");
jsOnEventById("click", "hubValidateButton",
"var validateText = document.getElementById('validateHubUrl');"
"validateText.value=$.trim(validateText.value);"
"if(validateUrl($('#validateHubUrl').val())) { "
" document.validateHubForm.elements['validateHubUrl'].value=validateText.value;"
" document.validateHubForm.submit(); return true; }"
"else { return false; }"
);
}
static void addPublicHubsToHubStatus(struct sqlConnection *conn, char *publicTable, char *statusTable)
/* Add urls in the hubPublic table to the hubStatus table if they aren't there already */
{
char query[1024];
sqlSafef(query, sizeof(query),
"select %s.hubUrl from %s left join %s on %s.hubUrl = %s.hubUrl where %s.hubUrl is NULL",
publicTable, publicTable, statusTable, publicTable, statusTable, statusTable);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
char *errorMessage = NULL;
char *url = row[0];
// add this url to the hubStatus table
hubFindOrAddUrlInStatusTable(database, cart, url, &errorMessage);
}
}
char *modifyTermsForHubSearch(char *hubSearchTerms, bool isStrictSearch)
/* This won't exactly be pretty. MySQL treats any sequence of alphanumerics and underscores
* as a word, and single apostrophes are allowed as long as they don't come back-to-back.
* Cut down to those characters, then add initial + (for requiring word) and * (for word
* expansion) as appropriate. */
{
char *cloneTerms = cloneString(hubSearchTerms);
struct dyString *modifiedTerms = dyStringNew(0);
if (isNotEmpty(cloneTerms))
{
int i;
for (i=0; itextLength == hubSearchTextLong) && isEmpty(hst->text))
continue;
char *hubUrl = hst->hubUrl;
struct hubEntry *hubInfo = hashFindVal(hubLookup, hubUrl);
if (hubInfo == NULL)
continue; // Search table evidently includes a hub that's not on this server. Skip it.
char *db = cloneString(hst->db);
tolowers(db);
if (isNotEmpty(dbFilter))
{
if (isNotEmpty(db))
{
if (stringIn(dbFilter, db) == NULL)
continue;
}
else
{
// no db in the hubSearchText means this is a top-level hub hit.
// filter by the db list associated with the hub instead
char *dbList = cloneString(hubInfo->dbList);
tolowers(dbList);
if (stringIn(dbFilter, dbList) == NULL)
continue;
}
}
// Add hst to the list to be returned
slAddHead(&hubSearchResultsList, hst);
}
slReverse(&hubSearchResultsList);
return hubSearchResultsList;
}
void printSearchAndFilterBoxes(int searchEnabled, char *hubSearchTerms, char *dbFilter)
/* Create the text boxes for search and database filtering along with the required
* javscript */
{
char event[4096];
if (searchEnabled)
{
safef(event, sizeof(event),
"document.searchHubForm.elements['hubSearchTerms'].value=$('#hubSearchTerms').val();"
"document.searchHubForm.elements['hubDbFilter'].value=$('#hubDbFilter').val();"
"document.searchHubForm.submit();return true;");
printf("Enter search terms to find in public track hub description pages: "
" \n",
hubSearchTerms!=NULL?hubSearchTerms:"");
printf(" \n");
}
else
{
safef(event, sizeof(event),
"document.searchHubForm.elements['hubDbFilter'].value=$('#hubDbFilter').val();"
"document.searchHubForm.submit();return true;");
}
printf("Filter hubs by assembly: "
" \n"
"\n",
hgHubDbFilter, dbFilter!=NULL?dbFilter:"");
jsOnEventById("click", "hubSearchButton", event);
puts("
\n");
}
void printSearchTerms(char *hubSearchTerms)
/* Write out a reminder about the current search terms and a note about
* how to navigate detailed search results */
{
printf("Displayed list restricted by search terms: %s\n", hubSearchTerms);
puts("\n");
jsOnEventById("click", "hubDeleteSearchButton",
"document.searchHubForm.elements['hubSearchTerms'].value='';"
"document.searchHubForm.elements['hubDbFilter'].value='';"
"document.searchHubForm.submit();return true;");
puts("
\n");
printf("When exploring the detailed search results for a hub, you may right-click "
"on an assembly or track line to open it in a new window.\n");
puts("
\n");
}
void printHubListHeader()
/* Write out the header for a list of hubs in its own table */
{
puts("Clicking Connect redirects to the gateway page of the selected hub's default assembly. ");
printf("
"
"
"
"
Display
"
"
Hub Name
"
"
Description
"
"
Assemblies
"
"
\n");
}
struct hash *buildPublicLookupHash(struct sqlConnection *conn, char *publicTable, char *statusTable,
