diff --git a/src/python/OBis/obis/dm/config.py b/src/python/OBis/obis/dm/config.py
index 4a552de59e0f8f535c729335b880eef5eba040ae..da0aaa36a556c4c846617d617009aba2b4013da3 100644
--- a/src/python/OBis/obis/dm/config.py
+++ b/src/python/OBis/obis/dm/config.py
@@ -30,7 +30,7 @@ class ConfigLocation(object):
class ConfigParam(object):
"""Class for configuration parameters."""
- def __init__(self, name, private, is_json=False):
+ def __init__(self, name, private, is_json=False, ignore_global=False):
"""
:param name: Name of the parameter.
:param private: Should the parameter be private to the repo or visible in the data set?
@@ -39,6 +39,7 @@ class ConfigParam(object):
self.name = name
self.private = private
self.is_json = is_json
+ self.ignore_global = ignore_global
def location_path(self, loc):
if loc == 'global':
@@ -88,7 +89,8 @@ class ConfigEnv(object):
self.add_param(ConfigParam(name='verify_certificates', private=True, is_json=True))
self.add_param(ConfigParam(name='external_dms_id', private=True))
self.add_param(ConfigParam(name='repository_id', private=True))
- self.add_param(ConfigParam(name='sample_id', private=False))
+ self.add_param(ConfigParam(name='sample_id', private=False, ignore_global=True))
+ self.add_param(ConfigParam(name='experiment_id', private=False, ignore_global=True))
self.add_param(ConfigParam(name='data_set_id', private=False))
self.add_param(ConfigParam(name='data_set_type', private=False))
self.add_param(ConfigParam(name='data_set_properties', private=False, is_json=True))
@@ -157,7 +159,7 @@ class ConfigResolver(object):
for name, param in env.params.items():
result[name] = None
for l in self.location_search_order:
- if local_only and l == 'global':
+ if l == 'global' and (local_only or param.ignore_global):
continue
val = self.value_for_parameter(param, l)
if val is not None:
@@ -215,4 +217,8 @@ class ConfigResolver(object):
# Do not overwrite existing values
if local_config.get(k) is not None:
continue
+ # Do not copy params which should not be taken from global
+ param = self.env.params[k]
+ if param.ignore_global:
+ continue
self.set_value_for_parameter(k, v, 'local')
diff --git a/src/python/OBis/obis/dm/data_mgmt.py b/src/python/OBis/obis/dm/data_mgmt.py
index a76f45b396978a52a9e345355a08127e4e419230..2f9c280d1b2f1951e2da507d3df1f20d75015016 100644
--- a/src/python/OBis/obis/dm/data_mgmt.py
+++ b/src/python/OBis/obis/dm/data_mgmt.py
@@ -417,6 +417,9 @@ class OpenbisSync(object):
def sample_id(self):
return self.config_dict.get('sample_id')
+ def experiment_id(self):
+ return self.config_dict.get('experiment_id')
+
def check_configuration(self):
missing_config_settings = []
if self.openbis is None:
@@ -425,8 +428,9 @@ class OpenbisSync(object):
missing_config_settings.append('user')
if self.data_set_type() is None:
missing_config_settings.append('data_set_type')
- if self.sample_id() is None:
+ if self.sample_id() is None and self.experiment_id() is None:
missing_config_settings.append('sample_id')
+ missing_config_settings.append('experiment_id')
if len(missing_config_settings) > 0:
return CommandResult(returncode=-1,
output="Missing configuration settings for {}.".format(missing_config_settings))
@@ -498,10 +502,11 @@ class OpenbisSync(object):
return result
commit_id = result.output
sample_id = self.sample_id()
+ experiment_id = self.experiment_id()
contents = GitRepoFileInfo(self.git_wrapper).contents()
try:
data_set = self.openbis.new_git_data_set(data_set_type, top_level_path, commit_id, repository_id, external_dms.code,
- sample_id, data_set_code=data_set_code, parents=parent_data_set_id,
+ sample_id, experiment_id, data_set_code=data_set_code, parents=parent_data_set_id,
properties=properties, contents=contents)
return CommandResult(returncode=0, output=""), data_set
except ValueError as e:
diff --git a/src/python/OBis/obis/scripts/cli.py b/src/python/OBis/obis/scripts/cli.py
index 6f56e10b1aa8d5fd0005e34448a2d66b24a9af42..4b256dee839de29124761f8c44c40d59a4c0df17 100644
--- a/src/python/OBis/obis/scripts/cli.py
+++ b/src/python/OBis/obis/scripts/cli.py
@@ -142,7 +142,7 @@ def init_data_impl(ctx, sample_id, folder, name):
with dm.cd(folder):
return check_result("init_data", set_property(data_mgmt, 'sample_id', sample_id, False))
-
+# TODO test and add param for experiment
@cli.command()
@click.pass_context
@click.option('-o', '--sample_id', help='Set the id of the owning object.')
