5194786c88bd4ab5e802eec79089897461389fe9
hiram
Fri Mar 22 14:52:22 2019 -0700
getting a little bit better refs #18869
diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c
index 410a905..76c7c93 100644
--- src/hg/hubApi/hubApi.c
+++ src/hg/hubApi/hubApi.c
@@ -1,1236 +1,1302 @@
/* hubApi - access mechanism to hub data resources. */
#include "dataApi.h"
/*
+------------------+------------------+------+-----+---------+-------+
| 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 | |
+------------------+------------------+------+-----+---------+-------+
*/
/* Global Variables for all modules */
int maxItemsOutput = 1000; /* can be set in URL maxItemsOutput=N */
+static int maxItemLimit = 1000000; /* maximum of 1,000,000 items returned */
/* Global only to this one source file */
-static boolean debug = FALSE; /* can be set in URL debug=1 */
+static boolean debug = TRUE; /* can be set in URL debug=1 */
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;
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 char *urlPrefix = ""; /* initalized to support self references */
static struct slName *supportedTypes = NULL;
/* will be initialized to a known supported set */
static void initSupportedTypes()
/* initalize the list of supported track types */
{
struct slName *el = newSlName("bed");
slAddHead(&supportedTypes, el);
el = newSlName("wig");
slAddHead(&supportedTypes, el);
el = newSlName("broadPeak");
slAddHead(&supportedTypes, el);
el = newSlName("narrowPeak");
slAddHead(&supportedTypes, el);
el = newSlName("bigBed");
slAddHead(&supportedTypes, el);
el = newSlName("bigWig");
slAddHead(&supportedTypes, el);
el = newSlName("bigNarrowPeak");
slAddHead(&supportedTypes, el);
el = newSlName("bigGenePred");
slAddHead(&supportedTypes, el);
// el = newSlName("bigPsl");
// slAddHead(&supportedTypes, el);
// el = newSlName("bigBarChart");
// slAddHead(&supportedTypes, el);
// el = newSlName("bigInteract");
// slAddHead(&supportedTypes, el);
// el = newSlName("bigMaf");
// slAddHead(&supportedTypes, el);
// el = newSlName("bigChain");
// slAddHead(&supportedTypes, el);
slNameSort(&supportedTypes);
}
static boolean isSupportedType(char *type)
/* is given type in the supportedTypes list ? */
{
boolean ret = FALSE;
if (startsWith("wigMaf", type)) /* not wigMaf at this time */
return ret;
struct slName *el;
for (el = supportedTypes; el; el = el->next)
{
if (startsWith(el->name, type))
{
ret = TRUE;
break;
}
}
return ret;
}
static int publicHubCmpCase(const void *va, const void *vb)
/* Compare two shortLabels, 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);
}
struct hubPublic *hubPublicDbLoadAll()
/* read entire hubPublic table in hgcentral and return resulting list */
{
char query[1024];
struct hubPublic *list = NULL;
struct sqlConnection *conn = hConnectCentral();
sqlSafef(query, sizeof(query), "select * from %s", hubPublicTableName());
struct sqlResult *sr = sqlGetResult(conn, query);
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;
}
static boolean timeOutReached()
/* see if the timeout has been reached to determine if an exit
* is appropriate at this time
*/
{
long nowTime = clock1000();
timedOut = FALSE;
if ((nowTime - enteredMainTime) > (1000 * timeOutSeconds))
timedOut= TRUE;
return timedOut;
}
#ifdef NOT
static void showCounts(struct hash *countTracks)
{
if (countTracks->elCount)
{
hPrintf("
\n");
struct hashEl *hel;
struct hashCookie hc = hashFirst(countTracks);
while ((hel = hashNext(&hc)) != NULL)
hPrintf(" - %d - %s
\n", ptToInt(hel->val), hel->name);
hPrintf("
\n");
}
}
#endif
static void hashCountTrack(struct trackDb *tdb, struct hash *countTracks)
/* this is counting up track types into the hash countTracks */
{
char *stripType = cloneString(tdb->type);
if (startsWith("chain ", tdb->type))
stripType = cloneString("chain");
else if (startsWith("netAlign ", tdb->type))
stripType = cloneString("netAlign");
else if (startsWith("genePred ", tdb->type))
stripType = cloneString("genePred");
else if (startsWith("bigWig ", tdb->type))
stripType = cloneString("bigWig");
else if (startsWith("wigMaf ", tdb->type))
stripType = cloneString("wigMaf");
else if (startsWith("wig ", tdb->type))
stripType = cloneString("wig");
else
stripType = cloneString(tdb->type);
// char *compositeTrack = trackDbLocalSetting(tdb, "compositeTrack");
boolean compositeContainer = tdbIsComposite(tdb);
boolean compositeView = tdbIsCompositeView(tdb);
// char *superTrack = trackDbLocalSetting(tdb, "superTrack");
boolean superChild = tdbIsSuperTrackChild(tdb);
if (compositeContainer)
hashIncInt(countTracks, "composite container");
else if (compositeView)
hashIncInt(countTracks, "composite view");
else if (superChild)
{
hashIncInt(countTracks, "superTrack child");
hashIncInt(countTracks, stripType);
hashIncInt(countTracks, "track count");
}
else if (isEmpty(tdb->type))
hashIncInt(countTracks, "no type specified");
else
{
hashIncInt(countTracks, stripType);
hashIncInt(countTracks, "track count");
}
freeMem(stripType);
// showCounts(countTracks);
}
-static void sampleUrl(struct trackHub *hub, char *db, struct trackDb *tdb, char *chrom, long long chromSize, char *errorString)
+static void sampleUrl(struct trackHub *hub, char *db, struct trackDb *tdb, char *chrom, unsigned chromSize, char *errorString)
/* print out a sample getData URL */
{
char errorPrint[2048];
errorPrint[0] = 0;
if (isNotEmpty(errorString))
{
safef(errorPrint, sizeof(errorPrint), " ERROR: %s", errorString);
}
