6cbe668f98ab263238542b8fd6bbf860db113930 angie Wed Jan 28 09:55:13 2015 -0800 Several major changes in the way data sources are represented: 1. Instead of the CGI sending menus for group, track and table, make it send the whole tree of groups, tracks, views, subtracks -- "groupedTrackDb". Now the client-side model can make menus that reflect the tree structure. This also gives us flexibility to tweak labels easily. 2. Instead of hardcoding group, track and table into elements of hgai_querySpec.dataSources, make each data source a proper object with a trackPath (path through groupedTrackDb), and for the UI, other attributes like label and URL for hgTables schema page. When the CGI unpacks hgai_querySpec.dataSources, it now uses trackPath and gets table from the leaf track or subtrack (the last item in trackPath). Note: this doesn't work for old Conservation tracks that don't have views/subtracks -- need to figure out how to fudge subtracks for those. 3. Limit the number of data sources to 5, don't let the user add the same data source twice, and remember which track the user most recently selected in the "Add Data Source" section. Also, in hgAi.jsx, I separated out a bunch of things that were rendered in the top-level AppComponent into subcomponents to add some granularity to "Loading..." sections (instead of making the whole page saying "Loading..." until everything is in place). diff --git src/hg/lib/cartJson.c src/hg/lib/cartJson.c index a0e4218..06cd76e 100644 --- src/hg/lib/cartJson.c +++ src/hg/lib/cartJson.c @@ -1,743 +1,787 @@ /* cartJson - parse and execute JSON commands to update cart and/or return cart data as JSON. */ #include "common.h" #include "cartJson.h" #include "cartTrackDb.h" #include "cheapcgi.h" #include "grp.h" #include "hdb.h" #include "hgFind.h" #include "htmshell.h" #include "hubConnect.h" #include "hui.h" #include "jsonParse.h" #include "obscure.h" #include "regexHelper.h" #include "suggest.h" #include "trackHub.h" #include "web.h" char *cartJsonOptionalParam(struct hash *paramHash, char *name) /* Convenience function for a CartJsonHandler function: Look up name in paramHash. * Return the string contained in its jsonElement value, or NULL if not found. */ { struct jsonElement *jel = hashFindVal(paramHash, name); if (jel) return jsonStringVal(jel, name); return NULL; } char *cartJsonRequiredParam(struct hash *paramHash, char *name, struct jsonWrite *jw, char *context) /* Convenience function for a CartJsonHandler function: Look up name in paramHash. * If found, return the string contained in its jsonElement value. * If not, write an error message (using context) and return NULL. */ { char *param = cartJsonOptionalParam(paramHash, name); if (param == NULL) jsonWriteStringf(jw, "error", "%s: required param %s is missing", context, name); return param; } static void printClade(struct jsonWrite *jw, char *clade) /* Print out clade menu's option list and selected item */ { struct slPair *cladeOptions = hGetCladeOptions(); jsonWriteValueLabelList(jw, "cladeOptions", cladeOptions); jsonWriteString(jw, "clade", clade); } static void printOrg(struct jsonWrite *jw, char *clade, char *org) /* Print out org menu's option list and selected item */ { struct slPair *orgOptions = hGetGenomeOptionsForClade(clade); jsonWriteValueLabelList(jw, "orgOptions", orgOptions); jsonWriteString(jw, "org", org); } static void printDb(struct jsonWrite *jw, char *org, char *db) /* Print out db menu's option list and selected item */ { struct slPair *dbOptions = hGetDbOptionsForGenome(org); jsonWriteValueLabelList(jw, "dbOptions", dbOptions); jsonWriteString(jw, "db", db); } static void printPosition(struct jsonWrite *jw, char *position) /* Print the position