void hubConnectStatusFree(struct hubConnectStatus **pHub)
/* Free hubConnectStatus */
{
struct hubConnectStatus *hub = *pHub;
if (hub != NULL)
{
freeMem(hub->hubUrl);
freeMem(hub->errorMessage);
trackHubClose(&hub->trackHub);
freez(pHub);
}
}
int trackHubCrawl(char *hubUrl)
/* Crawl a track data hub and output strings useful in a search */
{
struct errCatch *errCatch = errCatchNew();
struct trackHub *hub = NULL;
int retVal = 0;
if (errCatchStart(errCatch))
{
hub = trackHubOpen(hubUrl, "hub_0");
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
retVal = 1;
fprintf(stderr, "%s\n", errCatch->message->string);
}
errCatchFree(&errCatch);
if (hub == NULL)
return 1;
FILE *searchFp =stdout;
struct trackHubGenome *genomeList = hub->genomeList;
for(; genomeList ; genomeList = genomeList->next)
fprintf(searchFp, "%s\t%s\n",hub->url, trackHubSkipHubName(genomeList->name));
fprintf(searchFp, "%s\t%s\t%s\n",hub->url, hub->shortLabel, hub->longLabel);
if (hub->descriptionUrl != NULL)
{
char *html = netReadTextFileIfExists(hub->descriptionUrl);
char *stripHtml =htmlTextStripTags(html);
strSwapChar(stripHtml, '\n', ' ');
strSwapChar(stripHtml, '\t', ' ');
strSwapChar(stripHtml, '\015', ' ');
strSwapChar(stripHtml, ')', ' ');
strSwapChar(stripHtml, '(', ' ');
strSwapChar(stripHtml, '[', ' ');
strSwapChar(stripHtml, ']', ' ');
fprintf(searchFp, "%s\t%s\n",hub->url, stripHtml);
}
trackHubClose(&hub);
return retVal;
}
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;
}
int trackHubCheck(char *hubUrl, struct trackHubCheckOptions *options, struct dyString *errors)
/* Check a track data hub for integrity. Put errors in dyString.
* return 0 if hub has no errors, 1 otherwise
* if options->checkTracks is TRUE, check remote files of individual tracks
*/
{
struct errCatch *errCatch = errCatchNew();
struct trackHub *hub = NULL;
int retVal = 0;
if (errCatchStart(errCatch))
{
hub = trackHubOpen(hubUrl, "hub_0");
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
retVal = 1;
dyStringPrintf(errors, "%s\n", errCatch->message->string);
}
if (errCatch->gotWarning && !errCatch->gotError)
dyStringPrintf(errors, "%s", errCatch->message->string);
errCatchFree(&errCatch);
if (hub == NULL)
return 1;
if (options->checkSettings)
retVal |= hubSettingsCheckInit(hub, options, errors);
struct trackHubGenome *genome;
for (genome = hub->genomeList; genome != NULL; genome = genome->next)
{
retVal |= hubCheckGenome(hub, genome, options, errors);
}
trackHubClose(&hub);
return retVal;
}
int hubPublicCheck(char *table)
/* hubPublicCheck - checks that the labels in hubPublic match what is in the hub labels. */
{
struct sqlConnection *conn = hConnectCentral();
char query[512];
bool hasDescriptionUrl = sqlColumnExists(conn, table, "descriptionUrl");
if (hasDescriptionUrl)
sqlSafef(query, sizeof(query), "select hubUrl, shortLabel,longLabel,dbList,descriptionUrl from %s",
table);
else
sqlSafef(query, sizeof(query), "select hubUrl, shortLabel,longLabel,dbList from %s",
table);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
int differences = 0;
while ((row = sqlNextRow(sr)) != NULL)
{
char *url = row[0], *shortLabel = row[1], *longLabel = row[2], *dbList = row[3], *descriptionUrl = row[4];
struct errCatch *errCatch = errCatchNew();
boolean gotWarning = FALSE;
struct trackHub *tHub = NULL;
if (errCatchStart(errCatch))
tHub = trackHubOpen(url, "hub_1");
errCatchEnd(errCatch);
if (errCatch->gotError)
{
gotWarning = TRUE;
warn("%s", errCatch->message->string);
}
errCatchFree(&errCatch);
if (gotWarning)
{
continue;
}
if (!sameString(shortLabel, tHub->shortLabel))
{
differences++;
printf("update %s set shortLabel=\"%s\" where hubUrl=\"%s\";\n",table, tHub->shortLabel, url);
}
if (!sameString(longLabel, tHub->longLabel))
{
differences++;
printf("update %s set longLabel=\"%s\" where hubUrl=\"%s\";\n",table, tHub->longLabel, url);
}
struct hashCookie cookie = hashFirst(tHub->genomeHash);
struct dyString *dy = newDyString(1024);
struct hashEl *hel;
while ((hel = hashNext(&cookie)) != NULL)
dyStringPrintf(dy, "%s,", trackHubSkipHubName(hel->name));
if (!sameString(dy->string, dbList))
{
differences++;
printf("update %s set dbList=\"%s\" where hubUrl=\"%s\";\n",table, dy->string, url);
}
if (hasDescriptionUrl && !isEmpty(tHub->descriptionUrl) && ((descriptionUrl == NULL) || !sameString(descriptionUrl, tHub->descriptionUrl)))
{
differences++;
printf("update %s set descriptionUrl=\"%s\" where hubUrl=\"%s\";\n",table, tHub->descriptionUrl, url);
}
trackHubClose(&tHub);
}
return differences;
}
