char *identifierWhereClause(char *idField, struct hash *idHash)
/* If the number of pasted IDs is reasonably low, return a where-clause component for the IDs. */
{
if (idHash == NULL || idField == NULL)
return NULL;
int numIds = hashNumEntries(idHash);
int maxIdsInWhere = cartUsualInt(cart, "hgt_maxIdsInWhere", DEFAULT_MAX_IDS_IN_WHERE);
if (numIds > 0 && numIds <= maxIdsInWhere)
{
struct dyString *dy = dyStringNew(16 * numIds);
dyStringPrintf(dy, "%s in (", idField);
struct hashCookie hc = hashFirst(idHash);
boolean first = TRUE;
char *id;
while ((id = hashNextName(&hc)) != NULL)
{
if (first)
first = FALSE;
else
dyStringAppend(dy, ", ");
dyStringPrintf(dy, "'%s'", id);
}
dyStringAppend(dy, ")");
return dyStringCannibalize(&dy);
}
return NULL;
}
static void addExtras(char *extraFile, struct trackHubCheckOptions *checkOptions)
/* Add settings from extra file (e.g. for specific hub display site) */
{
verbose(2, "Accepting extra settings in '%s'\n", extraFile);
checkOptions->extraFile = extraFile;
checkOptions->extra = hashNew(0);
struct lineFile *lf = NULL;
if (startsWith("http", extraFile))
{
struct dyString *ds = netSlurpUrl(extraFile);
char *s = dyStringCannibalize(&ds);
lf = lineFileOnString(extraFile, TRUE, s);
}
else
{
lf = lineFileOpen(extraFile, TRUE);
}
char *line;
while (lineFileNextReal(lf, &line))
{
hashAdd(checkOptions->extra, line, NULL);
}
lineFileClose(&lf);
verbose(3, "Found %d extra settings\n", hashNumEntries(checkOptions->extra));
}
struct hash *raReadThreeLevels(char *fileName, char *lowKeyField, char *middleKeyField)
/* Return 3 level hash that contains all ra records in file keyed by lowKeyField, which must exist.
* and broken into sub hashes based upon middleKeyField that must exist.
* Example raReadThreeLevels("cv.ra","term","type"):
* returns hash of 'type' hashes of 'term' hashes of every stanza in cv.ra */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
struct hash *topHash = hashNew(0); // Not expecting that many types
struct hash *bottomHash;
while ((bottomHash = raNextRecord(lf)) != NULL)
{
char *lowKey = hashFindVal(bottomHash, lowKeyField);
if (lowKey == NULL)
errAbort("Couldn't find key field %s line %d of %s",
lowKeyField, lf->lineIx, lf->fileName);
char *middleKey = hashFindVal(bottomHash, middleKeyField);
if (middleKey == NULL)
errAbort("Couldn't find middle key field %s line %d of %s",
middleKeyField, lf->lineIx, lf->fileName);
struct hash *middleHash = hashFindVal(topHash, middleKey);
if (middleHash == NULL)
{
middleHash = hashNew(16); // could be quite a few terms per type.
hashAdd(topHash, middleKey, middleHash);
}
hashAdd(middleHash, lowKey, bottomHash);
}
lineFileClose(&lf);
if (hashNumEntries(topHash) == 0)
hashFree(&topHash);
return topHash;
}
struct hash *raReadWithFilter(char *fileName, char *keyField,char *filterKey,char *filterValue)
/* Return hash that contains all filtered ra records in file keyed by given field, which must exist.
* The values of the hash are themselves hashes. The filter is a key/value pair that must exist.