as given (it's up to caller to ensure this is consistent w/cart). */ { jsonWriteString(jw, "position", position); } static char *stripAnchor(char *textIn) /* If textIn contains an HTML anchor tag, strip it out (and its end tag). */ { regmatch_t matches[3]; if (regexMatchSubstrNoCase(textIn, "<a href[^>]+>", matches, ArraySize(matches))) { char *textOut = cloneString(textIn); memmove(textOut+matches[0].rm_so, textOut+matches[0].rm_eo, strlen(textOut) + 1 - matches[0].rm_eo); if (regexMatchSubstrNoCase(textOut, "</a>", matches, ArraySize(matches))) memmove(textOut+matches[0].rm_so, textOut+matches[0].rm_eo, strlen(textOut) + 1 - matches[0].rm_eo); return textOut; } return textIn; } static void hgPositionsJson(struct jsonWrite *jw, char *db, struct hgPositions *hgp, struct cart *cart) /* Write out JSON description of multiple position matches. */ { struct hgPosTable *table; jsonWriteListStart(jw, "positionMatches"); struct trackDb *tdbList = NULL; for (table = hgp->tableList; table != NULL; table = table->next) { if (table->posList != NULL) { char *tableName = table->name; // clear the tdb cache if this track is a hub track if (isHubTrack(tableName)) tdbList = NULL; struct trackDb *tdb = tdbForTrack(db, tableName, &tdbList); if (!tdb && startsWith("all_", tableName)) tdb = tdbForTrack(db, tableName+strlen("all_"), &tdbList); if (!tdb) errAbort("no track for table \"%s\" found via a findSpec", tableName); char *trackName = tdb->track; jsonWriteObjectStart(jw, NULL); jsonWriteString(jw, "name", table->name); jsonWriteString(jw, "trackName", trackName); jsonWriteString(jw, "description", table->description); jsonWriteString(jw, "vis", hCarefulTrackOpenVis(db, trackName)); jsonWriteListStart(jw, "matches"); struct hgPos *pos; for (pos = table->posList; pos != NULL; pos = pos->next) { char *encMatches = cgiEncode(pos->browserName); jsonWriteObjectStart(jw, NULL); // begin one match if (pos->chrom != NULL) jsonWriteStringf(jw, "position", "%s:%d-%d", pos->chrom, pos->chromStart+1, pos->chromEnd); else // GenBank results set position to GB accession instead of chr:s-e position. jsonWriteString(jw, "position", pos->name); // this is magic to tell the browser to make the // composite and this subTrack visible if (tdb->parent) { if (tdbIsSuperTrackChild(tdb)) jsonWriteStringf(jw, "extraSel", "%s=show&", tdb->parent->track); else { // tdb is a subtrack of a composite or a view jsonWriteStringf(jw, "extraSel", "%s_sel=1&%s_sel=1&", trackName, tdb->parent->track); } } jsonWriteString(jw, "hgFindMatches", encMatches); jsonWriteString(jw, "posName", htmlEncodeText(pos->name, FALSE)); if (pos->description) { stripString(pos->description, "\n"); jsonWriteString(jw, "description", stripAnchor(pos->description)); } jsonWriteObjectEnd(jw); // end one match } jsonWriteListEnd(jw); // end matches jsonWriteObjectEnd(jw); // end one table } } jsonWriteListEnd(jw); // end positionMatches } static struct hgPositions *genomePosCJ(struct jsonWrite *jw, char *db, char *spec, char **retChromName, int *retWinStart, int *retWinEnd, struct cart *cart) /* Search for positions in genome that match user query. * Return an hgp unless there is a problem. hgp->singlePos will be set if a single * position matched. * Otherwise display list of positions, put # of positions in retWinStart, * and return NULL. */ { char *hgAppName = "cartJson"; struct hgPositions *hgp = NULL; char *chrom = NULL; int start = BIGNUM; int end = 0; char *terms[16]; int termCount = chopByChar(cloneString(spec), ';', terms, ArraySize(terms)); boolean multiTerm = (termCount > 1); int i = 0; for (i = 0; i < termCount; i++) { trimSpaces(terms[i]); if (isEmpty(terms[i])) continue; hgp = hgPositionsFind(db, terms[i], "", hgAppName, cart, multiTerm); if (hgp == NULL || hgp->posCount == 0) { jsonWriteStringf(jw, "error", "Sorry, couldn't locate %s in genome database", htmlEncode(terms[i])); if (multiTerm) jsonWriteStringf(jw, "error", "%s not uniquely determined -- can't do multi-position search.", terms[i]); *retWinStart = 0; return NULL; } if (hgp->singlePos != NULL) { if (chrom != NULL && !sameString(chrom, hgp->singlePos->chrom)) { jsonWriteStringf(jw, "error", "Sites occur on different chromosomes: %s, %s.", chrom, hgp->singlePos->chrom); return NULL; } chrom = hgp->singlePos->chrom; if (hgp->singlePos->chromStart < start) start = hgp->singlePos->chromStart; if (hgp->singlePos->chromEnd > end) end = hgp->singlePos->chromEnd; } else { hgPositionsJson(jw, db, hgp, cart); if (multiTerm && hgp->posCount != 1) { jsonWriteStringf(jw, "error", "%s not uniquely determined (%d locations) -- " "can't do multi-position search.", terms[i], hgp->posCount); return NULL; } break; } } if (hgp != NULL) { *retChromName = chrom; *retWinStart = start; *retWinEnd = end; } return hgp; } static void changePosition(struct cartJson *cj, char *newPosition) /* Update position in cart, after performing lookup if necessary. * Usually we don't report what we just changed, but since we might modify it, * print out the final value. */ { char *db = cartString(cj->cart, "db"); char *chrom = NULL; int start=0, end=0; struct hgPositions *hgp = genomePosCJ(cj->jw, db, newPosition, &chrom, &start, &end, cj->cart); // If it resolved to a single position, update the cart; otherwise the app can // present the error (or list of matches) to the user. if (hgp && hgp->singlePos) { char newPosBuf[128]; safef(newPosBuf, sizeof(newPosBuf), "%s:%d-%d", chrom, start+1, end); cartSetString(cj->cart, "position", newPosBuf); printPosition(cj->jw, newPosBuf); } else // Search failed; restore position from cart jsonWriteString(cj->jw, "position", cartUsualString(cj->cart, "position", hDefaultPos(db))); } static void changePositionHandler(struct cartJson *cj, struct hash *paramHash) /* Update position in cart, after performing lookup if necessary. * Usually we don't report what we just changed, but since we might modify it, * print out the final value. */ { char *newPosition = cartJsonRequiredParam(paramHash, "newValue", cj->jw, "changePosition"); if (newPosition) changePosition(cj, newPosition); } static void printGeneSuggestTrack(struct cartJson *cj, char *db) /* Get the gene track used by hgSuggest for db (defaulting to cart db), or null if * there is none for this assembly. */ { if (isEmpty(db)) db = cartString(cj->cart, "db"); char *track = assemblyGeneSuggestTrack(db); jsonWriteString(cj->jw, "geneSuggestTrack", track); } static void changeDb(struct cartJson *cj, char *newDb) /* Change db to new value, update cart and print JSON of new position & gene suggest track. */ { cartSetString(cj->cart, "db", newDb); jsonWriteString(cj->jw, "db", newDb); char *defaultPosition = hDefaultPos(newDb); changePosition(cj, defaultPosition); printGeneSuggestTrack(cj, newDb); } void cartJsonChangeDb(struct cartJson *cj, struct hash *paramHash) /* Change db to new value, update cart and print JSON of new position & gene suggest track. */ { char *newDb = cartJsonRequiredParam(paramHash, "newValue", cj->jw, "changeDb"); if (newDb) changeDb(cj, newDb); } static void changeOrg(struct cartJson *cj, char *newOrg) /* Change org to new value, update cart variables and print JSON of new db menu etc. */ { char *newDb = hDefaultDbForGenome(newOrg); if (isEmpty(newDb)) { jsonWriteStringf(cj->jw, "error", "changeOrg: can't find default db for '%s'", newOrg); return; } cartSetString(cj->cart, "org", newOrg); jsonWriteString(cj->jw, "org", newOrg); printDb(cj->jw, newOrg, newDb); changeDb(cj, newDb); } void