pip install --upgrade pybis

pip install jupyter
pip install jupyterlab

from pybis import Openbis
o = Openbis('https://example.com')
o = Openbis('example.com')          # https:// is assumed

import getpass
password = getpass.getpass()

o.login('username', password, save_token=True)   # save the session token in ~/.pybis/example.com.token

from pybis import Openbis
o = Openbis(os.environ['OPENBIS_HOST'])

o.login(os.environ['OPENBIS_USERNAME'], os.environ['OPENBIS_PASSWORD'])

from pybis import Openbis
o = Openbis('https://test-openbis-instance.com', verify_certificates=False)

print(f"Session is active: {o.is_session_active()} and token is {o.token}")
o.logout()
print(f"Session is active: {o.is_session_active()"}

from pybis import Openbis
o = Openbis('https://test-openbis-instance.com')

o.login("username", "password")
# or
o.set_token("your_username-220808165456793xA3D0357C5DE66A5BAD647E502355FE2C")

pat = o.get_or_create_personal_access_token(sessionName="Project A")
o.set_token(pat, save_token=True)

o.get_personal_access_tokens()
o.get_personal_access_tokens(sessionName="APPLICATION_1")

o.get_personal_access_tokens()[0].delete('some reason')

o = Openbis('https://example.com', use_cache=False)

# or later in the script
o.use_cache = False
o.clear_cache()
o.clear_cache('sampleType')

$ sudo yum install epel-release
$ sudo yum --enablerepo=epel -y install fuse-sshfs
$ user="$(whoami)"
$ usermod -a -G fuse "$user"

o.mount()
o.mount(username, password, hostname, mountpoint, volname)
o.is_mounted()
o.unmount()
o.get_mountpoint()

sample_types = o.get_sample_types()  # get a list of sample types
sample_types.df                      # DataFrame object
st = o.get_sample_types()[3]         # get 4th element of that list
st = o.get_sample_type('YEAST')
st.code
st.generatedCodePrefix
st.attrs.all()                       # get all attributes as a dict
st.get_validationPlugin()            # returns a plugin object

st.get_property_assignments()        # show the list of properties
                                     # for that sample type
o.get_material_types()
o.get_dataset_types()
o.get_experiment_types()
o.get_collection_types()

o.get_property_types()
pt = o.get_property_type('BARCODE_COMPLEXITY_CHECKER')
pt.attrs.all()

o.get_plugins()
pl = o.get_plugin('Diff_time')
pl.script  # the Jython script that processes this property

o.get_vocabularies()
o.get_vocabulary('BACTERIAL_ANTIBIOTIC_RESISTANCE')
o.get_terms(vocabulary='STORAGE')
o.get_tags()

pt_text = o.new_property_type(
    code        = 'MY_NEW_PROPERTY_TYPE',
    label       = 'yet another property type',
    description = 'my first property',
    dataType    = 'VARCHAR',
)
pt_text.save()

pt_int = o.new_property_type(
    code        = 'MY_NUMBER',
    label       = 'property contains a number',
    dataType    = 'INTEGER',
)
pt_int.save()

pt_voc = o.new_property_type(
    code        = 'MY_CONTROLLED_VOCABULARY',
    label       = 'label me',
    description = 'give me a description',
    dataType    = 'CONTROLLEDVOCABULARY',
    vocabulary  = 'STORAGE',
)
pt_voc.save()

pt_richtext = o.new_property_type(
    code        = 'MY_RICHTEXT_PROPERTY',
    label       = 'richtext data',
    description = 'property contains rich text',
    dataType    = 'MULTILINE_VARCHAR',
    metaData    = {'custom_widget' : 'Word Processor'}
)
pt_richtext.save()

pt_spread = o.new_property_type(
    code        = 'MY_TABULAR_DATA',
    label       = 'data in a table',
    description = 'property contains a spreadsheet',
    dataType    = 'XML',
    metaData    = {'custom_widget': 'Spreadsheet'}
)
pt_spread.save()