struct hash **pHash)
/* Return a hash linking hub URLs to struct hubEntries. Also make pHash point to a hash that just stores
* the names of the public hubs (for use later when determining if hubs were added by the user) */
{
struct hash *hubLookup = newHash(5);
struct hash *publicLookup = newHash(5);
char query[512];
bool hasDescription = sqlColumnExists(conn, publicTable, "descriptionUrl");
if (hasDescription)
sqlSafef(query, sizeof(query), "select p.hubUrl,p.shortLabel,p.longLabel,p.dbList,"
"s.errorMessage,s.id,p.descriptionUrl from %s p,%s s where p.hubUrl = s.hubUrl",
publicTable, statusTable);
else
sqlSafef(query, sizeof(query), "select p.hubUrl,p.shortLabel,p.longLabel,p.dbList,"
"s.errorMessage,s.id from %s p,%s s where p.hubUrl = s.hubUrl",
publicTable, statusTable);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
struct hubEntry *hubInfo = hubEntryTextLoad(row, hasDescription);
hubInfo->tableHasDescriptionField = hasDescription;
hashAddUnique(hubLookup, hubInfo->hubUrl, hubInfo);
hashStore(publicLookup, hubInfo->hubUrl);
}
sqlFreeResult(&sr);
*pHash = publicLookup;
return hubLookup;
}
void outputPublicTableRow(struct hubEntry *hubInfo, int count)
/* Prints out a table row with basic information about a hub and a button
* to connect to that hub */
{
int id = hubInfo->id;
char jsId[256];
struct slName *dbListNames = slNameListFromComma(hubInfo->dbList);
printf("
\n");
if (id != 0)
{
ourCellStart();
char hubName[32];
safef(hubName, sizeof(hubName), "%s%u", hgHubConnectHubVarPrefix, id);
if (cartUsualBoolean(cart, hubName, FALSE))
{
safef(jsId, sizeof jsId, "hubDisconnectButtonP%d", count);
printf("\n", jsId);
jsOnEventByIdF("click", jsId,
"document.disconnectHubForm.elements['hubId'].value= '%d';"
"document.disconnectHubForm.submit();return true;", id);
}
else
{
// get first name off of list of supported databases
char * name = dbListNames->name;
// if the name isn't currently loaded, we assume it's a hub
if (!hDbExists(name))
{
char buffer[512];
safef(buffer, sizeof buffer, "hub_%d_%s", id, name);
name = cloneString(buffer);
}
safef(jsId, sizeof jsId, "hubConnectButton%d", count);
printf("\n", jsId);
jsOnEventByIdF("click", jsId,
"document.connectHubForm.elements['hubUrl'].value= '%s';"
"document.connectHubForm.elements['db'].value= '%s';"
"document.connectHubForm.submit();return true;", hubInfo->hubUrl,name);
}
ourCellEnd();
}
else
errAbort("cannot get id for hub with url %s\n", hubInfo->hubUrl);
ourPrintCellLink(hubInfo->shortLabel, hubInfo->hubUrl);
boolean hubHasNoError = isEmpty(hubInfo->errorMessage);
if (hubHasNoError)
{
if (hubInfo->tableHasDescriptionField && !isEmpty(hubInfo->descriptionUrl))
ourPrintCellLink(hubInfo->longLabel, hubInfo->descriptionUrl);
else
ourPrintCell(hubInfo->longLabel);
}
else
{
ourCellStart();
printf("ERROR: %s "
"Debug Help",
hubInfo->errorMessage);
safef(jsId, sizeof jsId, "hubClearButton%d", count);
printf(
""
, jsId);
jsOnEventByIdF("click", jsId,
"document.resetHubForm.elements['hubCheckUrl'].value='%s';"
"document.resetHubForm.submit();return true;", hubInfo->hubUrl);
ourCellEnd();
}
printGenomeList(hubInfo->hubUrl, dbListNames, count, hubHasNoError);
printf("
\n");
}
-
-void printSearchOutputForTrack(struct tdbOutputStructure *tdbOut)
-/* Write out a
entry for a search hit on a track, along with a nested
- *
for any included hits to subtracks */
-{
-printf("
\n");
-}
-
-
struct trackHub *fetchTrackHub(struct hubEntry *hubInfo)
/* Fetch the hub structure for a public hub, trapping the error
* if the hub cannot be reached */
{
struct errCatch *errCatch = errCatchNew();
struct trackHub *hub = NULL;
if (errCatchStart(errCatch))
{
char hubName[4096];
safef(hubName, sizeof(hubName), "hub_%d", hubInfo->id);
hub = trackHubOpen(hubInfo->hubUrl, hubName);
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
fprintf(stderr, "%s\n", errCatch->message->string);
}
errCatchFree(&errCatch);
return hub;
}
-
-struct tdbOutputStructure *addOrUpdateTrackOut(char *track, struct genomeOutputStructure *genomeOut,
- struct hash *tdbHash, struct trackHub *hub)
-/* If an output structure already exists for the track within genomeOut, return that. Otherwise,
- * create one for it and add it to genomeOut. Any missing parent tracks are also added at
- * the same time.
