diff --git a/app-openbis-command-line/src/python/obis/dm/data_mgmt_test.py b/app-openbis-command-line/src/python/obis/dm/data_mgmt_test.py
index 977f091a15bbd11105dfc60ab0edc9c4d46a4de3..99274b686a4f29dae7d6b252b1a596c70be723ae 100644
--- a/app-openbis-command-line/src/python/obis/dm/data_mgmt_test.py
+++ b/app-openbis-command-line/src/python/obis/dm/data_mgmt_test.py
@@ -24,21 +24,21 @@ data_mgmt_test.py
Created by Chandrasekhar Ramakrishnan on 2017-02-02.
Copyright (c) 2017 Chandrasekhar Ramakrishnan. All rights reserved.
"""
+import hashlib
import json
import os
import random
import shutil
import socket
-import hashlib
-
from datetime import datetime
+from unittest.mock import Mock, MagicMock, ANY
+from pybis.pybis import ExternalDMS, DataSet
+
+from . import CommandResult
from . import data_mgmt
from . import git
from . import utils
-from . import CommandResult
-from unittest.mock import Mock, MagicMock, ANY
-from pybis.pybis import ExternalDMS, DataSet
def generate_perm_id():
@@ -60,8 +60,23 @@ def shared_dm(path):
return dm
+def physical_dm(path):
+ openbis_config = {
+ 'allow_http_but_do_not_use_this_in_production_and_only_within_safe_networks': True
+ }
+ dm = data_mgmt.DataMgmt(openbis_config=openbis_config,
+ git_config={'data_path': path,
+ 'metadata_path': path,
+ 'invocation_path': path
+ },
+ repository_type=utils.Type.PHYSICAL)
+ dm.debug = True
+ return dm
+
+
def test_no_git(tmpdir):
- git_config = {'find_git': False, 'data_path': None, 'metadata_path': None, 'invocation_path': None}
+ git_config = {'find_git': False, 'data_path': None, 'metadata_path': None,
+ 'invocation_path': None}
dm = data_mgmt.DataMgmt(git_config=git_config)
try:
dm.init_data("")
@@ -99,16 +114,17 @@ def test_data_use_case(tmpdir):
dm = shared_dm(tmpdir)
tmp_dir_path = str(tmpdir)
- assert git_status(tmp_dir_path).returncode == 128 # The folder should not be a git repo at first.
+ assert git_status(
+ tmp_dir_path).returncode == 128 # The folder should not be a git repo at first.
with data_mgmt.cd(tmp_dir_path):
-
result = dm.init_data("test")
print(result.output)
assert result.returncode == 0
assert git_status(tmp_dir_path).returncode == 0 # The folder should be a git repo now
- assert git_status(tmp_dir_path, annex=True).returncode == 0 # ...and a git-annex repo as well.
+ assert git_status(tmp_dir_path,
+ annex=True).returncode == 0 # ...and a git-annex repo as well.
copy_test_data(tmpdir)
@@ -153,7 +169,6 @@ def test_child_data_set(tmpdir):
tmp_dir_path = str(tmpdir)
with data_mgmt.cd(tmp_dir_path):
-
result = dm.init_data("test")
assert result.returncode == 0
@@ -180,7 +195,8 @@ def test_child_data_set(tmpdir):
assert repository_id is not None
contents = git.GitRepoFileInfo(dm.git_wrapper).contents(git_annex_hash_as_checksum=True)
- check_new_data_set_expectations(dm, tmp_dir_path, commit_id, repository_id, ANY, child_ds_code, parent_ds_code,
+ check_new_data_set_expectations(dm, tmp_dir_path, commit_id, repository_id, ANY,
+ child_ds_code, parent_ds_code,
properties, contents)
@@ -215,9 +231,10 @@ def test_undo_commit_when_sync_fails(tmpdir):
# given
dm = shared_dm(tmpdir)
dm.git_wrapper = Mock()
- dm.git_wrapper.git_top_level_path = MagicMock(return_value = CommandResult(returncode=0, output=None))
- dm.git_wrapper.git_add = MagicMock(return_value = CommandResult(returncode=0, output=None))
- dm.git_wrapper.git_commit = MagicMock(return_value = CommandResult(returncode=0, output=None))
+ dm.git_wrapper.git_top_level_path = MagicMock(
+ return_value=CommandResult(returncode=0, output=None))
+ dm.git_wrapper.git_add = MagicMock(return_value=CommandResult(returncode=0, output=None))
+ dm.git_wrapper.git_commit = MagicMock(return_value=CommandResult(returncode=0, output=None))
dm._sync = lambda *args: CommandResult(returncode=-1, output="dummy error")
# when
result = dm.commit("Added data.")