sample_type = o.new_sample_type(
    code                = 'my_own_sample_type',  # mandatory
    generatedCodePrefix = 'S',                   # mandatory
    description         = '',
    autoGeneratedCode   = True,
    subcodeUnique       = False,
    listable            = True,
    showContainer       = False,
    showParents         = True,
    showParentMetadata  = False,
    validationPlugin    = 'Has_Parents'          # see plugins below
)
sample_type.save()

sample_type.get_next_sequence()    # eg. 67
sample_type.get_next_code()        # e.g. FLY77

sample_type.assign_property(
	prop                 = 'diff_time',           # mandatory
	section              = '',
	ordinal              = 5,
	mandatory            = True,
	initialValueForExistingEntities = 'initial value'
	showInEditView       = True,
	showRawValueInForms  = True
)
sample_type.revoke_property('diff_time')
sample_type.get_property_assignments()

dataset_type = o.new_dataset_type(
    code                = 'my_dataset_type',       # mandatory
    description         = None,
    mainDataSetPattern  = None,
    mainDataSetPath     = None,
    disallowDeletion    = False,
    validationPlugin    = None,
)
dataset_type.save()
dataset_type.assign_property('property_name')
dataset_type.revoke_property('property_name')
dataset_type.get_property_assignments()

experiment_type = o.new_experiment_type(
    code,
    description      = None,
    validationPlugin = None,
)
experiment_type.save()
experiment_type.assign_property('property_name')
experiment_type.revoke_property('property_name')
experiment_type.get_property_assignments()

material_type = o.new_material_type(
    code,
    description=None,
    validationPlugin=None,
)
material_type.save()
material_type.assign_property('property_name')
material_type.revoke_property('property_name')
material_type.get_property_assignments()

pl = o.new_plugin(
    name       ='my_new_entry_validation_plugin',
    pluginType ='ENTITY_VALIDATION',       # or 'DYNAMIC_PROPERTY' or 'MANAGED_PROPERTY',
    entityKind = None,                     # or 'SAMPLE', 'MATERIAL', 'EXPERIMENT', 'DATA_SET'
    script     = 'def calculate(): pass'   # a JYTHON script
)
pl.save()

o.get_groups()
group = o.new_group(code='group_name', description='...')
group = o.get_group('group_name')
group.save()
group.assign_role(role='ADMIN', space='DEFAULT')
group.get_roles()
group.revoke_role(role='ADMIN', space='DEFAULT')

group.add_members(['admin'])
group.get_members()
group.del_members(['admin'])
group.delete()

o.get_persons()
person = o.new_person(userId='username')
person.space = 'USER_SPACE'
person.save()
# person.delete() is currently not possible.

person.assign_role(role='ADMIN', space='MY_SPACE')
person.assign_role(role='OBSERVER')
person.get_roles()
person.revoke_role(role='ADMIN', space='MY_SPACE')
person.revoke_role(role='OBSERVER')

o.get_role_assignments()
o.get_role_assignments(space='MY_SPACE')
o.get_role_assignments(group='MY_GROUP')
ra = o.get_role_assignment(techId)
ra.delete()

space = o.new_space(code='space_name', description='')
space.save()
o.get_spaces(
    start_with = 0,                   # start_with and count
    count      = 10,                  # enable paging
)
space = o.get_space('MY_SPACE')

# get individual attributes
space.code
space.description
space.registrator
space.registrationDate
space.modifier
space.modificationDate

# set individual attribute
# most of the attributes above are set automatically and cannot be modified.
space.description = '...'

# get all attributes as a dictionary
space.attrs.all()

space.delete('reason for deletion')

project = o.new_project(
    space       = space,
    code        = 'project_name',
    description = 'some project description'
)
project = space.new_project(
	code         = 'project_code',
	description  = 'project description'
)
project.save()

o.get_projects(
    space       = 'MY_SPACE',         # show only projects in MY_SPACE
    start_with  = 0,                  # start_with and count
    count       = 10,                 # enable paging
)
o.get_projects(space='MY_SPACE')
space.get_projects()

project.get_experiments()

project.get_attachments()             # deprecated, as attachments are not compatible with ELN-LIMS.
                                      # Attachments are an old concept and should not be used anymore.
p.add_attachment(                     # deprecated, see above
    fileName='testfile',
     description= 'another file',
     title= 'one more attachment'
)
project.download_attachments(<path or cwd>)  # deprecated, see above

