def test_list_object_with_sets(self):
ws_name1 = self.createWs()
reads_obj_ref = self.__class__.example_reads_ref
set_obj_name = "MyReadsSet.1"
sapi = SetAPI(self.__class__.serviceWizardURL, token=self.getContext()['token'],
service_ver=self.__class__.SetAPI_version)
sapi.save_reads_set_v1({'workspace': ws_name1, 'output_object_name': set_obj_name,
'data': {'description': '', 'items': [{'ref': reads_obj_ref}]}})
list_ret = self.getImpl().list_objects_with_sets(self.getContext(),
{"ws_name": ws_name1})[0]
ret = list_ret['data']
self.assertTrue(len(ret) > 0)
set_count = 0
for item in ret:
self.assertTrue("object_info" in item)
if "set_items" in item:
set_count += 1
set_items = item["set_items"]["set_items_info"]
self.assertEqual(1, len(set_items))
self.assertEqual(1, set_count)
self.assertNotIn('data_palette_refs', list_ret)
ws_id = self.getWsClient().get_workspace_info({"workspace": ws_name1})[0]
list_ret = self.getImpl().list_objects_with_sets(self.getContext(),
{"ws_name": ws_name1,
"include_data_palettes": 1})[0]
ret = list_ret['data']
self.assertTrue(len(ret) > 0)
set_count = 0
for item in ret:
self.assertTrue("object_info" in item)
if "set_items" in item:
set_count += 1
set_items = item["set_items"]["set_items_info"]
self.assertEqual(1, len(set_items))
self.assertEqual(1, set_count)
self.assertIn('data_palette_refs', list_ret)
ws_id = self.getWsClient().get_workspace_info({"workspace": ws_name1})[0]
ret2 = self.getImpl().list_objects_with_sets(self.getContext(),
{"ws_id": ws_id})[0]["data"]
self.assertEqual(len(ret), len(ret2))
type_filter = "KBaseSets.ReadsSet"
ret3 = self.getImpl().list_objects_with_sets(self.getContext(),
{"types": [type_filter],
"workspaces": [str(ws_id)]})[0]["data"]
self.assertTrue(len(ret3) > 0)
for item in ret3:
info = item['object_info']
obj_type = info[2].split('-')[0]
self.assertEqual(type_filter, obj_type)
type_filter = "KBaseGenomes.Genome"
ret4 = self.getImpl().list_objects_with_sets(self.getContext(),
{"types": [type_filter],
"workspaces": [str(ws_id)]})[0]["data"]
self.assertTrue(len(ret4) == 0)
def loadReadsSet(self, fwd_reads, rev_reads, params):
if hasattr(self.__class__, 'reads_set_ref'):
return self.__class__.reads_set_ref
pe_reads_ref = self.loadPairedEndReads(fwd_reads, rev_reads, params)
reads_set_name = 'TestReadsSet'
# create the set object
reads_set_data = {
'description': 'Reads Set for testing Bwa',
'items': [{
'ref': pe_reads_ref,
'label': 'rs1'
}]
}
# test a save
set_api = SetAPI(self.srv_wiz_url)
res = set_api.save_reads_set_v1({
'data': reads_set_data,
'output_object_name': reads_set_name,
'workspace': params["workspace_name"]
})
reads_set_ref = res['set_ref']
# reads_set_ref = '5264/52/1'
print('Loaded ReadsSet: ' + reads_set_ref)
return reads_set_ref
def test_two_users_set_inside_dp(self):
ws_name1_1 = self.createWs()
# Injecting reads object (real copy) into workspace1
orig_reads_obj_ref = self.__class__.example_reads_ref
reads_obj_name = "TestReads"
self.getWsClient().copy_object({'from': {'ref': orig_reads_obj_ref},
'to': {'workspace': ws_name1_1,
'name': reads_obj_name}})
copy_reads_obj_ref = ws_name1_1 + '/' + reads_obj_name
ws_name1_2 = self.createWs()
set_obj_name = "MyReadsSet.1"
sapi = SetAPI(self.__class__.serviceWizardURL, token=self.getContext()['token'],
service_ver=self.__class__.SetAPI_version)
sapi.save_reads_set_v1({'workspace': ws_name1_2, 'output_object_name': set_obj_name,
