diff --git a/obis/src/python/integration_tests/integration_tests.py b/obis/src/python/integration_tests/integration_tests.py
index 4651f7e527716beaeefbe88432e9f1a5b10ae0a7..540a467e9bcd251330ee91ca4f461deced31482b 100644
--- a/obis/src/python/integration_tests/integration_tests.py
+++ b/obis/src/python/integration_tests/integration_tests.py
@@ -11,6 +11,7 @@ import subprocess
from subprocess import PIPE
from subprocess import SubprocessError
from contextlib import contextmanager
+from random import randrange
from pybis import Openbis
@@ -31,6 +32,7 @@ def test_obis(tmpdir):
o = Openbis('https://obisserver:8443', verify_certificates=False)
o.login('admin', 'admin', save_token=True)
+ setup_masterdata(o)
output_buffer = '=================== 1. Global settings ===================\n'
if os.path.exists('~/.obis'):
@@ -322,6 +324,18 @@ def test_obis(tmpdir):
timeout = True
assert timeout == True
+ output_buffer = '=================== 22. changing identifier ===================\n'
+ settings = create_repository_and_commit(tmpdir, o, 'data14', '/DEFAULT/BIGDATA2')
+ move_sample(o, settings['object']['permId'], 'BIGDATA')
+ try:
+ settings = commit_new_change(tmpdir, o, 'data14')
+ assert settings['object']['id'] == '/BIGDATA/BIGDATA2'
+ finally:
+ move_sample(o, settings['object']['permId'], 'DEFAULT')
+ with cd('data14'): assert get_settings()['object']['permId'] is not None
+ cmd('obis object set id=/DEFAULT/DEFAULT')
+ with cd('data14'): assert get_settings()['object']['permId'] is not None
+
def assert_file_paths(files, expected_paths):
paths = list(map(lambda file: file['path'], files))
@@ -373,5 +387,57 @@ def assert_matching(settings, data_set, tmpdir, path):
assert content_copy['gitRepositoryId'] == settings['repository']['id']
if settings['object']['id'] is not None:
assert data_set['sample']['identifier']['identifier'] == settings['object']['id']
+ assert data_set['sample']['permId']['permId'] == settings['object']['permId']
if settings['collection']['id'] is not None:
assert data_set['experiment']['identifier']['identifier'] == settings['collection']['id']
+ assert data_set['experiment']['permId']['permId'] == settings['collection']['permId']
+
+def move_sample(o, sample_permId, space):
+ field_update_value = {
+ "@type": "as.dto.common.update.FieldUpdateValue",
+ "value": {
+ "@type": "as.dto.space.id.SpacePermId",
+ "permId": space,
+ },
+ "isModified": True,
+ }
+ o.update_sample(sample_permId, space=field_update_value)
+
+def create_repository_and_commit(tmpdir, o, repo_name, object_id):
+ cmd('obis init ' + repo_name)
+ with cd(repo_name):
+ cmd('touch file')
+ result = cmd('obis status')
+ assert '? file' in result
+ cmd('obis object set id=' + object_id)
+ result = cmd('obis commit -m \'commit-message\'')
+ settings = get_settings()
+ assert settings['repository']['external_dms_id'].startswith('ADMIN-' + socket.gethostname().upper())
+ assert len(settings['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/' + repo_name)
+ return settings
+
+def commit_new_change(tmpdir, o, repo_name):
+ with cd(repo_name):
+ filename = 'file' + str(randrange(100000))
+ cmd('touch ' + filename)
+ result = cmd('obis status')
+ assert '? ' + filename in result
+ result = cmd('obis commit -m \'commit-message\'')
+ settings = get_settings()
+ assert settings['repository']['external_dms_id'].startswith('ADMIN-' + socket.gethostname().upper())
+ assert len(settings['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/' + repo_name)
+ return settings
+
+
+def setup_masterdata(o):
+ spaces = o.get_spaces()
+ if 'BIGDATA' not in o.get_spaces().df.code.values:
+ o.new_space(code='BIGDATA').save()
+ if '/DEFAULT/BIGDATA2' not in o.get_samples().df.identifier.values:
+ o.new_sample(type="UNKNOWN", code='BIGDATA2', space='DEFAULT').save()
diff --git a/obis/src/python/obis/dm/commands/openbis_command.py b/obis/src/python/obis/dm/commands/openbis_command.py
index 734282e8ae65563faa14df55a11600109c3236e2..599d66ca2400e5dda99a7e35d4daca1bb4814b6d 100644
--- a/obis/src/python/obis/dm/commands/openbis_command.py
+++ b/obis/src/python/obis/dm/commands/openbis_command.py
@@ -60,12 +60,18 @@ class OpenbisCommand(object):
def object_id(self):
return self.config_dict['object']['id']
+ def object_permId(self):
+ return self.config_dict['object']['permId']
+
def set_object_id(self, value):