@@ -153,6 +153,7 @@ def init(ctx, sample_id, folder, name):
return init_data_impl(ctx, sample_id, folder, name)
+# TODO test and add param for experiment
@cli.command()
@click.pass_context
@click.option('-o', '--sample_id', help='Set the id of the owning object.')
diff --git a/src/python/PyBis/pybis/data_set.py b/src/python/PyBis/pybis/data_set.py
index 3dc4bfe6b5f8fe167e28da47b7ac3ac2671a013c..d2b52fe8df02c8bb3b8bd2e7d613f840150910a8 100644
--- a/src/python/PyBis/pybis/data_set.py
+++ b/src/python/PyBis/pybis/data_set.py
@@ -20,8 +20,8 @@ def transfer_to_file_creation(content, file_creation, key, file_creation_key=Non
class GitDataSetCreation(object):
- def __init__(self, openbis, data_set_type, path, commit_id, repository_id, dms, sample=None, properties={},
- dss_code=None, parents=None, data_set_code=None, contents=[]):
+ def __init__(self, openbis, data_set_type, path, commit_id, repository_id, dms, sample=None, experiment = None,
+ properties={}, dss_code=None, parents=None, data_set_code=None, contents=[]):
"""Initialize the command object with the necessary parameters.
:param openbis: The openBIS API object.
:param data_set_type: The type of the data set
@@ -31,6 +31,7 @@ class GitDataSetCreation(object):
:param repository_id: The git repository id - same for copies
:param dms: An external data managment system object or external_dms_id
:param sample: A sample object or sample id.
+ :param experiment: An experiment or experiment id.
:param properties: Properties for the data set.
:param dss_code: Code for the DSS -- defaults to the first dss if none is supplied.
:param parents: Parents for the data set.
@@ -49,6 +50,7 @@ class GitDataSetCreation(object):
self.repository_id = repository_id
self.dms = dms
self.sample = sample
+ self.experiment = experiment
self.properties = properties
self.dss_code = dss_code
self.parents = parents
@@ -112,9 +114,6 @@ class GitDataSetCreation(object):
if dss_code is None:
dss_code = self.openbis.get_datastores()['code'][0]
- # if a sample identifier was given, use it as a string.