unsigned start = chromSize / 4;
unsigned end = start + 10000;
if (end > chromSize)
end = chromSize;
char *genome = NULL;
if (hub)
genome = hub->genomeList->name;
if (db)
{
if (hub)
{
if (tdb->parent)
hPrintf("%s : %s subtrack of parent: %s (sample getData)%s\n", tdb->track, tdb->type, tdb->parent->track, urlPrefix, hub->url, genome, chrom, tdb->track, start, end, errorPrint);
else
hPrintf("%s : %s (sample getData)%s\n", tdb->track, tdb->type, urlPrefix, hub->url, genome, chrom, tdb->track, start, end, errorPrint);
}
else
{
if (tdb->parent)
hPrintf("%s : %s subtrack of parent: %s (sample getData)%s\n", tdb->track, tdb->type, tdb->parent->track, urlPrefix, db, chrom, tdb->track, start, end, errorPrint);
else
hPrintf("%s : %s (sample getData)%s\n", tdb->track, tdb->type, urlPrefix, db, chrom, tdb->track, start, end, errorPrint);
}
}
else if (hub)
{
if (tdb->parent)
hPrintf("%s : %s subtrack of parent: %s (sample getData)%s\n", tdb->track, tdb->type, tdb->parent->track, urlPrefix, hub->url, genome, chrom, tdb->track, start, end, errorPrint);
else
hPrintf("%s : %s (sample getData)%s\n", tdb->track, tdb->type, urlPrefix, hub->url, genome, chrom, tdb->track, start, end, errorPrint);
}
else
hPrintf("%s : %s not db hub track ?\n", tdb->track, tdb->type);
}
-static void showSubTracks(struct trackHub *hub, char *db, struct trackDb *tdb, struct hash *countTracks,
- char *chromName, long long chromSize, char *errorString)
-/* tdb has subtracks, show only subTracks, no details */
-{
-hPrintf(" \n");
-if (debug)
- hPrintf(" - subtracks for '%s' db: '%s'
\n", tdb->track, db);
-if (tdb->subtracks)
+static void hubSampleUrl(struct trackHub *hub, struct trackDb *tdb,
+ long chromCount, long itemCount, char *chromName, unsigned chromSize,
+ char *genome, char *errorString)
{
- struct trackDb *tdbEl = NULL;
- for (tdbEl = tdb->subtracks; tdbEl; tdbEl = tdbEl->next)
+unsigned start = chromSize / 4;
+unsigned end = start + 10000;
+if (end > chromSize)
+ end = chromSize;
+
+char errorPrint[2048];
+errorPrint[0] = 0;
+
+if (isNotEmpty(errorString))
{
- if (tdbIsCompositeView(tdbEl))
- hPrintf("- %s : %s : composite view of parent: %s
\n", tdbEl->track, tdbEl->type, tdbEl->parent->track);
- else
+ safef(errorPrint, sizeof(errorPrint), " : ERROR: %s", errorString);
+ }
+
+char countsMessage[512];
+countsMessage[0] = 0;
+if (chromCount > 0 || itemCount > 0)
{
- if (isSupportedType(tdbEl->type))
- sampleUrl(hub, db, tdbEl, chromName, chromSize, errorString);
+ if (startsWithWord("bigBed", tdb->type))
+ safef(countsMessage, sizeof(countsMessage), " : %ld chroms : %ld item count ", chromCount, itemCount);
+ else if (startsWithWord("bigWig", tdb->type))
+ safef(countsMessage, sizeof(countsMessage), " : %ld chroms : %ld bases covered ", chromCount, itemCount);
else
- hPrintf("- %s : %s : subtrack of parent: %s
\n", tdbEl->track, tdbEl->type, tdbEl->parent->track);
- }
- hashCountTrack(tdbEl, countTracks);
- if (tdbEl->subtracks)
- showSubTracks(hub, db, tdbEl, countTracks, chromName, chromSize, errorString);
- }
- }
-hPrintf("
\n");
+ safef(countsMessage, sizeof(countsMessage), " : %ld chroms : %ld count ", chromCount, itemCount);
}
-static void trackSettings(struct trackDb *tdb, struct hash *countTracks)
-/* process the settingsHash for a trackDb, recursive when subtracks */
-{
-hPrintf(" \n");
-// if (tdb->children) haven't yet seen a track with children ?
-// hPrintf(" - %s: has children
\n", tdb->track);
-// else
-// hPrintf(" - %s: NO children
\n", tdb->track);
-struct hashEl *hel;
-struct hashCookie hc = hashFirst(tdb->settingsHash);
-while ((hel = hashNext(&hc)) != NULL)
+if (isSupportedType(tdb->type))
{
- if (sameWord("track", hel->name))
- continue; // already output in header
- if (isEmpty((char *)hel->val))
- hPrintf(" - %s : <empty>
\n", hel->name);
+ char urlReference[2048];
+ safef(urlReference, sizeof(urlReference), "(sample getData)%s\n", urlPrefix, hub->url, genome, tdb->track, chromName, start, end, errorPrint);
+
+ if (startsWithWord("bigBed", tdb->type))
+ hPrintf(" - %s : %s%s%s
\n", tdb->track, tdb->type, countsMessage, urlReference);
+ else if (startsWithWord("bigWig", tdb->type))
+ hPrintf(" - %s : %s%s%s
\n", tdb->track, tdb->type, countsMessage, urlReference);
else
- hPrintf(" - %s : '%s'
\n", hel->name, (char *)hel->val);
+ hPrintf(" - %s : %s%s%s
\n", tdb->track, tdb->type, countsMessage, urlReference);
}
-if (tdb->subtracks)
- {
- struct trackDb *tdbEl = NULL;
- if (debug)
- hPrintf(" - has %d subtrack(s)
\n", slCount(tdb->subtracks));
- for (tdbEl = tdb->subtracks; tdbEl; tdbEl = tdbEl->next)
+else
{
- hPrintf("- subtrack: %s of parent: %s : type: '%s'
\n", tdbEl->track, tdbEl->parent->track, tdbEl->type);
- hashCountTrack(tdbEl, countTracks);
- trackSettings(tdbEl, countTracks);
- }
- }
-hPrintf("
\n");
+ if (startsWithWord("bigBed", tdb->type))
+ hPrintf(" %s : %s%s\n", tdb->track, tdb->type, countsMessage);
+ else if (startsWithWord("bigWig", tdb->type))
+ hPrintf(" %s : %s%s\n", tdb->track, tdb->type, countsMessage);
+ else
+ hPrintf(" %s : %s%s\n", tdb->track, tdb->type, countsMessage);
}
+} /* static void hubSampleUrl(struct trackHub *hub, struct trackDb *tdb,
+ * long chromCount, long itemCount, char *chromName, unsigned chromSize,
+ * char *genome)
+ */
static void bbiBiggestChrom(struct bbiChromInfo *chromList, char **chromName,
unsigned *chromSize)
/* find largest chromosome name and size in the chromList */
{
if (chromName && chromSize)
{
*chromSize = 0;
