<IFRAME name=\"bigImg\" width=\"100%%\" height=\"90%%\" SRC=\"%s\"></IFRAME><BR>\n", buf);
fullCaption(conn, imageId);
safef(buf,sizeof(buf),"%s%s%s", dir, name, extension);
safef(url,sizeof(url),"%s?%s=go&%s&%s=%d",
hgVisiGeneCgiName(), hgpDoDownload, sidUrl, hgpId, imageId);
printf("<B>Full-size image:</B> %d x %d <A HREF='%s'> download </A> ", w, h, url);
/* Currently this is dangerous for users with less than 1 GB RAM to use
on large images, because their machines can thrash themselves into a coma.
X-windows (i.e. used by FireFox) will allocate 5 bytes per pixel.
If the image size in pixels times 5 exceeds real ram size, then
Linux thrashes incessantly. But you can hit ctrl-alt-F1 to
get a text only screen, then kill the bad processes (FF) and then
you can restore desktop with ctrl-alt-F7. Hiram says that's a
feature credited to SCO-Unix. On my 1GB machines at work/home,
I never encountered any problem what-so-ever, even with the
largest visiGene AllenBrain - about 19000x9000 pix.
printf(" <A HREF='%s'> view </A>\n", buf);
*/
printf("\n");
}
htmlEnd();
}
void loadCodeBlast(struct track *tg)
/* from the bed 6+1 codeBlast table, make a linkedFeaturesSeries and load it. */
{
struct linkedFeaturesSeries *lfs = NULL, *originalLfs, *codeLfs, *lfsList = NULL;
struct linkedFeatures *lf;
struct slName *codes = NULL, *track=NULL, *scores=NULL;
struct codeBlast *bedList;
struct codeBlast *cb, *list=NULL;
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char **temparray3;
char *temparray[32];
char *temparray2;
char **row;
char *tempstring;
int x;
int cutoff;
char cMode[64];
/*The most common names used to display method*/
char *codeNames[18] = {"within genus", "\t", "crenarchaea", "euryarchaea", "\t", "bacteria",
"\t", "eukarya", "\t", "thermophile", "hyperthermophile","acidophile",
"alkaliphile", "halophile", "methanogen", "strict aerobe",
"strict anaerobe", "anaerobe or aerobe"}; int i;
safef(cMode, sizeof(cMode), "%s.scoreFilter", tg->tdb->track);
cutoff=cartUsualInt(cart, cMode,0 );
sr=hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, 0);
while ((row = sqlNextRow(sr)) != NULL)
{
cb = codeBlastLoad(row);
slAddHead(&list, cb);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
slReverse(&list);
if(list == NULL)
return;
for(cb = list; cb != NULL; cb = cb->next)
{
AllocVar(lfs);
AllocVar(lf);
lfs->name = cloneString(cb->name);
lf = lfFromBed6(cb,0,1000);
lf->score = cb->score;
tempstring=cloneString(cb->code);
chopString(tempstring, "," , temparray, ArraySize(temparray));
if(sameWord(database, "pyrFur2"))
{
temparray3=(char**)calloc(19*8,sizeof(char**));
for(x=0; x<19; x++)
{
temparray3[x]=(char *)calloc(256, sizeof(char*));
/* Fix to cloneString problem when both patricia and my track was showing at the same time */
if(temparray[x]!=NULL)
{
if(atoi(temparray[x])==1000)
temparray3[x]="1000";
else if(atoi(temparray[x])==900)
temparray3[x]="900";
else if(atoi(temparray[x])==800)
temparray3[x]="800";
else if(atoi(temparray[x])==700)
temparray3[x]="700";
else if(atoi(temparray[x])==600)
temparray3[x]="600";
else if(atoi(temparray[x])==500)
temparray3[x]="500";
else if(atoi(temparray[x])==400)
