void doMiddle(struct cart *theCart)
/* Set up pretty web display and save cart in global. */
{
char *key = NULL;
char *file = NULL;
cart = theCart;
key = cartOptionalString(cart, "key");
if (isValidKey(key))
{
file = cartOptionalString(cart, "file");
if(NULL == file)
{
printIndexFile();
}
else
{
printFile(file);
}
}
else
{
cartWebStart(theCart, database, "SECURE CGI \n");
cartRemove(cart, "key");
printf("INVALID KEY\n");
cartWebEnd();
}
}
static boolean forCurTable()
/* Return TRUE if cart Identifier stuff is for curTable. */
{
char *identifierDb = cartOptionalString(cart, hgtaIdentifierDb);
char *identifierTable = cartOptionalString(cart, hgtaIdentifierTable);
return (identifierDb && identifierTable &&
sameString(identifierDb, database) &&
(sameString(identifierTable, curTable) ||
sameString(connectingTableForTrack(identifierTable), curTable)));
}
void doSetUserRegions(struct sqlConnection *conn)
/* Respond to set regions button. */
{
char *oldPasted = cartUsualString(cart, hgtaEnteredUserRegions, "");
char *db = cartOptionalString(cart, hgtaUserRegionsDb);
if (db && !sameString(db, database))
oldPasted = "";
htmlOpen("Enter region definition\n");
hPrintf("<FORM ACTION=\"%s\" METHOD=POST "
" ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n", getScriptName());
cartSaveSession(cart);
hPrintf("<TABLE><TR><TD ALIGN=LEFT>\n");
hPrintf("Paste regions:");
hPrintf("</TD><TD ALIGN=RIGHT>");
hPrintf("Or upload file: <INPUT TYPE=FILE NAME=\"%s\"> <BR>\n",
hgtaEnteredUserRegionFile);
hPrintf("</TD></TR><TR><TD COLSPAN=2 ALIGN=LEFT>\n");
cgiMakeTextArea(hgtaEnteredUserRegions, oldPasted, 10, 70);
hPrintf("</TD></TR><TR><TD COLSPAN=2 ALIGN=LEFT>\n");
cgiMakeButton(hgtaDoSubmitUserRegions, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearSetUserRegionsText, "clear");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</TD></TR></TABLE>");
hPrintf("</FORM><BR>\n");
webIncludeHelpFile("hgTbUserRegionsHelp", FALSE);
htmlClose();
}
void doMiddle(struct cart *cart)
/* Write body of web page. */
{
struct trackDb *tdbList = NULL;
char *organism = NULL;
char *db = NULL;
getDbAndGenome(cart, &db, &organism, NULL);
char *chrom = cartUsualString(cart, "c", hDefaultChrom(db));
measureTiming = isNotEmpty(cartOptionalString(cart, "measureTiming"));
// QUESTION: Do We need track list ??? trackHash ??? Can't we just get one track and no children
trackHash = trackHashMakeWithComposites(db,chrom,&tdbList,FALSE);
cartWebStart(cart, db, "Search for " FILE_SEARCH_WHAT " in the %s %s Assembly",
organism, hFreezeFromDb(db));
webIncludeResourceFile("HGStyle.css");
webIncludeResourceFile("jquery-ui.css");
webIncludeResourceFile("ui.dropdownchecklist.css");
jsIncludeFile("jquery.js", NULL);
jsIncludeFile("jquery-ui.js", NULL);
jsIncludeFile("ui.dropdownchecklist.js",NULL);
jsIncludeFile("utils.js",NULL);
// This line is needed to get the multi-selects initialized
jsIncludeFile("ddcl.js",NULL);
printf("<script type='text/javascript'>$(document).ready(function() "
"{ findTracks.updateMdbHelp(0); });</script>\n");
doFileSearch(db,organism,cart,tdbList);
printf("<BR>\n");
webEnd();
}
int bigFileMaxOutput()
/* return maxOut value (cart variable defined on curTable) */
{
char *maxOutputStr = NULL;
char *name;
int maxOut;
char *maxOutput = NULL;
if (isCustomTrack(curTable))
name = filterFieldVarName("ct", curTable, "_", filterMaxOutputVar);
else
name = filterFieldVarName(database, curTable, "_", filterMaxOutputVar);
maxOutputStr = cartOptionalString(cart, name);
/* Don't modify(stripChar) the values sitting in the cart hash */
if (NULL == maxOutputStr)
maxOutput = cloneString(maxOutMenu[0]);
else
maxOutput = cloneString(maxOutputStr);
stripChar(maxOutput, ',');
maxOut = sqlUnsigned(maxOutput);
freeMem(maxOutput);
return maxOut;
}
static void getVar(struct cartJson *cj, struct hash *paramHash)
/* Print out the requested cart var(s). varString may be a comma-separated list.