# get individual attributes
project.code
project.description

# set individual attribute
project.description = '...'

# get all attributes as a dictionary
project.attrs.all()

project.freeze = True
project.freezeForExperiments = True
project.freezeForSamples = True

exp = o.new_experiment
    code='MY_NEW_EXPERIMENT',
    type='DEFAULT_EXPERIMENT',
    space='MY_SPACE',
    project='YEASTS'
)
exp.save()

experiments = o.get_experiments(
    project       = 'YEASTS',
    space         = 'MY_SPACE',
    type          = 'DEFAULT_EXPERIMENT',
    tags          = '*',
    finished_flag = False,
    props         = ['name', 'finished_flag']
)
experiments = project.get_experiments()
experiment = experiments[0]        # get first experiment of result list
experiment = experiment
for experiment in experiments:     # iterate over search results
    print(experiment.props.all())
dataframe = experiments.df         # get Pandas DataFrame of result list

exp = o.get_experiment('/MY_SPACE/MY_PROJECT/MY_EXPERIMENT')

exp.attrs.all()                    # returns all attributes as a dict

exp.attrs.tags = ['some', 'tags']
exp.tags = ['some', 'tags']        # same thing
exp.save()

exp.code
exp.description
exp.registrator
...

exp.project = 'my_project'
exp.space   = 'my_space'
exp.freeze = True
exp.freezeForDataSets = True
exp.freezeForSamples = True

exp.save()                         # needed to save/update the changed attributes and properties

experiment.props == ds.p                  # you can use either .props or .p to access the properties
experiment.p                              # in Jupyter: show all properties in a nice table
experiment.p()                            # get all properties as a dict
experiment.props.all()                    # get all properties as a dict
experiment.p('prop1','prop2')             # get some properties as a dict
experiment.p.get('$name')                 # get the value of a property
experiment.p['property']                  # get the value of a property

experiment.experiment = 'first_exp'       # assign sample to an experiment
experiment.project = 'my_project'         # assign sample to a project

experiment.p. + TAB                       # in Jupyter/IPython: show list of available properties
experiment.p.my_property_ + TAB           # in Jupyter/IPython: show datatype or controlled vocabulary
experiment.p['my_property']= "value"      # set the value of a property
experiment.p.set('my_property, 'value')   # set the value of a property
experiment.p.my_property = "some value"   # set the value of a property
experiment.p.set({'my_property':'value'}) # set the values of some properties
experiment.set_props({ key: value })      # set the values of some properties

experiment.save()                         # needed to save/update the changed attributes and properties

sample = o.new_sample(
    type       = 'YEAST',
    space      = 'MY_SPACE',
    experiment = '/MY_SPACE/MY_PROJECT/EXPERIMENT_1',
    parents    = [parent_sample, '/MY_SPACE/YEA66'],   # you can use either permId, identifier
    children   = [child_sample],                       # or sample object
    props      = {"name": "some name", "description": "something interesting"}
)
sample = space.new_sample( type='YEAST' )
sample.save()

sample = o.get_sample('/MY_SPACE/MY_SAMPLE_CODE')
sample = o.get_sample('20170518112808649-52')
samples= o.get_samples(type='UNKNOWN')    # search for samples, see below

# get individual attributes
sample.space
sample.code
sample.permId
sample.identifier
sample.type  # once the sample type is defined, you cannot modify it

# set attribute
sample.space = 'MY_OTHER_SPACE'

sample.experiment    # a sample can belong to one experiment only
sample.experiment = '/MY_SPACE/MY_PROJECT/MY_EXPERIMENT'

sample.project
sample.project = '/MY_SPACE/MY_PROJECT'  # only works if project samples are
enabled

sample.tags
sample.tags = ['guten_tag', 'zahl_tag' ]

sample.attrs.all()                    # returns all attributes as a dict
sample.props.all()                    # returns all properties as a dict

sample.get_attachments()              # deprecated, as attachments are not compatible with ELN-LIMS.
                                      # Attachments are an old concept and should not be used anymore.
sample.download_attachments(<path or cwd>)  # deprecated, see above
sample.add_attachment('testfile.xls') # deprecated, see above