cartJsonChangeOrg(struct cartJson *cj, struct hash *paramHash) /* Change org to new value, update cart and print JSON of new db menu, new position etc. */ { char *newOrg = cartJsonRequiredParam(paramHash, "newValue", cj->jw, "changeOrg"); if (newOrg) changeOrg(cj, newOrg); } void cartJsonChangeClade(struct cartJson *cj, struct hash *paramHash) /* Change clade to new value, update cart, and print JSON of new org & db menus, new position etc */ { char *newClade = cartJsonRequiredParam(paramHash, "newValue", cj->jw, "changeClade"); if (! newClade) return; char *newOrg = hDefaultGenomeForClade(newClade); if (isEmpty(newOrg)) { jsonWriteStringf(cj->jw, "error", "changeClade: can't find default genome for '%s'", newClade); return; } cartSetString(cj->cart, "clade", newClade); jsonWriteString(cj->jw, "clade", newClade); printOrg(cj->jw, newClade, newOrg); changeOrg(cj, newOrg); } 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); } -static struct slPair *trackLabelPairsFromTdbRefs(struct slRef *tdbRefList) -/* For each tdb in tdbRefList, make a pair of {track, shortLabel}. */ +INLINE boolean nameIsTdbField(char *name) +/* Return TRUE if name is a tdb->{field}, e.g. "track" or "shortLabel" etc. */ { -struct slPair *pairList = NULL; -struct slRef *slr; -for (slr = tdbRefList; slr != NULL; slr = slr->next) - { - struct trackDb *tdb = slr->val; - slAddHead(&pairList, slPairNew(tdb->track, tdb->shortLabel)); +static char *tdbFieldNames[] = + { "track", "table", "shortLabel", "longLabel", "type", "priority", "grp", "parent", + "subtracks", "visibility" }; +return (stringArrayIx(name, tdbFieldNames, ArraySize(tdbFieldNames)) >= 0); } -slReverse(&pairList); -return pairList; + +INLINE boolean fieldOk(char *field, struct hash *fieldHash) +/* Return TRUE if fieldHash is NULL or field exists in fieldHash. */ +{ +return (fieldHash == NULL || hashLookup(fieldHash, field)); } -static int trackDbRefCmpShortLabel(const void *va, const void *vb) -/* Case-insensitive comparison of max 32 chars of tdb->shortLabel in slRefs. */ +static void writeTdbSimple(struct jsonWrite *jw, struct trackDb *tdb, struct hash *fieldHash) +/* Write JSON for the non-parent/child fields of tdb */ +{ +if (fieldOk("track", fieldHash)) + jsonWriteString(jw, "track", tdb->track); +if (fieldOk("table", fieldHash)) + jsonWriteString(jw, "table", tdb->table); +if (fieldOk("shortLabel", fieldHash)) + jsonWriteString(jw, "shortLabel", tdb->shortLabel); +if (fieldOk("longLabel", fieldHash)) + jsonWriteString(jw, "longLabel", tdb->longLabel); +if (fieldOk("type", fieldHash)) + jsonWriteString(jw, "type", tdb->type); +if (fieldOk("priority", fieldHash)) + jsonWriteDouble(jw, "priority", tdb->priority); +if (fieldOk("grp", fieldHash)) + jsonWriteString(jw, "grp", tdb->grp); +// NOTE: if you add a new field here, then also add it to nameIsTdbField above. +if (tdb->settingsHash) + { + struct hashEl *hel; + struct hashCookie cookie = hashFirst(tdb->settingsHash); + while ((hel = hashNext(&cookie)) != NULL) + { + if (! nameIsTdbField(hel->name) && fieldOk(hel->name, fieldHash)) { -const struct slRef *aRef = *((struct slRef **)va); -const struct slRef *bRef = *((struct slRef **)vb); -const struct trackDb *tdbA = aRef->val, *tdbB = bRef->val; -char shortLabelA[33], shortLabelB[33]; -strncpy(shortLabelA, tdbA->shortLabel, 32); -shortLabelA[32] = '\0'; -strncpy(shortLabelB, tdbB->shortLabel, 32); -shortLabelB[32] = '\0'; -tolowers(shortLabelA); -tolowers(shortLabelB); -return strcmp(shortLabelA, shortLabelB); + //#*** TODO: move jsonStringEscape inside jsonWriteString + char *encoded = jsonStringEscape((char *)hel->val); + jsonWriteString(jw, hel->name, encoded); + } + } + } } -static