* If a var is a list variable, prints out a list of values for that var. */
{
char *varString = cartJsonRequiredParam(paramHash, "var", cj->jw, "get");
if (! varString)
return;
struct slName *varList = slNameListFromComma(varString), *var;
for (var = varList; var != NULL; var = var->next)
{
if (cartListVarExists(cj->cart, var->name))
{
// Use cartOptionalSlNameList and return a list:
struct slName *valList = cartOptionalSlNameList(cj->cart, var->name);
jsonWriteSlNameList(cj->jw, var->name, valList);
slFreeList(&valList);
}
else
{
// Regular single-value variable (or not in the cart):
char *val = cartOptionalString(cj->cart, var->name);
//#*** TODO: move jsonStringEscape inside jsonWriteString
char *encoded = jsonStringEscape(val);
jsonWriteString(cj->jw, var->name, encoded);
freeMem(encoded);
}
}
slFreeList(&varList);
}
void dispatch()
/* Set up a connection to database and dispatch control
* based on hgpDo type var. */
{
struct sqlConnection *conn = sqlConnect(visiDb);
if (cartVarExists(cart, hgpDoThumbnails))
doThumbnails(conn);
else if (cartVarExists(cart, hgpDoImage))
doImage(conn);
else if (cartVarExists(cart, hgpDoProbe))
doProbe(conn);
else if (cartVarExists(cart, hgpDoControls))
doControls(conn);
else if (cartVarExists(cart, hgpDoId))
doId(conn);
#ifdef SOON
else if (cartVarExists(cart, hgpDoConfig))
configPage(conn);
#endif /* SOON */
else if (cartVarExists(cart, hgpDoSearch))
doDefault(conn, TRUE);
else
{
char *oldListSpec = hashFindVal(oldCart, hgpListSpec);
char *newListSpec = cartOptionalString(cart, hgpListSpec);
boolean isNew = differentStringNullOk(oldListSpec, newListSpec);
doDefault(conn, isNew);
}
cartRemovePrefix(cart, hgpDoPrefix);
}
struct slName *hubConnectHubsInCart(struct cart *cart)
/* Return list of track hub ids that are turned on. */
{
hubConnectRemakeTrackHubVar(cart);
char *trackHubString = cartOptionalString(cart, hubConnectTrackHubsVarName);
return slNameListFromString(trackHubString, ' ');
}
static void themeDropDown(struct cart* cart)
/* Create drop down for UI themes.
* specfied in hg.conf like this
* browser.theme.modern=background.png,HGStyle
* */
{
struct slName* themes = cfgNamesWithPrefix("browser.theme.");
//struct slName* themes = cfgNames();
if (themes==NULL)
return;
hPrintf("<TR><TD>website style:");
hPrintf("<TD style=\"text-align: right\">");
// create labels for drop down box by removing prefix from hg.conf keys
char *labels[50];
struct slName* el;
int i = 0;
el = themes;
for (el = themes; el != NULL && i<50; el = el->next)
{
char* name = el->name;
name = chopPrefix(name); // chop off first two words
name = chopPrefix(name);
labels[i] = name;
i++;
}
char* currentTheme = cartOptionalString(cart, "theme");
hDropList("theme", labels, i, currentTheme);
slFreeList(themes);
hPrintf("</TD>");
}
boolean userSettingsProcessForm(struct userSettings *us)
/* Handle button press in userSettings form.
