77f17523d1115eb2fb85eaf747a76db0c6328204 hiram Mon Jan 28 14:05:59 2019 -0800 ready to start listing other things refs #18869 diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c index ddec85b..1122600 100644 --- src/hg/hubApi/hubApi.c +++ src/hg/hubApi/hubApi.c @@ -1,659 +1,701 @@ /* hubApi - access mechanism to hub data resources. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "jksql.h" #include "htmshell.h" #include "web.h" #include "cheapcgi.h" #include "cart.h" #include "hui.h" #include "udc.h" #include "knetUdc.h" #include "genbank.h" #include "trackHub.h" #include "hgConfig.h" #include "hCommon.h" #include "hPrint.h" #include "bigWig.h" #include "hubConnect.h" #include "obscure.h" #include "errCatch.h" #include "vcf.h" #include "bedTabix.h" #include "bamFile.h" #ifdef USE_HAL #include "halBlockViz.h" #endif /* +------------------+------------------+------+-----+---------+-------+ | Field | Type | Null | Key | Default | Extra | +------------------+------------------+------+-----+---------+-------+ | hubUrl | longblob | NO | PRI | NULL | | | shortLabel | varchar(255) | NO | | NULL | | | longLabel | varchar(255) | NO | | NULL | | | registrationTime | varchar(255) | NO | | NULL | | | dbCount | int(10) unsigned | NO | | NULL | | | dbList | blob | YES | | NULL | | | descriptionUrl | longblob | YES | | NULL | | +------------------+------------------+------+-----+---------+-------+ */ struct hubPublic /* Table of public track data hub connections. */ { struct hubPublic *next; /* Next in singly linked list. */ char *hubUrl; /* URL to hub.ra file */ char *shortLabel; /* Hub short label. */ 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 */ -struct cart *cart; /* CGI and other variables */ -struct hash *oldVars = NULL; +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 */ static int publicHubCount = 0; static struct hubPublic *publicHubList = NULL; static char *defaultHub = "Plants"; 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 boolean jsonOutput = FALSE; /* turns on when pathInfo present */ /* ######################################################################### */ /* json output needs to encode special characters in strings: " - quotation mark / - forward slash \ - back slash \n - new line \r - carriage return \t - tab */ static char* jsonEscape(char *jsonString) /* escape any of the special characters in the string for json output */ { if (NULL == jsonString) return NULL; /* going to alternate the result string between a and b so the returned * string from replaceChars() can be freemem'ed * returned result from here should also be freemem'ed */ static char *a = NULL; static char *b = NULL; /* replace back slash first since the other encodings will be adding * the back slash */ a = replaceChars(jsonString, "\\", "\\\\"); /* \ -> \\ */ b = replaceChars(a, "\"", "\\\""); /* " -> \" */ freeMem(a); a = replaceChars(b, "/", "\\/"); /* / -> \/ */ freeMem(b); b = replaceChars(a, "\n", "\\\n"); /* \n -> \\n */ freeMem(a); a = replaceChars(b, "\r", "\\\r"); /* \r -> \\r */ freeMem(b); b = replaceChars(a, "\t", "\\\t"); /* \t -> \\t */ return b; } static void jsonInteger(FILE *f, char *tag, int value) /* output one json interger: "tag":value appropriately quoted and encoded */ { fprintf(f,"\"%s\":%d",tag, value); } static void jsonString(FILE *f, char *tag, char *value) /* output one json string: "tag":"value" appropriately quoted and encoded */ { fprintf(f,"\"%s\":",tag); char *a = jsonEscape(value); if (isEmpty(a)) fprintf(f, "%s", "null"); else