char *returnName = NULL;
struct bbiChromInfo *el;
for (el = chromList; el; el = el->next)
{
if (el->size > *chromSize)
{
*chromSize = el->size;
returnName = el->name;
}
}
if (chromSize > 0)
*chromName = cloneString(returnName);
}
}
static int bbiBriefMeasure(char *type, char *bigDataUrl, char *bigDataIndex, long *chromCount, long *itemCount, struct dyString *errors, char **chromName, unsigned *chromSize)
/* check a bigDataUrl to find chrom count and item count, return
* name of largest chrom and its size
*/
{
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);
bbiBiggestChrom(chromList, chromName, chromSize);
bbiChromInfoFreeList(&chromList);
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;
bbiBiggestChrom(chromList, chromName, chromSize);
bbiChromInfoFreeList(&chromList);
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 hubSampleUrl(struct trackHub *hub, struct trackDb *tdb,
- long chromCount, long itemCount, char *chromName, unsigned chromSize,
- char *genome, char *errorString)
+static void hubSubTracks(struct trackHub *hub, char *db, struct trackDb *tdb,
+ struct hash *countTracks, long chromCount, long itemCount,
+ char *chromName, unsigned chromSize, char *genome, char *errorString)
+/* tdb has subtracks, show only subTracks, no details */
{
-unsigned start = chromSize / 4;
-unsigned end = start + 10000;
-if (end > chromSize)
- end = chromSize;
-
-char errorPrint[2048];
-errorPrint[0] = 0;
-
-if (isNotEmpty(errorString))
+hPrintf(" \n");
+if (debug)
{
- safef(errorPrint, sizeof(errorPrint), " : ERROR: %s", errorString);
+ hPrintf(" - subtracks for '%s' db: '%s'
\n", tdb->track, db);
+ hPrintf(" - chrom: '%s' size: %u
\n", chromName, chromSize);
}
-
-if (isSupportedType(tdb->type))
+if (tdb->subtracks)
{
- if (startsWithWord("bigBed", tdb->type))
- hPrintf(" - %s : %s : %ld chroms : %ld item count (sample getData)%s
\n", tdb->track, tdb->type, chromCount, itemCount, urlPrefix, hub->url, genome, tdb->track, chromName, start, end, errorPrint);
- else if (startsWithWord("bigWig", tdb->type))
- hPrintf(" - %s : %s : %ld chroms : %ld bases covered (sample getData)%s
\n", tdb->track, tdb->type, chromCount, itemCount, urlPrefix, hub->url, genome, tdb->track, chromName, start, end, errorPrint);
+ struct trackDb *tdbEl = NULL;
+ for (tdbEl = tdb->subtracks; tdbEl; tdbEl = tdbEl->next)
+ {
+ boolean compositeContainer = tdbIsComposite(tdbEl);
+ boolean compositeView = tdbIsCompositeView(tdbEl);
+ if (! (compositeContainer || compositeView) )
+ {
+ if (chromSize < 1)
+ {
+ char *bigDataIndex = NULL;
+ char *relIdxUrl = trackDbSetting(tdbEl, "bigDataIndex");
+ if (relIdxUrl != NULL)
+ bigDataIndex = trackHubRelativeUrl(hub->genomeList->trackDbFile, relIdxUrl);
+ char *bigDataUrl = trackDbSetting(tdbEl, "bigDataUrl");
+ char *longName = NULL;
+ unsigned longSize = 0;
+ struct dyString *errors = newDyString(1024);
+ (void) bbiBriefMeasure(tdbEl->type, bigDataUrl, bigDataIndex, &chromCount, &itemCount, errors, &longName, &longSize);
+ chromSize = longSize;
+ chromName = longName;
+ }
+ }
+ if (tdbIsCompositeView(tdbEl))
+ hPrintf("- %s : %s : composite view of parent: %s
\n", tdbEl->track, tdbEl->type, tdbEl->parent->track);
else
- hPrintf(" - %s : %s : %ld chroms : %ld count <(sample getData)%s
\n", tdb->track, tdb->type, chromCount, itemCount, urlPrefix, hub->url, genome, tdb->track, chromName, start, end, errorPrint);
+ {
+ if (isSupportedType(tdbEl->type))
+ hubSampleUrl(hub, tdbEl, chromCount, itemCount, chromName, chromSize, genome, errorString);
+ else
+ hPrintf("- %s : %s : subtrack of parent: %s
\n", tdbEl->track, tdbEl->type, tdbEl->parent->track);
}
+ hashCountTrack(tdbEl, countTracks);
+ if (tdbEl->subtracks)
+ hubSubTracks(hub, db, tdbEl, countTracks, chromCount, itemCount, chromName, chromSize, genome, errorString);
+ }
+ }
+hPrintf("
\n");
+} /* hubSubTracks() */
+
+static void showSubTracks(struct trackHub *hub, char *db, struct trackDb *tdb, struct hash *countTracks,
+ char *chromName, unsigned chromSize, char *errorString)
+/* tdb has subtracks, show only subTracks, no details */
+{
+hPrintf(" \n");
+if (debug)
+ hPrintf(" - subtracks for '%s' db: '%s'
\n", tdb->track, db);
+if (tdb->subtracks)
+ {
+ struct trackDb *tdbEl = NULL;
+ for (tdbEl = tdb->subtracks; tdbEl; tdbEl = tdbEl->next)
+ {
+ if (tdbIsCompositeView(tdbEl))
+ hPrintf("- %s : %s : composite view of parent: %s
\n", tdbEl->track, tdbEl->type, tdbEl->parent->track);
else
{
- if (startsWithWord("bigBed", tdb->type))
- hPrintf(" - %s : %s : %ld chroms : %ld item count
\n", tdb->track, tdb->type, chromCount, itemCount);
- else if (startsWithWord("bigWig", tdb->type))
- hPrintf(" - %s : %s : %ld chroms : %ld bases covered
\n", tdb->track, tdb->type, chromCount, itemCount);
+ if (isSupportedType(tdbEl->type))
+ sampleUrl(hub, db, tdbEl, chromName, chromSize, errorString);
else
- hPrintf(" - %s : %s : %ld chroms : %ld count
\n", tdb->track, tdb->type, chromCount, itemCount);
+ hPrintf("- %s : %s : subtrack of parent: %s
\n", tdbEl->track, tdbEl->type, tdbEl->parent->track);
+ }
+ hashCountTrack(tdbEl, countTracks);
+ if (tdbEl->subtracks)
+ showSubTracks(hub, db, tdbEl, countTracks, chromName, chromSize, errorString);
+ }
+ }
+hPrintf("
\n");
+}
+
+static void trackSettings(struct trackDb *tdb, struct hash *countTracks)
+/* process the settingsHash for a trackDb, recursive when subtracks */
+{
+hPrintf(" \n");
+// if (tdb->children) haven't yet seen a track with children ?