self.config_dict['object']['id'] = value
def collection_id(self):
return self.config_dict['collection']['id']
+ def collection_permId(self):
+ return self.config_dict['collection']['permId']
+
def set_collection_id(self, value):
self.config_dict['collection']['id'] = value
diff --git a/obis/src/python/obis/dm/commands/openbis_sync.py b/obis/src/python/obis/dm/commands/openbis_sync.py
index e6e1476a2ec4cdaad5075a5cd252d009be5853f7..3cd70b28335d97e0b7e0ca6d4890620a796d2898 100644
--- a/obis/src/python/obis/dm/commands/openbis_sync.py
+++ b/obis/src/python/obis/dm/commands/openbis_sync.py
@@ -50,8 +50,7 @@ class OpenbisSync(OpenbisCommand):
if result.failure():
return result
commit_id = result.output
- sample_id = self.object_id()
- experiment_id = self.collection_id()
+ sample_id, experiment_id = self._update_and_get_object_or_collection_id()
contents = GitRepoFileInfo(self.git_wrapper).contents(git_annex_hash_as_checksum=self.git_annex_hash_as_checksum())
try:
data_set = self.openbis.new_git_data_set(data_set_type, top_level_path, commit_id, repository_id, external_dms.code,
@@ -62,8 +61,40 @@ class OpenbisSync(OpenbisCommand):
return CommandResult(returncode=-1, output=str(e)), None
- def commit_metadata_updates(self, msg_fragment=None):
- return self.data_mgmt.commit_metadata_updates(msg_fragment)
+ def _update_and_get_object_or_collection_id(self):
+ """ Updates identifier of object / collection in case it has changed in openBIS
+ if the permId is available. Returns sample / experiment identifier."""
+ sample_id = self.object_id()
+ experiment_id = self.collection_id()
+ if self.object_permId() is not None:
+ sample_id = self.openbis.get_sample(self.object_permId()).identifier
+ if sample_id != self.object_id():
+ self.settings_resolver.object.set_value_for_parameter('id', sample_id, 'local')
+ # permId is cleared when the id is set - set it again
+ self.settings_resolver.object.set_value_for_parameter('permId', self.object_permId(), 'local')
+ self.commit_metadata_updates("object identifier changed in openBIS")
+ if self.collection_permId() is not None:
+ experiment_id = self.openbis.get_experiment(self.collection_permId()).identifier
+ if experiment_id != self.collection_id():
+ self.settings_resolver.collection.set_value_for_parameter('id', experiment_id, 'local')
+ # permId is cleared when the id is set - set it again
+ self.settings_resolver.collection.set_value_for_parameter('permId', self.collection_permId(), 'local')
+ self.commit_metadata_updates("collection identifier changed in openBIS")
+ return sample_id, experiment_id
+
+ def _storePermId(self):
+ if self.object_permId() is None and self.object_id() is not None:
+ sample = self.openbis.get_sample(self.object_id())
+ self.settings_resolver.object.set_value_for_parameter('permId', sample.permId, 'local')
+ self.commit_metadata_updates("object permId", omit_usersettings=False)
+ if self.collection_permId() is None and self.collection_id() is not None:
+ experiment = self.openbis.get_experiment(self.collection_id())
+ self.settings_resolver.collection.set_value_for_parameter('permId', experiment.permId, 'local')
+ self.commit_metadata_updates("collection permId", omit_usersettings=False)
+
+
+ def commit_metadata_updates(self, msg_fragment=None, omit_usersettings=True):
+ return self.data_mgmt.commit_metadata_updates(msg_fragment, omit_usersettings=omit_usersettings)
def prepare_repository_id(self):
@@ -157,10 +188,14 @@ class OpenbisSync(OpenbisCommand):
self.commit_metadata_updates()
+ # store permId of object / collection so we can use those as a reference in the future
+ self._storePermId()
+
# Update data set id as last commit so we can easily revert it on failure
self.settings_resolver.repository.set_value_for_parameter('data_set_id', data_set_code, 'local')
self.commit_metadata_updates("data set id")
# create a data set, using the existing data set as a parent, if there is one
result, data_set = self.create_data_set(data_set_code, external_dms, repository_id, ignore_parent)
+
return result
diff --git a/obis/src/python/obis/dm/config.py b/obis/src/python/obis/dm/config.py
index 763404934fcc43312498e1170247f905a0da35ad..a2766838598ed8113034b539651007c7d98fe503 100644
--- a/obis/src/python/obis/dm/config.py
+++ b/obis/src/python/obis/dm/config.py
@@ -9,6 +9,7 @@ Configuration for obis.
