From 8075c740b72ffb0c442ea60d7493794bf5eb2fa1 Mon Sep 17 00:00:00 2001
From: Yves Noirjean <yves.noirjean@id.ethz.ch>
Date: Tue, 15 May 2018 14:29:35 +0200
Subject: [PATCH] SSDM-6476: fixing integration tests
---
.../integration_tests/integration_tests.py | 296 +++++++++---------
1 file changed, 148 insertions(+), 148 deletions(-)
diff --git a/src/python/OBis/integration_tests/integration_tests.py b/src/python/OBis/integration_tests/integration_tests.py
index 16f088aec0f..85d7c84d814 100644
--- a/src/python/OBis/integration_tests/integration_tests.py
+++ b/src/python/OBis/integration_tests/integration_tests.py
@@ -32,20 +32,20 @@ def test_obis(tmpdir):
o = Openbis('https://obisserver:8443', verify_certificates=False)
o.login('admin', 'admin', save_token=True)
- output_buffer = '=================== 1. Global configuration ===================\n'
+ output_buffer = '=================== 1. Global settings ===================\n'
if os.path.exists('~/.obis'):
os.rmdir('~/.obis')
- cmd('obis config -g openbis_url https://obisserver:8443')
- cmd('obis config -g user admin')
- cmd('obis config -g data_set_type UNKNOWN')
- cmd('obis config -g verify_certificates false')
- cmd('obis config -g hostname ' + socket.gethostname())
- config = get_config_global()
- assert config['openbis_url'] == 'https://obisserver:8443'
- assert config['user'] == 'admin'
- assert config['data_set_type'] == 'UNKNOWN'
- assert config['verify_certificates'] == False
- assert config['hostname'] == socket.gethostname()
+ cmd('obis config -g set openbis_url=https://obisserver:8443')
+ cmd('obis config -g set user=admin')
+ cmd('obis config -g set verify_certificates=false')
+ cmd('obis config -g set hostname=' + socket.gethostname())
+ cmd('obis data_set -g set data_set_type=UNKNOWN')
+ settings = get_settings_global()
+ assert settings['config']['openbis_url'] == 'https://obisserver:8443'
+ assert settings['config']['user'] == 'admin'
+ assert settings['config']['verify_certificates'] == False
+ assert settings['config']['hostname'] == socket.gethostname()
+ assert settings['data_set']['data_set_type'] == 'UNKNOWN'
with cd(tmpdir): cmd('mkdir obis_data')
with cd(tmpdir + '/obis_data'):
@@ -57,67 +57,67 @@ def test_obis(tmpdir):
result = cmd('obis status')
assert '?? .obis/config.json' in result
assert '?? file' in result
- cmd('obis config object_id /DEFAULT/DEFAULT')
+ cmd('obis object set object_id=/DEFAULT/DEFAULT')
result = cmd('obis commit -m \'commit-message\'')
- config = get_config()
- assert config['external_dms_id'].startswith('ADMIN-' + socket.gethostname().upper())
- assert len(config['repository_id']) == 36
- assert "Created data set {}.".format(config['data_set_id']) in result
- data_set = o.get_dataset(config['data_set_id']).data
- assert_matching(config, data_set, tmpdir, 'obis_data/data1')
+ settings = get_settings()
+ assert settings['repository']['external_dms_id'].startswith('ADMIN-' + socket.gethostname().upper())
+ assert len(settings['repository']['repository_id']) == 36
+ assert "Created data set {}.".format(settings['repository']['data_set_id']) in result
+ data_set = o.get_dataset(settings['repository']['data_set_id']).data
+ assert_matching(settings, data_set, tmpdir, 'obis_data/data1')
output_buffer = '=================== 3. Second commit ===================\n'
with cd('data1'):
- config_before = get_config()
+ settings_before = get_settings()
cmd('dd if=/dev/zero of=big_file bs=1000000 count=1')
result = cmd('obis commit -m \'commit-message\'')
- config = get_config()
- assert config['data_set_id'] != config_before['data_set_id']
- assert config['external_dms_id'].startswith('ADMIN-' + socket.gethostname().upper())
- assert config['external_dms_id'] == config_before['external_dms_id']
- assert config['repository_id'] == config_before['repository_id']
- assert "Created data set {}.".format(config['data_set_id']) in result
+ settings = get_settings()
+ assert settings['repository']['data_set_id'] != settings_before['repository']['data_set_id']