void printAllTracks(struct cartJson *cj, struct trackDb *trackList) -/* Print a mapping of "allTracks" to {track, shortLabel} for all tracks, - * alphabetized by shortLabel. */ +static void rWriteTdb(struct jsonWrite *jw, struct trackDb *tdb, struct hash *fieldHash, + int depth, int maxDepth) +/* Recursively write JSON for tdb and its subtracks if any. If fieldHash is non-NULL, + * include only the field names indexed in fieldHash. */ +{ +if (maxDepth >= 0 && depth > maxDepth) + return; +jsonWriteObjectStart(jw, NULL); +writeTdbSimple(jw, tdb, fieldHash); +if (tdb->parent && fieldOk("parent", fieldHash)) + { + // We can't link to an object in JSON and better not recurse here or else infinite loop. + if (tdbIsSuperTrackChild(tdb)) + { + // Supertracks have been omitted from fullTrackList, so add the supertrack object's + // non-parent/child info here. + jsonWriteObjectStart(jw, "parent"); + writeTdbSimple(jw, tdb->parent, fieldHash); + jsonWriteObjectEnd(jw); + } + else + // Just the name so we don't have infinite loops. + jsonWriteString(jw, "parent", tdb->parent->track); + } +if (tdb->subtracks && fieldOk("subtracks", fieldHash)) { -struct slRef *refList = refListFromSlList(trackList); -slSort(&refList, trackDbRefCmpShortLabel); -struct slPair *trackLabelPairs = trackLabelPairsFromTdbRefs(refList); -jsonWriteValueLabelList(cj->jw, "allTracks", trackLabelPairs); + jsonWriteListStart(jw, "subtracks"); + struct trackDb *subTdb; + for (subTdb = tdb->subtracks; subTdb != NULL; subTdb = subTdb->next) + rWriteTdb(jw, subTdb, fieldHash, depth+1, maxDepth); + jsonWriteListEnd(jw); + } +jsonWriteObjectEnd(jw); } -static void printOneGroupTracks(struct cartJson *cj, char *groupName, struct slRef *tdbRefList) -/* Given a group and value is an slRef list of trackDbs, sort the list by trackDb priority - * and print out JSON mapping the group name to list of trackDb {value, label} objects. */ +static struct hash *hashFromCommaString(char *commaString) +/* Return a hash that stores words in comma-separated string, or NULL if string is NULL or empty. */ +{ +struct hash *hash = NULL; +if (isNotEmpty(commaString)) { -slSort(&tdbRefList, trackDbRefCmp); -struct slPair *trackLabelPairs = trackLabelPairsFromTdbRefs(tdbRefList); -jsonWriteValueLabelList(cj->jw, groupName, trackLabelPairs); + hash = hashNew(0); + char *words[1024]; + int i, wordCount = chopCommas(commaString, words); + for (i = 0; i < wordCount; i++) + hashStoreName(hash, words[i]); + } +return hash; } -static void printGroupTracks(struct cartJson *cj, struct trackDb *trackList) -/* Hash group names to lists of tracks in those groups, and print out the structure as JSON. */ +static struct hash *hashTracksByGroup(struct trackDb *trackList) +/* Hash group names to lists of tracks in those groups; sort each list by trackDb priority. */ { struct hash *hash = hashNew(0); struct trackDb *tdb; for (tdb = trackList; tdb != NULL; tdb = tdb->next) { struct hashEl *hel = hashLookup(hash, tdb->grp); struct slRef *slr = slRefNew(tdb); if (hel) slAddHead(&(hel->val), slr); else hashAdd(hash, tdb->grp, slr); } -jsonWriteObjectStart(cj->jw, "groupTracks"); -printAllTracks(cj, trackList); struct hashCookie cookie = hashFirst(hash); struct hashEl *hel; while ((hel = hashNext(&cookie)) != NULL) - { - char *groupName = hel->name; - struct slRef *tdbRefList = hel->val; - printOneGroupTracks(cj, groupName, tdbRefList); - } -jsonWriteObjectEnd(cj->jw); -hashFree(&hash); -} - -static void printTrackTables(struct cartJson *cj, struct trackDb *trackList) -/* Hash track names to lists of tables in those tracks, and print out the structure as JSON. */ -{ -jsonWriteObjectStart(cj->jw, "trackTables"); -char *db = cartString(cj->cart, "db"); -struct trackDb *tdb; -for (tdb = trackList; tdb != NULL; tdb = tdb->next) - { - struct slName *tableList = cartTrackDbTablesForTrack(db, tdb, FALSE); // no useJoiner for now - jsonWriteSlNameList(cj->jw, tdb->track, tableList); - slFreeList(&tableList); - } -jsonWriteObjectEnd(cj->jw); + slSort(&hel->val, trackDbRefCmp); +return hash; } -void cartJsonGetGroupsTracksTables(struct cartJson *cj, struct hash *paramHash) -/* Print info necessary for group/track/table menus. */ +void cartJsonGetGroupedTrackDb(struct cartJson *cj, struct hash *paramHash) +/* Translate trackDb list (only a subset of the fields) into JSON array of track group objects; + * each group contains an array of track objects that may have subtracks. */ { struct trackDb *fullTrackList = NULL; struct grp *fullGroupList = NULL; cartTrackDbInit(cj->cart, &fullTrackList, &fullGroupList, /* useAccessControl=*/TRUE); -// Print out options for the track group menu: -// Remove All Tracks & All Tables from the end of the list for now. -struct grp *grp, *nextGrp = NULL; -for (grp = fullGroupList; grp != NULL; grp = nextGrp) +struct hash *groupedTrackRefList = hashTracksByGroup(fullTrackList); +// If the optional param 'fields' is given, hash the field names that should be returned. +char *fields = cartJsonOptionalParam(paramHash, "fields"); +struct hash *fieldHash = hashFromCommaString(fields); +// Also check for optional parameter 'maxDepth': +int maxDepth = -1; +char *maxDepthStr = cartJsonOptionalParam(paramHash, "maxDepth"); +if (isNotEmpty(maxDepthStr)) + maxDepth = atoi(maxDepthStr); +struct jsonWrite *jw = cj->jw; +jsonWriteListStart(jw, "groupedTrackDb"); +struct grp *grp; +for (grp = fullGroupList; grp != NULL; grp = grp->next) { - nextGrp = grp->next; - if (nextGrp && (sameString(nextGrp->name, "allTracks") || - sameString(nextGrp->name, "allTables"))) + jsonWriteObjectStart(jw, NULL); + jsonWriteString(jw, "name", grp->name); + jsonWriteString(jw, "label", grp->label); + jsonWriteListStart(jw, "tracks"); + struct slRef *tdbRefList = hashFindVal(groupedTrackRefList, grp->name); + struct slRef *tdbRef; + for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next) { - grp->next = nextGrp->next; - nextGrp = grp; + struct trackDb *tdb = tdbRef->val; + rWriteTdb(jw, tdb, fieldHash, 1, maxDepth); } + jsonWriteListEnd(jw); + jsonWriteObjectEnd(jw); } -jsonWriteObjectStart(cj->jw, "trackDbInfo"); -jsonWriteValueLabelList(cj->jw, "groupOptions", (struct slPair *)fullGroupList); -// Print out an object that maps group names to their tracks: -printGroupTracks(cj, fullTrackList); -// Print out an object that maps track names to tables: -printTrackTables(cj, fullTrackList); -jsonWriteObjectEnd(cj->jw); +jsonWriteListEnd(jw); } static char *hAssemblyDescription(char *db) /* Return a string containing db's description.html, or NULL if not found. */ //#*** LIBIFY: Code lifted from hgFind.c's hgPositionsHelpHtml. { char *htmlPath = hHtmlPath(db); char *htmlString = NULL; if (htmlPath != NULL) { if (fileExists(htmlPath)) readInGulp(htmlPath, &htmlString, NULL); else if (startsWith("http://" , htmlPath) || startsWith("https://", htmlPath) || startsWith("ftp://" , htmlPath)) { struct lineFile *lf = udcWrapShortLineFile(htmlPath, NULL, 256*1024); htmlString = lineFileReadAll(lf); lineFileClose(&lf); } } return htmlString; } static void getAssemblyInfo(struct cartJson *cj, struct hash *paramHash) /* Return useful things from dbDb (or track hub) and assembly description html (possibly NULL). * If db param is NULL, use db from cart. */ { char *db = cartJsonOptionalParam(paramHash, "db"); if (db == NULL) db = cartString(cj->cart, "db"); jsonWriteString(cj->jw, "db", db); jsonWriteString(cj->jw, "commonName", hGenome(db)); jsonWriteString(cj->jw, "scientificName", hScientificName(db)); jsonWriteString(cj->jw, "dbLabel", hFreezeDate(db)); //#*** TODO: move jsonStringEscape inside jsonWriteString jsonWriteString(cj->jw, "assemblyDescription", jsonStringEscape(hAssemblyDescription(db))); } static void getHasCustomTracks(struct cartJson *cj, struct hash *paramHash) /* Tell whether cart has custom tracks for db. If db param is NULL, use db from cart. */ { char *db = cartJsonOptionalParam(paramHash, "db"); if (db == NULL) db = cartString(cj->cart, "db"); jsonWriteBoolean(cj->jw, "hasCustomTracks", customTracksExistDb(cj->cart, db, NULL)); } static void getIsSpecialHost(struct cartJson *cj, struct hash *paramHash) /* Tell whether we're on a development host, preview, gsid etc. */ { jsonWriteBoolean(cj->jw, "isPrivateHost", hIsPrivateHost()); jsonWriteBoolean(cj->jw, "isBetaHost", hIsBetaHost()); jsonWriteBoolean(cj->jw, "isBrowserbox", hIsBrowserbox()); jsonWriteBoolean(cj->jw, "isPreviewHost", hIsPreviewHost()); } static void getHasHubTable(struct cartJson *cj, struct hash *paramHash) /* Tell whether central database has a hub table (i.e. server can do hubs). */ { jsonWriteBoolean(cj->jw, "hasHubTable", hubConnectTableExists()); } 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); } } } static void getCladeOrgDbPos(struct cartJson *cj, struct hash *paramHash) /* Get cart's current clade, org, db, position and geneSuggest track. */ { char *db = cartString(cj->cart, "db"); -char *genome = hGenome(db); -char *clade = hClade(genome); +char *genome = cartUsualString(cj->cart, "org", hGenome(db)); +char *clade = cartUsualString(cj->cart, "clade", hClade(genome)); printClade(cj->jw, clade); printOrg(cj->jw, clade, genome); printDb(cj->jw, genome, db); char *position = cartOptionalString(cj->cart, "position"); if (isEmpty(position)) position = hDefaultPos(db); printPosition(cj->jw, position); -printGeneSuggestTrack(cj, cartString(cj->cart, "db")); +printGeneSuggestTrack(cj, db); } static void getStaticHtml(struct cartJson *cj, struct hash *paramHash) /* Read HTML text from a relative path under browser.documentRoot and * write it as an encoded JSON string */ { char *tag = cartJsonOptionalParam(paramHash, "tag"); if (isEmpty(tag)) tag = "html"; char *file = cartJsonRequiredParam(paramHash, "file", cj->jw, "getStaticHtml"); char *html = hFileContentsOrWarning(file); //#*** TODO: move jsonStringEscape inside jsonWriteString char *encoded = jsonStringEscape(html); jsonWriteString(cj->jw, tag, encoded); } void cartJsonRegisterHandler(struct cartJson *cj, char *command, CartJsonHandler *handler) /* Associate handler with command; when javascript sends command, handler will be executed. */ { hashAdd(cj->handlerHash, command, handler); } struct cartJson *cartJsonNew(struct cart *cart) /* Allocate and return a cartJson object with default handlers. */ { struct cartJson *cj; AllocVar(cj); cj->handlerHash = hashNew(0); cj->jw = jsonWriteNew(); cj->cart = cart; +char *db = cartOptionalString(cj->cart, "db"); +if (isEmpty(db) || ! hDbIsActive(db)) + { + db = hDefaultDb(); + cartSetString(cj->cart, "db", db); + } cartJsonRegisterHandler(cj, "getCladeOrgDbPos", getCladeOrgDbPos); cartJsonRegisterHandler(cj, "changeClade", cartJsonChangeClade); cartJsonRegisterHandler(cj, "changeOrg", cartJsonChangeOrg); cartJsonRegisterHandler(cj, "changeDb", cartJsonChangeDb); cartJsonRegisterHandler(cj, "changePosition", changePositionHandler); cartJsonRegisterHandler(cj, "get", getVar); -cartJsonRegisterHandler(cj, "getGroupsTracksTables", cartJsonGetGroupsTracksTables); +cartJsonRegisterHandler(cj, "getGroupedTrackDb", cartJsonGetGroupedTrackDb); cartJsonRegisterHandler(cj, "getAssemblyInfo", getAssemblyInfo); cartJsonRegisterHandler(cj, "getHasCustomTracks", getHasCustomTracks); cartJsonRegisterHandler(cj, "getIsSpecialHost", getIsSpecialHost); cartJsonRegisterHandler(cj, "getHasHubTable", getHasHubTable); cartJsonRegisterHandler(cj, "setIfUnset", setIfUnset); cartJsonRegisterHandler(cj, "getStaticHtml", getStaticHtml); return