- * tdbHash takes track names to the struct trackDb * for that track */
-{
-struct tdbOutputStructure *tdbOut = hashFindVal(genomeOut->tdbOutHash, track);
-if (tdbOut == NULL)
- {
- genomeOut->trackCount++;
- AllocVar(tdbOut);
- tdbOut->shortLabel = dyStringNew(0);
- tdbOut->metaTags = dyStringNew(0);
- tdbOut->descriptionMatch = dyStringNew(0);
- tdbOut->configUrl = dyStringNew(0);
- struct trackDb *trackInfo = (struct trackDb *) hashFindVal(tdbHash, track);
- if (trackInfo == NULL)
- {
- // Some tracks are prefixed with the hub name; try that
- char withHubName[4096];
- safef(withHubName, sizeof(withHubName), "%s_%s", hub->name, track);
- trackInfo = hashFindVal(tdbHash, withHubName);
- if (trackInfo == NULL)
- {
- warn("Error: Unable to locate info for matching track '%s'. Skipping ...\n", withHubName);
- return NULL;
- }
- }
- if (isNotEmpty(trackInfo->longLabel))
- dyStringPrintf(tdbOut->shortLabel, "%s", trackInfo->longLabel);
- else if (isNotEmpty(trackInfo->shortLabel))
- dyStringPrintf(tdbOut->shortLabel, "%s", trackInfo->shortLabel);
- else
- dyStringPrintf(tdbOut->shortLabel, "%s", trackHubSkipHubName(trackInfo->track));
-
- if (tdbIsCompositeView(trackInfo) || tdbIsCompositeChild(trackInfo))
- {
- struct trackDb *parentTdb = tdbGetComposite(trackInfo);
- dyStringPrintf(tdbOut->configUrl, "../cgi-bin/hgTrackUi?hubUrl=%s&db=%s&g=%s&hgsid=%s&%s", hub->url,
- genomeOut->genomeName, parentTdb->track, cartSessionId(cart), genomeOut->positionString);
- }
- else
- {
- dyStringPrintf(tdbOut->configUrl, "../cgi-bin/hgTrackUi?hubUrl=%s&db=%s&g=%s&hgsid=%s&%s", hub->url,
- genomeOut->genomeName, trackInfo->track, cartSessionId(cart), genomeOut->positionString);
- }
-
- if (trackInfo->parent != NULL)
- {
- struct trackDb *parent = trackInfo->parent;
- struct tdbOutputStructure *parentOut = addOrUpdateTrackOut(parent->track, genomeOut, tdbHash, hub);
- if (parentOut != NULL)
- {
- // addOrUpdateTrackOut only returns NULL if it can't find the parent here.
- // This probably means the trackDb is corrupted, which should have already
- // generated a fatal error. All the same ...
- slAddTail(&(parentOut->children), tdbOut);
- parentOut->childCount++;
- }
- else
- {
- // If we can't find the track's rightful parent, we can't report its position
- // in the track hierarchy accurately. Time to abort. A warning will already
- // have been generated by addOrUpdateTrackOut(parent) failing.
- return NULL;
- }
- }
- else
- // No parent track, so add it to the root level track list for output
- slAddTail(&(genomeOut->tracks), tdbOut);
- hashAdd(genomeOut->tdbOutHash, track, tdbOut);
- }
-return tdbOut;
-}
-
-
-void buildTdbHash(struct hash *tdbHash, struct trackDb *tdbList)
-/* Recursively add all tracks from tdbList to the hash (indexed by track),
- * along with all parents and children of those tracks */
-{
-struct trackDb *tdb = tdbList;
-while (tdb != NULL)
- {
- hashAdd(tdbHash, tdb->track, tdb);
- if (tdb->subtracks != NULL)
- buildTdbHash(tdbHash, tdb->subtracks);
- if (tdb->parent != NULL)
- {
- // supertracks might be omitted from tdbList, but are still referred to by parent links
- if (hashFindVal(tdbHash, tdb->parent->track) == NULL)
- hashAdd(tdbHash, tdb->parent->track, tdb->parent);
- }
- tdb = tdb->next;
- }
-}
-
-
char *getPositionStringForDb(struct trackHubGenome *genome)
{
char positionVar[1024];
safef(positionVar, sizeof(positionVar), "position.%s", genome->name);
char *position = cartOptionalString(cart, positionVar);
if (position == NULL)
{
struct dyString *tmp = dyStringCreate("position=");
if (genome->defaultPos != NULL)
dyStringAppend(tmp, genome->defaultPos);
else
dyStringAppend(tmp, hDefaultPos(genome->name)); // memory leak from hDefaultPos return value
position = dyStringCannibalize(&tmp);
}
return position;
}
struct tdbOutputStructure *hstToTdbOutput(struct hubSearchText *hst, struct genomeOutputStructure *genomeOut, struct trackHub *hub)
/* Convert a hubSearchText entry to a (list of) tdbOutputStructure(s) */
{
struct tdbOutputStructure *tdbOut = hashFindVal(genomeOut->tdbOutHash, hst->track);
if (tdbOut == NULL)
{
genomeOut->trackCount++;
AllocVar(tdbOut);
tdbOut->shortLabel = dyStringNew(0);
tdbOut->metaTags = dyStringNew(0);
tdbOut->descriptionMatch = dyStringNew(0);
tdbOut->configUrl = dyStringNew(0);
dyStringPrintf(tdbOut->shortLabel, "%s", hst->label);
if (isNotEmpty(hst->parents))
{
// hst->parents is a comma-sep list like "track1","track1Label","track2","track2Label"
int i;
int parentCount;
char *parentTrack = NULL;
char *parentLabel = NULL;
char *parentTrackLabels[16]; // 2 slots per parent, can tracks nest more than 8 deep?