+ assert settings['repository']['external_dms_id'].startswith('ADMIN-' + socket.gethostname().upper())
+ assert settings['repository']['external_dms_id'] == settings_before['repository']['external_dms_id']
+ assert settings['repository']['repository_id'] == settings_before['repository']['repository_id']
+ assert "Created data set {}.".format(settings['repository']['data_set_id']) in result
result = cmd('git annex info big_file')
assert 'file: big_file' in result
assert 'key: MD5-s1000000--879f4bba57ed37c9ec5e5aedf9864698' in result
assert 'present: true' in result
- data_set = o.get_dataset(config['data_set_id']).data
- assert_matching(config, data_set, tmpdir, 'obis_data/data1')
- assert data_set['parents'][0]['code'] == config_before['data_set_id']
+ data_set = o.get_dataset(settings['repository']['data_set_id']).data
+ assert_matching(settings, data_set, tmpdir, 'obis_data/data1')
+ assert data_set['parents'][0]['code'] == settings_before['repository']['data_set_id']
output_buffer = '=================== 4. Second repository ===================\n'
cmd('obis init data2')
with cd('data2'):
- cmd('obis config object_id /DEFAULT/DEFAULT')
+ cmd('obis object set object_id=/DEFAULT/DEFAULT')
cmd('touch file')
result = cmd('obis commit -m \'commit-message\'')
- with cd('../data1'): config_data1 = get_config()
- config = get_config()
- assert config['external_dms_id'].startswith('ADMIN-' + socket.gethostname().upper())
- assert config['external_dms_id'] == config_data1['external_dms_id']
- assert len(config['repository_id']) == 36
- assert config['repository_id'] != config_data1['repository_id']
- assert "Created data set {}.".format(config['data_set_id']) in result
- data_set = o.get_dataset(config['data_set_id']).data
- assert_matching(config, data_set, tmpdir, 'obis_data/data2')
+ with cd('../data1'): settings_data1 = get_settings()
+ settings = get_settings()
+ assert settings['repository']['external_dms_id'].startswith('ADMIN-' + socket.gethostname().upper())
+ assert settings['repository']['external_dms_id'] == settings_data1['repository']['external_dms_id']
+ assert len(settings['repository']['repository_id']) == 36
+ assert settings['repository']['repository_id'] != settings_data1['repository']['repository_id']
+ assert "Created data set {}.".format(settings['repository']['data_set_id']) in result
+ data_set = o.get_dataset(settings['repository']['data_set_id']).data
+ assert_matching(settings, data_set, tmpdir, 'obis_data/data2')
output_buffer = '=================== 5. Second external dms ===================\n'
with cd(tmpdir): cmd('mkdir obis_data_b')
with cd(tmpdir + '/obis_data_b'):
cmd('obis init data3')
with cd('data3'):
- cmd('obis config object_id /DEFAULT/DEFAULT')
+ cmd('obis object set object_id=/DEFAULT/DEFAULT')
cmd('touch file')
result = cmd('obis commit -m \'commit-message\'')
- with cd('../../obis_data/data1'): config_data1 = get_config()
- config = get_config()
- assert config['external_dms_id'].startswith('ADMIN-' + socket.gethostname().upper())
- assert config['external_dms_id'] != config_data1['external_dms_id']
- assert len(config['repository_id']) == 36
- assert config['repository_id'] != config_data1['repository_id']
- assert "Created data set {}.".format(config['data_set_id']) in result
- data_set = o.get_dataset(config['data_set_id']).data
- assert_matching(config, data_set, tmpdir, 'obis_data_b/data3')
+ with cd('../../obis_data/data1'): settings_data1 = get_settings()
+ settings = get_settings()
+ assert settings['repository']['external_dms_id'].startswith('ADMIN-' + socket.gethostname().upper())
+ assert settings['repository']['external_dms_id'] != settings_data1['repository']['external_dms_id']
+ assert len(settings['repository']['repository_id']) == 36
+ assert settings['repository']['repository_id'] != settings_data1['repository']['repository_id']
+ assert "Created data set {}.".format(settings['repository']['data_set_id']) in result
