def test_create_action_invalid_schema():
schema = {'type': 'invalid'}
with pytest.raises(errors.ValidationError):
actions.create_action(sampledb.models.ActionType.SAMPLE_CREATION,
name="Example Action",
description="",
schema=schema)
def test_create_missing_instrument_action():
instrument = instruments.create_instrument(
"Example Instrument", "Example Instrument Description")
assert len(actions.get_actions()) == 0
with pytest.raises(errors.InstrumentDoesNotExistError):
actions.create_action(sampledb.models.ActionType.SAMPLE_CREATION,
name="Example Action",
description="",
schema=SCHEMA,
instrument_id=instrument.id + 1)
def test_get_missing_action():
assert len(actions.get_actions()) == 0
action = actions.create_action(sampledb.models.ActionType.SAMPLE_CREATION,
name="Example Action",
description="",
schema=SCHEMA)
with pytest.raises(errors.ActionDoesNotExistError):
actions.get_action(action.id + 1)
def test_get_actions():
measurement_action = actions.create_action(
sampledb.models.ActionType.MEASUREMENT,
name="Example Action",
description="",
schema=SCHEMA)
sample_action = actions.create_action(
sampledb.models.ActionType.SAMPLE_CREATION,
name="Example Action",
description="",
schema=SCHEMA)
assert actions.get_actions() == [
measurement_action, sample_action
] or actions.get_actions() == [sample_action, measurement_action]
assert actions.get_actions(
sampledb.models.ActionType.SAMPLE_CREATION) == [sample_action]
assert actions.get_actions(
sampledb.models.ActionType.MEASUREMENT) == [measurement_action]
def action(instrument, schema_file_name):
with open(schema_file_name) as schema_file:
schema = json.load(schema_file)
return actions.create_action(
action_type=actions.ActionType.SAMPLE_CREATION,
name='Example Action',
description='Example Action Description',
schema=schema,
instrument_id=instrument.id)
def test_update_missing_action():
action = actions.create_action(sampledb.models.ActionType.SAMPLE_CREATION,
name="Example Action",
description="",
schema=SCHEMA)
with pytest.raises(errors.ActionDoesNotExistError):
actions.update_action(action_id=action.id + 1,
name="Test",
description="desc",
schema=SCHEMA)
def test_create_independent_action():
assert len(actions.get_actions()) == 0
action = actions.create_action(sampledb.models.ActionType.SAMPLE_CREATION,
name="Example Action",
description="",
schema=SCHEMA)
assert action.name == "Example Action"
assert action.description == ""
assert action.schema == SCHEMA
assert len(actions.get_actions()) == 1
assert action == actions.get_action(action_id=action.id)
def action(instrument, schema_file_name):
with open(schema_file_name) as schema_file:
schema = json.load(schema_file)
action = actions.create_action(
action_type_id=sampledb.models.ActionType.SAMPLE_CREATION,
name='Example Action',
description='Example Action Description',
schema=schema,
instrument_id=instrument.id)
assert action.id is not None
db.session.expunge(action)
return action
def test_update_action():
action = actions.create_action(sampledb.models.ActionType.SAMPLE_CREATION,
name="Example Action",
description="",
schema=SCHEMA)
actions.update_action(action_id=action.id,
name="Test",
description="desc",
schema=SCHEMA)
action = actions.get_action(action_id=action.id)
assert action.name == "Test"
assert action.description == "desc"
assert action.schema == SCHEMA
def test_create_instrument_action():
instrument = instruments.create_instrument(
"Example Instrument", "Example Instrument Description")
assert len(actions.get_actions()) == 0
action = actions.create_action(sampledb.models.ActionType.SAMPLE_CREATION,
name="Example Action",
description="",
schema=SCHEMA,
instrument_id=instrument.id)
assert action.name == "Example Action"
assert action.description == ""
assert action.schema == SCHEMA
assert len(actions.get_actions()) == 1
assert action == actions.get_action(action_id=action.id)
assert action.instrument == instrument
def action():
action = actions.create_action(action_type=ActionType.SAMPLE_CREATION,
name='Example Action',
schema={
'title': 'Example Object',
'type': 'object',
'properties': {
'name': {
