diff --git a/src/python/OBis/integration_tests/00_get_config.sh b/src/python/OBis/integration_tests/00_get_config.sh
new file mode 100755
index 0000000000000000000000000000000000000000..7df8639dbc1125509232b47b959c542cc4e409d8
--- /dev/null
+++ b/src/python/OBis/integration_tests/00_get_config.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+cd $1
+obis config
diff --git a/src/python/OBis/integration_tests/00_get_config_global.sh b/src/python/OBis/integration_tests/00_get_config_global.sh
new file mode 100755
index 0000000000000000000000000000000000000000..13449f27ca4c4ba6fbee349bda810ad132ac7868
--- /dev/null
+++ b/src/python/OBis/integration_tests/00_get_config_global.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+obis config -g
diff --git a/src/python/OBis/integration_tests/01_global_config.sh b/src/python/OBis/integration_tests/01_global_config.sh
new file mode 100755
index 0000000000000000000000000000000000000000..ec95bed0b31bb2d1ff86c8aee5511018a8f0cbf0
--- /dev/null
+++ b/src/python/OBis/integration_tests/01_global_config.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+if [ -d "~/.obis" ]; then
+ rm -r ~/.obis
+fi
+
+obis config -g openbis_url https://localhost:8443
+obis config -g user admin
+obis config -g data_set_type UNKNOWN
+obis config -g verify_certificates false
+obis config -g hostname `hostname`
diff --git a/src/python/OBis/integration_tests/02_first_commit_1_create_repository.sh b/src/python/OBis/integration_tests/02_first_commit_1_create_repository.sh
new file mode 100755
index 0000000000000000000000000000000000000000..f507e0123b1580b5e46103317170a8a7dbb4425a
--- /dev/null
+++ b/src/python/OBis/integration_tests/02_first_commit_1_create_repository.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+rm -rf $1/obis_data
+mkdir $1/obis_data && cd $1/obis_data
+obis init data1 && cd data1
+echo content >> file
+obis status
diff --git a/src/python/OBis/integration_tests/02_first_commit_2_commit.sh b/src/python/OBis/integration_tests/02_first_commit_2_commit.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5a62ded9a6139a9f41a69f0910b83972fa8b9455
--- /dev/null
+++ b/src/python/OBis/integration_tests/02_first_commit_2_commit.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+cd $1/obis_data/data1
+
+obis config object_id /DEFAULT/DEFAULT
+obis commit -m 'commit message'
diff --git a/src/python/OBis/integration_tests/03_second_commit_1_commit.sh b/src/python/OBis/integration_tests/03_second_commit_1_commit.sh
new file mode 100755
index 0000000000000000000000000000000000000000..7488bbdcca86ffed934d76d12974e9e8315a556a
--- /dev/null
+++ b/src/python/OBis/integration_tests/03_second_commit_1_commit.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+cd $1/obis_data/data1
+
+dd if=/dev/zero of=big_file bs=1000000 count=1
+obis commit -m 'commit message'
diff --git a/src/python/OBis/integration_tests/03_second_commit_2_git_annex_info.sh b/src/python/OBis/integration_tests/03_second_commit_2_git_annex_info.sh
new file mode 100755
index 0000000000000000000000000000000000000000..f3e668bce882c1a334d1571a4518046d138af3b1
--- /dev/null
+++ b/src/python/OBis/integration_tests/03_second_commit_2_git_annex_info.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+cd $1/obis_data/data1
+
+git annex info big_file
diff --git a/src/python/OBis/integration_tests/04_second_repository.sh b/src/python/OBis/integration_tests/04_second_repository.sh
new file mode 100755
index 0000000000000000000000000000000000000000..903e8a64b9edf464cb80b91176e20363fd5ff2e3
--- /dev/null
+++ b/src/python/OBis/integration_tests/04_second_repository.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+cd $1/obis_data
+obis init data2 && cd data2
+obis config object_id /DEFAULT/DEFAULT
+echo content >> file
+obis commit -m 'commit message'
diff --git a/src/python/OBis/integration_tests/05_second_external_dms.sh b/src/python/OBis/integration_tests/05_second_external_dms.sh
new file mode 100755
index 0000000000000000000000000000000000000000..c7c4ef87969a50b551bd632d4fcbcd2c3a713782
--- /dev/null
+++ b/src/python/OBis/integration_tests/05_second_external_dms.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+mkdir $1/obis_data_b && cd $1/obis_data_b