cj; } void cartJsonFree(struct cartJson **pCj) /* Close **pCj's contents and nullify *pCj. */ { if (*pCj == NULL) return; struct cartJson *cj = *pCj; jsonWriteFree(&cj->jw); hashFree(&cj->handlerHash); freez(pCj); } static void doOneCommand(struct cartJson *cj, char *command, struct jsonElement *paramObject) /* Dispatch command by name, checking for required parameters. */ { CartJsonHandler *handler = hashFindVal(cj->handlerHash, command); if (handler) { struct hash *paramHash = jsonObjectVal(paramObject, command); handler(cj, paramHash); } else { jsonWriteStringf(cj->jw, "error", "cartJson: unrecognized command '%s'\"", command); return; } } static int commandCmp(const void *pa, const void *pb) /* Comparison function to put "change" commands ahead of other commands. */ { struct slPair *cmdA = *((struct slPair **)pa); struct slPair *cmdB = *((struct slPair **)pb); boolean aIsChange = startsWith("change", cmdA->name); boolean bIsChange = startsWith("change", cmdB->name); if (aIsChange && !bIsChange) return -1; if (!aIsChange && bIsChange) return 1; return strcmp(cmdA->name, cmdB->name); } // Accumulate warnings so they can be JSON-ified: static struct dyString *dyWarn = NULL; static void cartJsonVaWarn(char *format, va_list args) /* Save warnings for later. */ { dyStringVaPrintf(dyWarn, format, args); } static void cartJsonPrintWarnings(struct jsonWrite *jw) /* If there are warnings, write them out as JSON: */ { if (dyWarn && dyStringLen(dyWarn) > 0) { //#*** TODO: move jsonStringEscape inside jsonWriteString char *encoded = jsonStringEscape(dyWarn->string); jsonWriteString(jw, "warning", encoded); freeMem(encoded); } } static void cartJsonAbort() /* Print whatever warnings we have accumulated and exit. */ { if (dyWarn) puts(dyWarn->string); exit(0); } static void cartJsonPushErrHandlers() /* Push warn and abort handlers for errAbort. */ { if (dyWarn == NULL) dyWarn = dyStringNew(0); else dyStringClear(dyWarn); pushWarnHandler(cartJsonVaWarn); pushAbortHandler(cartJsonAbort); } static void cartJsonPopErrHandlers() /* Pop warn and abort handlers for errAbort. */ { popWarnHandler(); popAbortHandler(); } void cartJsonExecute(struct cartJson *cj) /* Get commands from cgi, print Content-type, execute commands, print results as JSON. */ { cartJsonPushErrHandlers(); puts("Content-Type:text/javascript\n"); // Initialize response JSON object: jsonWriteObjectStart(cj->jw, NULL); // Always send back hgsid: jsonWriteString(cj->jw, cartSessionVarName(), cartSessionId(cj->cart)); char *commandJson = cgiOptionalString(CARTJSON_COMMAND); if (commandJson) { struct jsonElement *commandObj = jsonParse(commandJson); struct hash *commandHash = jsonObjectVal(commandObj, "commandObj"); // change* commands need to go first! Really we need an ordered map type here... // for now, just make a list and sort to put change commands at the front. struct slPair *commandList = NULL, *cmd; struct hashCookie cookie = hashFirst(commandHash); struct hashEl *hel; while ((hel = hashNext(&cookie)) != NULL) slAddHead(&commandList, slPairNew(hel->name, hel->val)); slSort(&commandList, commandCmp); for (cmd = commandList; cmd != NULL; cmd = cmd->next) doOneCommand(cj, cmd->name, (struct jsonElement *)cmd->val); } cartJsonPrintWarnings(cj->jw); jsonWriteObjectEnd(cj->jw); puts(cj->jw->dy->string); cartJsonPopErrHandlers(); }