def test_two_users_sharing_dp(self):
dps = DataPaletteService(
self.__class__.serviceWizardURL,
token=self.getContext2()['token'],
service_ver=self.__class__.DataPalette_version)
ws_name1 = self.createWs()
# Injecting reads object (real copy) into workspace1
orig_reads_obj_ref = self.__class__.example_reads_ref
target_name = "TestReads"
self.getWsClient().copy_object({
'from': {
'ref': orig_reads_obj_ref
},
'to': {
'workspace': ws_name1,
'name': target_name
}
})
copy_reads_obj_ref = ws_name1 + '/' + target_name
# Making DP-copy of reads object by user2
ws_name2 = self.createWs2()
# Check that user2 can't import reads object until workspace is shared
try:
dps.add_to_palette({
'workspace': ws_name2,
'new_refs': [{
'ref': copy_reads_obj_ref
}]
})
raise ValueError(
"We shouldn't be able to import reads object to DataPalette")
except Exception, e:
self.assertTrue("Object TestReads cannot be accessed" in str(e))
def test_copy_object_two_users(self):
ws_name1 = self.createWs()
orig_reads_ref = self.__class__.example_reads_ref
# Adding DP object:
dps1 = DataPaletteService(self.__class__.serviceWizardURL,
token=self.getContext()['token'],
service_ver=self.__class__.DataPalette_version)
dps1.add_to_palette({'workspace': ws_name1, 'new_refs': [{'ref': orig_reads_ref}]})
# Share this workspace with user2 so that user2 can make DataPalette ref
ws1 = self.getWsClient()
ws1.set_permissions({'workspace': ws_name1, 'new_permission': 'r',
'users': [self.getContext2()['user_id']]})
# Get ref-path to reads object
ret = self.getImpl().list_objects_with_sets(self.getContext(),
{"ws_name": ws_name1})[0]['data']
reads_ref_path = None
for item in ret:
if 'dp_info' in item:
info = item['object_info']
reads_ref_path = (item['dp_info']['ref'] + ';' +
str(info[6]) + '/' + str(info[0]) + '/' + str(info[4]))
# Adding Reads to DP of second user
ws_name2 = self.createWs2()
dps2 = DataPaletteService(self.__class__.serviceWizardURL,
token=self.getContext2()['token'],
service_ver=self.__class__.DataPalette_version)
dps2.add_to_palette({'workspace': ws_name2, 'new_refs': [{'ref': reads_ref_path}]})
def test_copy_narrative_two_users(self):
# Create workspace with Reads object for user1
ws_name1 = self.createWs()
orig_reads_ref = self.__class__.example_reads_ref
target_reads_name = "MyReads.copy.1"
ws1 = self.getWsClient()
reads_info = ws1.copy_object({'from': {'ref': orig_reads_ref},
'to': {'workspace': ws_name1,
'name': target_reads_name}})
# Share this workspace with user2 so that user2 can make DataPalette ref
ws1.set_permissions({'workspace': ws_name1, 'new_permission': 'r',
'users': [self.getContext2()['user_id']]})
reads_ref = str(reads_info[6]) + '/' + str(reads_info[0]) + '/' + str(reads_info[4])
# Create workspace with Narrative for user2
ws2 = self.getWsClient2()
with open("/kb/module/test/data/narrative1.json", "r") as f1:
nar_obj_data = json.load(f1)
user_id = self.getContext2()['user_id']
ws_name2 = self.createWs2()
nar_obj_data['metadata']['creator'] = user_id
nar_obj_data['metadata']['ws_name'] = ws_name2
nar_obj_data['metadata']['kbase']['creator'] = user_id
nar_obj_data['metadata']['kbase']['ws_name'] = ws_name2
nar_obj_name = "Narrative." + str(int(round(time.time() * 1000)))
nar_obj_type = "KBaseNarrative.Narrative-4.0"
job_info = json.dumps({"queue_time": 0, "running": 0, "completed": 0,
"run_time": 0, "error": 0})
nar_obj_meta = {"description": "",
"format": "ipynb",
"creator": user_id,
"job_info": job_info,
"data_dependencies": "[]",
"jupyter.markdown": "1",
"ws_name": ws_name2,
"type": "KBaseNarrative.Narrative",
"name": "NarrativeCopyTest"}
ws2.save_objects({'workspace': ws_name2, 'objects':
[{'type': nar_obj_type,
'data': nar_obj_data,
'name': nar_obj_name,
'meta': nar_obj_meta}]})
# Adding DP object:
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': reads_ref}]})
target_reads_name2 = "MyReads.copy.2"
ws2.copy_object({'from': {'ref': reads_ref},
'to': {'workspace': ws_name2,
'name': target_reads_name2}})