'title': 'Sample Name',
'type': 'text'
}
},
'required': ['name']
},
description='',
instrument_id=None)
return action
def test_create_user_action():
user = users.User(name="Testuser",
email="*****@*****.**",
type=sampledb.models.UserType.PERSON)
sampledb.db.session.add(user)
sampledb.db.session.commit()
assert len(actions.get_actions()) == 0
action = actions.create_action(sampledb.models.ActionType.SAMPLE_CREATION,
name="Example Action",
description="",
schema=SCHEMA,
user_id=user.id)
assert action.name == "Example Action"
assert action.description == ""
assert action.schema == SCHEMA
assert action.user_id == user.id
assert len(actions.get_actions()) == 1
assert action == actions.get_action(action_id=action.id)
def main(arguments):
if len(arguments) != 0:
print(__doc__)
exit(1)
app = create_app()
if not app.config.get("SERVER_NAME"):
app.config["SERVER_NAME"] = "localhost:8000"
with app.app_context():
if sampledb.logic.actions.get_actions(
) or sampledb.logic.instruments.get_instruments() or len(
sampledb.logic.users.get_users()) > 1:
print("Error: database must be empty for demo", file=sys.stderr)
exit(1)
data_directory = os.path.abspath(
os.path.join(os.path.dirname(__file__), 'demo_data'))
schema_directory = os.path.join(data_directory, 'schemas')
objects_directory = os.path.join(data_directory, 'objects')
if sampledb.logic.users.get_users():
# admin might have been created from environment variables
admin = sampledb.logic.users.get_users()[0]
else:
admin = sampledb.logic.users.create_user(name="Administrator",
email="*****@*****.**",
type=UserType.PERSON)
sampledb.logic.users.set_user_administrator(admin.id, True)
instrument_responsible_user = sampledb.logic.users.create_user(
name="Instrument Scientist",
email="*****@*****.**",
type=UserType.PERSON)
basic_user = sampledb.logic.users.create_user(
name="Basic User", email="*****@*****.**", type=UserType.PERSON)
api_user = sampledb.logic.users.create_user(name="API User",
email="*****@*****.**",
type=UserType.OTHER)
sampledb.logic.authentication.add_other_authentication(
api_user.id, 'api', 'password')
group_id = groups.create_group(
"Example Group", "This is an example group for testing purposes.",
instrument_responsible_user.id).id
project_id = projects.create_project("Example Project",
"This is an example project",
instrument_responsible_user.id).id
project_id2 = projects.create_project(
"Example Project 2", "This is another example project",
instrument_responsible_user.id).id
projects.create_subproject_relationship(
parent_project_id=project_id,
child_project_id=project_id2,
child_can_add_users_to_parent=True)
markdown_notes = """# Header
This example shows how Markdown can be used for instrument Notes.
## Subheader
*italics* **bold**
| A | B | C |
|--:|:-:|---|
| Example | 100˚C | 5µm |
| Data | 110˚C | 6µm |
"""
instrument = create_instrument(
name="OMBE I",
description="This is an example instrument.",
users_can_create_log_entries=True,
notes=markdown_notes,
notes_is_markdown=True)
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
log_category_error = sampledb.logic.instrument_log_entries.create_instrument_log_category(
instrument_id=instrument.id,
title='Error',
theme=sampledb.logic.instrument_log_entries.
InstrumentLogCategoryTheme.RED)
log_category_warning = sampledb.logic.instrument_log_entries.create_instrument_log_category(
instrument_id=instrument.id,
title='Warning',
theme=sampledb.logic.instrument_log_entries.
InstrumentLogCategoryTheme.YELLOW)
log_category_success = sampledb.logic.instrument_log_entries.create_instrument_log_category(
instrument_id=instrument.id,
title='Success',
theme=sampledb.logic.instrument_log_entries.
InstrumentLogCategoryTheme.GREEN)
log_category_other = sampledb.logic.instrument_log_entries.create_instrument_log_category(
instrument_id=instrument.id,
title='Other',
theme=sampledb.logic.instrument_log_entries.
InstrumentLogCategoryTheme.BLUE)
log_category_normal = sampledb.logic.instrument_log_entries.create_instrument_log_category(
instrument_id=instrument.id,
title='Normal',
theme=sampledb.logic.instrument_log_entries.