+// hPrintf(" - %s: has children
\n", tdb->track);
+// else
+// hPrintf(" - %s: NO children
\n", tdb->track);
+struct hashEl *hel;
+struct hashCookie hc = hashFirst(tdb->settingsHash);
+while ((hel = hashNext(&hc)) != NULL)
+ {
+ if (sameWord("track", hel->name))
+ continue; // already output in header
+ if (isEmpty((char *)hel->val))
+ hPrintf(" - %s : <empty>
\n", hel->name);
+ else
+ hPrintf(" - %s : '%s'
\n", hel->name, (char *)hel->val);
+ }
+if (tdb->subtracks)
+ {
+ struct trackDb *tdbEl = NULL;
+ if (debug)
+ hPrintf(" - has %d subtrack(s)
\n", slCount(tdb->subtracks));
+ for (tdbEl = tdb->subtracks; tdbEl; tdbEl = tdbEl->next)
+ {
+ hPrintf("- subtrack: %s of parent: %s : type: '%s'
\n", tdbEl->track, tdbEl->parent->track, tdbEl->type);
+ hashCountTrack(tdbEl, countTracks);
+ trackSettings(tdbEl, countTracks);
+ }
+ }
+hPrintf("
\n");
}
-} /* static void hubSampleUrl(struct trackHub *hub, struct trackDb *tdb,
- * long chromCount, long itemCount, char *chromName, unsigned chromSize,
- * char *genome)
- */
static void hubCountOneTdb(struct trackHub *hub, char *db, struct trackDb *tdb,
char *bigDataIndex, struct hash *countTracks, char *chromName,
unsigned chromSize, char *genome)
{
char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl");
// char *compositeTrack = trackDbSetting(tdb, "compositeTrack");
boolean compositeContainer = tdbIsComposite(tdb);
boolean compositeView = tdbIsCompositeView(tdb);
// char *superTrack = trackDbSetting(tdb, "superTrack");
boolean superChild = tdbIsSuperTrackChild(tdb);
boolean depthSearch = cartUsualBoolean(cart, "depthSearch", FALSE);
hashCountTrack(tdb, countTracks);
-char *longName = NULL;
-unsigned longSize = 0;
long chromCount = 0;
long itemCount = 0;
struct dyString *errors = newDyString(1024);
+/* if given a chromSize, it belongs to a UCSC db and this is *not* an
+ * assembly hub, otherwise, look up a chrom and size in the bbi file
+ */
if (! (compositeContainer || compositeView) )
+ {
+ if (chromSize < 1 || depthSearch)
+ {
+ char *longName = NULL;
+ unsigned longSize = 0;
(void) bbiBriefMeasure(tdb->type, bigDataUrl, bigDataIndex, &chromCount, &itemCount, errors, &longName, &longSize);
+ chromSize = longSize;
+ chromName = longName;
+ }
+ }
if (depthSearch && bigDataUrl)
{
if (isSupportedType(tdb->type))
- {
- if (chromSize > 0)
hubSampleUrl(hub, tdb, chromCount, itemCount, chromName, chromSize, genome, errors->string);
- else
- hubSampleUrl(hub, tdb, chromCount, itemCount, longName, longSize, genome, errors->string);
- }
}
else
{
if (compositeContainer)
hPrintf(" %s : %s : composite track container has %d subtracks\n", tdb->track, tdb->type, slCount(tdb->subtracks));
else if (compositeView)
hPrintf(" %s : %s : composite view of parent: %s\n", tdb->track, tdb->type, tdb->parent->track);
else if (superChild)
hPrintf(" %s : %s : superTrack child of parent: %s (sample getData)\n", tdb->track, tdb->type, tdb->parent->track);
else if (! depthSearch && bigDataUrl)
{
if (isSupportedType(tdb->type))
{
- if (chromSize > 0)
hubSampleUrl(hub, tdb, chromCount, itemCount, chromName, chromSize, genome, errors->string);
- else
- hubSampleUrl(hub, tdb, chromCount, itemCount, longName, longSize, genome, errors->string);
}
- // hPrintf(" %s : %s : %s (maybe sample ?)\n", tdb->track, tdb->type, bigDataUrl);
}
else
{
if (isSupportedType(tdb->type))
{
- if (chromSize > 0)
hubSampleUrl(hub, tdb, chromCount, itemCount, chromName, chromSize, genome, errors->string);
- else
- hubSampleUrl(hub, tdb, chromCount, itemCount, longName, longSize, genome, errors->string);
}
else
hPrintf(" %s : %s (what is this)\n", tdb->track, tdb->type);
}
}
if (allTrackSettings)
{
hPrintf(" \n");
trackSettings(tdb, countTracks); /* show all settings */
hPrintf("
\n");
}
else if (tdb->subtracks)
{
- showSubTracks(hub, db, tdb, countTracks, chromName, chromSize, errors->string);
+ hubSubTracks(hub, db, tdb, countTracks, chromCount, itemCount, chromName, chromSize, genome, errors->string);
}
return;
} /* static void hubCountOneTdb(char *db, struct trackDb *tdb,