fprintf(f, "\"%s\"", a); freeMem(a); } static void hubPublicJsonOutput(struct hubPublic *el, FILE *f) /* Print out hubPublic element in JSON format. */ { fputc('{',f); jsonString(f, "hubUrl", el->hubUrl); fputc(',',f); jsonString(f, "shortLabel", el->shortLabel); fputc(',',f); jsonString(f, "longLabel", el->longLabel); fputc(',',f); jsonString(f, "registrationTime", el->registrationTime); fputc(',',f); jsonInteger(f, "dbCount", el->dbCount); fputc(',',f); jsonString(f, "dbList", el->dbList); fputc(',',f); jsonString(f, "descriptionUrl", el->descriptionUrl); fputc('}',f); } 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) /* Load a hubPublic from row fetched with select * from hubPublic * from database. Dispose of this with hubPublicFree(). */ { struct hubPublic *ret; AllocVar(ret); ret->hubUrl = cloneString(row[0]); ret->shortLabel = cloneString(row[1]); ret->longLabel = cloneString(row[2]); ret->registrationTime = cloneString(row[3]); ret->dbCount = sqlUnsigned(row[4]); ret->dbList = cloneString(row[5]); // if (row[6]) ret->descriptionUrl = cloneString(row[6]); // else // ret->descriptionUrl = cloneString(""); return ret; } static struct hubPublic *hubPublicLoadAll() { struct hubPublic *list = NULL; struct sqlConnection *conn = hConnectCentral(); // Build a query to find all public hub URL's struct dyString *query = sqlDyStringCreate("select * from %s", hubPublicTableName()); struct sqlResult *sr = sqlGetResult(conn, query->string); char **row; while ((row = sqlNextRow(sr)) != NULL) { struct hubPublic *el = hubPublicLoad(row); slAddHead(&list, el); } sqlFreeResult(&sr); hDisconnectCentral(&conn); publicHubSortCase(&list); int listSize = slCount(list); AllocArray(shortLabels, listSize); struct hubPublic *el = list; int i = 0; for ( ; el != NULL; el = el->next ) { shortLabels[i++] = el->shortLabel; ++publicHubCount; } return list; } #ifdef NOT static void startHtml(char *title) { printf ("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" \"http://www.w3.org/TR/html4/loose.dtd\">\n<html>\n<head><title>%s</title></head><body>\n", title); } static void endHtml() { printf ("</body></html>\n"); } #endif static boolean timeOutReached() { long nowTime = clock1000(); timedOut = FALSE; if ((nowTime - enteredMainTime) > (1000 * timeOutSeconds)) timedOut= TRUE; return timedOut; } static void trackSettings(struct trackDb *tdb) /* process the settingsHash for a track */ { hPrintf(" <ul>\n"); struct hashEl *hel; struct hashCookie hc = hashFirst(tdb->settingsHash); while ((hel = hashNext(&hc)) != NULL) { if (isEmpty((char *)hel->val)) hPrintf(" <li>%s : <empty></li>\n", hel->name); else hPrintf(" <li>%s : '%s'</li>\n", hel->name, (char *)hel->val); } hPrintf(" </ul>\n"); } static int bbiBriefMeasure(char *type, char *bigDataUrl, char *bigDataIndex, long *chromCount, long *itemCount, struct dyString *errors) /* check a bigDataUrl to find chrom count and item count */ { int retVal = 0; *chromCount = 0; *itemCount = 0; struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { if (startsWithWord("bigNarrowPeak", type) || startsWithWord("bigBed", type) || startsWithWord("bigGenePred", type) || startsWithWord("bigPsl", type) || startsWithWord("bigChain", type) || startsWithWord("bigMaf", type) || startsWithWord("bigBarChart", type) || startsWithWord("bigInteract", type)) { struct bbiFile *bbi = NULL; bbi = bigBedFileOpen(bigDataUrl); struct bbiChromInfo *chromList = bbiChromList(bbi); *chromCount = slCount(chromList); *itemCount = bigBedItemCount(bbi); bbiFileClose(&bbi); } else if (startsWithWord("bigWig", type)) { struct bbiFile *bwf = bigWigFileOpen(bigDataUrl); struct bbiChromInfo *chromList = bbiChromList(bwf); struct bbiSummaryElement sum = bbiTotalSummary(bwf); *chromCount = slCount(chromList); *itemCount = sum.validCount; bbiFileClose(&bwf); } else if (startsWithWord("vcfTabix", type)) { struct vcfFile *vcf = vcfTabixFileAndIndexMayOpen(bigDataUrl, bigDataIndex, NULL, 0, 0, 1, 1); if (vcf == NULL) { dyStringPrintf(errors, "Could not open %s and/or its tabix index (.tbi) file. See http://genome.ucsc.edu/goldenPath/help/vcf.html", bigDataUrl); retVal = 1; } else vcfFileFree(&vcf); } else if (startsWithWord("bam", type)) { bamFileAndIndexMustExist(bigDataUrl, bigDataIndex); } else if (startsWithWord("longTabix", type)) { struct bedTabixFile *btf = bedTabixFileMayOpen(bigDataUrl, NULL, 0, 0); if (btf == NULL) { dyStringPrintf(errors, "Couldn't open %s and/or its tabix index (.tbi) file.", bigDataUrl); retVal = 1; } else bedTabixFileClose(&btf); } #ifdef USE_HAL else if (startsWithWord("halSnake", type)) { char *errString; int handle = halOpenLOD(bigDataUrl, &errString); if (handle < 0) { dyStringPrintf(errors, "HAL open error: %s", errString); retVal = 1; } if (halClose(handle, &errString) < 0) { dyStringPrintf(errors, "HAL close error: %s", errString); retVal = 1; } } #endif else { dyStringPrintf(errors, "unrecognized type %s", type); retVal = 1; } } errCatchEnd(errCatch); if (errCatch->gotError) { retVal = 1; dyStringPrintf(errors, "%s", errCatch->message->string); } errCatchFree(&errCatch); return retVal; } /* static int bbiBriefMeasure() */ static void trackList(struct trackDb *tdb, struct trackHubGenome *genome) /* process the track list to show all tracks */ { if (tdb) { struct hash *countTracks = hashNew(0); hPrintf(" <ul>\n"); struct trackDb *track = tdb; for ( ; track; track = track->next ) { char *bigDataUrl = hashFindVal(track->settingsHash, "bigDataUrl"); char *compositeTrack = hashFindVal(track->settingsHash, "compositeTrack"); char *superTrack = hashFindVal(track->settingsHash, "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); long chromCount = 0; long itemCount = 0; struct dyString *errors = newDyString(1024); int retVal = bbiBriefMeasure(track->type, bigDataUrl, bigDataIndex, &chromCount, &itemCount, errors); if (retVal) { hPrintf(" <li>%s : %s : <font color='red'>ERROR: %s</font></li>\n", track->track, track->type, errors->string); } else { if (startsWithWord("bigBed", track->type)) hPrintf(" <li>%s : %s : %ld chroms : %ld item count</li>\n", track->track, track->type, chromCount, itemCount); else if (startsWithWord("bigWig", track->type)) hPrintf(" <li>%s : %s : %ld chroms : %ld bases covered</li>\n", track->track, track->type, chromCount, itemCount); else hPrintf(" <li>%s : %s : %ld chroms : %ld count</li>\n", track->track, track->type, chromCount, itemCount); } } else { if (compositeTrack) hPrintf(" <li>%s : %s : composite track container</li>\n", track->track, track->type); else if (superTrack) hPrintf(" <li>%s : %s : superTrack container</li>\n", track->track, track->type); else if (! depthSearch) hPrintf(" <li>%s : %s : %s</li>\n", track->track, track->type, bigDataUrl); else hPrintf(" <li>%s : %s</li>\n", track->track, track->type); } if (allTrackSettings) trackSettings(track); /* show all settings */ if (timeOutReached()) break; } /* for ( ; track; track = track->next ) */ hPrintf(" <li>%d different track types</li>\n", countTracks->elCount); if (countTracks->elCount) { 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"); } } /* static