* If this returns TRUE then form is finished processing
* and you can call something to make the next page. */
{
struct cart *cart = us->cart;
char *command = cartString(cart, us->formVar);
boolean retVal = TRUE;
char *name = cartNonemptyString(cart, us->nameVar);
command = trimSpaces(command);
if (sameWord(command, "save") && name != NULL)
{
char *varName = settingsVarName(us->savePrefix, name);
saveSettings(us, varName);
freez(&varName);
}
else if (startsWith(command, "load") && name != NULL)
{
userSettingsUseSelected(us);
}
else if (startsWith("delete", command))
{
char *which = cartOptionalString(cart, us->listDisplayVar);
if (which != NULL)
{
char *varName = settingsVarName(us->savePrefix, which);
cartRemove(cart, varName);
userSettingsSaveForm(us);
retVal = FALSE;
}
}
cartRemove(cart, us->formVar);
return retVal;
}
void doH1n1Gene(struct trackDb *tdb, char *item)
/* Show details page for H1N1 Genes and Regions annotations track. */
{
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char query[256];
char **row;
char *chrom, *chromStart, *chromEnd;
char *gene=NULL;
genericHeader(tdb, item);
gene = item;
printf("<B>Gene: </B> %s\n<BR>", gene);
sqlSafef(query, sizeof query, "select chrom, chromStart, chromEnd from h1n1Gene where name='%s';", gene);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL)
{
chrom = row[0];
chromStart = row[1];
chromEnd = row[2];
printPosOnChrom(chrom, atoi(chromStart), atoi(chromEnd), NULL, FALSE, item);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
htmlHorizontalLine();
printf("<H3>Protein Structure Analysis and Prediction</H3>");
printf("<B>3D Structure Prediction of consensus sequence (with variations of all selected sequences highlighted):");
printf("<BR>PDB file:</B> ");
char pdbUrl[PATH_LEN];
safef(pdbUrl, sizeof(pdbUrl), "%s/%s/decoys/%s.try1-opt3.pdb.gz", getH1n1StructUrl(), item, item);
// Modeller stuff
char modelPdbUrl[PATH_LEN];
if (getH1n1Model(gene, modelPdbUrl))
{
char *selectFile = cartOptionalString(cart, gisaidAaSeqList);
struct tempName imageFile, chimeraScript, chimerax;
mkH1n1StructData(gene, selectFile, NULL, &imageFile, &chimeraScript);
mkChimerax(gene, modelPdbUrl, chimeraScript.forCgi, &chimerax);
printf("<A HREF=\"%s\" TARGET=_blank>%s</A>, view with <A HREF=\"%s\">Chimera</A><BR>\n",
modelPdbUrl, gene, chimerax.forHtml);
printf("<TABLE>\n");
printf("<TR>\n");
printf("<TD ALIGN=\"center\"><img src=\"%s\"></TD>", imageFile.forHtml);
printf("</TR>\n");
printf("</TABLE>\n");
}
htmlHorizontalLine();
printTrackHtml(tdb);
sqlFreeResult(&sr);
hFreeConn(&conn);
}
void bigBedCustomClick(struct trackDb *tdb)
/* Display details for BigWig custom tracks. */
{
char *fileName = trackDbSetting(tdb, "bigDataUrl");
char *item = cartOptionalString(cart, "i");
int start = cartInt(cart, "o");
int end = cartInt(cart, "t");
bigBedClick(fileName, tdb, item, start, end, 0);
}
void userSettingsUseSelected(struct userSettings *us)
/* Use currently selected user settings. */
{
char *setName = cartOptionalString(us->cart, us->nameVar);
if (setName != NULL)
{
userSettingsUseNamed(us, setName);
}
}
char *userRegionsFileName()
/* File name defined regions are in, or NULL if no such file. */
{