temparray3[x]="400";
else if(atoi(temparray[x])==300)
temparray3[x]="300";
else if(atoi(temparray[x])==200)
temparray3[x]="200";
else if(atoi(temparray[x])==100)
temparray3[x]="100";
else
temparray3[x]="0";
}
}
}
else
{
temparray3=(char**)calloc(18*8,sizeof(char**));
for(x=0; x<18; x++)
{
temparray3[x]=(char *)calloc(256, sizeof(char*));
/* Fix to cloneString problem when both patricia and my track was showing at the same time */
if(temparray[x]!=NULL)
{
if(atoi(temparray[x])==1000)
temparray3[x]="1000";
else if(atoi(temparray[x])==900)
temparray3[x]="900";
else if(atoi(temparray[x])==800)
temparray3[x]="800";
else if(atoi(temparray[x])==700)
temparray3[x]="700";
else if(atoi(temparray[x])==600)
temparray3[x]="600";
else if(atoi(temparray[x])==500)
temparray3[x]="500";
else if(atoi(temparray[x])==400)
temparray3[x]="400";
else if(atoi(temparray[x])==300)
temparray3[x]="300";
else if(atoi(temparray[x])==200)
temparray3[x]="200";
else if(atoi(temparray[x])==100)
temparray3[x]="100";
else
temparray3[x]="0";
}
}
}
lf->extra = temparray3;
lfs->start = lf->start;
lfs->end = lf->end;
lfs->features= lf;
slAddHead(&lfsList, lfs);
}
tg->items=lfsList;
bedList=tg->items;
lfsList=NULL;
if(tg->limitedVis != tvDense)
{
originalLfs = tg->items;
if(sameWord(database, "pyrFur2"))
{
for (i = 0; i < 19; i++)
{
struct linkedFeatures *lfList = NULL;
AllocVar(codeLfs);
/*When doing abyssi displays differnt names at the begining*/
if(i == 0)
codeLfs->name="within Pho";
else if (i==1)
codeLfs->name="within Pab";
else if (i==2)
codeLfs->name="\t";
else
codeLfs->name = cloneString(codeNames[i-1]);
codeLfs->noLine = TRUE;
for (lfs = originalLfs; lfs != NULL; lfs = lfs->next)
{
lf = lfsToLf(lfs);
if(i>2)
temparray2=((char**)(lfs->features->extra))[i-0];
else temparray2=((char**)(lfs->features->extra))[i];
if (i!=2 && i!=5 && i!=7 && i!=9 && atoi(temparray2)>-9997 && atoi(temparray2)!=0 && atoi(temparray2)>=cutoff)
{
lf->score=atoi(temparray2);
slAddHead(&lfList,lf);
}
}
slReverse(&lfList);
codeLfs->features = lfList;
slAddHead(&lfsList,codeLfs);
}
}
else
{
for (i = 0; i < 18; i++)
{
struct linkedFeatures *lfList = NULL;
AllocVar(codeLfs);
codeLfs->name = cloneString(codeNames[i]);
codeLfs->noLine = TRUE;
for (lfs = originalLfs; lfs != NULL; lfs = lfs->next)
{
lf = lfsToLf(lfs);
temparray2=((char**)(lfs->features->extra))[i];
if (i!=1 && i!=4 && i!=6 && i!=8 && atoi(temparray2)>-9997 && atoi(temparray2)!=0 && atoi(temparray2)>=cutoff)
{
lf->score=atoi(temparray2);
slAddHead(&lfList,lf);
}
}
slReverse(&lfList);
codeLfs->features = lfList;
slAddHead(&lfsList,codeLfs);
}
}
freeLinkedFeaturesSeries(&originalLfs);
slReverse(&lfsList);
tg->items=lfsList;
}
slFreeList(&track);
slFreeList(&scores);
slFreeList(&codes);
codeBlastFree(&list);
}
void doFrame(struct sqlConnection *conn, boolean forceImageToList)
/* Make a html frame page. Fill frame with thumbnail, control bar,
* and image panes. */
{
int imageId = cartUsualInt(cart, hgpId, 0);
char *sidUrl = cartSidUrlString(cart);
char *listSpec = cartUsualString(cart, hgpListSpec, "");
struct tempName matchTempName;
char *matchFile = NULL;