- # if a sample object was given, take its identifier
- sample_id = self.openbis.sample_to_sample_id(self.sample)
dms_id = self.openbis.external_data_managment_system_to_dms_id(self.dms)
parents = self.parents
parentIds = []
@@ -139,7 +138,6 @@ class GitDataSetCreation(object):
"@type": "as.dto.entitytype.id.EntityTypePermId",
"permId": self.data_set_type
},
- "sampleId": sample_id,
"dataStoreId": {
"permId": dss_code,
"@type": "as.dto.datastore.id.DataStorePermId"
@@ -149,6 +147,14 @@ class GitDataSetCreation(object):
"properties": self.properties,
"@type": "as.dto.dataset.create.DataSetCreation"
}
+
+ if self.sample is not None:
+ sample_id = self.openbis.sample_to_sample_id(self.sample)
+ data_set_creation['sampleId'] = sample_id
+ elif self.experiment is not None:
+ experiment_id = self.openbis.experiment_to_experiment_id(self.experiment)
+ data_set_creation['experimentId'] = experiment_id
+
if self.data_set_code is not None:
data_set_creation['code'] = self.data_set_code
data_set_creation["autoGeneratedCode"] = False
diff --git a/src/python/PyBis/pybis/pybis.py b/src/python/PyBis/pybis/pybis.py
index 5833dfa3473a16773d4e71be06a82e98eeba456e..ee0f4cf256360ac54c268dd51ed48c033a4cf39e 100644
--- a/src/python/PyBis/pybis/pybis.py
+++ b/src/python/PyBis/pybis/pybis.py
@@ -1835,7 +1835,7 @@ class Openbis:
except:
return resp
- def new_git_data_set(self, data_set_type, path, commit_id, repository_id, dms, sample=None, properties={},
+ def new_git_data_set(self, data_set_type, path, commit_id, repository_id, dms, sample=None, experiment=None, properties={},
dss_code=None, parents=None, data_set_code=None, contents=[]):
""" Create a link data set.
:param data_set_type: The type of the data set
@@ -1856,30 +1856,39 @@ class Openbis:
'path': [the relative path string]}
:return: A DataSet object
"""
- return pbds.GitDataSetCreation(self, data_set_type, path, commit_id, repository_id, dms, sample,
+ return pbds.GitDataSetCreation(self, data_set_type, path, commit_id, repository_id, dms, sample, experiment,
properties, dss_code, parents, data_set_code, contents).new_git_data_set()
@staticmethod
def sample_to_sample_id(sample):
"""Take sample which may be a string or object and return an identifier for it."""
- sample_id = None
- if isinstance(sample, str):
- if (is_identifier(sample)):
- sample_id = {
- "identifier": sample,
- "@type": "as.dto.sample.id.SampleIdentifier"
+ return Openbis._object_to_object_id(sample, "as.dto.sample.id.SampleIdentifier", "as.dto.sample.id.SamplePermId");
+
+ @staticmethod
+ def experiment_to_experiment_id(experiment):
+ """Take experiment which may be a string or object and return an identifier for it."""
+ return Openbis._object_to_object_id(experiment, "as.dto.experiment.id.ExperimentIdentifier", "as.dto.experiment.id.SamplePermId");
+
+ @staticmethod
+ def _object_to_object_id(obj, identifierType, permIdType):
+ object_id = None
+ if isinstance(obj, str):
+ if (is_identifier(obj)):
+ object_id = {
+ "identifier": obj,
+ "@type": identifierType
}
else:
- sample_id = {
- "permId": sample,
- "@type": "as.dto.sample.id.SamplePermId"
+ object_id = {
+ "permId": obj,
+ "@type": permIdType
}
else:
- sample_id = {
- "identifier": sample.identifier,
- "@type": "as.dto.sample.id.SampleIdentifier"
+ object_id = {
+ "identifier": obj.identifier,
+ "@type": identifierType
}
- return sample_id
+ return object_id
@staticmethod
def data_set_to_data_set_id(data_set):
diff --git a/src/vagrant/obis/README.md b/src/vagrant/obis/README.md
index 2f23656f60d7d34a08d186e1c75e7ccf84a4ca0c..a51ee548624015ae2dd1a1e5847ac4eec7facff1 100644
--- a/src/vagrant/obis/README.md
+++ b/src/vagrant/obis/README.md
@@ -64,7 +64,7 @@ Now create a file and put some content into it. E.g.,
vi info.txt
-When finished, we need to set the sample_id this data set should be associated with. Then we can commit it.
+When finished, we need to set the sample_id or experiment_id this data set should be associated with. Then we can commit it.
obis config sample_id /DEMO/BIGDATA
obis commit -m"Initial data commit."