struct tdbOutputStructure *parentTdbOut = NULL;
struct tdbOutputStructure *savedParent = NULL;
parentCount = chopByCharRespectDoubleQuotes(cloneString(hst->parents), ',', parentTrackLabels, sizeof(parentTrackLabels));
if (parentCount == 0 || parentCount % 2 != 0)
{
errAbort("error parsing hubSearchText->parents for %s.%s in hub: '%s'",
genomeOut->genomeName, hst->track, hub->url);
}
dyStringPrintf(tdbOut->configUrl, "../cgi-bin/hgTrackUi?hubUrl=%s&db=%s&g=%s&hgsid=%s&%s",
hub->url, genomeOut->genomeName, parentTrackLabels[0], cartSessionId(cart),
genomeOut->positionString);
boolean foundParent = FALSE;
boolean doAddSaveParent = FALSE;
for (i = 0; i < parentCount; i += 2)
{
parentTrack = stripEnclosingDoubleQuotes(cloneString(parentTrackLabels[i]));
parentLabel = stripEnclosingDoubleQuotes(cloneString(parentTrackLabels[i+1]));
parentTdbOut = hashFindVal(genomeOut->tdbOutHash, parentTrack);
if (parentTdbOut != NULL)
{
foundParent = TRUE; // don't add this track to the genomeOut->tracks hash again
if (savedParent && doAddSaveParent)
{
parentTdbOut->childCount += 1;
slAddHead(&(parentTdbOut->children), savedParent);
}
else if (!savedParent)
{
parentTdbOut->childCount += 1;
slAddHead(&(parentTdbOut->children), tdbOut);
}
savedParent = parentTdbOut;
doAddSaveParent = FALSE;
}
else
{
AllocVar(parentTdbOut);
parentTdbOut->shortLabel = dyStringNew(0);
parentTdbOut->metaTags = dyStringNew(0);
parentTdbOut->descriptionMatch = dyStringNew(0);
parentTdbOut->configUrl = dyStringNew(0);
dyStringPrintf(tdbOut->configUrl,
"../cgi-bin/hgTrackUi?hubUrl=%s&db=%s&g=%s&hgsid=%s&%s",
hub->url, genomeOut->genomeName, parentTrack, cartSessionId(cart), genomeOut->positionString);
dyStringPrintf(parentTdbOut->shortLabel, "%s", parentLabel);
parentTdbOut->childCount += 1;
if (savedParent)
slAddHead(&(parentTdbOut->children), savedParent);
else
slAddHead(&(parentTdbOut->children), tdbOut);
savedParent = parentTdbOut;
doAddSaveParent = TRUE;
hashAdd(genomeOut->tdbOutHash, parentTrack, parentTdbOut);
}
}
if (!foundParent)
{
slAddHead(&(genomeOut->tracks), parentTdbOut);
}
}
else
{
dyStringPrintf(tdbOut->configUrl, "../cgi-bin/hgTrackUi?hubUrl=%s&db=%s&g=%s&hgsid=%s&%s",
hub->url, genomeOut->genomeName, hst->track, cartSessionId(cart),
genomeOut->positionString);
slAddHead(&(genomeOut->tracks), tdbOut);
}
hashAdd(genomeOut->tdbOutHash, hst->track, tdbOut);
}
return tdbOut;
}
struct hubOutputStructure *buildHubSearchOutputStructure(struct trackHub *hub,
struct hubSearchText *searchResults)
/* Build a structure that contains the data for writing out the hub search results for this hub */
{
struct hash *missingGenomes = hashNew(0);
struct hubOutputStructure *hubOut = NULL;
AllocVar(hubOut);
hubOut->metaTags = dyStringNew(0);
hubOut->descriptionMatch = dyStringNew(0);
hubOut->genomeOutHash = newHash(5);
struct hubSearchText *hst = NULL;
for (hst = searchResults; hst != NULL; hst = hst->next)
{
if (isEmpty(hst->db))
{
// must be a hit to the hub itself, not an assembly or track within it
if (hst->textLength == hubSearchTextLong)
{
dyStringPrintf(hubOut->descriptionMatch, "%s", hst->text);
}
else if (hst->textLength == hubSearchTextMeta)
{
if (isNotEmpty(dyStringContents(hubOut->metaTags)))
dyStringPrintf(hubOut->metaTags, ", %s", hst->text);
else
dyStringPrintf(hubOut->metaTags, "%s", hst->text);
}
continue;
}
char *db = cloneString(hst->db);
if (hashLookup(missingGenomes, db) != NULL)
continue;
struct trackHubGenome *genome = hashFindVal(hub->genomeHash, db);
if (genome == NULL)
{
// assembly hub genomes are stored with a prefix; try that
char withHubName[4096];
safef(withHubName, sizeof(withHubName), "%s_%s", hub->name, db);
genome = hashFindVal(hub->genomeHash, withHubName);
if (genome == NULL)
{
hashStoreName(missingGenomes, db);
warn("Error: Unable to find info for matching assembly '%s'. Skipping ...\n", withHubName);
continue;
}
}
struct genomeOutputStructure *genomeOut = hashFindVal(hubOut->genomeOutHash, db);
if (genomeOut == NULL)
{
AllocVar(genomeOut);
genomeOut->tdbOutHash = newHash(5);
genomeOut->metaTags = dyStringNew(0);
genomeOut->descriptionMatch = dyStringNew(0);
genomeOut->shortLabel = dyStringNew(0);
genomeOut->assemblyLink = dyStringNew(0);
genomeOut->positionString = getPositionStringForDb(genome);
dyStringPrintf(genomeOut->assemblyLink, "../cgi-bin/hgTracks?hubUrl=%s&db=%s&hgsid=%s&%s",
hub->url, genome->name, cartSessionId(cart), genomeOut->positionString);
char *name = trackHubSkipHubName(genome->name);