sample.delete('deleted for some reason')

trans = o.new_transaction()
for i in range (0, 100):
    sample = o.new_sample(...)
    trans.add(sample)

trans.commit()

trans = o.new_transaction()
for sample in o.get_samples(count=100):
    sample.prop.some_property = 'different value'
    trans.add(sample)

trans.commit()

trans = o.new_transaction()
for sample in o.get_samples(count=100):
    sample.mark_to_be_deleted()
    trans.add(sample)

trans.reason('go what has to go')
trans.commit()

sample.get_parents()
sample.set_parents(['/MY_SPACE/PARENT_SAMPLE_NAME')
sample.add_parents('/MY_SPACE/PARENT_SAMPLE_NAME')
sample.del_parents('/MY_SPACE/PARENT_SAMPLE_NAME')

sample.get_children()
sample.set_children('/MY_SPACE/CHILD_SAMPLE_NAME')
sample.add_children('/MY_SPACE/CHILD_SAMPLE_NAME')
sample.del_children('/MY_SPACE/CHILD_SAMPLE_NAME')

# A Sample may belong to another Sample, which acts as a container.
# As opposed to DataSets, a Sample may only belong to one container.
sample.container    # returns a sample object
sample.container = '/MY_SPACE/CONTAINER_SAMPLE_NAME'   # watch out, this will change the identifier of the sample to:
                                                       # /MY_SPACE/CONTAINER_SAMPLE_NAME:SAMPLE_NAME
sample.container = ''                                  # this will remove the container.

# A Sample may contain other Samples, in order to act like a container (see above)
# caveat: containers are NOT compatible with ELN-LIMS
# The Sample-objects inside that Sample are called «components» or «contained Samples»
# You may also use the xxx_contained() functions, which are just aliases.
sample.get_components()
sample.set_components('/MY_SPACE/COMPONENT_NAME')
sample.add_components('/MY_SPACE/COMPONENT_NAME')
sample.del_components('/MY_SPACE/COMPONENT_NAME')

sample.get_tags()
sample.set_tags('tag1')
sample.add_tags(['tag2','tag3'])
sample.del_tags('tag1')

sample.attrs.all()                    # returns all attributes as a dict
sample.attribute_name                 # return the attribute value

sample.props == ds.p                  # you can use either .props or .p to access the properties
sample.p                              # in Jupyter: show all properties in a nice table
sample.p()                            # get all properties as a dict
sample.props.all()                    # get all properties as a dict
sample.p('prop1','prop2')             # get some properties as a dict
sample.p.get('$name')                 # get the value of a property
sample.p['property']                  # get the value of a property

sample.experiment = 'first_exp'       # assign sample to an experiment
sample.project = 'my_project'         # assign sample to a project

sample.p. + TAB                       # in Jupyter/IPython: show list of available properties
sample.p.my_property_ + TAB           # in Jupyter/IPython: show datatype or controlled vocabulary
sample.p['my_property']= "value"      # set the value of a property
sample.p.set('my_property, 'value')   # set the value of a property
sample.p.my_property = "some value"   # set the value of a property
sample.p.set({'my_property':'value'}) # set the values of some properties
sample.set_props({ key: value })      # set the values of some properties

sample.save()                         # needed to save/update the attributes and properties

samples = o.get_samples(
    space      ='MY_SPACE',
    type       ='YEAST',
    tags       =['*'],                # only sample with existing tags
    start_with = 0,                   # start_with and count
    count      = 10,                  # enable paging
    where = {
        "$SOME.WEIRD-PROP": "hello"   # only receive samples where properties match
    }

    registrationDate = "2020-01-01",  # date format: YYYY-MM-DD
    modificationDate = "<2020-12-31", # use > or < to search for specified date and later / earlier
    attrs=[                           # show these attributes in the dataFrame
        'sample.code',
        'registrator.email',
        'type.generatedCodePrefix'
    ],
    parent_property = 'value',        # search in a parent's property
    child_property  = 'value',        # search in a child's property
    container_property = 'value'      # search in a container's property
    parent = '/MY_SPACE/PARENT_SAMPLE', # sample has this as its parent
    parent = '*',                     # sample has at least one parent
    child  = '/MY_SPACE/CHILD_SAMPLE',
    child  = '*',                     # sample has at least one child
    container = 'MY_SPACE/CONTAINER',
    container = '*'                   # sample lives in a container
    props=['$NAME', 'MATING_TYPE']    # show these properties in the result
)