struct visiMatch *matchList = visiSearch(conn, listSpec);
#ifdef SOON
if (!cartUsualBoolean(cart, hgpIncludeMutants, FALSE))
matchList = removeMutants(conn, matchList);
#endif /* SOON */
matchList = onePerImageFile(conn, matchList);
weighMatches(conn, matchList);
slSort(&matchList, visiMatchCmpWeight);
if (forceImageToList)
{
if (matchList != NULL)
imageId = matchList->imageId;
else
imageId = 0;
}
trashDirFile(&matchTempName, "vg", "visiMatch", ".tab");
matchFile = matchTempName.forCgi;
saveMatchFile(matchFile, matchList);
cartSetString(cart, hgpMatchFile, matchFile);
cartSetInt(cart, hgpId, imageId);
//puts("\n");
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Frameset//EN\" \"http://www.w3.org/TR/html4/frameset.dtd\">");
printf("<HTML>\n");
printf("<HEAD>\n");
printf("<TITLE>\n");
printf("%s ", hgVisiGeneShortName());
printf("%s",titleMessage);
printf("</TITLE>\n");
printf("</HEAD>\n");
printf(" <frameset rows=\"27,*\">\n");
printf(" <frame name=\"controls\" src=\"%s?%s=go&%s&%s=%d\" noresize marginwidth=\"0\" marginheight=\"0\" frameborder=\"0\">\n",
hgVisiGeneCgiName(), hgpDoControls, sidUrl, hgpId, imageId);
printf(" <frameset cols=\"230,*\"> \n");
printf(" <frame src=\"%s?%s=go&%s&%s=%d\" noresize frameborder=\"0\" name=\"list\">\n",
hgVisiGeneCgiName(), hgpDoThumbnails, sidUrl, hgpId, imageId);
printf(" <frame src=\"%s?%s=go&%s&%s=%d\" name=\"image\" noresize frameborder=\"0\">\n",
hgVisiGeneCgiName(), hgpDoImage, sidUrl, hgpId, imageId);
printf(" </frameset>\n");
printf(" <noframes>\n");
printf(" <body>\n");
printf(" <p>This web page uses frames, but your browser doesn't support them.</p>\n");
printf(" </body>\n");
printf(" </noframes>\n");
printf("</frameset>\n");
printf("</HTML>\n");
}
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");
}
void doPastedIdentifiers(struct sqlConnection *conn)
/* Process submit in paste identifiers page. */
{
char *idText = trimSpaces(cartString(cart, hgtaPastedIdentifiers));
htmlOpen("Table Browser (Input Identifiers)");
if (isNotEmpty(idText))
{
/* Write terms to temp file, checking whether they have matches, and
* save temp file name. */
boolean saveIdText = (strlen(idText) < MAX_IDTEXT);
char *idTextForLf = saveIdText ? cloneString(idText) : idText;
struct lineFile *lf = lineFileOnString("idText", TRUE, idTextForLf);
char *line, *word;
struct tempName tn;
FILE *f;
int totalTerms = 0, foundTerms = 0;
struct slName* missingTerms = NULL;
struct dyString *exampleMissingIds = dyStringNew(256);
char *actualDb = database;
if (sameWord(curTable, WIKI_TRACK_TABLE))
actualDb = wikiDbName();
struct hTableInfo *hti = maybeGetHti(actualDb, curTable, conn);
char *idField = getIdField(actualDb, curTrack, curTable, hti);
if (idField == NULL)
{
warn("Sorry, I can't tell which field of table %s to treat as the "
"identifier field.", curTable);
webNewSection("Table Browser");
cartRemove(cart, hgtaIdentifierDb);
cartRemove(cart, hgtaIdentifierTable);
cartRemove(cart, hgtaIdentifierFile);
mainPageAfterOpen(conn);
htmlClose();
return;
}
struct slName *allTerms = NULL, *term;
while (lineFileNext(lf, &line, NULL))
{
while ((word = nextWord(&line)) != NULL)
{
term = slNameNew(word);
