Exemple #1
0
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;
}
Exemple #3
0
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;
}
Exemple #4
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;
}