fa326179d9bd70fb1fb1d2fe4996c3a5545257aa hiram Tue Feb 12 14:57:50 2019 -0800 now traversing trackDb recursively to show all composite tracks refs #18869 diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c index a554615..ba07c64 100644 --- src/hg/hubApi/hubApi.c +++ src/hg/hubApi/hubApi.c @@ -54,87 +54,102 @@ char *longLabel; /* Hub long label. */ char *registrationTime; /* Time first registered */ unsigned dbCount; /* Number of databases hub has data for. */ char *dbList; /* Comma separated list of databases. */ char *descriptionUrl; /* URL to description HTML */ }; /* Global Variables */ static struct cart *cart; /* CGI and other variables */ static struct hash *oldVars = NULL; static struct hash *trackCounter = NULL; static long totalTracks = 0; static boolean measureTiming = FALSE; /* set by CGI parameters */ static boolean allTrackSettings = FALSE; /* checkbox setting */ static char **shortLabels = NULL; /* public hub short labels in array */ -struct hubPublic *publicHubList = NULL; +// struct hubPublic *publicHubList = NULL; static int publicHubCount = 0; static char *defaultHub = "Plants"; static char *defaultDb = "ce11"; static long enteredMainTime = 0; /* will become = clock1000() on entry */ /* to allow calculation of when to bail out, taking too long */ static long timeOutSeconds = 100; static boolean timedOut = FALSE; /* ######################################################################### */ static struct jsonWrite *jsonStartOutput() -/* begin json output */ +/* begin json output with standard header information for all requests */ { time_t timeNow = time(NULL); // struct tm tm; // gmtime_r(&timeNow, &tm); struct jsonWrite *jw = jsonWriteNew(); jsonWriteObjectStart(jw, NULL); jsonWriteString(jw, "apiVersion", "0.1"); jsonWriteString(jw, "source", "UCSantaCruz"); jsonWriteDateFromUnix(jw, "downloadTime", (long long) timeNow); jsonWriteNumber(jw, "downloadTimeStamp", (long long) timeNow); return jw; } static void jsonErrAbort(char *format, ...) -/* Issue an error message in json format. */ +/* Issue an error message in json format, and exit(0) */ { char errMsg[2048]; va_list args; va_start(args, format); vsnprintf(errMsg, sizeof(errMsg), format, args); struct jsonWrite *jw = jsonStartOutput(); jsonWriteString(jw, "error", errMsg); jsonWriteObjectEnd(jw); fputs(jw->dy->string,stdout); exit(0); } static void hubPublicJsonData(struct jsonWrite *jw, struct hubPublic *el) /* Print array data for one row from hubPublic table, order here * must be same as was stated in the columnName header element * TODO: need to figure out how to use the order of the columns as * they are in the 'desc' request */ { jsonWriteListStart(jw, NULL); jsonWriteString(jw, NULL, el->hubUrl); jsonWriteString(jw, NULL, el->shortLabel); jsonWriteString(jw, NULL, el->longLabel); jsonWriteString(jw, NULL, el->registrationTime); jsonWriteNumber(jw, NULL, (long long)el->dbCount); jsonWriteString(jw, NULL, el->dbList); jsonWriteString(jw, NULL, el->descriptionUrl); jsonWriteListEnd(jw); } +int trackDbTrackCmp(const void *va, const void *vb) +/* Compare to sort based on 'track' name; use shortLabel as secondary sort key. + * Note: parallel code to hgTracks.c:tgCmpPriority */ +{ +const struct trackDb *a = *((struct trackDb **)va); +const struct trackDb *b = *((struct trackDb **)vb); +int dif = strcmp(a->track, b->track); +if (dif < 0) + return -1; +else if (dif == 0.0) + return strcasecmp(a->shortLabel, b->shortLabel); +else + return 1; +} + static int publicHubCmpCase(const void *va, const void *vb) /* Compare two slNames, ignore case. */ { const struct hubPublic *a = *((struct hubPublic **)va); const struct hubPublic *b = *((struct hubPublic **)vb); return strcasecmp(a->shortLabel, b->shortLabel); } static void publicHubSortCase(struct hubPublic **pList) /* Sort slName list, ignore case. */ { slSort(pList, publicHubCmpCase); } static struct hubPublic *hubPublicLoad(char **row) @@ -293,46 +308,73 @@ retVal = 1; } } errCatchEnd(errCatch); if (errCatch->gotError) { retVal = 1; dyStringPrintf(errors, "%s", errCatch->message->string); } errCatchFree(&errCatch); return retVal; } /* static int bbiBriefMeasure() */ -static struct slName *trackList(struct trackDb *tdb, struct trackHubGenome *genome) -/* process the track list to show all tracks */ +#ifdef NOT +static void cloneTdb(struct trackDb *source, struct trackDb *destination) +/* TBD: is there a cloneTdb() function somewhere else ? */ +{ +destination->track = cloneString(source->track); +destination->shortLabel = cloneString(source->shortLabel); +destination->type = cloneString(source->type); +destination->longLabel = cloneString(source->longLabel); +destination->visibility = source->visibility; +destination->priority = source->priority; +destination->colorR = source->colorR; +destination->colorG = source->colorG; +destination->colorB = source->colorB; +destination->altColorR = source->altColorR; +destination->altColorG = source->altColorG; +destination->altColorB = source->altColorB; +destination->useScore = source->useScore; +destination->private = source->private; +destination->url = cloneString(source->url); +destination->html = cloneString(source->html); +destination->grp = cloneString(source->grp); +destination->canPack = source->canPack; +destination->settings = cloneString(source->settings); +destination->settingsHash = source->settingsHash; +} +#endif + +static void hubTrackList(struct trackDb *tdb, struct trackHubGenome *genome) +/* process the track list to show all tracks, return trackDb list */ { -struct slName *retList = NULL; /* for return of track list for 'genome' */ if (tdb) { struct hash *countTracks = hashNew(0); hPrintf(" <ul>\n"); struct trackDb *track = tdb; for ( ; track; track = track->next ) { - struct slName *el = slNameNew(track->track); - slAddHead(&retList, el); - char *bigDataUrl = hashFindVal(track->settingsHash, "bigDataUrl"); - char *compositeTrack = hashFindVal(track->settingsHash, "compositeTrack"); - char *superTrack = hashFindVal(track->settingsHash, "superTrack"); +// char *bigDataUrl = hashFindVal(track->settingsHash, "bigDataUrl"); + char *bigDataUrl = trackDbSetting(track, "bigDataUrl"); +// char *compositeTrack = hashFindVal(track->settingsHash, "compositeTrack"); + char *compositeTrack = trackDbSetting(track, "compositeTrack"); +// char *superTrack = hashFindVal(track->settingsHash, "superTrack"); + char *superTrack = trackDbSetting(track, "superTrack"); boolean depthSearch = cartUsualBoolean(cart, "depthSearch", FALSE); if (compositeTrack) hashIncInt(countTracks, "composite container"); else if (superTrack) hashIncInt(countTracks, "superTrack container"); else if (isEmpty(track->type)) hashIncInt(countTracks, "no type specified"); else hashIncInt(countTracks, track->type); if (depthSearch && bigDataUrl) { char *bigDataIndex = NULL; char *relIdxUrl = trackDbSetting(tdb, "bigDataIndex"); if (relIdxUrl != NULL) bigDataIndex = trackHubRelativeUrl(genome->trackDbFile, relIdxUrl); @@ -376,56 +418,56 @@ { hPrintf(" <ul>\n"); struct hashEl *hel; struct hashCookie hc = hashFirst(countTracks); while ((hel = hashNext(&hc)) != NULL) { int prevCount = ptToInt(hashFindVal(trackCounter, hel->name)); totalTracks += ptToInt(hel->val); hashReplace(trackCounter, hel->name, intToPt(prevCount + ptToInt(hel->val))); hPrintf(" <li>%d - %s</li>\n", ptToInt(hel->val), hel->name); } hPrintf(" </ul>\n"); } hPrintf(" </ul>\n"); } -return retList; -} /* static struct slName *trackList() */ +} /* static struct trackDb *hubTrackList() */ -static struct slName *assemblySettings(struct trackHubGenome *genome) +static struct trackDb * assemblySettings(struct trackHubGenome *genome) /* display all the assembly 'settingsHash' */ { -struct slName *retList = NULL; +struct trackDb *retTbd = NULL; hPrintf(" <ul>\n"); struct hashEl *hel; struct hashCookie hc = hashFirst(genome->settingsHash); while ((hel = hashNext(&hc)) != NULL) { hPrintf(" <li>%s : %s</li>\n", hel->name, (char *)hel->val); if (sameWord("trackDb", hel->name)) /* examine the trackDb structure */ { struct trackDb *tdb = trackHubTracksForGenome(genome->trackHub, genome); - retList = trackList(tdb, genome); + retTbd = tdb; + hubTrackList(tdb, genome); } if (timeOutReached()) break; } hPrintf(" </ul>\n"); -return retList; +return retTbd; } -static struct slName *genomeList(struct trackHub *hubTop, struct slName **dbTrackList, char *selectGenome) +static struct slName *genomeList(struct trackHub *hubTop, struct trackDb **dbTrackList, char *selectGenome) /* follow the pointers from the trackHub to trackHubGenome and around * in a circle from one to the other to find all hub resources * return slName list of the genomes in this track hub * optionally, return the trackList from this hub for the specified genome */ { struct slName *retList = NULL; long totalAssemblyCount = 0; struct trackHubGenome *genome = hubTop->genomeList; hPrintf("<h4>genome sequences (and tracks) present in this track hub</h4>\n"); hPrintf("<ul>\n"); long lastTime = clock1000(); for ( ; genome; genome = genome->next ) @@ -435,35 +477,31 @@ if ( differentStringNullOk(selectGenome, genome->name) ) continue; } ++totalAssemblyCount; struct slName *el = slNameNew(genome->name); slAddHead(&retList, el); if (genome->organism) { hPrintf("<li>%s - %s - %s</li>\n", genome->organism, genome->name, genome->description); } else { /* can there be a description when organism is empty ? */ hPrintf("<li>%s</li>\n", genome->name); } if (genome->settingsHash) - { - struct slName *trackList = assemblySettings(genome); - if (dbTrackList) - *dbTrackList = trackList; - } + *dbTrackList = assemblySettings(genome); if (measureTiming) { long thisTime = clock1000(); hPrintf("<em>processing time %s: %ld millis</em><br>\n", genome->name, thisTime - lastTime); } if (timeOutReached()) break; } if (trackCounter->elCount) { hPrintf(" <li>total genome assembly count: %ld</li>\n", totalAssemblyCount); hPrintf(" <li>%ld total tracks counted, %d different track types:</li>\n", totalTracks, trackCounter->elCount); hPrintf(" <ul>\n"); struct hashEl *hel; struct hashCookie hc = hashFirst(trackCounter); @@ -541,31 +579,31 @@ jsonWriteString(jw, NULL, row[0]); sqlFreeResult(&sr); hDisconnectCentral(&conn); jsonWriteListEnd(jw); return FALSE; } static void jsonPublicHubs() /* output the hubPublic SQL table */ { struct sqlConnection *conn = hConnectCentral(); char *dataTime = sqlTableUpdate(conn, hubPublicTableName()); hDisconnectCentral(&conn); time_t dataTimeStamp = sqlDateToUnixTime(dataTime); replaceChar(dataTime, ' ', 'T'); -struct hubPublic *el = publicHubList; +struct hubPublic *el = hubPublicLoadAll(); struct jsonWrite *jw = jsonStartOutput(); jsonWriteString(jw, "dataTime", dataTime); jsonWriteNumber(jw, "dataTimeStamp", (long