+obis init data3 && cd data3
+obis config object_id /DEFAULT/DEFAULT
+echo content >> file
+obis commit -m 'commit message'
diff --git a/src/python/OBis/integration_tests/06_error_on_first_commit_1_error.sh b/src/python/OBis/integration_tests/06_error_on_first_commit_1_error.sh
new file mode 100755
index 0000000000000000000000000000000000000000..3c58d80edce46b66c55023226dbdcacba101fe9f
--- /dev/null
+++ b/src/python/OBis/integration_tests/06_error_on_first_commit_1_error.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+cd $1/obis_data
+obis init data4 && cd data4
+echo content >> file
+obis commit -m 'commit message'
diff --git a/src/python/OBis/integration_tests/06_error_on_first_commit_2_status.sh b/src/python/OBis/integration_tests/06_error_on_first_commit_2_status.sh
new file mode 100755
index 0000000000000000000000000000000000000000..8815e2f5b74ac894b2b9705c27e44176752026f6
--- /dev/null
+++ b/src/python/OBis/integration_tests/06_error_on_first_commit_2_status.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+cd $1/obis_data/data4
+obis status
diff --git a/src/python/OBis/integration_tests/06_error_on_first_commit_3_commit.sh b/src/python/OBis/integration_tests/06_error_on_first_commit_3_commit.sh
new file mode 100755
index 0000000000000000000000000000000000000000..6cb1ce4b2cd566ebdc8ca368aff6a8c757a346c6
--- /dev/null
+++ b/src/python/OBis/integration_tests/06_error_on_first_commit_3_commit.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+cd $1/obis_data/data4
+obis config object_id /DEFAULT/DEFAULT
+obis commit -m 'commit message'
diff --git a/src/python/OBis/integration_tests/07_attach_to_collection.sh b/src/python/OBis/integration_tests/07_attach_to_collection.sh
new file mode 100755
index 0000000000000000000000000000000000000000..3ea844b98ecdd347c4adbecf0ec9cbfb361eb7cc
--- /dev/null
+++ b/src/python/OBis/integration_tests/07_attach_to_collection.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+cd $1/obis_data
+obis init data5 && cd data5
+echo content >> file
+obis config collection_id /DEFAULT/DEFAULT/DEFAULT
+obis commit -m 'msg'
+
diff --git a/src/python/OBis/integration_tests/08_addref_1_success.sh b/src/python/OBis/integration_tests/08_addref_1_success.sh
new file mode 100755
index 0000000000000000000000000000000000000000..f368719c5a216c3305eb2b72e71d53e619665cc5
--- /dev/null
+++ b/src/python/OBis/integration_tests/08_addref_1_success.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+cd $1/obis_data
+cp -r data1 data6
+obis addref data6
+
diff --git a/src/python/OBis/integration_tests/08_addref_2_duplicate.sh b/src/python/OBis/integration_tests/08_addref_2_duplicate.sh
new file mode 100755
index 0000000000000000000000000000000000000000..0429bbf6221c3c75e7202b7fb862c4abbd3c0f68
--- /dev/null
+++ b/src/python/OBis/integration_tests/08_addref_2_duplicate.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+cd $1/obis_data
+obis addref data6
+
diff --git a/src/python/OBis/integration_tests/08_addref_3_non-existent.sh b/src/python/OBis/integration_tests/08_addref_3_non-existent.sh
new file mode 100755
index 0000000000000000000000000000000000000000..363cc3d7027d1c2a456db0081595550a4d65cab2
--- /dev/null
+++ b/src/python/OBis/integration_tests/08_addref_3_non-existent.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+cd $1/obis_data
+obis addref data7
+
diff --git a/src/python/OBis/integration_tests/09_local_clone.sh b/src/python/OBis/integration_tests/09_local_clone.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5e2a031aa69de85754f86032b4aaed67717da288
--- /dev/null
+++ b/src/python/OBis/integration_tests/09_local_clone.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+data_set_id=$2
+
+cd $1/obis_data_b
+obis clone $data_set_id
+
diff --git a/src/python/OBis/integration_tests/11_init_analysis_1_external.sh b/src/python/OBis/integration_tests/11_init_analysis_1_external.sh
new file mode 100755
index 0000000000000000000000000000000000000000..d585576488124351ea0804d4881ffeea57a6375b
--- /dev/null
+++ b/src/python/OBis/integration_tests/11_init_analysis_1_external.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+cd $1/obis_data
