def orth_result(request, resultId):
'''
GET: return an orthology result page
'''
logging.debug('orth_result resultId={}'.format(resultId))
if orthresult.resultExists(resultId):
resultType = request.GET.get('rt', orthresult.ORTH_RESULT)
templateType = request.GET.get('tt', orthresult.WIDE_TEMPLATE)
def urlFunc(resultId):
return django.core.urlresolvers.reverse(orth_result, kwargs={'resultId': resultId})
page = orthresult.renderResult(resultId, urlFunc, resultType=resultType, otherParams=request.GET)
# page = orthresult.resultToAllGenesView(resultId)
if templateType == orthresult.WIDE_TEMPLATE:
return django.shortcuts.render(request, 'wide.html', {'html': page, 'nav_id': 'browse'})
elif templateType == orthresult.DOWNLOAD_TEMPLATE:
response = django.http.HttpResponse(page, content_type='text/plain')
full_filename = 'roundup-{}-gene_clusters_for_result_{}.txt'.format(webconfig.CURRENT_RELEASE, resultId)
response['Content-Disposition'] = 'attachment; filename={}'.format(full_filename)
return response
elif templateType == orthresult.DOWNLOAD_XML_TEMPLATE:
response = django.http.HttpResponse(page, content_type='text/xml')
full_filename = 'roundup-{}-gene_clusters_for_result_{}.xml'.format(webconfig.CURRENT_RELEASE, resultId)
response['Content-Disposition'] = 'attachment; filename={}'.format(full_filename)
return response
else:
raise django.http.Http404
else:
raise django.http.Http404
def orth_query(request, queryId):
'''
run an orthology query to create a "result".
GET: return a page which will get the result of the query. either gets result from the cache or runs the query and stores the result in the cache.
'''
logging.debug('orth_query queryId={}'.format(queryId))
if not roundup_util.cacheHasKey(queryId):
raise django.http.Http404
orthQuery = roundup_util.cacheGet(queryId)
querySize = len(orthQuery['limit_genomes']) + len(orthQuery['genomes'])
resultId = getResultId(queryId)
resultPath = orthresult.getResultFilename(resultId)
logging.debug(u'orth_query():\northQuery={}\nresultId={}\nqueryId={}\nresultPath={}'.format(orthQuery, resultId, queryId, resultPath))
if USE_CACHE and roundup_util.cacheHasKey(resultId) and orthresult.resultExists(resultId):
logging.debug('cache hit.')
return django.shortcuts.redirect(django.core.urlresolvers.reverse(orth_result, kwargs={'resultId': resultId}))
elif not webconfig.NO_LSF and lsf.isJobNameOn(resultId, retry=True, delay=0.2):
logging.debug('cache miss. job is already running. go to waiting page.')
return django.shortcuts.redirect(django.core.urlresolvers.reverse(orth_wait, kwargs={'resultId': resultId}))
elif webconfig.NO_LSF or querySize <= SYNC_QUERY_LIMIT:
logging.debug('cache miss. run job sync.')
# wait for query to run and store query
roundup_util.do_orthology_query(cache_key=resultId,
cache_file=resultPath,
query_kws=orthQuery)
return django.shortcuts.redirect(
django.core.urlresolvers.reverse(orth_result,
kwargs={'resultId': resultId}))
else:
logging.debug('cache miss. run job async.')
# run on lsf and have result page poll for job completion
roundup_util.bsub_orthology_query(cache_key=resultId,
cache_file=resultPath,
query_kws=orthQuery,
job_name=resultId)
return django.shortcuts.redirect(
django.core.urlresolvers.reverse(orth_wait,
kwargs={'resultId': resultId}))