struct hash *hashUpPositions(struct bed **pBedList)
/* Add beds to a hash of lists. */
{
struct bed *popped;
struct hash *theHash = hashNew(22);
while ((popped = slPopHead(pBedList)) != NULL)
{
struct slRef *ref = slRefNew(popped);
struct slRef *list = (struct slRef *)hashFindVal(theHash, popped->name);
ref->next = list;
hashReplace(theHash, popped->name, ref);
}
return theHash;
}
int oneHubTrackSettings(char *hubUrl, struct hash *totals)
/* Read hub trackDb files, noting settings used */
{
struct trackHub *hub = NULL;
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
hub = trackHubOpen(hubUrl, "hub_0");
errCatchEnd(errCatch);
errCatchFree(&errCatch);
if (hub == NULL)
return 1;
printf("%s (%s)\n", hubUrl, hub->shortLabel);
struct trackHubGenome *genome;
struct hash *counts;
if (totals)
counts = totals;
else
counts = newHash(0);
struct hashEl *el;
for (genome = hub->genomeList; genome != NULL; genome = genome->next)
{
struct trackDb *tdb, *tdbs = trackHubTracksForGenome(hub, genome);
for (tdb = tdbs; tdb != NULL; tdb = tdb->next)
{
struct hashCookie cookie = hashFirst(trackDbHashSettings(tdb));
verbose(2, " track: %s\n", tdb->shortLabel);
while ((el = hashNext(&cookie)) != NULL)
{
int count = hashIntValDefault(counts, el->name, 0);
count++;
hashReplace(counts, el->name, intToPt(count));
}
}
}
if (!totals)
printCounts(counts);
trackHubClose(&hub);
return 0;
}
struct trackHubSettingSpec *trackHubSettingsForVersion(char *specHost, char *version)
/* Return list of settings with support level. Version can be version string or spec url */
{
struct htmlPage *page = NULL;
if (version == NULL)
{
version = trackHubVersionDefault(specHost, &page);
if (version == NULL)
errAbort("Can't get default spec from host %s", specHost);
}
/* Retrieve specs from file url.
* Settings are the first text word within any <code> tag having class="level-" attribute.
* The level represents the level of support for the setting (e.g. base, full, deprecated)
* The support level ('level-*') is the class value of the * <code> tag.
* E.g. <code class="level-full">boxedConfig on</code> produces:
* setting=boxedConfig, class=full */
if (page == NULL)
page = trackHubVersionSpecMustGet(specHost, version);
if (page == NULL)
errAbort("Can't get settings spec for version %s from host %s", version, specHost);
verbose(5, "Found %d tags\n", slCount(page->tags));
struct trackHubSettingSpec *spec, *savedSpec;
struct hash *specHash = hashNew(0);
struct htmlTag *tag;
struct htmlAttribute *attr;
char buf[256];
for (tag = page->tags; tag != NULL; tag = tag->next)
{
if (differentWord(tag->name, "code"))
continue;
attr = tag->attributes;
if (attr == NULL || differentString(attr->name, "class") || !startsWith("level-", attr->val))
continue;
AllocVar(spec);
int len = min(tag->next->start - tag->end, sizeof buf - 1);
memcpy(buf, tag->end, len);
buf[len] = 0;
verbose(6, "Found spec: %s\n", buf);
spec->name = cloneString(firstWordInLine(buf));
if (spec->name == NULL || strlen(spec->name) == 0)
{
warn("ERROR: format problem with trackDbHub.html -- contact UCSC.");
continue;
}
spec->level = cloneString(chopPrefixAt(attr->val, '-'));
verbose(6, "spec: name=%s, level=%s\n", spec->name, spec->level);
savedSpec = (struct trackHubSettingSpec *)hashFindVal(specHash, spec->name);
if (savedSpec != NULL)
verbose(6, "found spec %s level %s in hash\n", savedSpec->name, savedSpec->level);
if (savedSpec == NULL)
{
hashAdd(specHash, spec->name, spec);
verbose(6, "added spec %s at level %s\n", spec->name, spec->level);
}
else if (trackHubSettingLevelCmp(spec, savedSpec) > 0)
{
hashReplace(specHash, spec->name, spec);
verbose(6, "replaced spec %s at level %s, was %s\n",
spec->name, spec->level, savedSpec->level);
}
}
struct hashEl *el, *list = hashElListHash(specHash);
int settingsCt = slCount(list);
verbose(5, "Found %d settings's\n", slCount(list));
if (settingsCt == 0)
errAbort("Can't find hub setting info for version %s (host %s)."
" Use -version to indicate a different version number or url.", version, specHost);
slSort(&list, hashElCmp);
struct trackHubSettingSpec *specs = NULL;
int baseCt = 0;
int requiredCt = 0;
int deprecatedCt = 0;
for (el = list; el != NULL; el = el->next)
{
if (sameString(((struct trackHubSettingSpec *)el->val)->level, "base"))
baseCt++;
else if (sameString(((struct trackHubSettingSpec *)el->val)->level, "required"))
requiredCt++;
else if (sameString(((struct trackHubSettingSpec *)el->val)->level, "deprecated"))
deprecatedCt++;
slAddHead(&specs, el->val);
}
slReverse(&specs);
verbose(3,
"Found %d supported settings for this version (%d required, %d base, %d deprecated)\n",
slCount(specs), requiredCt, baseCt, deprecatedCt);
return specs;
}