Created by Chandrasekhar Ramakrishnan on 2017-02-10.
Copyright (c) 2017 Chandrasekhar Ramakrishnan. All rights reserved.
"""
+import abc
import json
import os
@@ -78,8 +79,10 @@ class ConfigEnv(object):
def __init__(self):
self.locations = {}
self.params = {}
+ self.rules = []
self.initialize_locations()
self.initialize_params()
+ self.initialize_rules()
def initialize_locations(self):
self.add_location(ConfigLocation(['global'], 'user_home', '.obis'))
@@ -120,17 +123,31 @@ class ConfigEnv(object):
def is_usersetting(self):
return True
+ def add_rule(self, rule):
+ self.rules.append(rule)
+
+ def initialize_rules(self):
+ pass
+
class CollectionEnv(ConfigEnv):
def initialize_params(self):
self.add_param(ConfigParam(name='id', private=False, ignore_global=True))
+ self.add_param(ConfigParam(name='permId', private=False, ignore_global=True))
+
+ def initialize_rules(self):
+ self.add_rule(ClearPermIdRule())
class ObjectEnv(ConfigEnv):
def initialize_params(self):
self.add_param(ConfigParam(name='id', private=False, ignore_global=True))
+ self.add_param(ConfigParam(name='permId', private=False, ignore_global=True))
+
+ def initialize_rules(self):
+ self.add_rule(ClearPermIdRule())
class DataSetEnv(ConfigEnv):
@@ -244,6 +261,9 @@ class ConfigResolver(object):
with open(config_path, "w") as f:
json.dump(location_config_dict, f, sort_keys=True, indent=4)
+ for rule in self.env.rules:
+ rule.on_set(self, name, value, loc)
+
def set_value_for_json_parameter(self, json_param_name, name, value, loc):
"""Set one field for the json parameter
:param json_param_name: Name of the json parameter
@@ -331,10 +351,10 @@ class SettingsResolver(object):
combined_dict[resolver.categoty] = resolver.config_dict(local_only=local_only)
return combined_dict
- def local_public_properties_paths(self, get_usersettings=False):
+ def local_public_properties_paths(self, omit_usersettings=True):
paths = []
for resolver in self.resolvers:
- if get_usersettings == resolver.is_usersetting():
+ if omit_usersettings == False or resolver.is_usersetting() == False:
paths.append(resolver.local_public_properties_path())
return paths
@@ -349,3 +369,19 @@ class SettingsResolver(object):
def set_location_search_order(self, order):
for resolver in self.resolvers:
resolver.location_search_order = order
+
+
+class SettingRule(object):
+ """ Setting rules can react to setting changes and trigger further actions. """
+
+ @abc.abstractmethod
+ def on_set(self, setting, value):
+ pass
+
+
+class ClearPermIdRule(SettingRule):
+ """ When the user sets a new id, the permId might be invalid, so it will be cleared. """
+
+ def on_set(self, config_resolver, name, value, loc):
+ if name == "id":
+ config_resolver.set_value_for_parameter("permId", None, loc)
diff --git a/obis/src/python/obis/dm/data_mgmt.py b/obis/src/python/obis/dm/data_mgmt.py
index c5ec2315d74ec31164d741764a018293e22f077e..339bb2f40b8016b119352f3ba0cace732c649a85 100644
--- a/obis/src/python/obis/dm/data_mgmt.py
+++ b/obis/src/python/obis/dm/data_mgmt.py
@@ -365,8 +365,8 @@ class GitDataMgmt(AbstractDataMgmt):
output += sync_status.output
return CommandResult(returncode=0, output=output)
- def commit_metadata_updates(self, msg_fragment=None):
- properties_paths = self.settings_resolver.local_public_properties_paths()
+ def commit_metadata_updates(self, msg_fragment=None, omit_usersettings=True):
+ properties_paths = self.settings_resolver.local_public_properties_paths(omit_usersettings=omit_usersettings)
total_status = ''
for properties_path in properties_paths:
status = self.git_wrapper.git_status(properties_path).output.strip()