def test_url_rotate(self):
''' Test the url rotates from http://xxx:9200 to correct url. '''
query = ElasticQuery.filtered(Query.term("seqid", 1),
Filter(Query.term("id", "rs768019142")))
elastic = Search(query, idx=ElasticSettings.idx('DEFAULT'))
self.assertTrue(elastic.search().hits_total == 1,
"Elastic filtered query retrieved marker")
Search.index_exists('test', 'test2')
ElasticUrl.URL_INDEX = 0 # reset
def test_region_idx_loader(self):
''' Test loader has created and populated indices. '''
key = 'PRIVATE_REGIONS_GFF'
if key in IDX.keys():
idx = IDX[key]['indexName']
Search.index_refresh(idx)
self.assertTrue(Search.index_exists(idx=idx), 'Index exists: '+idx)
ndocs = Search(idx=idx).get_count()['count']
self.assertTrue(ndocs > 0, "Elastic count documents in " + idx + ": " + str(ndocs))
def test_idx_loader(self):
''' Test loader has created and populated indices. '''
for key in IDX:
idx = IDX[key]['indexName']
# check the index has documents, allow for the indexing to complete if necessary
# Search.index_refresh(idx)
self.assertTrue(Search.index_exists(idx=idx),
'Index exists: ' + idx)
ndocs = Search(idx=idx).get_count()['count']
self.assertTrue(
ndocs > 0,
"Elastic count documents in " + idx + ": " + str(ndocs))
def test_region_idx_loader(self):
''' Test loader has created and populated indices. '''
key = 'PRIVATE_REGIONS_GFF'
if key in IDX.keys():
idx = IDX[key]['indexName']
Search.index_refresh(idx)
self.assertTrue(Search.index_exists(idx=idx),
'Index exists: ' + idx)
ndocs = Search(idx=idx).get_count()['count']
self.assertTrue(
ndocs > 0,
"Elastic count documents in " + idx + ": " + str(ndocs))
def test_create_restore_delete_snapshot(self):
self.wait_for_running_snapshot()
snapshot = 'test_' + ElasticSettings.getattr('TEST')
repo = SnapshotTest.TEST_REPO
# create a snapshot
call_command('snapshot',
snapshot,
indices=IDX['MARKER']['indexName'],
repo=repo)
Snapshot.wait_for_snapshot(repo, snapshot)
self.assertTrue(Snapshot.exists(repo, snapshot),
"Created snapshot " + snapshot)
# snapshot already exist so return false
self.assertFalse(
Snapshot.create_snapshot(repo, snapshot,
IDX['MARKER']['indexName']))
# delete index
requests.delete(ElasticSettings.url() + '/' +
IDX['MARKER']['indexName'])
self.assertFalse(Search.index_exists(IDX['MARKER']['indexName']),
"Removed index")
# restore from snapshot
call_command('restore_snapshot',
snapshot,
repo=repo,
indices=IDX['MARKER']['indexName'])
Search.index_refresh(IDX['MARKER']['indexName'])
self.assertTrue(Search.index_exists(IDX['MARKER']['indexName']),
"Restored index exists")
# remove snapshot
call_command('snapshot', snapshot, delete=True, repo=repo)
Snapshot.wait_for_snapshot(repo, snapshot, delete=True, count=10)
self.assertFalse(Snapshot.exists(repo, snapshot),
"Deleted snapshot " + snapshot)
def marker_page(request, marker):
''' Render a marker page '''
query = ElasticQuery.query_match("id", marker)
elastic = Search(query)
context = elastic.get_result()
_add_info(context)
# rs history lookup
if Search.index_exists(
idx=ElasticSettings.idx(name='MARKER', idx_type='HISTORY')):
query = ElasticQuery.query_match("rscurrent", marker)
rs_history = Search(query,
idx=ElasticSettings.idx(name='MARKER',
idx_type='HISTORY'))
context['history'] = rs_history.get_result()
# get gene(s) overlapping position
position = context['data'][0]['start']
chrom = 'chr' + str(context['data'][0]['seqid'])
featurelocs = (
Featureloc.objects.filter(fmin__lt=position) # @UndefinedVariable
.filter(fmax__gt=position) # @UndefinedVariable
.filter(srcfeature__uniquename=chrom) # @UndefinedVariable
.filter(feature__type__name='gene')) # @UndefinedVariable
genes = []
for loc in featurelocs:
genes.append(loc.feature)
context['genes'] = genes
# page title
if len(context["data"]) == 1 and "id" in context["data"][0]:
context['title'] = "Marker - " + context["data"][0]["id"]
return render(request,
'marker/marker.html',
context,
content_type='text/html')
def test_idx_exists(self):
''' Test that index_exists() method. '''
self.assertTrue(Search.index_exists(idx=ElasticSettings.idx('DEFAULT')),
"Index exists")
self.assertFalse(Search.index_exists("xyz123"))