slAddHead(&allTerms, term);
totalTerms++;
}
}
slReverse(&allTerms);
lineFileClose(&lf);
char *extraWhere = NULL;
int maxIdsInWhere = cartUsualInt(cart, "hgt_maxIdsInWhere", DEFAULT_MAX_IDS_IN_WHERE);
if (totalTerms > 0 && totalTerms <= maxIdsInWhere)
extraWhere = slNameToInExpression(idField, allTerms);
struct lm *lm = lmInit(0);
struct hash *matchHash = getAllPossibleIds(conn, lm, idField, extraWhere);
trashDirFile(&tn, "hgtData", "identifiers", ".key");
f = mustOpen(tn.forCgi, "w");
for (term = allTerms; term != NULL; term = term->next)
{
struct slName *matchList = NULL, *match;
if (matchHash == NULL)
{
matchList = slNameNew(term->name);
}
else
{
/* Support multiple alias->id mappings: */
char upcased[1024];
safecpy(upcased, sizeof(upcased), term->name);
touppers(upcased);
struct hashEl *hel = hashLookup(matchHash, upcased);
if (hel != NULL)
{
matchList = slNameNew((char *)hel->val);
while ((hel = hashLookupNext(hel)) != NULL)
{
match = slNameNew((char *)hel->val);
slAddHead(&matchList, match);
}
}
}
if (matchList != NULL)
{
foundTerms++;
for (match = matchList; match != NULL; match = match->next)
{
mustWrite(f, match->name, strlen(match->name));
mustWrite(f, "\n", 1);
}
}
else
{
slAddHead(&missingTerms, slNameNew(term->name));
}
}
slReverse(&missingTerms);
carefulClose(&f);
cartSetString(cart, hgtaIdentifierDb, database);
cartSetString(cart, hgtaIdentifierTable, curTable);
cartSetString(cart, hgtaIdentifierFile, tn.forCgi);
if (saveIdText)
freez(&idTextForLf);
else
cartRemove(cart, hgtaPastedIdentifiers);
int missingCount = totalTerms - foundTerms;
if (missingCount > 0)
{
char *xrefTable, *aliasField;
getXrefInfo(conn, &xrefTable, NULL, &aliasField);
boolean xrefIsSame = xrefTable && sameString(curTable, xrefTable);
struct tempName tn;
trashDirFile(&tn, "hgt/missingIds", cartSessionId(cart), ".tmp");
FILE *f = mustOpen(tn.forCgi, "w");
int exampleCount = 0;
for (term = missingTerms; term != NULL; term = term->next)
{
if (exampleCount < 10)
{
++exampleCount;
dyStringPrintf(exampleMissingIds, "%s\n", term->name);
}
fprintf(f, "%s\n", term->name);
}
carefulClose(&f);
dyStringPrintf(exampleMissingIds, "\n<a href=%s>Complete list of missing identifiers<a>\n", tn.forHtml);
warn("Note: %d of the %d given identifiers have no match in "
"table %s, field %s%s%s%s%s. "
"Try the \"describe table schema\" button for more "
"information about the table and field.\n"
"%d %smissing identifier(s):\n"
"%s\n",
(totalTerms - foundTerms), totalTerms,
curTable, idField,
(xrefTable ? (xrefIsSame ? "" : " or in alias table ") : ""),
(xrefTable ? (xrefIsSame ? "" : xrefTable) : ""),
(xrefTable ? (xrefIsSame ? " or in field " : ", field ") : ""),
(xrefTable ? aliasField : ""),
exampleCount,
exampleCount < missingCount ? "example " : "",
exampleMissingIds->string
);
webNewSection("Table Browser");
}
lmCleanup(&lm);
hashFree(&matchHash);
}
else
{
cartRemove(cart, hgtaIdentifierFile);
}
mainPageAfterOpen(conn);
htmlClose();
}
static void displayFoundTracks(struct cart *cart, struct slRef *tracks, int tracksFound,
enum sortBy sortBy)
// Routine for displaying found tracks
{