InstrumentLogCategoryTheme.GRAY)
for category in sampledb.logic.instrument_log_entries.get_instrument_log_categories(
instrument.id):
sampledb.logic.instrument_log_entries.create_instrument_log_entry(
instrument.id, basic_user.id,
"This is an example instrument log entry", [category.id])
sampledb.logic.instrument_log_entries.create_instrument_log_entry(
instrument.id, basic_user.id,
"This is an example instrument log entry")
sampledb.logic.instrument_log_entries.create_instrument_log_entry(
instrument.id, basic_user.id,
"This is an example instrument log entry", [log_category_other.id])
log_entry = sampledb.logic.instrument_log_entries.create_instrument_log_entry(
instrument.id, basic_user.id,
"This is an example instrument log entry", [
log_category_error.id, log_category_warning.id,
log_category_normal.id, log_category_success.id
])
sampledb.logic.instrument_log_entries.create_instrument_log_file_attachment(
instrument_log_entry_id=log_entry.id,
file_name="ghs01.png",
content=open(
os.path.join(os.path.dirname(sampledb.__file__),
'static/img/ghs01.png'), 'rb').read())
sampledb.logic.instrument_log_entries.create_instrument_log_file_attachment(
instrument_log_entry_id=log_entry.id,
file_name="ghs02.png",
content=open(
os.path.join(os.path.dirname(sampledb.__file__),
'static/img/ghs02.png'), 'rb').read())
sampledb.logic.instrument_log_entries.create_instrument_log_file_attachment(
instrument_log_entry_id=log_entry.id,
file_name="test.txt",
content="This is a test".encode('utf-8'))
with open(os.path.join(schema_directory,
'ombe_measurement.sampledb.json'),
'r',
encoding='utf-8') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.SAMPLE_CREATION,
"Sample Creation",
"This is an example action", schema,
instrument.id)
sampledb.logic.action_permissions.set_action_public(
instrument_action.id)
independent_action = create_action(ActionType.SAMPLE_CREATION,
"Alternative Process",
"This is an example action", schema)
sampledb.logic.action_permissions.set_action_public(
independent_action.id)
with open(os.path.join(schema_directory,
'ombe_measurement_batch.sampledb.json'),
'r',
encoding='utf-8') as schema_file:
batch_schema = json.load(schema_file)
action = create_action(ActionType.SAMPLE_CREATION,
"Sample Creation (Batch)",
"This is an example action", batch_schema,
instrument.id)
sampledb.logic.action_permissions.set_action_public(action.id)
sampledb.db.session.commit()
with open(os.path.join(objects_directory, 'ombe-1.sampledb.json'),
'r',
encoding='utf-8') as data_file:
data = json.load(data_file)
instrument_object = Objects.create_object(
data=data,
schema=schema,
user_id=instrument_responsible_user.id,
action_id=instrument_action.id,
connection=sampledb.db.engine)
create_object(object_id=instrument_object.object_id,
user_id=instrument_responsible_user.id)
independent_object = Objects.create_object(
data=data,
schema=schema,
user_id=instrument_responsible_user.id,
action_id=independent_action.id,
connection=sampledb.db.engine)
create_object(object_id=independent_object.object_id,
user_id=instrument_responsible_user.id)
comments.create_comment(
instrument_object.id, instrument_responsible_user.id,
'This comment is very long. ' * 20 + '\n' +
'This comment has three paragraphs. ' * 20 + '\n' + '\n' +
'This comment has three paragraphs. ' * 20)
comments.create_comment(instrument_object.id,
instrument_responsible_user.id,
'This is another, shorter comment')
files.create_local_file(
instrument_object.id, instrument_responsible_user.id,
'example.txt',
lambda stream: stream.write("Dies ist ein Test".encode('utf-8')))
files.create_local_file(
instrument_object.id, instrument_responsible_user.id, 'demo.png',
lambda stream: stream.write(
open(
os.path.join(os.path.dirname(sampledb.__file__),
'static/img/ghs01.png'), 'rb').read()))
files.update_file_information(instrument_object.id, 1,
instrument_responsible_user.id,
'Example File',
'This is a file description.')
files.create_url_file(instrument_object.id,
instrument_responsible_user.id,
'http://iffsamples.fz-juelich.de/')
projects.link_project_and_object(project_id,
instrument_object.object_id,
instrument_responsible_user.id)
with open(os.path.join(schema_directory,
'ombe_measurement_updated.sampledb.json'),
'r',
encoding='utf-8') as schema_file:
schema = json.load(schema_file)
sampledb.logic.actions.update_action(instrument_action.id,
"Updated Sample Creation", "",
schema)
object_permissions.set_group_object_permissions(
independent_object.object_id, group_id,
object_permissions.Permissions.READ)
instrument = create_instrument(name="XRR",
description="X-Ray Reflectometry")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open(os.path.join(schema_directory,
'xrr_measurement.sampledb.json'),
'r',
encoding='utf-8') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.MEASUREMENT,
"XRR Measurement", "", schema,
instrument.id)
sampledb.logic.action_permissions.set_action_public(
instrument_action.id)
with open(os.path.join(schema_directory, 'searchable_quantity.json'),
'r',
encoding='utf-8') as schema_file:
schema = json.load(schema_file)
action = create_action(ActionType.SAMPLE_CREATION, "Searchable Object",
"", schema, None)
sampledb.logic.action_permissions.set_action_public(action.id)
independent_object = Objects.create_object(
data={
"name": {