long)dataTimeStamp); freeMem(dataTime); jsonWriteString(jw, "tableName", hubPublicTableName()); tableColumns(jw, hubPublicTableName()); jsonWriteListStart(jw, "publicHubData"); for ( ; el != NULL; el = el->next ) { hubPublicJsonData(jw, el); } jsonWriteListEnd(jw); jsonWriteObjectEnd(jw); fputs(jw->dy->string,stdout); } @@ -687,54 +725,90 @@ jsonWriteNumber(jw, "dataTimeStamp", (long long)dataTimeStamp); freeMem(dataTime); jsonWriteNumber(jw, "chromCount", (long long)slCount(ciList)); jsonWriteObjectStart(jw, "chromosomes"); for ( ; el != NULL; el = el->next ) { jsonWriteNumber(jw, el->chrom, (long long)el->size); } jsonWriteObjectEnd(jw); /* chromosomes */ jsonWriteObjectEnd(jw); /* top level */ fputs(jw->dy->string,stdout); } hFreeConn(&conn); } +static void recursiveTrackList(struct jsonWrite *jw, struct trackDb *tdb, char *type) +{ +jsonWriteListStart(jw, type); +struct trackDb *el; +for (el = tdb; el != NULL; el = el->next ) + { + jsonWriteObjectStart(jw, NULL); + jsonWriteString(jw, "track", el->track); + jsonWriteString(jw, "shortLabel", el->shortLabel); + jsonWriteString(jw, "type", el->type); + jsonWriteString(jw, "longLabel", el->longLabel); + if (tdbIsComposite(el)) + { + recursiveTrackList(jw, el->subtracks, "subtracks"); + } + if (tdb->parent && tdbIsSuperTrackChild(el)) + jsonWriteString(jw, "superTrack", "TRUE"); + jsonWriteObjectEnd(jw); + } +jsonWriteListEnd(jw); +} + static void trackDbJsonOutput(char *db, FILE *f) /* return track list from specified UCSC database name */ { struct sqlConnection *conn = hAllocConn(db); char *dataTime = sqlTableUpdate(conn, "trackDb"); time_t dataTimeStamp = sqlDateToUnixTime(dataTime); replaceChar(dataTime, ' ', 'T'); hFreeConn(&conn); struct trackDb *tdbList = hTrackDb(db); -struct trackDb *el; struct jsonWrite *jw = jsonStartOutput(); jsonWriteString(jw, "db", db); jsonWriteString(jw, "dataTime", dataTime); jsonWriteNumber(jw, "dataTimeStamp", (long long)dataTimeStamp); freeMem(dataTime); -jsonWriteListStart(jw, "tracks"); -for (el = tdbList; el != NULL; el = el->next ) - jsonWriteString(jw, NULL, el->track); -jsonWriteListEnd(jw); +recursiveTrackList(jw, tdbList, "tracks"); jsonWriteObjectEnd(jw); fputs(jw->dy->string,stdout); } /* static void trackDbJsonOutput(char *db, FILE *f) */ +static void getTrackData() +{ +} + +static void getSequenceData() +{ +} + #define MAX_PATH_INFO 32 +static void apiGetData(char *words[MAX_PATH_INFO]) +/* 'getData' function, words[1] is the subCommand */ +{ +if (sameWord("track", words[1])) + getTrackData(); +if (sameWord("sequence", words[1])) + getSequenceData(); +jsonErrAbort("do not recognize endpoint function: '/%s/%s'", words[0], words[1]); +} + static void apiList(char *words[MAX_PATH_INFO]) /* 'list' function words[1] is the subCommand */ { if (sameWord("publicHubs", words[1])) jsonPublicHubs(); else if (sameWord("ucscGenomes", words[1])) jsonDbDb(); else if (sameWord("hubGenomes", words[1])) { char *hubUrl = cgiOptionalString("hubUrl"); if (isEmpty(hubUrl)) jsonErrAbort("ERROR: must supply hubUrl='http:...' some URL to a hub for /list/genomes"); struct trackHub *hub = trackHubOpen(hubUrl, ""); if (hub->genomeList) @@ -764,74 +838,70 @@ if (isEmpty(hubUrl)) // missing hubUrl implies UCSC database { trackDbJsonOutput(db, stdout); // only need db for this function return; } if (isEmpty(genome) || isEmpty(hubUrl)) { if (isEmpty(genome)) warn("# must supply genome='someName' the name of a genome in a hub for /list/tracks\n"); if (isEmpty(hubUrl)) jsonErrAbort("ERROR: must supply hubUrl='http:...' some URL to a hub for /list/genomes"); } struct trackHub *hub = trackHubOpen(hubUrl, ""); if (hub->genomeList) { - struct slName *dbTrackList = NULL; + struct trackDb *dbTrackList = NULL; (void) genomeList(hub, &dbTrackList, genome); + slSort(dbTrackList, trackDbTrackCmp); struct jsonWrite *jw = jsonStartOutput(); jsonWriteString(jw, "hubUrl", hubUrl); - jsonWriteListStart(jw, "genome"); - slNameSort(&dbTrackList); - struct slName *el = dbTrackList; - for ( ; el != NULL; el = el->next ) - { - jsonWriteString(jw, NULL, el->name); - } - jsonWriteListEnd(jw); + jsonWriteString(jw, "genome", genome); + recursiveTrackList(jw, dbTrackList, "tracks"); jsonWriteObjectEnd(jw); fputs(jw->dy->string,stdout); } } else if (sameWord("chromosomes", words[1])) { char *hubUrl = cgiOptionalString("hubUrl"); // char *genome = cgiOptionalString("genome"); char *db = cgiOptionalString("db"); if (isEmpty(hubUrl) && isEmpty(db)) jsonErrAbort("ERROR: must supply hubUrl or db name to return chromosome list"); if (isEmpty(hubUrl)) // missing hubUrl implies UCSC database { chromInfoJsonOutput(stdout, db); return; } } else - jsonErrAbort("do not recognize endpoint: '/list/%s' request", words[1]); + jsonErrAbort("do not recognize endpoint function: '/%s/%s'", words[0], words[1]); } static struct hash *apiFunctionHash = NULL; static void setupFunctionHash() /* initialize the apiFunctionHash */ { if (apiFunctionHash) - return; + return; /* already done */ apiFunctionHash = hashNew(0); hashAdd(apiFunctionHash, "list", &apiList); +hashAdd(apiFunctionHash, "getData", &apiGetData); } static void apiFunctionSwitch(char *pathInfo) /* given a pathInfo string: /command/subCommand/etc... * parse that and decide on which function to acll */ { hPrintDisable(); /* turn off all normal HTML output, doing JSON output */ /* the leading slash has been removed from the pathInfo, therefore, the * chop will have the first word in words[0] */ char *words[MAX_PATH_INFO];/*expect no more than MAX_PATH_INFO number of words*/ int wordCount = chopByChar(pathInfo, '/', words, ArraySize(words)); if (wordCount < 2) @@ -854,32 +924,30 @@ struct trackDb *track; hPrintf("<ul>\n"); for (track = tdbList; track != NULL; track = track->next ) { hPrintf("<li>%s</li>\n", track->track); if (allTrackSettings) trackSettings(track); /* show all settings */ } hPrintf("</ul>\n"); hPrintf("</p>\n"); } static void doMiddle(struct cart *theCart) /* Set up globals and make web page */ { -// struct hubPublic *hubList = hubPublicLoadAll(); -publicHubList = hubPublicLoadAll(); cart = theCart; measureTiming = hPrintStatus() && isNotEmpty(cartOptionalString(cart, "measureTiming")); measureTiming = TRUE; char *database = NULL; char *genome = NULL; getDbAndGenome(cart, &database, &genome, oldVars); initGenbankTableNames(database); char *docRoot = cfgOptionDefault("browser.documentRoot", DOCUMENT_ROOT); int timeout = cartUsualInt(cart, "udcTimeout", 300); if (udcCacheTimeout() < timeout) udcSetCacheTimeout(timeout); knetUdcInstall(); @@ -887,30 +955,32 @@ char *pathInfo = getenv("PATH_INFO"); if (isNotEmpty(pathInfo)) { puts("Content-Type:application/json"); puts("\n"); /* skip the first leading slash to simplify chopByChar parsing */ pathInfo += 1; setupFunctionHash(); apiFunctionSwitch(pathInfo); return; } puts("Content-Type:text/html"); puts("\n"); +(void) hubPublicLoadAll(); + struct dbDb *dbList = ucscDbDb(); char **ucscDbList = NULL; int listSize = slCount(dbList); AllocArray(ucscDbList, listSize); struct dbDb *el = dbList; int ucscDataBaseCount = 0; int maxDbNameWidth = 0; for ( ; el != NULL; el = el->next ) { ucscDbList[ucscDataBaseCount++] = el->name; if (strlen(el->name) > maxDbNameWidth) maxDbNameWidth = strlen(el->name); } maxDbNameWidth += 1;