+ data_set = o.get_dataset(settings['repository']['data_set_id']).data
+ assert_matching(settings, data_set, tmpdir, 'obis_data_b/data3')
output_buffer = '=================== 6. Error on first commit ===================\n'
with cd(tmpdir + '/obis_data'):
@@ -128,102 +128,102 @@ def test_obis(tmpdir):
assert 'Missing configuration settings for [\'object_id\', \'collection_id\'].' in result
result = cmd('obis status')
assert '?? file' in result
- cmd('obis config object_id /DEFAULT/DEFAULT')
+ cmd('obis object set object_id=/DEFAULT/DEFAULT')
result = cmd('obis commit -m \'commit-message\'')
- config = get_config()
- assert "Created data set {}.".format(config['data_set_id']) in result
- data_set = o.get_dataset(config['data_set_id']).data
- assert_matching(config, data_set, tmpdir, 'obis_data/data4')
+ settings = get_settings()
+ assert "Created data set {}.".format(settings['repository']['data_set_id']) in result
+ data_set = o.get_dataset(settings['repository']['data_set_id']).data
+ assert_matching(settings, data_set, tmpdir, 'obis_data/data4')
output_buffer = '=================== 7. Attach data set to a collection ===================\n'
cmd('obis init data5')
with cd('data5'):
cmd('touch file')
- cmd('obis config collection_id /DEFAULT/DEFAULT/DEFAULT')
+ cmd('obis collection set collection_id=/DEFAULT/DEFAULT/DEFAULT')
result = cmd('obis commit -m \'commit-message\'')
- config = get_config()
- assert config['external_dms_id'].startswith('ADMIN-' + socket.gethostname().upper())
- assert len(config['repository_id']) == 36
- assert "Created data set {}.".format(config['data_set_id']) in result
- data_set = o.get_dataset(config['data_set_id']).data
- assert_matching(config, data_set, tmpdir, 'obis_data/data5')
+ settings = get_settings()
+ assert settings['repository']['external_dms_id'].startswith('ADMIN-' + socket.gethostname().upper())
+ assert len(settings['repository']['repository_id']) == 36
+ assert "Created data set {}.".format(settings['repository']['data_set_id']) in result
+ data_set = o.get_dataset(settings['repository']['data_set_id']).data
+ assert_matching(settings, data_set, tmpdir, 'obis_data/data5')
output_buffer = '=================== 8. Addref ===================\n'
cmd('cp -r data1 data6')
cmd('obis addref data6')
- with cd('data1'): config_data1 = get_config()
- with cd('data6'): config_data6 = get_config()
- assert config_data6 == config_data1
+ with cd('data1'): settings_data1 = get_settings()
+ with cd('data6'): settings_data6 = get_settings()
+ assert settings_data6 == settings_data1
result = cmd('obis addref data6')
assert 'DataSet already exists in the database' in result
result = cmd('obis addref data7')
assert 'Invalid value' in result
- data_set = o.get_dataset(config_data6['data_set_id']).data
- with cd('data6'): assert_matching(config_data6, data_set, tmpdir, 'obis_data/data6')
+ data_set = o.get_dataset(settings_data6['repository']['data_set_id']).data
+ with cd('data6'): assert_matching(settings_data6, data_set, tmpdir, 'obis_data/data6')
output_buffer = '=================== 9. Local clone ===================\n'
- with cd('data2'): config_data2 = get_config()
+ with cd('data2'): settings_data2 = get_settings()
with cd('../obis_data_b'):
- cmd('obis clone ' + config_data2['data_set_id'])
+ cmd('obis clone ' + settings_data2['repository']['data_set_id'])
with cd('data2'):
- config_data2_clone = get_config()
- assert config_data2_clone['external_dms_id'].startswith('ADMIN-' + socket.gethostname().upper())
- assert config_data2_clone['external_dms_id'] != config_data2['external_dms_id']
- data_set = o.get_dataset(config_data2_clone['data_set_id']).data
- assert_matching(config_data2_clone, data_set, tmpdir, 'obis_data_b/data2')
- del config_data2['external_dms_id']
- del config_data2_clone['external_dms_id']
- assert config_data2_clone == config_data2
+ settings_data2_clone = get_settings()