"_type": "text",
"text": "TEST-1"
},
"tags": {
"_type": "tags",
"tags": ["tag1", "tag2"]
},
"mass": {
"_type": "quantity",
"dimensionality": "[mass]",
"magnitude_in_base_units": 0.00001,
"units": "mg"
}
},
schema=schema,
user_id=instrument_responsible_user.id,
action_id=action.id,
connection=sampledb.db.engine)
create_object(object_id=independent_object.object_id,
user_id=instrument_responsible_user.id)
object_permissions.set_group_object_permissions(
independent_object.object_id, group_id,
object_permissions.Permissions.READ)
object_permissions.set_user_object_permissions(
independent_object.object_id, api_user.id,
object_permissions.Permissions.WRITE)
independent_object = Objects.create_object(
data={
"name": {
"_type": "text",
"text": "TEST-2"
},
"tags": {
"_type": "tags",
"tags": ["tag2", "tag3"]
},
"mass": {
"_type": "quantity",
"dimensionality": "[mass]",
"magnitude_in_base_units": 0.000005,
"units": "mg"
}
},
schema=schema,
user_id=instrument_responsible_user.id,
action_id=action.id,
connection=sampledb.db.engine)
create_object(object_id=independent_object.object_id,
user_id=instrument_responsible_user.id)
object_permissions.set_group_object_permissions(
independent_object.object_id, group_id,
object_permissions.Permissions.READ)
sampledb.db.session.commit()
instrument = create_instrument(
name="MPMS SQUID", description="MPMS SQUID Magnetometer JCNS-2")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open(os.path.join(schema_directory,
'squid_measurement.sampledb.json'),
'r',
encoding='utf-8') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.MEASUREMENT,
"Perform Measurement", "", schema,
instrument.id)
sampledb.logic.action_permissions.set_action_public(
instrument_action.id)
sampledb.db.session.commit()
instrument = create_instrument(
name="Powder Diffractometer",
description="Huber Imaging Plate Guinier Camera G670 at JCNS-2")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open(os.path.join(
schema_directory,
'powder_diffractometer_measurement.sampledb.json'),
'r',
encoding='utf-8') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.MEASUREMENT,
"Perform Measurement", "", schema,
instrument.id)
sampledb.logic.action_permissions.set_action_public(
instrument_action.id)
sampledb.db.session.commit()
instrument = create_instrument(
name="GALAXI",
description="Gallium Anode Low-Angle X-ray Instrument")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open(os.path.join(schema_directory,
'galaxi_measurement.sampledb.json'),
'r',
encoding='utf-8') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.MEASUREMENT,
"Perform Measurement", "", schema,
instrument.id)
sampledb.logic.action_permissions.set_action_public(
instrument_action.id)
sampledb.db.session.commit()
with open(os.path.join(schema_directory, 'other_sample.sampledb.json'),
'r',
encoding='utf-8') as schema_file:
schema = json.load(schema_file)
action = create_action(ActionType.SAMPLE_CREATION, "Other Sample", "",
schema, None)
sampledb.logic.action_permissions.set_action_public(action.id)
sampledb.db.session.commit()
sample_action = sampledb.logic.actions.create_action(
action_type_id=ActionType.SAMPLE_CREATION,
name="sample_action",
description="",
schema={
'title': 'Example Object',
'type': 'object',
'properties': {
'name': {
'title': 'Object Name',
'type': 'text'
},
'sample': {
'title': 'Sample',
'type': 'sample'
}
},
'required': ['name']
})
sampledb.logic.action_permissions.set_action_public(sample_action.id)
measurement_action = sampledb.logic.actions.create_action(
action_type_id=ActionType.MEASUREMENT,
name="measurement_action",
description="",
schema={
'title': 'Example Object',
'type': 'object',
'properties': {
'name': {
'title': 'Object Name',
'type': 'text'
},
'sample': {
'title': 'Sample',
'type': 'sample'
},
'comment': {
'title': 'Comment',
'type': 'text',
'markdown': True
}
},
'required': ['name']
})
sampledb.logic.action_permissions.set_action_public(
measurement_action.id)
data = {'name': {'_type': 'text', 'text': 'Object 1'}}
object = sampledb.logic.objects.create_object(sample_action.id, data,
basic_user.id)
sampledb.logic.object_permissions.set_object_public(object.id, True)
data = {
'name': {
'_type': 'text',
'text': 'Object 2'
},
'sample': {
'_type': 'sample',
'object_id': object.id
}
}
sample = sampledb.logic.objects.create_object(sample_action.id, data,
basic_user.id)
sampledb.logic.object_permissions.set_object_public(sample.id, True)
data = {
'name': {
'_type': 'text',
'text': 'Object 1'
},
'sample': {
'_type': 'sample',
'object_id': sample.id
}
}
sampledb.logic.objects.update_object(object.id, data, basic_user.id)
data = {
'name': {
'_type': 'text',
'text': 'Measurement'
},
'sample': {
'_type': 'sample',
'object_id': object.id
},
'comment': {
'_type': 'text',
'text':
'This is a test.\nThis **is** a *second* line.\n\nThis line follows an empty line.',
'is_markdown': True
}
}
measurement = sampledb.logic.objects.create_object(
measurement_action.id, data, basic_user.id)
sampledb.logic.object_permissions.set_object_public(
measurement.id, True)
data = {
'name': {
'_type': 'text',
'text': 'Measurement 2'
},
'sample': {
'_type': 'sample',
'object_id': sample.id
},
'comment': {
'_type':
'text',
'text':
'This is a test.\nThis is a second line.\n\nThis line follows an empty line.'