char *fileName = cartOptionalString(cart, hgtaUserRegionsFile);
char *db = cartOptionalString(cart, hgtaUserRegionsDb);
if (db && !sameString(database, db))
return NULL;
if (fileName == NULL)
return NULL;
if (fileExists(fileName))
return fileName;
else
{
cartRemove(cart, hgtaUserRegionsFile);
cartRemove(cart, hgtaRegionType);
return NULL;
}
}
static char *checkForNew( struct cart *cart)
/* see if the user just typed in a new hub url, return id if so */
{
struct hubConnectStatus *hub;
char *url = cartOptionalString(cart, hgHubDataClearText);
if (url != NULL)
disconnectHubsSamePrefix(cart, url);
else
url = cartOptionalString(cart, hgHubDataText);
if (url == NULL)
return NULL;
trimSpaces(url);
gNewHub = hub = getAndSetHubStatus( cart, url, TRUE);
cartRemove(cart, hgHubDataClearText);
cartRemove(cart, hgHubDataText);
char *wantFirstDb = cartOptionalString(cart, hgHubDoFirstDb);
char *newDatabase = NULL;
if ((wantFirstDb != NULL) && (hub->trackHub != NULL))
newDatabase = hub->trackHub->defaultDb;
else
{
// Check to see if the user specified an assembly within
// an assembly hub.
char *assemblyDb = cartOptionalString(cart, hgHubGenome);
if (assemblyDb != NULL)
{
char buffer[512];
safef(buffer, sizeof buffer, "hub_%d_%s", hub->id, assemblyDb);
newDatabase = cloneString(buffer);
}
}
cartRemove(cart, hgHubDoFirstDb);
cartRemove(cart, hgHubGenome);
return newDatabase;
}
static void doClearHub(struct cart *theCart)
{
char *url = cartOptionalString(cart, hgHubDataText);
printf("<pre>clearing hub %s\n",url);
if (url != NULL)
hubClearStatus(url);
else
errAbort("must specify url in %s\n", hgHubDataText);
printf("<pre>Completed\n");
}
static void doResetHub(struct cart *theCart)
{
char *url = cartOptionalString(cart, hgHubDataText);
if (url != NULL)
{
unsigned id = hubResetError(url);
tryHubOpen(id);
}
else
errAbort("must specify url in %s\n", hgHubDataText);
}
void copyCartVars(struct cart *cart, char **source, char **dest, int count)
/* Copy from source to dest. */
{
int i;
for (i=0; i<count; ++i)
{
char *s = cartOptionalString(cart, source[i]);
if (s != NULL)
cartSetString(cart, dest[i], s);
else
cartRemove(cart, dest[i]);
}
}
static void doDisconnectHub(struct cart *theCart)
{
char *id = cartOptionalString(cart, "hubId");
if (id != NULL)
{
char buffer[1024];
safef(buffer, sizeof buffer, "hgHubConnect.hub.%s", id);
cartRemove(cart, buffer);
}
cartRemove(theCart, "hubId");
}
boolean anySubtrackMerge(char *db, char *table)
/* Return TRUE if a subtrack merge has been specified on db.table. */
{
char *smp = cartOptionalString(cart, hgtaSubtrackMergePrimary);
if (smp == NULL)
return FALSE;
else
{
char *dbTable = getDbTable(db, table);
boolean curTableHasMerge = sameString(smp, dbTable);
freez(&dbTable);
return curTableHasMerge;
}
}
void refineVisibility(struct column *colList)
/* Consult cart to set on/off visibility. */
{
char varName[128], *val;
struct column *col;
for (col = colList; col != NULL; col = col->next)
{
safef(varName, sizeof(varName), "%s%s.vis", colConfigPrefix, col->name);
val = cartOptionalString(cart, varName);
if (val != NULL)
col->on = sameString(val, "1");
}
}
static void setIfUnset(struct cartJson *cj, struct hash *paramHash)