+ assert settings_data2_clone['repository']['external_dms_id'].startswith('ADMIN-' + socket.gethostname().upper())
+ assert settings_data2_clone['repository']['external_dms_id'] != settings_data2['repository']['external_dms_id']
+ data_set = o.get_dataset(settings_data2_clone['repository']['data_set_id']).data
+ assert_matching(settings_data2_clone, data_set, tmpdir, 'obis_data_b/data2')
+ del settings_data2['repository']['external_dms_id']
+ del settings_data2_clone['repository']['external_dms_id']
+ assert settings_data2_clone == settings_data2
output_buffer = '=================== 11. Init analysis ===================\n'
cmd('obis init_analysis -p data1 analysis1')
with cd('analysis1'):
- cmd('obis config object_id /DEFAULT/DEFAULT')
+ cmd('obis object set object_id=/DEFAULT/DEFAULT')
cmd('touch file')
result = cmd('obis commit -m \'commit-message\'')
- with cd('data1'): config_data1 = get_config()
+ with cd('data1'): settings_data1 = get_settings()
with cd('analysis1'):
- config_analysis1 = get_config()
- assert "Created data set {}.".format(config_analysis1['data_set_id']) in result
- assert len(config_analysis1['repository_id']) == 36
- assert config_analysis1['repository_id'] != config_data1['repository_id']
- assert config_analysis1['data_set_id'] != config_data1['data_set_id']
- data_set = o.get_dataset(config_analysis1['data_set_id']).data
- assert_matching(config_analysis1, data_set, tmpdir, 'obis_data/analysis1')
- assert data_set['parents'][0]['code'] == config_data1['data_set_id']
+ settings_analysis1 = get_settings()
+ assert "Created data set {}.".format(settings_analysis1['repository']['data_set_id']) in result
+ assert len(settings_analysis1['repository']['repository_id']) == 36
+ assert settings_analysis1['repository']['repository_id'] != settings_data1['repository']['repository_id']
+ assert settings_analysis1['repository']['data_set_id'] != settings_data1['repository']['data_set_id']
+ data_set = o.get_dataset(settings_analysis1['repository']['data_set_id']).data
+ assert_matching(settings_analysis1, data_set, tmpdir, 'obis_data/analysis1')
+ assert data_set['parents'][0]['code'] == settings_data1['repository']['data_set_id']
with cd('data1'):
cmd('obis init_analysis analysis2')
with cd('analysis2'):
- cmd('obis config object_id /DEFAULT/DEFAULT')
+ cmd('obis object set object_id=/DEFAULT/DEFAULT')
cmd('touch file')
result = cmd('obis commit -m \'commit-message\'')
- config_analysis2 = get_config()
- assert "Created data set {}.".format(config_analysis2['data_set_id']) in result
- assert len(config_analysis2['repository_id']) == 36
- assert config_analysis2['repository_id'] != config_data1['repository_id']
- assert config_analysis2['data_set_id'] != config_data1['data_set_id']
- data_set = o.get_dataset(config_analysis2['data_set_id']).data
- assert_matching(config_analysis2, data_set, tmpdir, 'obis_data/data1/analysis2')
- assert data_set['parents'][0]['code'] == config_data1['data_set_id']
+ settings_analysis2 = get_settings()
+ assert "Created data set {}.".format(settings_analysis2['repository']['data_set_id']) in result
+ assert len(settings_analysis2['repository']['repository_id']) == 36
+ assert settings_analysis2['repository']['repository_id'] != settings_data1['repository']['repository_id']
+ assert settings_analysis2['repository']['data_set_id'] != settings_data1['repository']['data_set_id']
+ data_set = o.get_dataset(settings_analysis2['repository']['data_set_id']).data
+ assert_matching(settings_analysis2, data_set, tmpdir, 'obis_data/data1/analysis2')
+ assert data_set['parents'][0]['code'] == settings_data1['repository']['data_set_id']
result = cmd('git check-ignore analysis2')
assert 'analysis2' in result
output_buffer = '=================== 12. Metadata only commit ===================\n'
cmd('obis init data7')
with cd('data7'):
- cmd('obis config object_id /DEFAULT/DEFAULT')
+ cmd('obis object set object_id=/DEFAULT/DEFAULT')
cmd('touch file')
result = cmd('obis commit -m \'commit-message\'')