}
}
measurement = sampledb.logic.objects.create_object(
measurement_action.id, data, instrument_responsible_user.id)
sampledb.logic.object_permissions.set_object_public(
measurement.id, True)
with open(os.path.join(schema_directory, 'plotly.json'),
'r',
encoding='utf-8') as schema_file:
schema = json.load(schema_file)
plotly_action = create_action(ActionType.SAMPLE_CREATION,
"Plotly Example Action", "", schema,
None)
sampledb.logic.action_permissions.set_action_public(plotly_action.id)
with open(os.path.join(objects_directory,
'plotly-example-data1.sampledb.json'),
'r',
encoding='utf-8') as data_file:
example_data = json.load(data_file)
data = {
"name": {
"_type": "text",
"text": "Plotly Example Data #1"
},
"plot1": {
"_type": "plotly_chart",
"plotly": example_data
}
}
plotly_object = sampledb.logic.objects.create_object(
plotly_action.id, data, basic_user.id)
sampledb.logic.object_permissions.set_object_public(
plotly_object.id, True)
with open(os.path.join(schema_directory, 'plotly_array.json'),
'r',
encoding='utf-8') as schema_file:
schema = json.load(schema_file)
plotly_array_action = create_action(ActionType.SAMPLE_CREATION,
"Plotly Array Example Action", "",
schema, None)
sampledb.logic.action_permissions.set_action_public(
plotly_array_action.id)
with open(os.path.join(objects_directory,
'plotly-example-data2.sampledb.json'),
'r',
encoding='utf-8') as data_file:
example_data2 = json.load(data_file)
with open(os.path.join(objects_directory,
'plotly-example-data3.sampledb.json'),
'r',
encoding='utf-8') as data_file:
example_data3 = json.load(data_file)
data = {
"name": {
"_type": "text",
"text": "Plotly Array Example"
},
"plotlist": [{
"_type": "plotly_chart",
"plotly": example_data
}, {
"_type": "plotly_chart",
"plotly": example_data2
}, {
"_type": "plotly_chart",
"plotly": example_data3
}]
}
plotly_object = sampledb.logic.objects.create_object(
plotly_array_action.id, data, basic_user.id)
sampledb.logic.object_permissions.set_object_public(
plotly_object.id, True)
sampledb.db.session.commit()
campus = sampledb.logic.locations.create_location(
"Campus", "Max Mustermann Campus", None,
instrument_responsible_user.id)
building_a = sampledb.logic.locations.create_location(
"Building A", "Building A on Max Mustermann Campus", campus.id,
instrument_responsible_user.id)
room_42a = sampledb.logic.locations.create_location(
"Room 42a", "Building A, Room 42a", building_a.id,
instrument_responsible_user.id)
room_42b = sampledb.logic.locations.create_location(
"Room 42b", "Building A, Room 42b", building_a.id,
instrument_responsible_user.id)
sampledb.logic.locations.assign_location_to_object(
measurement.id, room_42a.id, None, instrument_responsible_user.id,
"Temporarily stored on table\n\nSome other text")
sampledb.logic.locations.assign_location_to_object(
measurement.id, room_42b.id, instrument_responsible_user.id,
basic_user.id, "Stored in shelf K")
sampledb.logic.notifications.create_other_notification(
instrument_responsible_user.id, "This is a demo.")