* char *bigDataIndex, struct hash *countTracks,
- * char *chromName, long long chromSize)
+ * char *chromName, unsigned chromSize)
*/
static void countOneTdb(char *db, struct trackDb *tdb,
struct hash *countTracks, char *chromName, unsigned chromSize,
char *errorString)
/* for this tdb in this db, count it up and provide a sample */
{
char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl");
// char *compositeTrack = trackDbSetting(tdb, "compositeTrack");
boolean compositeContainer = tdbIsComposite(tdb);
boolean compositeView = tdbIsCompositeView(tdb);
// char *superTrack = trackDbSetting(tdb, "superTrack");
boolean superChild = tdbIsSuperTrackChild(tdb);
boolean depthSearch = cartUsualBoolean(cart, "depthSearch", FALSE);
hashCountTrack(tdb, countTracks);
if (compositeContainer)
hPrintf(" %s : %s : composite track container has %d subtracks\n", tdb->track, tdb->type, slCount(tdb->subtracks));
else if (compositeView)
hPrintf(" %s : %s : composite view of parent: %s\n", tdb->track, tdb->type, tdb->parent->track);
else if (superChild)
hPrintf(" %s : %s : superTrack child of parent: %s\n", tdb->track, tdb->type, tdb->parent->track);
else if (! depthSearch && bigDataUrl)
hPrintf(" %s : %s : %s\n", tdb->track, tdb->type, bigDataUrl);
else
{
if (isSupportedType(tdb->type))
sampleUrl(NULL, db, tdb, chromName, chromSize, errorString);
else
hPrintf(" %s : %s\n", tdb->track, tdb->type);
}
if (allTrackSettings)
{
hPrintf(" \n");
trackSettings(tdb, countTracks); /* show all settings */
hPrintf("
\n");
}
else if (tdb->subtracks)
{
showSubTracks(NULL, db, tdb, countTracks, chromName, chromSize, NULL);
}
return;
} /* static void countOneTdb(char *db, struct trackDb *tdb,
* struct hash *countTracks, char *chromName,
* unsigned chromSize)
*/
static unsigned largestChrom(char *db, char **nameReturn)
/* return the length and get the chrom name for the largest chrom
* from chromInfo table. For use is sample getData URLs
*/
{
char query[1024];
struct sqlConnection *conn = hAllocConn(db);
sqlSafef(query, sizeof(query), "select chrom,size from chromInfo order by size desc limit 1");
struct sqlResult *sr = sqlGetResult(conn, query);
char **row = sqlNextRow(sr);
unsigned length = 0;
if (row)
{
*nameReturn = cloneString(row[0]);
length = sqlLongLong(row[1]);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
return length;
}
static void hubTrackList(struct trackHub *hub, struct trackDb *topTrackDb, struct trackHubGenome *genome)
/* process the track list in a hub to show all tracks */
{
hPrintf(" \n");
if (topTrackDb)
{
struct hash *countTracks = hashNew(0);
struct trackDb *tdb = NULL;
for ( tdb = topTrackDb; tdb; tdb = tdb->next )
{
char *bigDataIndex = NULL;
char *relIdxUrl = trackDbSetting(topTrackDb, "bigDataIndex");
if (relIdxUrl != NULL)
bigDataIndex = trackHubRelativeUrl(genome->trackDbFile, relIdxUrl);
char *defaultGenome = NULL;
if (isNotEmpty(genome->name))
defaultGenome = genome->name;
char *chromName = NULL;
unsigned chromSize = 0;
if (isEmpty(genome->twoBitPath))
chromSize = largestChrom(defaultGenome, &chromName);
hubCountOneTdb(hub, defaultGenome, tdb, bigDataIndex, countTracks, chromName, chromSize, defaultGenome);
if (timeOutReached())
break;
} /* for ( tdb = topTrackDb; tdb; tdb = tdb->next ) */
hPrintf(" - %d different track types
\n",countTracks->elCount - 1);
/* add this single genome count to the overall multi-genome counts */
if (countTracks->elCount)
{
hPrintf(" \n");
struct hashEl *hel, *helList = hashElListHash(countTracks);
slSort(&helList, hashElCmpIntValDesc);
for (hel = helList; hel; hel = hel->next)
{
if (sameOk("track count", hel->name))
continue;
int prevCount = ptToInt(hashFindVal(trackCounter, hel->name));
if (differentStringNullOk("track count", hel->name))
totalTracks += ptToInt(hel->val);
hashReplace(trackCounter, hel->name, intToPt(prevCount + ptToInt(hel->val)));
if (isSupportedType(hel->name))
hPrintf(" - %d - %s - supported
\n", ptToInt(hel->val), hel->name);
else
hPrintf(" - %d - %s
\n", ptToInt(hel->val), hel->name);
}
hPrintf("
\n");
}
}
else
hPrintf(" - no trackTopDb ?