- config = get_config()
- assert "Created data set {}.".format(config['data_set_id']) in result
- data_set = o.get_dataset(config['data_set_id']).data
- assert_matching(config, data_set, tmpdir, 'obis_data/data7')
- cmd('obis config collection_id /DEFAULT/DEFAULT/DEFAULT')
+ settings = get_settings()
+ assert "Created data set {}.".format(settings['repository']['data_set_id']) in result
+ data_set = o.get_dataset(settings['repository']['data_set_id']).data
+ assert_matching(settings, data_set, tmpdir, 'obis_data/data7')
+ cmd('obis collection set collection_id=/DEFAULT/DEFAULT/DEFAULT')
result = cmd('obis commit -m \'commit-message\'')
- config = get_config()
- assert "Created data set {}.".format(config['data_set_id']) in result
- data_set = o.get_dataset(config['data_set_id']).data
- assert_matching(config, data_set, tmpdir, 'obis_data/data7')
+ settings = get_settings()
+ assert "Created data set {}.".format(settings['repository']['data_set_id']) in result
+ data_set = o.get_dataset(settings['repository']['data_set_id']).data
+ assert_matching(settings, data_set, tmpdir, 'obis_data/data7')
output_buffer = '=================== 13. obis sync ===================\n'
with cd('data7'):
@@ -231,37 +231,37 @@ def test_obis(tmpdir):
cmd('git add file2')
cmd('git commit -m \'msg\'')
result = cmd('obis sync')
- config = get_config()
- assert "Created data set {}.".format(config['data_set_id']) in result
- data_set = o.get_dataset(config['data_set_id']).data
- assert_matching(config, data_set, tmpdir, 'obis_data/data7')
+ settings = get_settings()
+ assert "Created data set {}.".format(settings['repository']['data_set_id']) in result
+ data_set = o.get_dataset(settings['repository']['data_set_id']).data
+ assert_matching(settings, data_set, tmpdir, 'obis_data/data7')
result = cmd('obis sync')
assert 'Nothing to sync' in result
- output_buffer = '=================== 14. Configure data set properties ===================\n'
+ output_buffer = '=================== 14. Set data set properties ===================\n'
cmd('obis init data8')
with cd('data8'):
- result = cmd('obis config -p a 0')
- config = get_config()
- assert config['data_set_properties'] == { 'A': '0' }
- cmd('obis config data_set_properties {"a":"0","b":"1","c":"2"}')
- cmd('obis config -p c 3')
- config = get_config()
- assert config['data_set_properties'] == { 'A': '0', 'B': '1', 'C': '3' }
- result = cmd('obis config data_set_properties {"a":"0","A":"1"}')
+ result = cmd('obis data_set -p set a=0')
+ settings = get_settings()
+ assert settings['data_set']['data_set_properties'] == { 'A': '0' }
+ cmd('obis data_set set data_set_properties={"a":"0","b":"1","c":"2"}')
+ cmd('obis data_set -p set c=3')
+ settings = get_settings()
+ assert settings['data_set']['data_set_properties'] == { 'A': '0', 'B': '1', 'C': '3' }
+ result = cmd('obis data_set set data_set_properties={"a":"0","A":"1"}')
assert 'Duplicate key after capitalizing JSON config: A' in result
output_buffer = '=================== 15. Removeref ===================\n'
- with cd('data6'): config = get_config()
- content_copies = get_data_set(o, config)['linkedData']['contentCopies']
+ with cd('data6'): settings = get_settings()
+ content_copies = get_data_set(o, settings)['linkedData']['contentCopies']
assert len(content_copies) == 2
cmd('obis removeref data6')
- content_copies = get_data_set(o, config)['linkedData']['contentCopies']
+ content_copies = get_data_set(o, settings)['linkedData']['contentCopies']
assert len(content_copies) == 1
assert content_copies[0]['path'].endswith('data1')
cmd('obis addref data6')
cmd('obis removeref data1')
- content_copies = get_data_set(o, config)['linkedData']['contentCopies']
+ content_copies = get_data_set(o, settings)['linkedData']['contentCopies']
assert len(content_copies) == 1
assert content_copies[0]['path'].endswith('data6')
result = cmd('obis removeref data1')
@@ -272,23 +272,23 @@ def test_obis(tmpdir):
cmd('obis init data10')