/* For each name in paramHash, if that cart variable doesn't already have a non-empty
* value, set it to the value. */
{
struct hashCookie cookie = hashFirst(paramHash);
struct hashEl *hel;
while ((hel = hashNext(&cookie)) != NULL)
{
if (isEmpty(cartOptionalString(cj->cart, hel->name)))
{
char *val = jsonStringVal((struct jsonElement *)(hel->val), hel->name);
if (val)
cartSetString(cj->cart, hel->name, val);
}
}
}
char *identifierFileName()
/* File name identifiers are in, or NULL if not for curTable or no such file. */
{
char *fileName = cartOptionalString(cart, hgtaIdentifierFile);
if (fileName == NULL)
return NULL;
if (! forCurTable())
return NULL;
if (fileExists(fileName))
return fileName;
else
{
cartRemove(cart, hgtaIdentifierFile);
return NULL;
}
}
void doMiddle(struct cart *theCart)
/* Write header and body of html page. */
{
char *userSeq;
char *db, *organism;
boolean clearUserSeq = cgiBoolean("Clear");
cart = theCart;
dnaUtilOpen();
orgChange = sameOk(cgiOptionalString("changeInfo"),"orgChange");
if (orgChange)
{
cgiVarSet("db", hDefaultDbForGenome(cgiOptionalString("org")));
}
getDbAndGenome(cart, &db, &organism, oldVars);
char *oldDb = cloneString(db);
findClosestServer(&db, &organism);
/* Get sequence - from userSeq variable, or if
* that is empty from a file. */
if (clearUserSeq)
{
cartSetString(cart, "userSeq", "");
cartSetString(cart, "seqFile", "");
}
userSeq = cartUsualString(cart, "userSeq", "");
if (isEmpty(userSeq))
{
userSeq = cartOptionalString(cart, "seqFile");
}
if (isEmpty(userSeq) || orgChange)
{
cartWebStart(theCart, db, "%s BLAT Search", trackHubSkipHubName(organism));
if (differentString(oldDb, db))
printf("<HR><P><EM><B>Note:</B> BLAT search is not available for %s %s; "
"defaulting to %s %s</EM></P><HR>\n",
hGenome(oldDb), hFreezeDate(oldDb), organism, hFreezeDate(db));
askForSeq(organism,db);
cartWebEnd();
}
else
{
blatSeq(skipLeadingSpaces(userSeq), organism);
}
}
static void pubsPslLoadItems(struct track *tg)
/* load only psl items from a single article */
{
// get articleId to filter on
char *articleId = cartOptionalString(cart, PUBSFILTERNAME);
if (articleId==NULL)
return;
struct sqlConnection *conn = hAllocConn(database);
char *dispLabel = pubsArticleDispId(tg, conn, articleId);
struct hash *idToSnip = pubsLookupSequences(tg, conn, articleId, TRUE);
struct hash *idToSeq = pubsLookupSequences(tg, conn, articleId, FALSE);
// change track label
char *oldLabel = tg->longLabel;
tg->longLabel = catTwoStrings("Individual matches for article ", dispLabel);
freeMem(oldLabel);
// filter and load items for this articleId
char where[256];
safef(where, sizeof(where), " articleId=%s ", articleId);
int rowOffset = 0;
struct sqlResult *sr = NULL;
sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, where, &rowOffset);
struct linkedFeatures *lfList = NULL;
char **row = NULL;
while ((row = sqlNextRow(sr)) != NULL)
{
struct psl *psl = pslLoad(row+rowOffset);
slAddHead(&lfList, lfFromPsl(psl, TRUE));
char *shortSeq = hashFindVal(idToSeq, lfList->name);
char *snip = hashFindVal(idToSnip, lfList->name);
struct pubsExtra *extra = needMem(sizeof(struct pubsExtra));
extra->mouseOver=snip;
extra->label=shortSeq;
lfList->extra = extra;
}
sqlFreeResult(&sr);
slReverse(&lfList);