@@ -230,7 +247,6 @@ def test_init_analysis(tmpdir):
tmp_dir_path = str(tmpdir)
with data_mgmt.cd(tmp_dir_path):
-
dm = shared_dm(tmp_dir_path)
prepare_registration_expectations(dm)
openbis = dm.openbis
@@ -250,7 +266,6 @@ def test_init_analysis(tmpdir):
os.mkdir(analysis_repo)
with data_mgmt.cd(analysis_repo):
-
dm = shared_dm(os.path.join(tmpdir, analysis_repo))
dm.openbis = openbis
prepare_new_data_set_expectations(dm)
@@ -269,10 +284,27 @@ def test_init_analysis(tmpdir):
assert repository_id is not None
contents = git.GitRepoFileInfo(dm.git_wrapper).contents(git_annex_hash_as_checksum=True)
- check_new_data_set_expectations(dm, tmp_dir_path + '/' + analysis_repo, commit_id, repository_id, ANY, child_ds_code, parent_ds_code,
+ check_new_data_set_expectations(dm, tmp_dir_path + '/' + analysis_repo, commit_id,
+ repository_id, ANY, child_ds_code, parent_ds_code,
None, contents)
+def test_init_physical(tmpdir):
+ tmp_dir_path = str(tmpdir)
+
+ with data_mgmt.cd(tmp_dir_path):
+ dm = physical_dm(tmp_dir_path)
+ init_result = dm.init_data("")
+ assert init_result.returncode == 0
+
+ files = os.listdir(os.path.join(tmp_dir_path, ".obis"))
+ assert files == ['config.json']
+
+ with open(os.path.join(tmp_dir_path, ".obis", "config.json")) as f:
+ config_local = json.load(f)
+ assert config_local.get('is_physical') is True
+
+
# TODO Test that if the data set registration fails, the data_set_id is reverted
def set_registration_configuration(dm, properties=None):
@@ -288,10 +320,11 @@ def set_registration_configuration(dm, properties=None):
def prepare_registration_expectations(dm):
dm.openbis = Mock()
dm.openbis.is_session_active = MagicMock(return_value=True)
- edms = ExternalDMS(dm.openbis, {'code': 'AUSER-MACHINE-ffffffff', 'label': 'AUSER-MACHINE-ffffffff'})
+ edms = ExternalDMS(dm.openbis,
+ {'code': 'AUSER-MACHINE-ffffffff', 'label': 'AUSER-MACHINE-ffffffff'})
dm.openbis.create_external_data_management_system = MagicMock(return_value=edms)
dm.openbis.get_external_data_management_system = MagicMock(return_value=edms)
- dm.openbis.create_permId.side_effect = [0, 1, 2 , 3, 4, 5, 6, 7, 8, 9]
+ dm.openbis.create_permId.side_effect = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
prepare_new_data_set_expectations(dm)
@@ -301,8 +334,8 @@ def prepare_new_data_set_expectations(dm, properties={}):
data_set = DataSet(dm.openbis, None,
{'code': perm_id, 'properties': properties, 'components': [],
"parents": [], "children": [], "samples": [], 'tags': [], 'containers': [],
- 'physicalData': None, 'linkedData': { 'contentCopies': []}},
- kind='LINK')
+ 'physicalData': None, 'linkedData': {'contentCopies': []}},
+ kind='LINK')
dm.openbis.new_git_data_set = MagicMock(return_value=data_set)
dm.openbis.get_dataset = MagicMock(return_value=data_set)
@@ -312,11 +345,13 @@ def prepare_new_data_set_expectations(dm, properties={}):
dm.openbis.get_sample = MagicMock(return_value=sample)
-
-def check_new_data_set_expectations(dm, tmp_dir_path, commit_id, repository_id, external_dms, data_set_id, parent_id, properties,
+def check_new_data_set_expectations(dm, tmp_dir_path, commit_id, repository_id, external_dms,
+ data_set_id, parent_id, properties,
contents):
- dm.openbis.new_git_data_set.assert_called_with('DS_TYPE', tmp_dir_path, commit_id, repository_id, external_dms,
- data_set_code=data_set_id, experiment=None, parents=parent_id, properties=properties,
+ dm.openbis.new_git_data_set.assert_called_with('DS_TYPE', tmp_dir_path, commit_id,
+ repository_id, external_dms,
+ data_set_code=data_set_id, experiment=None,
+ parents=parent_id, properties=properties,
contents=contents, sample="/SAMPLE/ID")