sample = samples[9]                   # get the 10th sample
                                      # of the search results
sample = samples['/SPACE/AABC']       # same, fetched by identifier
for sample in samples:                # iterate over the
   print(sample.code)                 # search results


samples.df                            # returns a Pandas DataFrame object

samples = o.get_samples(props="*")    # retrieve all properties of all samples

sample.freeze = True
sample.freezeForComponents = True
sample.freezeForChildren = True
sample.freezeForParents = True
sample.freezeForDataSets = True

datasets = sample.get_datasets(type='SCANS', start_with=0, count=10)
for dataset in datasets:
    print(dataset.props())
    print(dataset.file_list)
    dataset.download()
dataset = datasets[0]

ds = o.get_dataset('20160719143426517-259')
ds.get_parents()
ds.get_children()
ds.sample
ds.experiment
ds.physicalData
ds.status                         # AVAILABLE   LOCKED   ARCHIVED
                                  # ARCHIVE_PENDING   UNARCHIVE_PENDING
                                  # BACKUP_PENDING
ds.archive()                      # archives a dataset, i.e. moves it to a slower but cheaper diskspace (tape).
                                  # archived datasets cannot be downloaded, they need to be unarchived first.
                                  # This is an asynchronous process,
                                  # check ds.status regularly until the dataset becomes 'ARCHIVED'
ds.unarchive()                    # this starts an asynchronous process which gets the dataset from the tape.
                                  # Check ds.status regularly until it becomes 'AVAILABLE'

ds.attrs.all()                    # returns all attributes as a dict
ds.props.all()                    # returns all properties as a dict

ds.add_attachment()               # Deprecated. Attachments usually contain meta-data
ds.get_attachments()              # about the dataSet, not the data itself.
ds.download_attachments(<path or cwd>)  # Deprecated, as attachments are not compatible with ELN-LIMS.
                                  # Attachments are an old concept and should not be used anymore.

o.download_prefix                  # used for download() and symlink() method.
                                   # Is set to data/hostname by default, but can be changed.
ds.get_files(start_folder="/")     # get file list as Pandas dataFrame
ds.file_list                       # get file list as array
ds.file_links                      # file list as a dict containing direct https links

ds.download()                      # simply download all files to data/hostname/permId/
ds.download(
	destination = 'my_data',        # download files to folder my_data/
	create_default_folders = False, # ignore the /original/DEFAULT folders made by openBIS
	wait_until_finished = False,    # download in background, continue immediately
	workers = 10                    # 10 downloads parallel (default)
)
ds.download_path                   # returns the relative path (destination) of the files after a ds.download()
ds.is_physical()                   # TRUE if dataset is physically

o.download_prefix                  # used for download() and symlink() method.
                                   # Is set to data/hostname by default, but can be changed.
ds.symlink()                       # creates a symlink for this dataset: data/hostname/permId
                                   # tries to mount openBIS instance
                                   # in case it is not mounted yet
ds.symlink(
   target_dir = 'data/dataset_1/', # default target_dir is: data/hostname/permId
   replace_if_symlink_exists=True
)
ds.is_symlink()

ds.attrs.all()                    # returns all attributes as a dict
ds.attribute_name                 # return the attribute value

ds.props == ds.p                  # you can use either .props or .p to access the properties
ds.p                              # in Jupyter: show all properties in a nice table
ds.p()                            # get all properties as a dict
ds.props.all()                    # get all properties as a dict
ds.p('prop1','prop2')             # get some properties as a dict
ds.p.get('$name')                 # get the value of a property
ds.p['property']                  # get the value of a property

ds.experiment = 'first_exp'       # assign dataset to an experiment
ds.sample = 'my_sample'           # assign dataset to a sample