if (isNotEmpty(genome->description))
dyStringPrintf(genomeOut->shortLabel, "%s (%s)", genome->description, name);
else if (isNotEmpty(genome->organism))
dyStringPrintf(genomeOut->shortLabel, "%s %s", genome->organism, name);
else
dyStringPrintf(genomeOut->shortLabel, "%s", name);
genomeOut->genomeName = cloneString(genome->name);
hashAdd(hubOut->genomeOutHash, db, genomeOut);
slAddTail(&(hubOut->genomes), genomeOut);
hubOut->genomeCount++;
}
if (isEmpty(hst->track))
{
if (hst->textLength == hubSearchTextLong) // Genome description match
dyStringPrintf(genomeOut->descriptionMatch, "%s", hst->text);
else if (hst->textLength == hubSearchTextMeta)
{
if (isNotEmpty(dyStringContents(genomeOut->metaTags)))
dyStringPrintf(genomeOut->metaTags, ", %s", hst->text);
else
dyStringPrintf(genomeOut->metaTags, "%s", hst->text);
}
}
if (isNotEmpty(hst->track))
{
// Time to add a track! (or add info to one, maybe)
struct tdbOutputStructure *tdbOut = hstToTdbOutput(hst, genomeOut, hub);
if (tdbOut != NULL)
{
if (hst->textLength == hubSearchTextLong)
dyStringPrintf(tdbOut->descriptionMatch, "%s", hst->text);
else if (hst->textLength == hubSearchTextMeta)
{
if (isNotEmpty(dyStringContents(tdbOut->metaTags)))
dyStringPrintf(tdbOut->metaTags, ", %s", hst->text);
else
dyStringPrintf(tdbOut->metaTags, "%s", hst->text);
}
}
}
}
return hubOut;
}
static char *tdbOutputStructureLabelToId(struct tdbOutputStructure *tdbOut)
/* Make an array name out of a tdbOutputStruct */
{
struct dyString *id = dyStringNew(0);
dyStringPrintf(id, "%s", htmlEncode(dyStringContents(tdbOut->shortLabel)));
if (tdbOut->childCount > 0)
{
dyStringPrintf(id, " (%d subtrack%s)", tdbOut->childCount,
tdbOut->childCount == 1 ? "" : "s");
}
return dyStringCannibalize(&id);
}
static void printTdbOutputStructureToDyString(struct tdbOutputStructure *tdbOut, struct dyString *dy, char *arrayName)
-/* Print a tdbOutputStructure to a dyString*/
+/* Print a tdbOutputStructure to a dyString, recursive for subtracks. */
{
dyStringPrintf(dy, "trackData['%s'] = [", arrayName);
if (tdbOut->childCount > 0)
{
struct dyString *subtrackDy = dyStringNew(0);
struct tdbOutputStructure *child = tdbOut->children;
while (child != NULL)
{
char *childId = tdbOutputStructureLabelToId(child);
dyStringPrintf(dy, "\n\t{\n\tid: '%s',\n\tparent: '%s',\n\t"
"li_attr: {nodetype:'track', configlink:'%s'},\n\ttext: \'%s ",
childId, arrayName, dyStringContents(child->configUrl), childId);
if (isNotEmpty(dyStringContents(child->metaTags)))
{
dyStringPrintf(dy, " Metadata: %s",
htmlEncode(dyStringContents(child->metaTags)));
}
if (isNotEmpty(dyStringContents(child->descriptionMatch)))
{
dyStringPrintf(dy, " Description: %s",
htmlEncode(dyStringContents(child->descriptionMatch)));
}
dyStringPrintf(dy, "\'");
if (child->childCount > 0)
{
dyStringPrintf(dy, ",\n\tchildren: true");
printTdbOutputStructureToDyString(child, subtrackDy, childId);
}
dyStringPrintf(dy, "\n\t},");
child = child->next;
}
dyStringPrintf(dy, "];\n");
if (isNotEmpty(dyStringContents(subtrackDy)))
dyStringPrintf(dy, "%s", subtrackDy->string);
}
else
dyStringPrintf(dy, "];\n");
}
-
void printGenomeOutputStructureToDyString(struct genomeOutputStructure *genomeOut, struct dyString *dy, char *genomeNameId)
-/* Print a genomeOutputStructure to a dyString */
+/* Print a genomeOutputStructure to a dyString. The structure here is:
+ * trackData[genome] = [{track 1 obj}, {track2 obj}, {track3 obj}, ... ]
+ * trackData[track1] = [{search hit text}, {subtrack1 obj}, {subtrack2 obj}, ... ]
+ *
+ * if track1, track2, track3 are container tracks, then the recursive function
+ * tdbOutputStructureToDystring creates the above trackData[track1] = [{}] for
+ * each of the containers, otherwise a single child of the genome is sufficient */
{
struct tdbOutputStructure *tdbOut = NULL;
static struct dyString *tdbArrayDy = NULL; // the dyString for all of the tdb objects
static struct dyString *idString = NULL; // the special id of this track
if (tdbArrayDy == NULL)
tdbArrayDy = dyStringNew(0);
if (idString == NULL)
idString = dyStringNew(0);
-// The structure here is:
-// trackData[genome] = [{track 1 obj}, {track2 obj}, {track3 obj}, ... ]
-// trackData[track1] = [{search hit text}, {subtrack1 search hit}, {subtrack2 search hit}, ... ]
-//
-// if track1, track2, track3 are container tracks, then the recursive function
-// tdbOutputStructureToDystring creates the above trackData[track1] = [{}] for
-// each of the containers, otherwise a single child of the genome is sufficient