void trackList(struct trackDb *tdb) */ static void assemblySettings(struct trackHubGenome *genome) /* display all the assembly 'settingsHash' */ { 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); trackList(tdb, genome); } if (timeOutReached()) break; } hPrintf(" </ul>\n"); } static void genomeList (struct trackHub *hubTop) /* follow the pointers from the trackHub to trackHubGenome and around * in a circle from one to the other to find all hub resources */ { 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 ) { ++totalAssemblyCount; 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) 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 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); while ((hel = hashNext(&hc)) != NULL) { hPrintf(" <li>%d - %s - total</li>\n", ptToInt(hel->val), hel->name); } hPrintf(" </ul>\n"); } hPrintf("</ul>\n"); } static char *urlFromShortLabel(char *shortLabel) { char hubUrl[1024]; char query[1024]; struct sqlConnection *conn = hConnectCentral(); // Build a query to select the hubUrl for the given shortLabel sqlSafef(query, sizeof(query), "select hubUrl from %s where shortLabel='%s'", hubPublicTableName(), shortLabel); if (! sqlQuickQuery(conn, query, hubUrl, sizeof(hubUrl))) hubUrl[0] = 0; hDisconnectCentral(&conn); return cloneString(hubUrl); } -void jsonPublicHubs() +static void jsonPublicHubs() { struct hubPublic *el = publicHubList; hPrintf("{\"publicHubs\":["); for ( ; el != NULL; el = el->next ) { hubPublicJsonOutput(el, stdout); if (el->next) hPrintf(","); } hPrintf("]}\n"); } -void doMiddle(struct cart *theCart) +#define MAX_PATH_INFO 32 +static void apiList(char *words[MAX_PATH_INFO]) +/* 'list' function */ +{ +if (sameWord("publicHubs", words[1])) + jsonPublicHubs(); +else if (sameWord("genomes", words[1])) + { + char *hubUrl = cgiOptionalString("hubUrl"); + if (isNotEmpty(hubUrl)) + { + hPrintf("# list genomes for hubUrl: '%s'\n", hubUrl); + } + else + errAbort("# must supply hubUrl='http:...' some URL to a hub for /list/genomes\n"); + } +else + errAbort("# ERROR: do not recognize '%s' for 'list' function\n", words[1]); +} + +static struct hash *apiFunctionHash = NULL; + +static void setupFunctionHash() +{ +if (apiFunctionHash) + return; + +apiFunctionHash = hashNew(0); +hashAdd(apiFunctionHash, "list", &apiList); +} + +static void apiFunctionSwitch(char *pathInfo) +/* given a pathInfo string: /command/subCommand/etc... + * parse that and decide on which function to acll + */ +{ +/* 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) + errAbort("ERROR: no commands found in path info\n"); + +void (*apiFunction)(char **) = hashMustFindVal(apiFunctionHash, words[0]); + +(*apiFunction)(words); + +} + +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(); char *pathInfo = getenv("PATH_INFO"); -if ((NULL == pathInfo) || strlen(pathInfo) < 1) +if (isNotEmpty(pathInfo)) { - pathInfo = cloneString("noPathInfo"); - } -else - { - jsonOutput = TRUE; - } - -if (jsonOutput) - { -// startHtml("json output example"); -// hPrintf("<br><a href='http://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi'>return to hubApi</a><br><br>\n"); - jsonPublicHubs(); -// endHtml(); + /* skip the first leading slash to simplify chopByChar parsing */ + pathInfo += 1; + setupFunctionHash(); + apiFunctionSwitch(pathInfo); return; } + cartWebStart(cart, database, "access mechanism to hub data resources"); char *goOtherHub = cartUsualString(cart, "goOtherHub", defaultHub); char *otherHubUrl = cartUsualString(cart, "urlHub", defaultHub); char *goPublicHub = cartUsualString(cart, "goPublicHub", defaultHub); char *hubDropDown = cartUsualString(cart, "publicHubs", defaultHub); char *urlDropDown = urlFromShortLabel(hubDropDown); char *urlInput = urlDropDown; /* assume public hub */ if (sameWord("go", goOtherHub)) /* requested other hub URL */ urlInput = otherHubUrl; hPrintf("<h2>Example URLs to return json data structures:</h2>\n"); hPrintf("<ul>\n"); hPrintf("<li><a href='/cgi-bin/hubApi/list/publicHubs'>list public hubs</a> <em>/cgi-bin/hubApi/list/publicHubs</em></li>\n"); +hPrintf("<li><a href='/cgi-bin/hubApi/list/genomes?hubUrl=%s'>list genomes from specified hub</a> <em>/cgi-bin/hubApi/list/genomes?hubUrl='%s'</em></li>\n", urlInput, urlInput); hPrintf("</ul>\n"); long lastTime = clock1000(); struct trackHub *hub = trackHubOpen(urlInput, ""); if (measureTiming) { long thisTime = clock1000(); hPrintf("<em>hub open time: %ld millis</em><br>\n", thisTime - lastTime); } hPrintf("<h4>cart dump</h4>"); hPrintf("<pre>\n"); cartDump(cart); hPrintf("</pre>\n"); hPrintf("<form action='%s' name='hubApiUrl' id='hubApiUrl' method='GET'>\n\n", "../cgi-bin/hubApi"); hPrintf("<b>Select public hub: </b>"); #define JBUFSIZE 2048 char javascript[JBUFSIZE]; struct slPair *events = NULL; safef(javascript, sizeof(javascript), "this.lastIndex=this.selectedIndex;"); slPairAdd(&events, "focus", cloneString(javascript)); #define SMALLBUF 256 // char class[SMALLBUF]; // safef(class, sizeof(class), "viewDD normalText %s", "class"); cgiMakeDropListClassWithIdStyleAndJavascript("publicHubs", "publicHubs", shortLabels, publicHubCount, hubDropDown, NULL, "width: 400px", events); hWrites(" "); hButton("goPublicHub", "go"); hPrintf("<br>Or, enter a hub URL: "); hPrintf("<input type='text' name='urlHub' id='urlHub' size='60' value='%s'>\n", urlInput); hWrites(" "); hButton("goOtherHub", "go"); boolean depthSearch = cartUsualBoolean(cart, "depthSearch", FALSE); hPrintf("<br>\n "); hCheckBox("depthSearch", cartUsualBoolean(cart, "depthSearch", FALSE)); hPrintf(" perform full bbi file measurement : %s (will time out if taking longer than %ld seconds)<br>\n", depthSearch ? "TRUE" : "FALSE", timeOutSeconds); hPrintf("\n "); allTrackSettings = cartUsualBoolean(cart, "allTrackSettings", FALSE); hCheckBox("allTrackSettings", allTrackSettings); hPrintf(" display all track settings for each track : %s<br>\n", allTrackSettings ? "TRUE" : "FALSE"); hPrintf("<br>\n</form>\n"); hPrintf("<p>URL: %s - %s<br>\n", urlInput, sameWord("go",goPublicHub) ? "public hub" : "other hub"); hPrintf("name: %s<br>\n", hub->shortLabel); hPrintf("description: %s<br>\n", hub->longLabel); hPrintf("default db: '%s'<br>\n", isEmpty(hub->defaultDb) ? "(none available)" : hub->defaultDb); -printf("pathInfo:'%s'<br>\ndocRoot:'%s'<br>\n", pathInfo, docRoot); +printf("docRoot:'%s'<br>\n", docRoot); if (hub->genomeList) genomeList(hub); hPrintf("</p>\n"); if (timedOut) hPrintf("<h1>Reached time out %ld seconds</h1>", timeOutSeconds); if (measureTiming) hPrintf("<em>Overall total time: %ld millis</em><br>\n", clock1000() - enteredMainTime); cartWebEnd(); } /* void doMiddle(struct cart *theCart) */ /* Null terminated list of CGI Variables we don't want to save * permanently. */ char *excludeVars[] = {"Submit", "submit", NULL,}; int main(int argc, char *argv[]) /* Process command line. */ { enteredMainTime = clock1000(); cgiSpoof(&argc, argv); measureTiming = TRUE; verboseTimeInit(); trackCounter = hashNew(0); cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars); return 0; }