+obis init_analysis -p data1 analysis1
+cd analysis1
+obis config object_id /DEFAULT/DEFAULT
+echo content >> file
+obis commit -m 'commit message'
+
diff --git a/src/python/OBis/integration_tests/11_init_analysis_2_internal.sh b/src/python/OBis/integration_tests/11_init_analysis_2_internal.sh
new file mode 100755
index 0000000000000000000000000000000000000000..311d53e0579a468d5e97bff5f2b0bf92ba29cb57
--- /dev/null
+++ b/src/python/OBis/integration_tests/11_init_analysis_2_internal.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+cd $1/obis_data/data1
+obis init_analysis analysis2
+cd analysis2
+obis config object_id /DEFAULT/DEFAULT
+echo content >> file
+obis commit -m 'commit message'
+
diff --git a/src/python/OBis/integration_tests/11_init_analysis_3_git_check_ignore.sh b/src/python/OBis/integration_tests/11_init_analysis_3_git_check_ignore.sh
new file mode 100755
index 0000000000000000000000000000000000000000..bb597b8aae1c371242fb65c77948ed523f826008
--- /dev/null
+++ b/src/python/OBis/integration_tests/11_init_analysis_3_git_check_ignore.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+cd $1/obis_data/data1
+git check-ignore analysis2
+
diff --git a/src/python/OBis/integration_tests/12_metadata_only_1_commit.sh b/src/python/OBis/integration_tests/12_metadata_only_1_commit.sh
new file mode 100755
index 0000000000000000000000000000000000000000..2a7d6560f3b989acde69e0b20a61b108f1eb7ffc
--- /dev/null
+++ b/src/python/OBis/integration_tests/12_metadata_only_1_commit.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+cd $1/obis_data
+obis init data7 && cd data7
+obis config object_id /DEFAULT/DEFAULT
+echo content >> file
+obis commit -m 'commit message'
+
diff --git a/src/python/OBis/integration_tests/12_metadata_only_2_metadata_commit.sh b/src/python/OBis/integration_tests/12_metadata_only_2_metadata_commit.sh
new file mode 100755
index 0000000000000000000000000000000000000000..086383272c5210ed109876d98c346f59f5df0375
--- /dev/null
+++ b/src/python/OBis/integration_tests/12_metadata_only_2_metadata_commit.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+cd $1/obis_data/data7
+obis config collection_id /DEFAULT/DEFAULT/DEFAULT
+obis commit -m 'commit message'
+
diff --git a/src/python/OBis/integration_tests/13_sync_1_git_commit_and_sync.sh b/src/python/OBis/integration_tests/13_sync_1_git_commit_and_sync.sh
new file mode 100755
index 0000000000000000000000000000000000000000..590f099d3a1be607a7f28a2b24fa3406f33d8e4d
--- /dev/null
+++ b/src/python/OBis/integration_tests/13_sync_1_git_commit_and_sync.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+cd $1/obis_data/data7
+echo content >> file2
+git add file2
+git commit -m 'msg'
+obis sync
+
diff --git a/src/python/OBis/integration_tests/13_sync_2_only_sync.sh b/src/python/OBis/integration_tests/13_sync_2_only_sync.sh
new file mode 100755
index 0000000000000000000000000000000000000000..615a994c45922bba9ff223f2879c7ca8ad59416c
--- /dev/null
+++ b/src/python/OBis/integration_tests/13_sync_2_only_sync.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+cd $1/obis_data/data7
+obis sync
+
diff --git a/src/python/OBis/integration_tests/big_file b/src/python/OBis/integration_tests/big_file
new file mode 100644
index 0000000000000000000000000000000000000000..7c2624a6b9687e88178638cd95b609c329177ade
Binary files /dev/null and b/src/python/OBis/integration_tests/big_file differ
diff --git a/src/python/OBis/integration_tests/integration_tests.py b/src/python/OBis/integration_tests/integration_tests.py
new file mode 100644
index 0000000000000000000000000000000000000000..ecc169c64788738ea69f052726d82b979d82a45a
--- /dev/null
+++ b/src/python/OBis/integration_tests/integration_tests.py
@@ -0,0 +1,140 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import json
+import subprocess
+import socket
+
+
+def run(cmd, tmpdir="", params=[]):
+ completed_process = subprocess.run([cmd, tmpdir] + params, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ result = ''
+ if completed_process.stderr:
+ result += completed_process.stderr.decode('utf-8').strip()
+ if completed_process.stdout:
+ result += completed_process.stdout.decode('utf-8').strip()
+ print('-------------------' + cmd + '------------------- ' + str(tmpdir))
+ print(result)
+ return result
+
+
+def test_obis(tmpdir):
+ # 1. Global configuration
+ result = run('./01_global_config.sh', tmpdir)
+ config = json.loads(run('./00_get_config_global.sh'))
+ assert config['openbis_url'] == 'https://localhost:8443'
+ assert config['user'] == 'admin'
+ assert config['data_set_type'] == 'UNKNOWN'
+ assert config['verify_certificates'] == False
+
+ # 2. First commit
+ result = run('./02_first_commit_1_create_repository.sh', tmpdir)
+ assert '?? .obis/config.json' in result
+ assert '?? file' in result
+ result = run('./02_first_commit_2_commit.sh', tmpdir)
+ config = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data1'))
+ 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
+
+ # 3. Second commit
+ config_before = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data1'))
+ result = run('./03_second_commit_1_commit.sh', tmpdir)
+ config = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data1'))
+ 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
+ result = run('./03_second_commit_2_git_annex_info.sh', tmpdir)
+ assert 'file: big_file' in result
+ assert 'key: SHA256E-s1000000--d29751f2649b32ff572b5e0a9f541ea660a50f94ff0beedfb0b692b924cc8025' in result
+ assert 'present: true' in result
+
+ # 4. Second repository
+ result = run('./04_second_repository.sh', tmpdir)
+ config_data1 = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data1'))
+ config = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data2'))
+ 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
+
+ # 5. Second external dms
+ result = run('./05_second_external_dms.sh', tmpdir)
+ config_data1 = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data1'))
+ config = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data_b/data3'))
+ 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
+
+ # 6. Error on first commit
+ result = run('./06_error_on_first_commit_1_error.sh', tmpdir)
+ assert 'Missing configuration settings for [\'object_id\', \'collection_id\'].' in result
+ result = run('./06_error_on_first_commit_2_status.sh', tmpdir)
+ assert '?? file' in result
+ 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
+
+ # 7. Attach data set to a collection
+ result = run('./07_attach_to_collection.sh', tmpdir)
+ config = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data5'))
+ 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
+
+ # 8. Addref
+ result = run('./08_addref_1_success.sh', tmpdir)
+ config_data1 = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data1'))
+ config_data6 = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data6'))
+ assert config_data6 == config_data1
+ result = run('./08_addref_2_duplicate.sh', tmpdir)
+ assert 'DataSet already exists in the database' in result
+ result = run('./08_addref_3_non-existent.sh', tmpdir)
+ assert 'Invalid value' in result
+
+ # 9. Local clone
+ config_data2 = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data2'))
+ result = run('./09_local_clone.sh', tmpdir, [config_data2['data_set_id']])
+ 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']
+ del config_data2['external_dms_id']
+ del config_data2_clone['external_dms_id']
+ assert config_data2_clone == config_data2
+
+ # 11. Init analysis
+ result = run('./11_init_analysis_1_external.sh', tmpdir, [config_data2['data_set_id']])
+ config_data1 = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data1'))
+ config_analysis1 = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/analysis1'))
+ 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']
+ 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
+ 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']
+ result = run('./11_init_analysis_3_git_check_ignore.sh', tmpdir)
+ assert 'analysis2' in result
+
+ # 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
+ 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
+
+ # 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
+ result = run('./13_sync_2_only_sync.sh', tmpdir)
+ assert 'Nothing to sync' in result