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);\" " \
"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("</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);\"");
hPrintf("by Relevance");
cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "1", (sortBy == sbAbc),
"onclick=\"findTracks.sortNow(this);\"");
hPrintf("Alphabetically");
cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "2",(sortBy == sbHierarchy),
"onclick=\"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>"
hPrintf(CB_SEEN,track->track,(checked?" CHECKED":""));
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);
hideShowDropDownWithClassAndExtra(track->track, (track->visibility != tvHide),
"normalText visDD",extra);
}
else
{
safef(extra,sizeof(extra),"id='%s_id' onchange='findTracks.changeVis(this)'",
track->track);
hTvDropDownClassWithJavascript(NULL, track->visibility,track->canPack,
"normalText seenVis",extra);
}
// 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);
}
//#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;\" "
"href='%s' title='Display track details'>%s</a></td>\n",
track->track, trackUrl(track->track, NULL), track->shortLabel);
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)
{
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();
}
static void doThumbnails(struct sqlConnection *conn)
/* Write out list of thumbnail images. */
{
char *sidUrl = cartSidUrlString(cart);
char *listSpec = cartUsualString(cart, hgpListSpec, "");
char *matchFile = cartString(cart, hgpMatchFile);
struct visiMatch *matchList = NULL, *match;
int maxCount = 25, count = 0;
int startAt = cartUsualInt(cart, hgpStartAt, 0);
int imageCount;
htmlSetStyle(
"<STYLE TYPE=\"text/css\">\n"
" BODY {margin: 2px}\n"
" </STYLE>\n"
);
htmlSetBgColor(0xC0C0D6);
htmStart(stdout, "doThumbnails");
matchList = readMatchFile(matchFile);
imageCount = slCount(matchList);
if (imageCount > 0)
{
printf(
" <DIV"
" ID='perspClip'"
" STYLE='position:absolute;left:-1000px;top:-1000px;z-index:2;visibility:visible;overflow:hidden!important;'"
" onmouseover='this.style.left=\"-1000px\";' "
" >"
" <DIV"
" ID='perspective'"
" STYLE='position:absolute;left:0px;top:0px;'"
" >"
" <IMG ID='perspBox' SRC='../images/dot_clear.gif' STYLE='position:absolute;left:0px;top:0px;width:100px;height:100px;border-style:solid;border-color:#8080FF;border-width:1px' "
">"
" </DIV>"
" </DIV>"
);
printf("<TABLE>\n");
printf("<TR><TD><B>");
printf("%d images match<BR>\n", imageCount);
printf("</B></TD></TR>\n");
for (match = slElementFromIx(matchList, startAt);
match != NULL; match = match->next)
{
int id = match->imageId;
char *imageFile = visiGeneThumbSizePath(conn, id);
printf("<TR>");
printf("<TD>");
printf("<A HREF=\"%s?%s&%s=%d&%s=do\" target=\"image\" >",
hgVisiGeneCgiName(),
sidUrl, hgpId, id, hgpDoImage);
printf("<IMG SRC=\"%s\"></A><BR>\n", imageFile);
smallCaption(conn, id);
printf("<BR>\n");
printf("</TD>");
printf("</TR>");
if (++count >= maxCount)
break;
}
printf("</TABLE>\n");
printf("<HR>\n");
}
if (count != imageCount)
{
int start;
int page = 0;
printf("%d-%d of %d for:<BR>", startAt+1,
startAt+count, imageCount);
printf(" %s<BR>\n", listSpec);