* Example raReadWithFilter(file,"term","type","antibody"): returns hash of hashes of every term with type=antibody */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
struct hash *bigHash = hashNew(14);
struct hash *hash;
while ((hash = raNextRecord(lf)) != NULL)
{
char *key = hashFindVal(hash, keyField);
if (key == NULL)
errAbort("Couldn't find key field %s line %d of %s",
keyField, lf->lineIx, lf->fileName);
if (filterKey != NULL)
{
char *filter = hashFindVal(hash, filterKey);
if (filter == NULL)
{
hashFree(&hash);
continue;
}
if (filterValue != NULL && differentString(filterValue,filter))
{
hashFree(&hash);
continue;
}
}
hashAdd(bigHash, key, hash);
}
lineFileClose(&lf);
if (hashNumEntries(bigHash) == 0)
hashFree(&bigHash);
return bigHash;
}
int hubCheckTrack(struct trackHub *hub, struct trackHubGenome *genome, struct trackDb *tdb,
struct trackHubCheckOptions *options, struct dyString *errors)
/* Check track settings and optionally, files */
{
int retVal = 0;
if (options->checkSettings && options->settings)
{
//verbose(3, "Found %d settings to check to spec\n", slCount(settings));
verbose(3, "Checking track: %s\n", tdb->shortLabel);
verbose(3, "Found %d settings to check to spec\n", hashNumEntries(tdb->settingsHash));
struct hashEl *hel;
struct hashCookie cookie = hashFirst(tdb->settingsHash);
while ((hel = hashNext(&cookie)) != NULL)
retVal |= hubCheckTrackSetting(hub, tdb, hel->name, options, errors);
/* TODO: ? also need to check settings not in this list (other tdb fields) */
}
if (options->printMeta)
{
struct slPair *metaPairs = trackDbMetaPairs(tdb);
if (metaPairs != NULL)
{
printf("%s\n", trackHubSkipHubName(tdb->track));
struct slPair *pair;
for(pair = metaPairs; pair; pair = pair->next)
{
printf("\t%s : %s\n", pair->name, (char *)pair->val);
}
printf("\n");
}
slPairFreeValsAndList(&metaPairs);
}
if (!options->checkFiles)
return retVal;
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
hubCheckBigDataUrl(hub, genome, tdb);
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
retVal = 1;
dyStringPrintf(errors, "%s", errCatch->message->string);
}
errCatchFree(&errCatch);
return retVal;
}
static void jsonDyStringPrintRecurse(struct dyString *dy, struct jsonElement *ele, int indentLevel)
{
if (indentLevel >= -1) // Note that < -1 will result in no indenting
indentLevel++;
char *tab = "\t";
char *nl = "\n";
if (indentLevel < 0)
{
tab = "";
nl = "";
}
char *indentBuf = makeIndentBuf(indentLevel);
switch (ele->type)
{
case jsonObject:
{
dyStringPrintf(dy,"{%s",nl);
if(hashNumEntries(ele->val.jeHash))
{
struct hashEl *el, *list = hashElListHash(ele->val.jeHash);
slSort(&list, hashElCmp);
for (el = list; el != NULL; el = el->next)
{
struct jsonElement *val = el->val;
dyStringPrintf(dy,"%s%s\"%s\": ", indentBuf, tab, el->name);
jsonDyStringPrintRecurse(dy, val, indentLevel);
dyStringPrintf(dy,"%s%s", el->next == NULL ? "" : ",",nl);
}
hashElFreeList(&list);
}
dyStringPrintf(dy,"%s}", indentBuf);
break;
}
case jsonList:
{
struct slRef *el;
dyStringPrintf(dy,"[%s",nl);
if(ele->val.jeList)
{
for (el = ele->val.jeList; el != NULL; el = el->next)
{
struct jsonElement *val = el->val;
dyStringPrintf(dy,"%s%s", indentBuf,tab);
jsonDyStringPrintRecurse(dy, val, indentLevel);