\n");
hPrintf("
\n");
} /* static struct trackDb *hubTrackList() */
static void hubAssemblySettings(struct trackHub *hub, struct trackHubGenome *genome)
/* display all the assembly 'settingsHash' */
{
struct trackDb *tdb = obtainTdb(genome, NULL);
hPrintf(" \n");
struct hashEl *hel;
struct hashCookie hc = hashFirst(genome->settingsHash);
while ((hel = hashNext(&hc)) != NULL)
{
hPrintf(" - %s : %s
\n", hel->name, (char *)hel->val);
if (sameWord("trackDb", hel->name)) /* examine the trackDb structure */
{
hubTrackList(hub, tdb, genome);
}
if (timeOutReached())
break;
}
hPrintf("
\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("genome sequences (and tracks) present in this track hub
\n");
if (NULL == genome)
{
hPrintf("odd error, can not find a gnomeList ? at url: '%s'
\n", hubTop->url);
return;
}
hPrintf("\n");
long lastTime = clock1000();
for ( ; genome; genome = genome->next )
{
++totalAssemblyCount;
-#ifdef NOT
- char *twoBitPath; /* URL to twoBit. If not null, this is an assmebly hub*/
- struct twoBitFile *tbf; /* open handle to two bit file */
- char *groups; /* URL to group.txt file */
- char *defaultPos; /* default position */
- char *organism; /* organism name, like Human */
- char *description; /* description, also called freeze name */
- struct trackHub *trackHub; /* associated track hub */
-#endif
if (isNotEmpty(genome->twoBitPath))
{
hPrintf("- assembly hub twoBitFile: %s
\n", genome->twoBitPath);
}
if (genome->organism)
{
hPrintf("- %s - %s - %s
\n", genome->organism, genome->name, genome->description);
}
else
{ /* can there be a description when organism is empty ? */
hPrintf("- name: %s
\n", genome->name);
}
hubAssemblySettings(hubTop, genome);
- if (measureTiming)
+ if (measureTiming || debug)
{
long thisTime = clock1000();
hPrintf("- processing time %s: %ld millis
\n", genome->name, thisTime - lastTime);
}
if (timeOutReached())
break;
}
if (trackCounter->elCount)
{
hPrintf(" - total genome assembly count: %ld
\n", totalAssemblyCount);
hPrintf(" - %ld total tracks counted, %d different track types:
\n", totalTracks, trackCounter->elCount);
hPrintf(" \n");
struct hashEl *hel, *helList = hashElListHash(trackCounter);
slSort(&helList, hashElCmpIntValDesc);
for (hel = helList; hel; hel = hel->next)
{
hPrintf(" - %d - %s - total
\n", ptToInt(hel->val), hel->name);
}
hPrintf("
\n");
}
hPrintf("
\n");
} /* static void genomeList (hubTop) */
static char *urlFromShortLabel(char *shortLabel)
/* this is not a fair way to get the URL since shortLabel's are not
* necessarily unique. This is temporary. TBD: need to always use URL
* and then get the 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);
}
static int dbDbCmpName(const void *va, const void *vb)
/* Compare two dbDb elements: name, ignore case. */
{
const struct dbDb *a = *((struct dbDb **)va);
const struct dbDb *b = *((struct dbDb **)vb);
return strcasecmp(a->name, b->name);
}
struct dbDb *ucscDbDb()
/* return the dbDb table as an slList */
{
char query[1024];
struct sqlConnection *conn = hConnectCentral();
sqlSafef(query, sizeof(query), "select * from dbDb");
struct dbDb *dbList = NULL, *el = NULL;
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
el = dbDbLoad(row);
slAddHead(&dbList, el);
}
sqlFreeResult(&sr);
hDisconnectCentral(&conn);
slSort(&dbList, dbDbCmpName);
return dbList;
}
static struct hash *apiFunctionHash = NULL;
static void setupFunctionHash()
/* initialize the apiFunctionHash */
{
if (apiFunctionHash)
return; /* already done */
apiFunctionHash = hashNew(0);
hashAdd(apiFunctionHash, "list", &apiList);
hashAdd(apiFunctionHash, "getData", &apiGetData);
}
static struct hashEl *parsePathInfo(char *pathInfo, char *words[MAX_PATH_INFO])
/* given a pathInfo string: /command/subCommand/etc...
* parse that and return a function pointer and the parsed words
* Returns NULL if not recognized
*/
{
char *tmp = cloneString(pathInfo);
/* skip the first leading slash to simplify chopByChar parsing */
tmp += 1;
int wordCount = chopByChar(tmp, '/', words, MAX_PATH_INFO);
if (wordCount < 1)
return NULL;
struct hashEl *hel = hashLookup(apiFunctionHash, words[0]);
return hel;
}
static void tracksForUcscDb(char *db)
/* scan the specified database for all tracks */
{
struct hash *countTracks = hashNew(0);
char *chromName = NULL;
unsigned chromSize = largestChrom(db, &chromName);
hPrintf("Tracks in UCSC genome: '%s', longest chrom: %s:%u
\n", db, chromName, chromSize);
struct trackDb *tdbList = obtainTdb(NULL, db);
struct trackDb *tdb;
hPrintf("\n");
hPrintf("- %s:%u
\n", chromName, chromSize);
for (tdb = tdbList; tdb != NULL; tdb = tdb->next )
{
countOneTdb(db, tdb, countTracks, chromName, chromSize, NULL);
if (timeOutReached())
break;
}
int trackCount = ptToInt(hashFindVal(countTracks, "track count"));
/* elCount - 1 since the 'track count' element isn't a track */
hPrintf(" - %d total tracks counted, %d different track types
\n", trackCount, countTracks->elCount - 1);
if (countTracks->elCount)
{
hPrintf(" \n");
struct hashEl *hel, *helList = hashElListHash(countTracks);
slSort(&helList, hashElCmpIntValDesc);
for (hel = helList; hel; hel = hel->next)
{
if (sameOk("track count", hel->name))
continue;
if (isSupportedType(hel->name))
hPrintf(" - %d - %s - supported
\n", ptToInt(hel->val), hel->name);
else
hPrintf(" - %d - %s
\n", ptToInt(hel->val), hel->name);
}
hPrintf("
\n");
}
hPrintf("
\n");
hPrintf("\n");
} // static void tracksForUcscDb(char * db)
static void introductionText()
/* output explanation text */
{
char *scriptUri = getenv("SCRIPT_URI");
hPrintf("JSON data API interface to U.C. Santa Cruz genome browser data
\n");
hPrintf("Data access URL: %s
\n", scriptUri);
hPrintf("Endpoint functions:
\n");
hPrintf("\n");
hPrintf("- /list/...
\n");
hPrintf("\n");
hPrintf("- /list/publicHubs - list public hubs
\n");
hPrintf("- /list/ucscGenomes - list UCSC database genomes
\n");
hPrintf("- /list/hubGenomes - list genomes from specified hub
\n");
hPrintf("- /list/tracks - list data tracks available in specified hub or database genome
\n");
hPrintf("- /list/chromosomes - list chromosomes from specified data track in specified hub or database genome
\n");
hPrintf("
\n");
hPrintf("- /getData/...