with cd('data10'):
cmd('touch file')
- cmd('obis config object_id /DEFAULT/DEFAULT')
+ cmd('obis object set object_id=/DEFAULT/DEFAULT')
# use MD5 form git annex by default
result = cmd('obis commit -m \'commit-message\'')
- config = get_config()
- search_result = o.search_files(config['data_set_id'])
+ settings = get_settings()
+ search_result = o.search_files(settings['repository']['data_set_id'])
files = list(filter(lambda file: file['fileLength'] > 0, search_result['objects']))
- assert len(files) == 3
+ assert len(files) == 5
for file in files:
assert file['checksumType'] == "MD5"
assert len(file['checksum']) == 32
# don't use git annex hash - use default CRC32
- cmd('obis config git_annex_hash_as_checksum false')
+ cmd('obis config set git_annex_hash_as_checksum=false')
result = cmd('obis commit -m \'commit-message\'')
- config = get_config()
- search_result = o.search_files(config['data_set_id'])
+ settings = get_settings()
+ search_result = o.search_files(settings['repository']['data_set_id'])
files = list(filter(lambda file: file['fileLength'] > 0, search_result['objects']))
- assert len(files) == 3
+ assert len(files) == 5
for file in files:
assert file['checksumType'] is None
assert file['checksum'] is None
@@ -298,12 +298,12 @@ def test_obis(tmpdir):
cmd('obis init data9')
with cd('data9'):
cmd('touch file')
- cmd('obis config object_id /DEFAULT/DEFAULT')
+ cmd('obis object set object_id=/DEFAULT/DEFAULT')
result = cmd('obis commit -m \'commit-message\'')
- config = get_config()
- assert "Created data set {}.".format(config['data_set_id']) in result
+ settings = get_settings()
+ assert "Created data set {}.".format(settings['repository']['data_set_id']) in result
cmd('touch file2')
- cmd('obis config user watney')
+ cmd('obis config user=watney')
# expect timeout because obis is asking for the password of the new user
try:
timeout = False
@@ -313,14 +313,14 @@ def test_obis(tmpdir):
assert timeout == True
-def get_config():
- return json.loads(cmd('obis config'))
+def get_settings():
+ return json.loads(cmd('obis settings get'))
-def get_config_global():
- return json.loads(cmd('obis config -g'))
+def get_settings_global():
+ return json.loads(cmd('obis settings -g get'))
-def get_data_set(o, config):
- return o.get_dataset(config['data_set_id']).data
+def get_data_set(o, settings):
+ return o.get_dataset(settings['repository']['data_set_id']).data
@contextmanager
def cd(newdir):
@@ -348,14 +348,14 @@ def get_cmd_result(completed_process, tmpdir=''):
result += completed_process.stdout.decode('utf-8').strip()
return result
-def assert_matching(config, data_set, tmpdir, path):
+def assert_matching(settings, data_set, tmpdir, path):
content_copies = data_set['linkedData']['contentCopies']
content_copy = list(filter(lambda cc: cc['path'].endswith(path) == 1, content_copies))[0]
- assert data_set['type']['code'] == config['data_set_type']
- assert content_copy['externalDms']['code'] == config['external_dms_id']
+ assert data_set['type']['code'] == settings['data_set']['data_set_type']
+ assert content_copy['externalDms']['code'] == settings['repository']['external_dms_id']
assert content_copy['gitCommitHash'] == cmd('git rev-parse --short HEAD')
- assert content_copy['gitRepositoryId'] == config['repository_id']
- if config['object_id'] is not None:
- assert data_set['sample']['identifier']['identifier'] == config['object_id']
- if config['collection_id'] is not None:
- assert data_set['experiment']['identifier']['identifier'] == config['collection_id']
+ assert content_copy['gitRepositoryId'] == settings['repository']['repository_id']
+ if settings['object']['object_id'] is not None:
+ assert data_set['sample']['identifier']['identifier'] == settings['object']['object_id']
+ if settings['collection']['collection_id'] is not None:
+ assert data_set['experiment']['identifier']['identifier'] == settings['collection']['collection_id']
--
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