printf("Page:\n");
for (start=0; start<imageCount; start += maxCount)
{
++page;
if (start != startAt)
{
printf("<A HREF=\"%s?", hgVisiGeneCgiName());
printf("%s&", sidUrl);
printf("%s=on&", hgpDoThumbnails);
printf("%s=%s&", hgpListSpec, listSpec);
if (start != 0)
printf("%s=%d", hgpStartAt, start);
printf("\">");
}
printf("%d", page);
if (start != startAt)
printf("</A>");
printf(" ");
}
}
else
{
printf("%d images for:<BR>", imageCount);
printf(" %s<BR>\n", listSpec);
}
cartRemove(cart, hgpStartAt);
htmlEnd();
}
void configurePage()
/* Put up configuration page. */
{
cartWebStart(cart, database, "Configure Genome Graphs");
hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\" METHOD=GET>\n");
cartSaveSession(cart);
hPrintf("<TABLE>\n");
hPrintf("<TR>\n");
hPrintf("<TD>\n");
hPrintf("image width: ");
cgiMakeIntVar(hggImageWidth, cartUsualInt(cart, hggImageWidth, hgDefaultPixWidth), 4);
hPrintf("</TD>\n");
hPrintf("<TD>\n");
hPrintf("graph height: ");
cgiMakeIntVar(hggGraphHeight, graphHeight(), 3);
hPrintf("</TD>\n");
hPrintf("<TD>\n");
hPrintf(" graphs per line: ");
makeNumMenu(hggGraphsPerLine, minGraphsPerLine, maxGraphsPerLine,
graphsPerLine());
hPrintf("</TD>\n");
hPrintf("<TD>\n");
hPrintf(" lines of graphs: ");
makeNumMenu(hggLinesOfGraphs, minLinesOfGraphs, maxLinesOfGraphs,
linesOfGraphs());
hPrintf("</TD>\n");
hPrintf("</TR>\n");
hPrintf("</TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
hPrintf("chromosome layout: ");
cgiMakeDropList(hggChromLayout, chromLayouts, ArraySize(chromLayouts),
chromLayout());
hPrintf("</TD></TR></TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
hPrintf("numerical labels: ");
cartMakeCheckBox(cart, hggLabels, TRUE);
hPrintf(" <I>Label axis on left for first graph and on right for last graph</I>");
hPrintf("</TD></TR></TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
hPrintf("highlight missing: ");
cartMakeCheckBox(cart, hggYellowMissing, FALSE);
hPrintf(" <I>Highlight background in yellow/gray if there is missing data in first graph</I>");
hPrintf("</TD></TR></TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
hPrintf("region padding: ");
cgiMakeIntVar(hggRegionPad, regionPad(), 6);
hPrintf(" <I>Number of bases to add to either side of regions over threshold</I>");
hPrintf("</TD></TR></TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
cgiMakeButton("submit", "submit");
hPrintf("</TD></TR></TABLE>\n");
hPrintf("</TD>\n");
hPrintf("</FORM>\n");
webNewSection("Configure Graphs");
hPrintf("Click on the hyperlink by the graph name to configure it.");
hTableStart();
hPrintf("<TR><TH>name</TH>");
hPrintf("<TH>description</TH></TR>");
struct slRef *ref;
for (ref = ggList; ref != NULL; ref = ref->next)
{
struct genoGraph *gg = ref->val;
/* Only show custom graphs, stand-alone DB graphs, and composite */
/* graphs. Don't show subGraphs part of a composite. */
if (gg->isSubGraph == FALSE)
{
char *tmp = cgiEncode(gg->name);
hPrintf("<TR><TD><A HREF=\"../cgi-bin/hgGenome?%s&%s=on&g=%s\">",
cartSidUrlString(cart), hggConfigureOne, tmp);
freeMem(tmp);
hPrintf("%s</A></TD>", gg->shortLabel);
hPrintf("<TD>%s</TD></TR>\n", gg->longLabel);