sampledb.logic.object_permissions.set_user_object_permissions(
independent_object.id, instrument_responsible_user.id,
sampledb.models.Permissions.GRANT)
sampledb.logic.notifications.create_notification_for_having_received_an_objects_permissions_request(
instrument_responsible_user.id, independent_object.id, admin.id)
for object in sampledb.logic.objects.get_objects():
sampledb.logic.instrument_log_entries.create_instrument_log_object_attachment(
instrument_log_entry_id=log_entry.id, object_id=object.id)
print("Success: set up demo data")
def setup_data(app):
# TODO: replace using user management logic
admin = User(name="Administrator",
email="*****@*****.**",
type=UserType.PERSON)
admin.is_admin = True
instrument_responsible_user = User(name="Instrument Responsible User",
email="*****@*****.**",
type=UserType.PERSON)
basic_user = User(name="Basic User",
email="*****@*****.**",
type=UserType.PERSON)
for user in (admin, instrument_responsible_user, basic_user):
sampledb.db.session.add(user)
sampledb.db.session.commit()
api_user = sampledb.logic.users.create_user(name="API User",
email="*****@*****.**",
type=UserType.OTHER)
sampledb.logic.authentication.add_other_authentication(
api_user.id, 'api', 'password')
group_id = groups.create_group(
"Example Group", "This is an example group for testing purposes.",
instrument_responsible_user.id).id
project_id = projects.create_project("Example Project",
"This is an example project",
instrument_responsible_user.id).id
project_id2 = projects.create_project("Example Project 2",
"This is another example project",
instrument_responsible_user.id).id
projects.create_subproject_relationship(parent_project_id=project_id,
child_project_id=project_id2,
child_can_add_users_to_parent=True)
# Setup autologin for testing
@app.route('/users/me/autologin')
@app.route('/users/<int:user_id>/autologin')
def autologin(user_id=instrument_responsible_user.id):
user = User.query.get(user_id)
assert user is not None
flask_login.login_user(user)
# Remove the message asking the user to sign in
flask.session.pop('_flashes', None)
flask.flash(
'You have been signed in automatically as part of the SampleDB Demo.',
'info')
return flask.redirect(
os.environ.get('SAMPLEDB_DEMO_REDIRECT_URI',
flask.url_for('frontend.index')))
sampledb.login_manager.login_view = 'autologin'
markdown_notes = """
This example shows how Markdown can be used for instrument Notes.
## Header
*italics* **bold**
| A | B | C |
|--:|:-:|---|
| Example | 100˚C | 5µm |
| Data | 110˚C | 6µm |
"""
instrument = create_instrument(
name="OMBE I",
description="This is an example instrument.",
users_can_create_log_entries=True,
notes=markdown_notes,
notes_as_html=sampledb.frontend.utils.markdown_to_safe_html(
markdown_notes))
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
log_category_error = sampledb.logic.instrument_log_entries.create_instrument_log_category(
instrument_id=instrument.id,
title='Error',
theme=sampledb.logic.instrument_log_entries.InstrumentLogCategoryTheme.
RED)
log_category_warning = sampledb.logic.instrument_log_entries.create_instrument_log_category(
instrument_id=instrument.id,
title='Warning',
theme=sampledb.logic.instrument_log_entries.InstrumentLogCategoryTheme.
YELLOW)
log_category_success = sampledb.logic.instrument_log_entries.create_instrument_log_category(
instrument_id=instrument.id,
title='Success',
theme=sampledb.logic.instrument_log_entries.InstrumentLogCategoryTheme.
GREEN)
log_category_other = sampledb.logic.instrument_log_entries.create_instrument_log_category(
instrument_id=instrument.id,
title='Other',
theme=sampledb.logic.instrument_log_entries.InstrumentLogCategoryTheme.
BLUE)
log_category_normal = sampledb.logic.instrument_log_entries.create_instrument_log_category(
instrument_id=instrument.id,
title='Normal',
theme=sampledb.logic.instrument_log_entries.InstrumentLogCategoryTheme.
GRAY)
for category in sampledb.logic.instrument_log_entries.get_instrument_log_categories(
instrument.id):
sampledb.logic.instrument_log_entries.create_instrument_log_entry(
instrument.id, basic_user.id,
"This is an example instrument log entry", [category.id])
sampledb.logic.instrument_log_entries.create_instrument_log_entry(
instrument.id, basic_user.id,
"This is an example instrument log entry")
log_entry = sampledb.logic.instrument_log_entries.create_instrument_log_entry(
instrument.id, basic_user.id,
"This is an example instrument log entry", [
log_category_error.id, log_category_warning.id,
log_category_normal.id, log_category_success.id
])
sampledb.logic.instrument_log_entries.create_instrument_log_file_attachment(
instrument_log_entry_id=log_entry.id,
file_name="ghs01.png",
content=open('sampledb/static/img/ghs01.png', 'rb').read())
sampledb.logic.instrument_log_entries.create_instrument_log_file_attachment(