ds.p. + TAB                       # in Jupyter/IPython: show list of available properties
ds.p.my_property_ + TAB           # in Jupyter/IPython: show datatype or controlled vocabulary
ds.p['my_property']= "value"      # set the value of a property
ds.p.set('my_property, 'value')   # set the value of a property
ds.p.my_property = "some value"   # set the value of a property
ds.p.set({'my_property':'value'}) # set the values of some properties
ds.set_props({ key: value })      # set the values of some properties

datasets = o.get_datasets(
    type  ='MY_DATASET_TYPE',
    **{ "SOME.WEIRD:PROP": "value"},  # property name contains a dot or a
                                      # colon: cannot be passed as an argument
    start_with = 0,                   # start_with and count
    count      = 10,                  # enable paging
    registrationDate = "2020-01-01",  # date format: YYYY-MM-DD
    modificationDate = "<2020-12-31", # use > or < to search for specified date and later / earlier
    parent_property = 'value',        # search in a parent's property
    child_property  = 'value',        # search in a child's property
    container_property = 'value'      # search in a container's property
    parent = '/MY_SPACE/PARENT_DS',   # has this dataset as its parent
    parent = '*',                     # has at least one parent dataset
    child  = '/MY_SPACE/CHILD_DS',
    child  = '*',                     # has at least one child dataset
    container = 'MY_SPACE/CONTAINER_DS',
    container = '*',                  # belongs to a container dataset
    attrs=[                           # show these attributes in the dataFrame
        'sample.code',
        'registrator.email',
        'type.generatedCodePrefix'
    ],
    props=['$NAME', 'MATING_TYPE']    # show these properties in the result
)
datasets = o.get_datasets(props="*")  # retrieve all properties of all dataSets
dataset = datasets[0]                 # get the first dataset in the search result
for dataset in datasets:              # iterate over the datasets
    ...
df = datasets.df                      # returns a Pandas dataFrame object of the search results

datasets = o.get_experiments(project='YEASTS')\
			 .get_samples(type='FLY')\
			 .get_datasets(
					type='ANALYZED_DATA',
					props=['MY_PROPERTY'],
					MY_PROPERTY='some analyzed data'
		 	 )

datasets = o.get_experiment('/MY_NEW_SPACE/MY_PROJECT/MY_EXPERIMENT4')\
           .get_samples(type='UNKNOWN')\
           .get_parents()\
           .get_datasets(type='RAW_DATA')

ds.freeze = True
ds.freezeForChildren = True
ds.freezeForParents = True
ds.freezeForComponents = True
ds.freezeForContainers = True
ds.save()

ds_new = o.new_dataset(
    type       = 'ANALYZED_DATA',
    experiment = '/SPACE/PROJECT/EXP1',
    sample     = '/SPACE/SAMP1',
    files      = ['my_analyzed_data.dat'],
    props      = {'name': 'some good name', 'description': '...' }
)
ds_new.save()

ds_new = o.new_dataset(
    type       = 'RAW_DATA',
    sample     = '/SPACE/SAMP1',
    zipfile    = 'my_zipped_folder.zip',
)
ds_new.save()

ds_new = o.new_dataset(
    type       = 'RAW_DATA',
    sample     = '/SPACE/SAMP1',
    files     = ['../measurements/', 'my_analyis.ipynb', 'results/']
)
ds_new.save()

ds_new = o.new_dataset(
    type       = 'ANALYZED_DATA',
    experiment = '/SPACE/PROJECT/EXP1',
    sample     = '/SPACE/SAMP1',
    kind       = 'CONTAINER',
    props      = {'name': 'some good name', 'description': '...' }
)
ds_new.save()

dataset.get_parents()
dataset.set_parents(['20170115220259155-412'])
dataset.add_parents(['20170115220259155-412'])
dataset.del_parents(['20170115220259155-412'])

dataset.get_children()
dataset.set_children(['20170115220259155-412'])
dataset.add_children(['20170115220259155-412'])
dataset.del_children(['20170115220259155-412'])

dataset.get_containers()
dataset.set_containers(['20170115220259155-412'])
dataset.add_containers(['20170115220259155-412'])
dataset.del_containers(['20170115220259155-412'])