dyStringPrintf(dy, "trackData['%s'] = [", genomeNameId);
if (genomeOut->tracks != NULL)
{
tdbOut = genomeOut->tracks;
slReverse(&tdbOut);
while (tdbOut != NULL)
{
dyStringPrintf(idString, "%s", tdbOutputStructureLabelToId(tdbOut));
dyStringPrintf(dy, "\n\t{\n\t'id': '%s',\n\t'parent': '%s',\n\t"
"'li_attr': {'nodetype':'track', configlink: '%s'},\n\t'text': \'%s ",
idString->string, genomeNameId, dyStringContents(tdbOut->configUrl), idString->string);
if (isNotEmpty(dyStringContents(tdbOut->metaTags)))
{
dyStringPrintf(dy, " Metadata: %s",
htmlEncode(dyStringContents(tdbOut->metaTags)));
}
if (isNotEmpty(dyStringContents(tdbOut->descriptionMatch)))
{
dyStringPrintf(dy, " Description: %s",
htmlEncode(dyStringContents(tdbOut->descriptionMatch)));
}
dyStringPrintf(dy, "\'");
// above we took care of both non-heirarchical tracks and the top-level containers,
// now do container children, which also takes care of any deeper heirarchies
if (tdbOut->childCount > 0)
dyStringPrintf(dy, ",\n\t'children': true");
dyStringPrintf(dy, "\n\t},\n");
if (tdbOut->childCount > 0)
printTdbOutputStructureToDyString(tdbOut, tdbArrayDy, idString->string);
tdbOut = tdbOut->next;
dyStringClear(idString);
}
}
dyStringPrintf(dy, "];\n"); // close off genome node
dyStringPrintf(dy, "%s\n", tdbArrayDy->string);
dyStringClear(tdbArrayDy);
-dyStringClear(idString);
}
void printHubOutputStructure(struct hubOutputStructure *hubOut, struct hubEntry *hubInfo)
-/* Convert a hubOutputStructure to a jstree-readable string */
+/* Convert a hubOutputStructure to a jstree-readable string. This function forms the root
+ * node for each hub search tree, whose children are the hub description match and each individual
+ * genome node. A simplified structure is:
+ * trackData['#_hubId'] = [{id:'descriptionMatch',...},{id:'assembly1',...},...]
+ *
+ * The id's become new "trackData[id]" entries with their own arrays later if they have
+ * sub-trees (via printGenomeOutputStructureToDyString() and printTdbOutputStructureToDyString(). */
{
struct dyString *dy = dyStringNew(0);
// The leading '#' tells the javascript this is a 'root' node
dyStringPrintf(dy, "trackData['#_%d'] = [", hubInfo->id);
if (isNotEmpty(dyStringContents(hubOut->descriptionMatch)))
{
dyStringPrintf(dy, "{'id':'%d_descriptionMatchText','parent':'#_%d',"
"'state':{'opened': true},'text': 'Hub Description: "
"%s'},",
hubInfo->id, hubInfo->id, htmlEncode(dyStringContents(hubOut->descriptionMatch)));
}
struct genomeOutputStructure *genomeOut = hubOut->genomes;
struct dyString *genomeDy = dyStringNew(0);
if (genomeOut != NULL)
{
dyStringPrintf(dy, "{'id':'%d_assemblies', 'text':'%d Matching Assembl%s', 'parent':'#_%d', "
"'children':true, 'li_attr': {'state':{'opened': 'false'}}}];\n",
hubInfo->id, hubOut->genomeCount, hubOut->genomeCount == 1 ? "y" : "ies", hubInfo->id);
dyStringPrintf(dy, "trackData['%d_assemblies'] = [", hubInfo->id);
while (genomeOut != NULL)
{
char *assemblyName = htmlEncode(dyStringContents(genomeOut->shortLabel));
char genomeNameId[512];
safef(genomeNameId, sizeof(genomeNameId), "%d_%s", hubInfo->id, assemblyName);
dyStringPrintf(dy, "{'id': '%s', 'parent': '%d_assemblies', 'children': true, "
"'li_attr': {'assemblylink': '%s','nodetype': 'assembly'},"
"'text': \"%s",
genomeNameId, hubInfo->id, dyStringContents(genomeOut->assemblyLink), assemblyName);
if (genomeOut->trackCount > 0)
{
dyStringPrintf(dy, " (%d track%s) ", genomeOut->trackCount,
genomeOut->trackCount == 1 ? "" : "s");
}
if (isNotEmpty(dyStringContents(genomeOut->metaTags)))
{
dyStringPrintf(dy, " %s",
htmlEncode(dyStringContents(genomeOut->metaTags)));
}
if (isNotEmpty(dyStringContents(genomeOut->descriptionMatch)))
{
dyStringPrintf(dy, " Assembly Description: %s",
htmlEncode(dyStringContents(genomeOut->descriptionMatch)));
}
dyStringPrintf(dy, "\"},");
printGenomeOutputStructureToDyString(genomeOut, genomeDy, genomeNameId);
genomeOut = genomeOut->next;
}
}
dyStringPrintf(dy, "];\n");
dyStringPrintf(dy, "%s", genomeDy->string);
jsInline(dy->string);
dyStringClear(dy);
}
static void printOutputForHub(struct hubEntry *hubInfo, struct hubSearchText *hubSearchResult, int count)
/* Given a hub's info and a structure listing the search hits within the hub, first print
* a basic line of hub information with a "connect" button. Then, if the search results
* are non-NULL, write out information about the genomes and tracks from the search hits that
* match the db filter.