instrument_log_entry_id=log_entry.id,
file_name="ghs02.png",
content=open('sampledb/static/img/ghs02.png', 'rb').read())
sampledb.logic.instrument_log_entries.create_instrument_log_file_attachment(
instrument_log_entry_id=log_entry.id,
file_name="test.txt",
content="This is a test".encode('utf-8'))
with open('sampledb/schemas/ombe_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.SAMPLE_CREATION,
"Sample Creation",
"This is an example action", schema,
instrument.id)
independent_action = create_action(ActionType.SAMPLE_CREATION,
"Alternative Process",
"This is an example action", schema)
with open('sampledb/schemas/ombe_measurement_batch.sampledb.json',
'r') as schema_file:
batch_schema = json.load(schema_file)
create_action(ActionType.SAMPLE_CREATION, "Sample Creation (Batch)",
"This is an example action", batch_schema, instrument.id)
sampledb.db.session.commit()
with open('example_data/ombe-1.sampledb.json', 'r') as data_file:
data = json.load(data_file)
instrument_object = Objects.create_object(
data=data,
schema=schema,
user_id=instrument_responsible_user.id,
action_id=instrument_action.id,
connection=sampledb.db.engine)
create_object(object_id=instrument_object.object_id,
user_id=instrument_responsible_user.id)
data['multilayer'][0]['repetitions']['magnitude_in_base_units'] = 20000
data['multilayer'][1]['films'][0]['thickness'][
'magnitude_in_base_units'] = 1
independent_object = Objects.create_object(
data=data,
schema=schema,
user_id=instrument_responsible_user.id,
action_id=independent_action.id,
connection=sampledb.db.engine)
create_object(object_id=independent_object.object_id,
user_id=instrument_responsible_user.id)
comments.create_comment(
instrument_object.id, instrument_responsible_user.id,
'This comment is very long. ' * 20 + '\n' +
'This comment has three paragraphs. ' * 20 + '\n' + '\n' +
'This comment has three paragraphs. ' * 20)
comments.create_comment(instrument_object.id,
instrument_responsible_user.id,
'This is another, shorter comment')
files.create_local_file(
instrument_object.id, instrument_responsible_user.id, 'example.txt',
lambda stream: stream.write("Dies ist ein Test".encode('utf-8')))
files.create_local_file(
instrument_object.id, instrument_responsible_user.id, 'demo.png',
lambda stream: stream.write(
open('sampledb/static/img/ghs01.png', 'rb').read()))
files.update_file_information(instrument_object.id, 1,
instrument_responsible_user.id,
'Example File',
'This is a file description.')
files.create_url_file(instrument_object.id, instrument_responsible_user.id,
'http://iffsamples.fz-juelich.de/')
with open('server_schemas/ombe_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
sampledb.logic.actions.update_action(instrument_action.id,
"Updated Sample Creation", "", schema)
object_permissions.set_group_object_permissions(
independent_object.object_id, group_id,
object_permissions.Permissions.READ)
instrument = create_instrument(name="XRR",
description="X-Ray Reflectometry")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open('sampledb/schemas/xrr_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.MEASUREMENT,
"XRR Measurement", "", schema,
instrument.id)
with open('sampledb/schemas/searchable_quantity.json', 'r') as schema_file:
schema = json.load(schema_file)
action = create_action(ActionType.SAMPLE_CREATION, "Searchable Object", "",
schema, None)
independent_object = Objects.create_object(
data={
"name": {
"_type": "text",
"text": "TEST-1"
},
"tags": {
"_type": "tags",
"tags": ["tag1", "tag2"]
},
"mass": {
"_type": "quantity",
"dimensionality": "[mass]",
"magnitude_in_base_units": 0.00001,
"units": "mg"
}
},
schema=schema,
user_id=instrument_responsible_user.id,
action_id=action.id,
connection=sampledb.db.engine)
create_object(object_id=independent_object.object_id,
user_id=instrument_responsible_user.id)
object_permissions.set_group_object_permissions(
independent_object.object_id, group_id,
object_permissions.Permissions.READ)
object_permissions.set_user_object_permissions(
independent_object.object_id, api_user.id,
object_permissions.Permissions.WRITE)
independent_object = Objects.create_object(
data={
"name": {
"_type": "text",
"text": "TEST-2"
},
"tags": {
"_type": "tags",
"tags": ["tag2", "tag3"]
},
"mass": {
"_type": "quantity",
"dimensionality": "[mass]",
"magnitude_in_base_units": 0.000005,
"units": "mg"
}
},
schema=schema,
user_id=instrument_responsible_user.id,
action_id=action.id,
connection=sampledb.db.engine)
create_object(object_id=independent_object.object_id,
user_id=instrument_responsible_user.id)
object_permissions.set_group_object_permissions(
independent_object.object_id, group_id,
object_permissions.Permissions.READ)
sampledb.db.session.commit()
instrument = create_instrument(