dyStringPrintf(dy,"%s%s", el->next == NULL ? "" : ",",nl);
}
}
dyStringPrintf(dy,"%s]", indentBuf);
break;
}
case jsonString:
{
dyStringPrintf(dy,"\"%s\"", jsonStringEscape(ele->val.jeString));
break;
}
case jsonBoolean:
{
dyStringPrintf(dy,"%s", ele->val.jeBoolean ? "true" : "false");
break;
}
case jsonNumber:
{
char buf[256];
safef(buf, sizeof(buf), "%ld", ele->val.jeNumber);
dyStringPrintf(dy,"%s", buf);
break;
}
case jsonDouble:
{
char buf[256];
safef(buf, sizeof(buf), "%g", ele->val.jeDouble);
dyStringPrintf(dy,"%s", buf);
break;
}
default:
{
errAbort("jsonPrintRecurse; invalid type: %d", ele->type);
break;
}
}
if (indentLevel >= 0)
freez(&indentBuf);
}
void doBamDetails(struct trackDb *tdb, char *item)
/* Show details of an alignment from a BAM file. */
{
if (item == NULL)
errAbort("doBamDetails: NULL item name");
int start = cartInt(cart, "o");
if (!tdb || !trackDbSetting(tdb, "bamSkipPrintQualScore"))
skipQualityScore = FALSE;
else
skipQualityScore = TRUE;
// TODO: libify tdb settings table_pairEndsByName, stripPrefix and pairSearchRange
knetUdcInstall();
if (udcCacheTimeout() < 300)
udcSetCacheTimeout(300);
if (sameString(item, "zoom in"))
printf("Zoom in to a region with fewer items to enable 'detail page' links for individual items.<BR>");
char varName[1024];
safef(varName, sizeof(varName), "%s_pairEndsByName", tdb->track);
boolean isPaired = cartUsualBoolean(cart, varName,
(trackDbSetting(tdb, "pairEndsByName") != NULL));
char position[512];
safef(position, sizeof(position), "%s:%d-%d", seqName, winStart, winEnd);
struct hash *pairHash = isPaired ? hashNew(0) : NULL;
struct bamTrackData btd = {start, item, pairHash};
char *fileName = hReplaceGbdb(trackDbSetting(tdb, "bigDataUrl"));
if (fileName == NULL)
{
if (isCustomTrack(tdb->table))
{
errAbort("bamLoadItemsCore: can't find bigDataUrl for custom track %s", tdb->track);
}
else
{
struct sqlConnection *conn = hAllocConnTrack(database, tdb);
fileName = hReplaceGbdb(bamFileNameFromTable(conn, tdb->table, seqName));
hFreeConn(&conn);
}
}
char *indexName = hReplaceGbdb(trackDbSetting(tdb, "bigDataIndex"));
char *cacheDir = cfgOption("cramRef");
char *refUrl = trackDbSetting(tdb, "refUrl");
bamAndIndexFetchPlus(fileName, indexName, position, oneBam, &btd, NULL, refUrl, cacheDir);
if (isPaired)
{
char *setting = trackDbSettingOrDefault(tdb, "pairSearchRange", "20000");
int pairSearchRange = atoi(setting);
if (pairSearchRange > 0 && hashNumEntries(pairHash) > 0)
{
// Repeat the search for item in a larger window:
struct hash *newPairHash = hashNew(0);
btd.pairHash = newPairHash;
safef(position, sizeof(position), "%s:%d-%d", seqName,
max(0, winStart-pairSearchRange), winEnd+pairSearchRange);
bamFetch(fileName, position, oneBam, &btd, NULL);
}
struct hashEl *hel;
struct hashCookie cookie = hashFirst(btd.pairHash);
while ((hel = hashNext(&cookie)) != NULL)
{
bam1_t *bam = hel->val;
const bam1_core_t *core = &bam->core;
if (! (core->flag & BAM_FMUNMAP))
printf("<B>Note: </B>unable to find paired end for %s "
"within +-%d bases of viewing window %s<BR>\n",
item, pairSearchRange, addCommasToPos(database, cartString(cart, "position")));
else
printf("<B>Paired read name:</B> %s<BR>\n", item);
singleBamDetails(bam);
}
}
}