\n");
hPrintf("\n");
hPrintf("- /getData/sequence - return sequence from specified hub or database genome
\n");
hPrintf("- /getData/track - return data from specified track in hub or database genome
\n");
hPrintf("
\n");
hPrintf("
\n");
hPrintf("Parameters to endpoint functions:
\n");
hPrintf("\n");
hPrintf("- hubUrl=<url> - specify track hub or assembly hub URL
\n");
hPrintf("- genome=<name> - specify genome assemby in track or assembly hub
\n");
hPrintf("- db=<ucscDb> - specify database (aka genome assembly) in UCSC genome browser
\n");
hPrintf("- track=<trackName> - specify data track in hub or UCSC database genome assembly
\n");
hPrintf("- chrom=<chrN> - specify chromosome name for sequence or track data
\n");
hPrintf("- start=<123> - specify start coordinate (0 relative) for data from track or sequence retrieval
\n");
hPrintf("- end=<456> - specify end coordinate (1 relative) for data from track or sequence retrieval
\n");
hPrintf("- (see also: UCSC browser coordinate counting systems)
");
hPrintf("
\n");
hPrintf("Supported track types, at this time, for getData functions:
\n");
hPrintf("\n");
static struct slName *el;
for (el = supportedTypes; el; el = el->next)
{
hPrintf("- %s
\n", el->name);
}
hPrintf("
\n");
}
static void initUrlPrefix()
/* set up urlPrefix for self referenes */
{
char *httpHost = getenv("HTTP_HOST");
+if (isEmpty(httpHost))
+ urlPrefix = "";
+else
+ {
if (! startsWith("hgwdev-api", httpHost))
{
if (startsWith("hgwdev",httpHost) || startsWith("genome-test", httpHost))
{
urlPrefix = "../cgi-bin/hubApi";
}
}
}
+}
static void showExamples(char *url, struct trackHubGenome *hubGenome, char *ucscDb)
{
hPrintf("Example URLs to return json data structures:
\n");
hPrintf("listing functions
\n");
hPrintf("\n");
hPrintf("- list public hubs %s/list/publicHubs
\n", urlPrefix, urlPrefix);
hPrintf("- list database genomes %s/list/ucscGenomes
\n", urlPrefix, urlPrefix);
hPrintf("- list genomes from specified hub %s/list/hubGenomes?hubUrl=%s
\n", urlPrefix, url, urlPrefix, url);
hPrintf("- list tracks from specified hub and genome %s/list/tracks?hubUrl=%s&genome=%s
\n", urlPrefix, url, hubGenome->name, urlPrefix, url, hubGenome->name);
hPrintf("- list tracks from specified UCSC database %s/list/tracks?db=%s
\n", urlPrefix, ucscDb, urlPrefix, ucscDb);
hPrintf("- list chromosomes from specified UCSC database %s/list/chromosomes?db=%s
\n", urlPrefix, ucscDb, urlPrefix, ucscDb);
hPrintf("- list chromosomes from specified track from UCSC databaset %s/list/chromosomes?db=%s&track=gold
\n", urlPrefix, ucscDb, urlPrefix, ucscDb);
hPrintf("
\n");
hPrintf("getData functions
\n");
hPrintf("\n");
hPrintf("- get sequence from specified database and chromosome %s/getData/sequence?db=%s&chrom=chrM
\n", urlPrefix, ucscDb, urlPrefix, ucscDb);
hPrintf("- get sequence from specified database, chromosome with start,end coordinates %s/getData/sequence?db=%s&chrom=chrM&start=0&end=128
\n", urlPrefix, ucscDb, urlPrefix, ucscDb);
hPrintf("- get entire track data from specified database and track name (gold == Assembly) %s/getData/track?db=%s&track=gold
\n", urlPrefix, ucscDb, urlPrefix, ucscDb);
hPrintf("- get track data from specified database, chromosome and track name (gold == Assembly) %s/getData/track?db=%s&chrom=chrM&track=gold
\n", urlPrefix, ucscDb, urlPrefix, ucscDb);
hPrintf("- get track data from specified database, chromosome, track name, start and end coordinates %s/getData/track?db=%s&chrom=chrI&track=gold&start=107680&end=186148
\n", urlPrefix, defaultDb, urlPrefix, defaultDb);
hPrintf("- get entire track data from specified hub and track name %s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt&genome=hg19&track=ultraConserved
\n", urlPrefix, urlPrefix);
hPrintf("- get track data from specified hub, chromosome and track name (full chromosome) %s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrCp&track=assembly_
\n", urlPrefix, urlPrefix);
hPrintf("- get track data from specified hub, chromosome, track name, start and end coordinates %s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chr1&track=assembly_&start=0&end=14309681
\n", urlPrefix, urlPrefix);
hPrintf("- get all track data from specified hub and track name %s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&track=gc5Base
\n", urlPrefix, urlPrefix);
hPrintf("- get track data from specified hub, chromosome, track name, start and end coordinates %s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrMt&track=gc5Base&start=143600&end=143685
\n", urlPrefix, urlPrefix);
hPrintf("- get bigWig track data from specified database, chromosome, track name, start and end coordinates %s/getData/track?db=%s&chrom=chrI&track=gc5BaseBw&start=107680&end=186148
\n", urlPrefix, defaultDb, urlPrefix, defaultDb);
hPrintf("- get bigBed track data from specified database, chromosome, track name, start and end coordinates %s/getData/track?db=%s&chrom=chrII&track=ncbiRefSeqOther&start=14334626&end=14979625
\n", urlPrefix, defaultDb, urlPrefix, defaultDb);
hPrintf("- get narrowPeak track data from specified database, chromosome, track name, start and end coordinates %s/getData/track?db=%s&chrom=chr1&track=wgEncodeAwgDnaseDuke8988tUniPk&start=14334626&end=14979625
\n", urlPrefix, "hg19", urlPrefix, "hg19");
hPrintf("- get broadPeak track data from specified database, chromosome, track name, start and end coordinates %s/getData/track?db=%s&chrom=chr1&track=wgEncodeBroadHistoneOsteoP300kat3bPk&start=14334626&end=14979625
\n", urlPrefix, "hg19", urlPrefix, "hg19");
hPrintf("
\n");
hPrintf("Example URLs to generate errors:
\n");
hPrintf("\n");
hPrintf("- get track data from specified hub, chromosome, track name, start and end coordinates %s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrI&track=assembly_&start=0&end=14309681
\n", urlPrefix, urlPrefix);
hPrintf("
\n");
} /* static void showExamples() */
static void showCartDump()
/* for information purposes only during development, will become obsolete */
{
hPrintf("cart dump
");
hPrintf("\n");
cartDump(cart);
hPrintf("
\n");
}
static void doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
cart = theCart;
measureTiming = hPrintStatus() && isNotEmpty(cartOptionalString(cart, "measureTiming"));
measureTiming = TRUE;
char *database = NULL;
char *genome = NULL;
cgiVarSet("ignoreCookie", "1");
getDbAndGenome(cart, &database, &genome, oldVars);
initGenbankTableNames(database);
initSupportedTypes();
initUrlPrefix();
/* global variable for all workers to honor this limit */
maxItemsOutput = cartUsualInt(cart, "maxItemsOutput", maxItemsOutput);
+if (maxItemsOutput > maxItemLimit) /* safety check */
+ maxItemsOutput = maxItemLimit;
+if (maxItemsOutput < 1) /* safety check */
+ maxItemsOutput = 1;
debug = cartUsualBoolean(cart, "debug", debug);
int timeout = cartUsualInt(cart, "udcTimeout", 300);
if (udcCacheTimeout() < timeout)
udcSetCacheTimeout(timeout);
knetUdcInstall();
char *pathInfo = getenv("PATH_INFO");
/* nothing on incoming path, then display the WEB page instead */
if (sameOk("/",pathInfo))
pathInfo = NULL;
boolean commandError = FALSE;
/*expect no more than MAX_PATH_INFO number of words*/
char *words[MAX_PATH_INFO];
if (isNotEmpty(pathInfo))
{
setupFunctionHash();
struct hashEl *hel = parsePathInfo(pathInfo, words);
/* verify valid API command */
if (hel) /* have valid command */
{
hPrintDisable();
puts("Content-Type:application/json");
puts("\n");
void (*apiFunction)(char **) = hel->val;
(*apiFunction)(words);
return;
}
else
commandError = TRUE;
}
puts("Content-Type:text/html");
puts("\n");
(void) hubPublicDbLoadAll();
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;
cartWebStart(cart, database, "UCSC JSON API interface");
if (debug)
{
hPrintf("\n");
char *envVar = getenv("BROWSER_HOST");
hPrintf("- BROWSER_HOST:%s
\n", envVar);
envVar = getenv("CONTEXT_DOCUMENT_ROOT");
hPrintf("- CONTEXT_DOCUMENT_ROOT:%s
\n", envVar);
envVar = getenv("CONTEXT_PREFIX");
hPrintf("- CONTEXT_PREFIX:%s
\n", envVar);
envVar = getenv("DOCUMENT_ROOT");
hPrintf("- DOCUMENT_ROOT:%s
\n", envVar);
envVar = getenv("HTTP_HOST");
hPrintf("- HTTP_HOST:%s
\n", envVar);
envVar = getenv("REQUEST_URI");
hPrintf("- REQUEST_URI:%s
\n", envVar);
envVar = getenv("SCRIPT_FILENAME");
hPrintf("- SCRIPT_FILENAME:%s
\n", envVar);
envVar = getenv("SCRIPT_NAME");
hPrintf("- SCRIPT_NAME:%s
\n", envVar);
envVar = getenv("SCRIPT_URI");
hPrintf("- SCRIPT_URI:%s
\n", envVar);
envVar = getenv("SCRIPT_URL");
hPrintf("- SCRIPT_URL:%s
\n", envVar);
envVar = getenv("SERVER_NAME");
hPrintf("- SERVER_NAME:%s
\n", envVar);
envVar = getenv("PATH_INFO");
if (isNotEmpty(envVar))
hPrintf("- PATH_INFO:'%s'
\n", envVar);
else
hPrintf("- PATH_INFO:<empty>
\n");
hPrintf("
\n");
}
char *goOtherHub = cartUsualString(cart, "goOtherHub", defaultHub);
char *goUcscDb = cartUsualString(cart, "goUcscDb", "");
char *otherHubUrl = cartUsualString(cart, "urlHub", defaultHub);
char *goPublicHub = cartUsualString(cart, "goPublicHub", defaultHub);
char *hubDropDown = cartUsualString(cart, "publicHubs", defaultHub);
char *urlDropDown = urlFromShortLabel(hubDropDown);
char *ucscDb = cartUsualString(cart, "ucscGenomes", defaultDb);
char *urlInput = urlDropDown; /* assume public hub */
if (sameWord("go", goOtherHub)) /* requested other hub URL */
urlInput = otherHubUrl;
else if (isEmpty(otherHubUrl))
otherHubUrl = urlInput;
if (commandError)
{
hPrintf("ERROR: no such command: '%s/%s' for endpoint '%s'
", words[0], words[1], pathInfo);
}
long lastTime = clock1000();
struct trackHub *hub = errCatchTrackHubOpen(urlInput);
-if (measureTiming)
+if (measureTiming || debug)
{
long thisTime = clock1000();
if (debug)
hPrintf("hub open time: %ld millis
\n", thisTime - lastTime);
}
// hPrintf("ucscDb: '%s'\n", ucscDb);
struct trackHubGenome *hubGenome = hub->genomeList;
introductionText();
showExamples(urlInput, hubGenome, ucscDb);
if (debug)
showCartDump();
hPrintf("Explore hub or database assemblies and tracks
\n");
// hPrintf("
\n");
hPrintf("\n");
if (sameWord("go", goUcscDb)) /* requested UCSC db track list */
{
tracksForUcscDb(ucscDb);
}
else
{
hPrintf("
Examine %s at: %s
\n", sameWord("go",goPublicHub) ? "public hub" : "other hub", urlInput);
hPrintf("\n");
hPrintf("- %s
\n", hub->shortLabel);
hPrintf("- %s
\n", hub->longLabel);
if (isNotEmpty(hub->defaultDb))
hPrintf("- %s - default database
\n", hub->defaultDb);
hPrintf("
\n");
genomeList(hub);
}
if (timedOut)
hPrintf("Reached time out %ld seconds
", timeOutSeconds);
-if (measureTiming)
+if (measureTiming || debug)
hPrintf("Overall total time: %ld millis
\n", clock1000() - enteredMainTime);
hPrintf("\n");
cartWebEnd();
} /* void doMiddle(struct cart *theCart) */
/* Null terminated list of CGI Variables we don't want to save
* permanently. */
static char *excludeVars[] = {"Submit", "submit", "goOtherHub", "goPublicHub", "goUcscDb", "ucscGenomes", "publicHubs", NULL,};
int main(int argc, char *argv[])
/* Process command line. */
{
enteredMainTime = clock1000();
cgiSpoof(&argc, argv);
measureTiming = TRUE;
verboseTimeInit();
trackCounter = hashNew(0);
cartEmptyShellNoContent(doMiddle, hUserCookie(), excludeVars, oldVars);
return 0;
}