diff --git a/src/python/OBis/integration_tests/00_get_commit_hash.sh b/src/python/OBis/integration_tests/00_get_commit_hash.sh
new file mode 100755
index 0000000000000000000000000000000000000000..c48c86179e413effa41cd256fd994408ad5879a2
--- /dev/null
+++ b/src/python/OBis/integration_tests/00_get_commit_hash.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+cd $1
+git rev-parse --short HEAD
+
diff --git a/src/python/OBis/integration_tests/integration_tests.py b/src/python/OBis/integration_tests/integration_tests.py
index 3cfa87ae1479ecc60c6b8f7731c259908176eb33..f134ba5a8e92e1013e5e47f41e1d76e0d6bff502 100644
--- a/src/python/OBis/integration_tests/integration_tests.py
+++ b/src/python/OBis/integration_tests/integration_tests.py
@@ -1,6 +1,9 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
+# can be run on vagrant like this:
+# vagrant ssh obisserver -c 'cd /vagrant_python/OBis/integration_tests && pytest ./integration_tests.py'
+
import json
import subprocess
import socket
@@ -19,6 +22,19 @@ def run(cmd, tmpdir="", params=[]):
return result
+def assert_matching(config, 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 content_copy['gitCommitHash'] == run('./00_get_commit_hash.sh', str(tmpdir) + '/' + path)
+ 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']
+
+
def test_obis(tmpdir):
# 0. pybis login
o = Openbis('https://localhost:8443', verify_certificates=False)
@@ -41,6 +57,9 @@ def test_obis(tmpdir):
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')
+
# 3. Second commit
config_before = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data1'))
@@ -55,6 +74,9 @@ def test_obis(tmpdir):
assert 'file: big_file' in result
assert 'key: SHA256E-s1000000--d29751f2649b32ff572b5e0a9f541ea660a50f94ff0beedfb0b692b924cc8025' 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']
# 4. Second repository
result = run('./04_second_repository.sh', tmpdir)
@@ -65,6 +87,8 @@ def test_obis(tmpdir):
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')
# 5. Second external dms
result = run('./05_second_external_dms.sh', tmpdir)
@@ -75,6 +99,8 @@ def test_obis(tmpdir):
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')
# 6. Error on first commit
result = run('./06_error_on_first_commit_1_error.sh', tmpdir)
@@ -84,6 +110,8 @@ def test_obis(tmpdir):
result = run('./06_error_on_first_commit_3_commit.sh', tmpdir)
config = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data4'))
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')
# 7. Attach data set to a collection
result = run('./07_attach_to_collection.sh', tmpdir)
@@ -91,6 +119,8 @@ def test_obis(tmpdir):
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')
# 8. Addref
result = run('./08_addref_1_success.sh', tmpdir)
@@ -101,6 +131,8 @@ def test_obis(tmpdir):
assert 'DataSet already exists in the database' in result
result = run('./08_addref_3_non-existent.sh', tmpdir)
assert 'Invalid value' in result
+ data_set = o.get_dataset(config_data6['data_set_id']).data
+ assert_matching(config_data6, data_set, tmpdir, 'obis_data/data6')
# 9. Local clone
config_data2 = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data2'))
@@ -108,6 +140,8 @@ def test_obis(tmpdir):
config_data2_clone = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data_b/data2'))
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
@@ -120,6 +154,9 @@ def test_obis(tmpdir):
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']
result = run('./11_init_analysis_2_internal.sh', tmpdir)
config_analysis2 = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data1/analysis2'))
assert "Created data set {}.".format(config_analysis2['data_set_id']) in result
@@ -128,18 +165,27 @@ def test_obis(tmpdir):
assert config_analysis2['data_set_id'] != config_data1['data_set_id']
result = run('./11_init_analysis_3_git_check_ignore.sh', tmpdir)
assert 'analysis2' in result
+ 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']
# 12. Metadata only commit
result = run('./12_metadata_only_1_commit.sh', tmpdir)
config = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data7'))
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')
result = run('./12_metadata_only_2_metadata_commit.sh', tmpdir)
config = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data7'))
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')
# 13. obis sync
result = run('./13_sync_1_git_commit_and_sync.sh', tmpdir)
config = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data7'))
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')
result = run('./13_sync_2_only_sync.sh', tmpdir)
assert 'Nothing to sync' in result
diff --git a/src/vagrant/obis/initialize/install_openbis.sh b/src/vagrant/obis/initialize/install_openbis.sh
index 7df0a7802ea5d7b0d018686280113043bee27605..480c8f141db15749140c7d0f1d365a395b30cc30 100755
--- a/src/vagrant/obis/initialize/install_openbis.sh
+++ b/src/vagrant/obis/initialize/install_openbis.sh
@@ -13,6 +13,7 @@ if [ ! -L /openbis_installed ]; then
sudo su openbis -c "export ADMIN_PASSWORD=admin && export ETLSERVER_PASSWORD=etlserver && $ob_dir/run-console.sh"
sudo touch /openbis_installed
+ sudo chmod 777 /openbis_installed
popd $@ > /dev/null