}
}
hTableEnd();
cartWebEnd();
}
int palOutPredList(struct sqlConnection *conn, struct cart *cart,
struct genePred *list)
/* output a list of genePreds in pal format */
{
if (list == NULL)
return 0;
char *mafTable = cartString(cart, hgtaCGIGeneMafTable);
char *database = sqlGetDatabase(conn);
struct trackDb *maftdb = hTrackDbForTrack(database, mafTable);
struct wigMafSpecies *wmSpecies;
int groupCnt;
/* get maf parent (if any) */
maftdb->parent = hCompositeTrackDbForSubtrack(database,maftdb);
/* this queries the state of the getSpecies dialog */
wigMafGetSpecies(cart, maftdb, maftdb->track, database, &wmSpecies, &groupCnt);
/* since the species selection dialog doesn't list
* the reference species, we just automatically include
* it */
struct slName *includeList = slNameNew(database);
/* now make a list of all species that are on */
for(; wmSpecies; wmSpecies = wmSpecies->next)
{
if (wmSpecies->on)
{
struct slName *newName = slNameNew(wmSpecies->name);
slAddHead(&includeList, newName);
}
}
slReverse(&includeList);
boolean inExons = cartUsualBoolean(cart, hgtaCGIGeneExons , FALSE);
boolean noTrans = cartUsualBoolean(cart, hgtaCGIGeneNoTrans, FALSE);
boolean outBlank = cartUsualBoolean(cart, hgtaCGIGeneOutBlank, FALSE);
boolean outTable = cartUsualBoolean(cart, hgtaCGIOutTable, FALSE);
boolean truncHeader = cartUsualBoolean(cart, hgtaCGITruncHeader, FALSE);
int numCols = cartUsualInt(cart, hgtaCGINumColumns, 20);
unsigned options = 0;
if (inExons) options |= MAFGENE_EXONS;
if (noTrans) options |= MAFGENE_NOTRANS;
if (outBlank) options |= MAFGENE_OUTBLANK;
if (outTable) options |= MAFGENE_OUTTABLE;
if (!truncHeader)
numCols = -1;
/* send out the alignments */
int outCount = 0;
for( ; list ; list = list->next)
{
if (list->cdsStart != list->cdsEnd)
{
outCount++;
mafGeneOutPred(stdout, list, database, mafTable,
includeList, options, numCols);
}
}
slNameFreeList(&includeList);
return outCount;
}
static void doDownload(struct sqlConnection *conn)
/* Try to force user's browser to download by giving special response headers */
{
int imageId = cartUsualInt(cart, hgpId, 0);
char url[1024];
char *p = NULL;
char dir[256];
char name[128];
char extension[64];
int w = 0, h = 0;
int sd = -1;
if (!visiGeneImageSize(conn, imageId, &w, &h))
imageId = 0;
if (imageId == 0)
{
problemPage("invalid imageId","");
}
else
{
p=visiGeneFullSizePath(conn, imageId);
splitPath(p, dir, name, extension);
safef(url,sizeof(url),"%s%s%s", dir, name, extension);
sd = netUrlOpen(url);
if (sd < 0)
{
problemPage("Couldn't open", url);
}
else
{
char *newUrl = NULL;
int newSd = 0;
/* url needed for err msgs and redirect url*/
if (netSkipHttpHeaderLinesHandlingRedirect(sd, url, &newSd, &newUrl))
{
char buf[32*1024];
int readSize;
if (newUrl)
{
freeMem(newUrl);
sd = newSd;
}
printf("Content-Type: application/octet-stream\n");
printf("Content-Disposition: attachment; filename=%s%s\n", name, extension);
printf("\n");
while ((readSize = read(sd, buf, sizeof(buf))) > 0)
fwrite(buf, 1, readSize, stdout);
close(sd);
sd = -1;
fflush(stdout);
fclose(stdout);
}
else
{
problemPage("Skip http header problem", url);
}
freeMem(newUrl);
}
}
}