* If there are no search results to print, the basic hub lines are combined into a single HTML table
* that is defined outside this function.
* Otherwise, each hub line is printed in its own table followed by a
containing details
* about the search results. */
{
if (hubSearchResult != NULL)
printf("
\n");
outputPublicTableRow(hubInfo, count);
if (hubSearchResult != NULL)
{
printf("
\n");
printf("
\n");
printf("", hubInfo->id); // div for the jstree for this hub's search result(s)
printf("
\n");
struct trackHub *hub = fetchTrackHub(hubInfo);
struct hubOutputStructure *hubOut = buildHubSearchOutputStructure(hub, hubSearchResult);
if (dyStringIsEmpty(hubOut->descriptionMatch) && (hubOut->genomes == NULL))
return; // no detailed search results; hit must have been to hub short label or something
printHubOutputStructure(hubOut, hubInfo);
}
}
int hubEntryCmp(const void *va, const void *vb)
/* Compare to sort based on shortLabel */
{
const struct hubEntry *a = *((struct hubEntry **)va);
const struct hubEntry *b = *((struct hubEntry **)vb);
return strcasecmp(a->shortLabel, b->shortLabel);
}
void printHubList(struct slName *hubsToPrint, struct hash *hubLookup, struct hash *searchResultHash)
/* Print out a list of hubs, possibly along with search hits to those hubs.
* hubLookup takes hub URLs to struct hubEntry
* searchResultHash takes hub URLs to struct hubSearchText * (list of hits on that hub)
*/
{
int count = 0;
int udcTimeoutVal = udcCacheTimeout();
char *udcOldDir = cloneString(udcDefaultDir());
char *searchUdcDir = cfgOptionDefault("hgHubConnect.cacheDir", udcOldDir);
udcSetDefaultDir(searchUdcDir);
udcSetCacheTimeout(1<<30);
struct hubEntry *hubList = NULL;
struct hubEntry *hubInfo;
long slTime;
long printOutputForHubTime;
boolean measureTiming = cartUsualBoolean(cart, "measureTiming", FALSE);
if (hubsToPrint != NULL)
{
printHubListHeader();
if (searchResultHash == NULL) // if not displaying search results, join the hub
s into one table
printf("
\n");
struct slName *thisHubName = NULL;
for (thisHubName = hubsToPrint; thisHubName != NULL; thisHubName = thisHubName->next)
{
hubInfo = (struct hubEntry *) hashFindVal(hubLookup, thisHubName->name);
if (hubInfo == NULL)
{
/* This shouldn't happen often, but maybe the search hits list was built from an outdated
* search text file that includes hubs for which no info is available.
* Skip this hub. */
continue;
}
slAddHead(&hubList, hubInfo);
}
slSort(&hubList, hubEntryCmp);
slTime = clock1000();
for (hubInfo = hubList; hubInfo != NULL; hubInfo = hubInfo->next)
{
struct hubSearchText *searchResult = NULL;
if (searchResultHash != NULL)
{
searchResult = (struct hubSearchText *) hashMustFindVal(searchResultHash, hubInfo->hubUrl);
}
printOutputForHub(hubInfo, searchResult, count);
count++;
}
printOutputForHubTime = clock1000();
if (measureTiming)
printf("hgHubConnect: printOutputForHubTime before js execution: %lu millis \n", printOutputForHubTime - slTime);
if (searchResultHash == NULL)
printf("
\n");
}
udcSetCacheTimeout(udcTimeoutVal);
udcSetDefaultDir(udcOldDir);
if (hubsToPrint != NULL)
{
/* Write out the list of hubs in a single table inside a div that will be hidden by
* javascript. This table is used (before being hidden) to set common column widths for
* the individual hub tables when they're split by detailed search results. */
printf("
\n");
}
jsInline(
"function lineUpCols()\n"
" {\n"
" var tableList = $('table.hubList');\n"
" if (tableList.length == 0)\n"
" return;\n"
" var colWidths = new Array();\n"
" var combinedTrackTable = $('#hideThisTable');\n"
" for (i=0; i \n");
char *hubSearchTableName = cfgOptionDefault("hubSearchTextTable", "hubSearchText");
int searchEnabled = sqlTableExists(conn, hubSearchTableName);
printSearchAndFilterBoxes(searchEnabled, hubSearchTerms, dbFilter);
struct hash *searchResultHash = NULL;
struct slName *hubsToPrint = NULL;
if (searchEnabled && !isEmpty(hubSearchTerms))
{
printSearchTerms(hubSearchTerms);
// Forcing checkDescriptions to TRUE right now, but we might want to add this as a
// checkbox option for users in the near future.