slSort(&lfList, linkedFeaturesCmp);
tg->items = lfList;
hFreeConn(&conn);
}
static void getCladeOrgDbPos(struct cartJson *cj, struct hash *paramHash)
/* Get cart's current clade, org, db, position and geneSuggest track. */
{
jsonWriteObjectStart(cj->jw, "cladeOrgDb");
printCladeOrgDbTree(cj->jw);
char *db = cartString(cj->cart, "db");
jsonWriteString(cj->jw, "db", db);
char *org = cartUsualString(cj->cart, "org", hGenome(db));
jsonWriteString(cj->jw, "org", org);
char *clade = cartUsualString(cj->cart, "clade", hClade(org));
jsonWriteString(cj->jw, "clade", clade);
jsonWriteObjectEnd(cj->jw);
char *position = cartOptionalString(cj->cart, "position");
if (isEmpty(position))
position = hDefaultPos(db);
jsonWriteString(cj->jw, "position", position);
printGeneSuggestTrack(cj, db);
}
void userSettingsUseNamed(struct userSettings *us, char *setName)
/* Use named collection of settings. */
{
struct cart *cart = us->cart;
char *varName = settingsVarName(us->savePrefix, setName);
char *settings = cartOptionalString(cart, varName);
if (settings != NULL)
{
struct hash *hash = hashVarLine(settings, 1);
struct hashEl *list = hashElListHash(hash);
struct hashEl *el;
for (el = list; el != NULL; el = el->next)
cartSetString(cart, el->name, el->val);
slFreeList(&list);
hashFree(&hash);
}
freez(&varName);
}
static void saveSettings(struct userSettings *us, char *varName)
/* Save captured settings to varName. */
{
struct cart *cart = us->cart;
struct slName *capture;
struct dyString *dy = dyStringNew(4*1024);
for (capture = us->saveList; capture != NULL; capture = capture->next)
{
char *name = capture->name;
char *val = cartOptionalString(cart, name);
if (val != NULL)
{
dyStringPrintf(dy, "%s=", name);
dyStringAppendQuoted(dy, val);
}
}
cartSetString(cart, varName, dy->string);
dyStringFree(&dy);
}
static char * outMafTableDrop(struct cart *cart, struct sqlConnection *conn)
{
struct slName *list = hTrackTablesOfType(conn, "wigMaf%%");
int count = slCount(list);
if (count == 0)
errAbort("There are no multiple alignments available for this genome.");
char **tables = needMem(sizeof(char *) * count);
char **tb = tables;
char *mafTable = cartOptionalString(cart, hgtaCGIGeneMafTable);
if (mafTable != NULL)
{
struct slName *l = list;
for(; l; l=l->next)
if (sameString(l->name, mafTable))
break;
/* didn't find mafTable in list, reset it */
if (l == NULL)
mafTable = NULL;
}
if (mafTable == NULL)
{
if ((mafTable = getConservationTrackName(conn)) == NULL)
mafTable = list->name;
cartSetString(cart, hgtaCGIGeneMafTable, mafTable);
}
for(; list; list = list->next)
*tb++ = list->name;
printf("<B>MAF table: </B>\n");
cgiMakeDropListFull(hgtaCGIGeneMafTable, tables, tables,
count , mafTable, onChangeGenome());
return mafTable;
}
boolean anyFilter()
/* Return TRUE if any filter set. If there is filter state from a filter
* defined on a different table, clear it. */
{
char *filterTable = cartOptionalString(cart, hgtaFilterTable);
if (filterTable == NULL)
return FALSE;
else
{
char *dbTable = getDbTable(database, curTable);
boolean curTableHasFilter = sameString(filterTable, dbTable);
freez(&dbTable);
if (curTableHasFilter)
return TRUE;
else
{
removeFilterVars();
return FALSE;
}
}
}