'data': {'description': '', 'items': [{'ref': copy_reads_obj_ref}]}})
orig_set_ref = ws_name1_2 + '/' + set_obj_name
# Making DP-copy of reads set object by user2
ws_name2 = self.createWs2()
# Let's share workspace containing set with user2
self.getWsClient().set_permissions({'workspace': ws_name1_2, 'new_permission': 'r',
'users': [self.getContext2()['user_id']]})
# Import reads set ref into DataPalette of third workspace
dps = DataPaletteService(self.__class__.serviceWizardURL,
token=self.getContext2()['token'],
service_ver=self.__class__.DataPalette_version)
dps.add_to_palette({'workspace': ws_name2, 'new_refs': [{'ref': orig_set_ref}]})
dp_ref_map = dps.list_data({'workspaces': [ws_name2]})['data_palette_refs']
set_ref_path = next(iter(dp_ref_map.values())) + ';' + orig_set_ref
reads_ref_path = set_ref_path + ';' + copy_reads_obj_ref
# Un-share original workspace
self.getWsClient().set_permissions({'workspace': ws_name1_2, 'new_permission': 'n',
'users': [self.getContext2()['user_id']]})
# Let's check that we can list set and see reads object as set item
ret = self.getImpl().list_objects_with_sets(self.getContext2(),
{"ws_name": ws_name2})[0]["data"]
self.assertEqual(1, len(ret))
item = ret[0]
self.assertTrue('set_items' in item)
self.assertTrue('set_items_info' in item['set_items'])
self.assertEqual(1, len(item['set_items']['set_items_info']))
# Check access to reads and to set objects
info = self.getWsClient2().get_object_info_new({'objects': [{'ref': set_ref_path}]})[0]
self.assertEqual(set_obj_name, info[1])
info = self.getWsClient2().get_object_info_new({'objects': [{'ref': reads_ref_path}]})[0]
self.assertEqual(reads_obj_name, info[1])
def test_unique_items(self):
# Create original workspace with reads object + ReadsSet object
ws_name1 = self.createWs()
foft = FakeObjectsForTests(os.environ['SDK_CALLBACK_URL'])
reads_obj_name = "testreads1"
foft.create_fake_reads({'ws_name': ws_name1, 'obj_names': [reads_obj_name]})
reads_obj_ref = ws_name1 + '/' + reads_obj_name
set_obj_name = "testreads_set1"
sapi = SetAPI(self.__class__.serviceWizardURL, token=self.getContext()['token'],
service_ver=self.__class__.SetAPI_version)
sapi.save_reads_set_v1({'workspace': ws_name1, 'output_object_name': set_obj_name,
'data': {'description': '', 'items': [{'ref': reads_obj_ref}]}})
set_obj_ref = ws_name1 + '/' + set_obj_name
# Create workspace with DataPalette copy of Reads object and copy of ReadsSet
ws_name2 = self.createWs()
dps = DataPaletteService(self.__class__.serviceWizardURL, token=self.getContext()['token'],
service_ver=self.__class__.DataPalette_version)
dps.add_to_palette({'workspace': ws_name2, 'new_refs': [{'ref': reads_obj_ref},
{'ref': set_obj_ref}]})
# Check if listing in both these workspaces at the same time gives unique items
ret = self.getImpl().list_objects_with_sets(self.getContext(),
{"workspaces": [ws_name1, ws_name2]})[0]["data"]
self.assertEqual(2, len(ret))
def load_reads_set(srv_wiz_url, ws_name, reads_set, target_name):
"""
Combine a list of reads references into a ReadsSet.
if file_rev is None or not a present key, then this is treated as a single end reads.
"""
set_client = SetAPI(srv_wiz_url)
set_output = set_client.save_reads_set_v1({
"workspace": ws_name,
"output_object_name": target_name,
"data": {
"description": "reads set for testing",
"items": reads_set
}
})
return set_output["set_ref"]