dataset.get_components()
dataset.set_components(['20170115220259155-412'])
dataset.add_components(['20170115220259155-412'])
dataset.del_components(['20170115220259155-412'])

sa = o.new_semantic_annotation(
	entityType = 'UNKNOWN',
	predicateOntologyId = 'po_id',
	predicateOntologyVersion = 'po_version',
	predicateAccessionId = 'pa_id',
	descriptorOntologyId = 'do_id',
	descriptorOntologyVersion = 'do_version',
	descriptorAccessionId = 'da_id'
)
sa.save()

sa = o.new_semantic_annotation(propertyType = 'DESCRIPTION', ...)
sa.save()

sa = o.new_semantic_annotation(
	entityType = 'UNKNOWN',
	propertyType = 'DESCRIPTION',
	...
)
sa.save()

st = o.get_sample_type("ORDER")
st.new_semantic_annotation(...)

o.get_semantic_annotations()

sa = o.get_semantic_annotation("20171015135637955-30")

sa.predicateOntologyId = 'new_po_id'
sa.descriptorOntologyId = 'new_do_id'
sa.save()

sa.delete('reason')

new_tag = o.new_tag(
	code        = 'my_tag',
	description = 'some descriptive text'
)
new_tag.description = 'some new description'
new_tag.save()
o.get_tags()
o.get_tag('/username/TAG_Name')
o.get_tag('TAG_Name')

tag.get_experiments()
tag.get_samples()
tag.get_owner()   # returns a person object
tag.delete('why?')

voc = o.new_vocabulary(
    code = 'BBB',
    description = 'description of vocabulary aaa',
    urlTemplate = 'https://ethz.ch',
    terms = [
        { "code": 'term_code1', "label": "term_label1", "description": "term_description1"},
        { "code": 'term_code2', "label": "term_label2", "description": "term_description2"},
        { "code": 'term_code3', "label": "term_label3", "description": "term_description3"}
    ]
)
voc.save()

voc.vocabulary = 'description of vocabulary BBB'
voc.chosenFromList = True
voc.save() # update

term = o.new_term(
	code='TERM_CODE_XXX',
	vocabularyCode='BBB',
	label='here comes a label',
	description='here might appear a meaningful description'
)
term.save()

voc = o.get_vocabulary('STORAGE')
term = voc.get_terms()['RT']
term.label = "Room Temperature"
term.official = True
term.move_to_top()
term.move_after_term('-40')
term.save()
term.delete()

import json
settings_sample = o.get_sample("/ELN_SETTINGS/GENERAL_ELN_SETTINGS")
settings = json.loads(settings_sample.props["$eln_settings"])
print(settings["mainMenu"])
{'showLabNotebook': True,
 'showInventory': True,
 'showStock': True,
 'showObjectBrowser': True,
 'showExports': True,
 'showStorageManager': True,
 'showAdvancedSearch': True,
 'showUnarchivingHelper': True,
 'showTrashcan': False,
 'showVocabularyViewer': True,
 'showUserManager': True,
 'showUserProfile': True,
 'showZenodoExportBuilder': False,
 'showBarcodes': False,
 'showDatasets': True}

settings['mainMenu']['showTrashcan'] = False
settings_sample.props['$eln_settings'] = json.dumps(settings)
settings_sample.save()

o.get_samples(project='/ELN_SETTINGS/STORAGES')

sto = o.get_sample('/ELN_SETTINGS/STORAGES/BENCH')
sto.props()
{'$name': 'Bench',
 '$storage.row_num': '1',
 '$storage.column_num': '1',
 '$storage.box_num': '9999',
 '$storage.storage_space_warning': '80',
 '$storage.box_space_warning': '80',
 '$storage.storage_validation_level': 'BOX_POSITION',
 '$xmlcomments': None,
 '$annotations_state': None}
 sto.props['$storage.box_space_warning']= '80'
 sto.save()

o.get_samples(project='/ELN_SETTINGS/TEMPLATES')

pt = o.get_property_type('YEAST.SOURCE')
pt.metaData = {'custom_widget': 'Spreadsheet'}
pt.save()