bool checkDescriptions = TRUE;
struct hubSearchText *hubSearchResults = getHubSearchResults(conn, hubSearchTableName,
hubSearchTerms, checkDescriptions, lcDbFilter, hubLookup);
searchResultHash = newHash(5);
struct hubSearchText *hst = hubSearchResults;
while (hst != NULL)
{
struct hubSearchText *nextHst = hst->next;
hst->next = NULL;
struct hashEl *hubHashEnt = hashLookup(searchResultHash, hst->hubUrl);
if (hubHashEnt == NULL)
{
slNameAddHead(&hubsToPrint, hst->hubUrl);
hashAdd(searchResultHash, hst->hubUrl, hst);
}
else
slAddHead(&(hubHashEnt->val), hst);
hst = nextHst;
}
struct hashEl *hel;
struct hashCookie cookie = hashFirst(searchResultHash);
while ((hel = hashNext(&cookie)) != NULL)
slReverse(&(hel->val));
}
else
{
// There is no active search, so just add all hubs to the list
struct hashEl *hel;
struct hashEl *helList;
helList = hashElListHash(hubLookup);
for (hel = helList; hel != NULL; hel = hel->next)
{
if (isNotEmpty(lcDbFilter))
{
struct hubEntry *hubEnt = (struct hubEntry *) hel->val;
char *lcDbList = cloneString(hubEnt->dbList);
if (isNotEmpty(lcDbList))
tolowers(lcDbList);
if ((lcDbList == NULL) || (stringIn(lcDbFilter, lcDbList) == NULL))
continue;
}
slNameAddHead(&hubsToPrint, hel->name);
}
}
slReverse(&hubsToPrint);
printHubList(hubsToPrint, hubLookup, searchResultHash);
printf("");
return (hubsToPrint != NULL);
}
struct hash *hgHubConnectPublic()
/* Put up the list of public hubs and other controls for the page. */
{
struct hash *retHash = NULL;
struct sqlConnection *conn = hConnectCentral();
char *publicTable = cfgOptionEnvDefault("HGDB_HUB_PUBLIC_TABLE",
hubPublicTableConfVariable, defaultHubPublicTableName);
char *statusTable = cfgOptionEnvDefault("HGDB_HUB_STATUS_TABLE",
hubStatusTableConfVariable, defaultHubStatusTableName);
if (!(sqlTableExists(conn, publicTable) &&
outputPublicTable(conn, publicTable,statusTable, &retHash)) )
{
printf("
\n");
printf("No Public Track Hubs found that match search criteria. ");
printf("
");
}
hDisconnectCentral(&conn);
return retHash;
}
static void tryHubOpen(unsigned id)
/* try to open hub, leaks trackHub structure */
{
/* try opening this again to reset error */
struct sqlConnection *conn = hConnectCentral();
struct errCatch *errCatch = errCatchNew();
struct hubConnectStatus *hub = NULL;
if (errCatchStart(errCatch))
hub = hubConnectStatusForId(conn, id);
errCatchEnd(errCatch);
if (errCatch->gotError)
hubUpdateStatus( errCatch->message->string, NULL);
else
hubUpdateStatus(NULL, hub);
errCatchFree(&errCatch);
hDisconnectCentral(&conn);
}
static int doRedirect(struct cart *theCart)
{
struct hubConnectStatus *hub = hubConnectNewHub();
if (hub == NULL)
return 0;
char headerText[1024];
char *errorMessage;
hubFindOrAddUrlInStatusTable(database, cart, hub->hubUrl, &errorMessage);
// if there is an error message, we stay in hgHubConnect
if (errorMessage != NULL)
return 0;
getDbAndGenome(cart, &database, &organism, oldVars);
int redirDelay = 3;
printf( "",
redirDelay,"../cgi-bin/hgGateway",cartSidUrlString(cart));
safef(headerText, sizeof(headerText), "Hub Connect Successful");
cartWebStart(cart, NULL, "%s", headerText);
hPrintf("You will be automatically redirected to the gateway page for this hub's default database "
"(%s) in %d seconds.
",
cartSidUrlString(cart),trackHubSkipHubName(database),redirDelay);
struct trackHub *tHub = hub->trackHub;
if (tHub->email != NULL)
{
hPrintf("This hub is provided courtesy of %s. Please contact them with any questions.", tHub->email, tHub->email);
}
hPrintf("
Track data hubs are collections of external tracks that can be imported into the UCSC Genome Browser. "
"Hub tracks show up under the hub's own blue label bar on the main browser page, "
"as well as on the configure page. For more information, including where to "
"host your track hub, see the "
""
"User's Guide."
"To import a public hub click its \"Connect\" button below.
"
"
NOTE: Because Track Hubs are created and maintained by external sources,"
" UCSC is not responsible for their content.
"
);
printf("
\n");
// this variable is used by hub search and hub validate, initialize here so we don't
// overwrite it unintentionally depending on which path the CGI takes
jsInline("trackData = [];\n");
getDbAndGenome(cart, &database, &organism, oldVars);
char *survey = cfgOptionEnv("HGDB_HUB_SURVEY", "hubSurvey");
char *surveyLabel = cfgOptionEnv("HGDB_HUB_SURVEY_LABEL", "hubSurveyLabel");
if (survey && differentWord(survey, "off"))
hPrintf("%s\n", survey, surveyLabel ? surveyLabel : "Take survey");
hPutc('\n');
// grab all the hubs that are listed in the cart
struct hubConnectStatus *hubList = hubConnectStatusListFromCartAll(cart);
checkTrackDbs(hubList);
slSort(&hubList, hubConnectStatusCmp);
// here's a little form for the add new hub button
printf("");
// this is the form for the connect hub button
printf("");
// this is the form for the disconnect hub button
printf("");
// this is the form for the reset hub button
printf("");
// this is the form for the search hub button
printf("");
// this is the form for the validate button
boolean doValidate = cfgOptionBooleanDefault("hgHubConnect.validateHub", FALSE);
if (doValidate)
{
printf("");
}
// ... and now the main form
printf("");
printf("