#Un-share ws_name1 with user2
ws1.set_permissions({'workspace': ws_name1, 'new_permission': 'n',
'users': [self.getContext2()['user_id']]})
try:
self.getWsClient2().get_object_info_new({'objects': [{'ref': reads_ref}]})
raise ValueError("We shouldn't be able to access reads object")
except Exception, e:
self.assertTrue("cannot be accessed" in str(e))
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 = dp_ref_map.itervalues().next() + ';' + 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 = "test.reads.1"
foft.create_fake_reads({
'ws_name': ws_name1,
'obj_names': [reads_obj_name]
})
reads_obj_ref = ws_name1 + '/' + reads_obj_name
set_obj_name = "test.reads_set.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
}]
}
})
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 test_list_sets(self):
workspace = self.getWsName()
setAPI = self.getImpl()
# make sure we can see an empty list of sets before WS has any
res = setAPI.list_sets(self.getContext(), {
'workspace': workspace,
'include_set_item_info': 1
})[0]
# create the test sets
self.create_sets()
res = setAPI.list_sets(self.getContext(), {
'workspace': workspace,
'include_set_item_info': 1
})[0]
self.assertTrue('sets' in res)
self.assertEqual(len(res['sets']), len(self.setNames))
for s in res['sets']:
self.assertTrue('ref' in s)
self.assertTrue('info' in s)
self.assertTrue('items' in s)
self.assertEqual(len(s['info']), 11)
self.assertEqual(len(s['items']), 2)
for item in s['items']:
self.assertTrue('ref' in item)
self.assertTrue('info' in item)
self.assertEqual(len(item['info']), 11)
res2 = setAPI.list_sets(self.getContext(), {'workspace': workspace})[0]
self.assertTrue('sets' in res2)
self.assertEqual(len(res2['sets']), len(self.setNames))
for s in res2['sets']:
self.assertTrue('ref' in s)
self.assertTrue('info' in s)
self.assertTrue('items' in s)
self.assertEqual(len(s['info']), 11)
self.assertEqual(len(s['items']), 2)
for item in s['items']:
self.assertTrue('ref' in item)
self.assertTrue('info' not in item)
res = setAPI.get_set_items(self.getContext(),
{'set_refs': [{
'ref': self.setRefs[0]
}]})[0]
self.assertEqual(len(res['sets']), 1)
for s in res['sets']:
self.assertTrue('ref' in s)
self.assertTrue('info' in s)
self.assertTrue('items' in s)
self.assertEqual(len(s['info']), 11)
self.assertEqual(len(s['items']), 2)
for item in s['items']:
self.assertTrue('ref' in item)
self.assertTrue('info' in item)
self.assertEqual(len(item['info']), 11)
set_obj_name = self.setNames[0]
wsName2 = "test_SetAPI_" + str(int(time.time() * 1000)) + "_two"
self.getWsClient().create_workspace({'workspace': wsName2})
try:
set_obj_ref = self.getWsName() + '/' + set_obj_name
dps = DataPaletteService(
self.serviceWizardURL,
token=self.getContext()['token'],
service_ver=self.dataPaletteServiceVersion)
dps.add_to_palette({
'workspace': wsName2,
'new_refs': [{
'ref': set_obj_ref
}]
})
ret = self.getImpl().list_sets(
self.getContext(), {
'workspace': wsName2,
'include_set_item_info': 1,
'include_raw_data_palettes': 1
})[0]
set_list = ret['sets']
self.assertEqual(1, len(set_list))
set_info = set_list[0]
info = set_info['info']
self.assertEqual(self.getWsName(), info[7])
self.assertEqual(set_obj_name, info[1])
self.assertTrue('raw_data_palettes' in ret)
self.assertEqual(1, len(ret['raw_data_palettes']))
self.assertIn('info', ret['raw_data_palettes'][0])
self.assertIn('ref', ret['raw_data_palettes'][0])
self.assertTrue('raw_data_palette_refs' in ret)
self.assertEqual(1, len(ret['raw_data_palette_refs']))
set_list2 = self.getImpl().list_sets(
self.getContext(), {
'workspaces': [workspace, wsName2],
'include_set_item_info': 1,
'include_metadata': 1
})[0]['sets']
self.assertEqual(len(set_list2), len(self.setNames))
self.assertTrue(len(set_list2) > 0)
for set_obj in set_list2:
self.assertIsNotNone(set_obj['info'][10])
for item in set_obj['items']:
self.assertIsNotNone(item['info'][10])
finally:
self.getWsClient().delete_workspace({'workspace': wsName2})