name="MPMS SQUID", description="MPMS SQUID Magnetometer JCNS-2")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open('server_schemas/squid_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.MEASUREMENT,
"Perform Measurement", "", schema,
instrument.id)
sampledb.db.session.commit()
instrument = create_instrument(
name="Powder Diffractometer",
description="Huber Imaging Plate Guinier Camera G670 at JCNS-2")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open('server_schemas/powder_diffractometer_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.MEASUREMENT,
"Perform Measurement", "", schema,
instrument.id)
sampledb.db.session.commit()
instrument = create_instrument(
name="GALAXI", description="Gallium Anode Low-Angle X-ray Instrument")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open('server_schemas/galaxi_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.MEASUREMENT,
"Perform Measurement", "", schema,
instrument.id)
sampledb.db.session.commit()
with open('server_schemas/other_sample.sampledb.json', 'r') as schema_file:
schema = json.load(schema_file)
create_action(ActionType.SAMPLE_CREATION, "Other Sample", "", schema, None)
sampledb.db.session.commit()
sample_action = sampledb.logic.actions.create_action(
action_type_id=ActionType.SAMPLE_CREATION,
name="sample_action",
description="",
schema={
'title': 'Example Object',
'type': 'object',
'properties': {
'name': {
'title': 'Object Name',
'type': 'text'
},
'sample': {
'title': 'Sample',
'type': 'sample'
}
},
'required': ['name']
})
measurement_action = sampledb.logic.actions.create_action(
action_type_id=ActionType.MEASUREMENT,
name="measurement_action",
description="",
schema={
'title': 'Example Object',
'type': 'object',
'properties': {
'name': {
'title': 'Object Name',
'type': 'text'
},
'sample': {
'title': 'Sample',
'type': 'sample'
},
'comment': {
'title': 'Comment',
'type': 'text',
'multiline': True
}
},
'required': ['name']
})
data = {'name': {'_type': 'text', 'text': 'Object 1'}}
object = sampledb.logic.objects.create_object(sample_action.id, data,
user.id)
sampledb.logic.object_permissions.set_object_public(object.id, True)
data = {
'name': {
'_type': 'text',
'text': 'Object 2'
},
'sample': {
'_type': 'sample',
'object_id': object.id
}
}
sample = sampledb.logic.objects.create_object(sample_action.id, data,
user.id)
sampledb.logic.object_permissions.set_object_public(sample.id, True)
data = {
'name': {
'_type': 'text',
'text': 'Object 1'
},
'sample': {
'_type': 'sample',
'object_id': sample.id
}
}
sampledb.logic.objects.update_object(object.id, data, user.id)
data = {
'name': {
'_type': 'text',
'text': 'Measurement'
},
'sample': {
'_type': 'sample',
'object_id': object.id
},
'comment': {
'_type':
'text',
'text':
'This is a test.\nThis is a second line.\n\nThis line follows an empty line.'
}
}
measurement = sampledb.logic.objects.create_object(measurement_action.id,
data, user.id)
sampledb.logic.object_permissions.set_object_public(measurement.id, True)
data = {
'name': {
'_type': 'text',
'text': 'Measurement 2'
},
'sample': {
'_type': 'sample',
'object_id': sample.id
},
'comment': {
'_type':
'text',
'text':
'This is a test.\nThis is a second line.\n\nThis line follows an empty line.'
}
}
measurement = sampledb.logic.objects.create_object(
measurement_action.id, data, instrument_responsible_user.id)
sampledb.logic.object_permissions.set_object_public(measurement.id, True)
juelich = sampledb.logic.locations.create_location(
"FZJ", "Forschungszentrum Jülich", None,
instrument_responsible_user.id)
building_04_8 = sampledb.logic.locations.create_location(
"Building 04.8", "Building 04.8 at Forschungszentrum Jülich",
juelich.id, instrument_responsible_user.id)
room_139 = sampledb.logic.locations.create_location(
"Room 139b", "Building 04.8, Room 139", building_04_8.id,
instrument_responsible_user.id)
room_141 = sampledb.logic.locations.create_location(
"Room 141", "Building 04.8, Room 141", building_04_8.id,
instrument_responsible_user.id)
sampledb.logic.locations.assign_location_to_object(
measurement.id, room_141.id, None, instrument_responsible_user.id,
"Temporarily stored on table\n\nSome other text")
sampledb.logic.locations.assign_location_to_object(
measurement.id, room_141.id, instrument_responsible_user.id,
basic_user.id, "Stored in shelf K")
sampledb.logic.notifications.create_other_notification(
instrument_responsible_user.id, "This is a demo.")
sampledb.logic.object_permissions.set_user_object_permissions(
independent_object.id, instrument_responsible_user.id,
sampledb.models.Permissions.GRANT)
sampledb.logic.notifications.create_notification_for_having_received_an_objects_permissions_request(
instrument_responsible_user.id, independent_object.id, admin.id)
for i in range(1, 8):
sampledb.logic.instrument_log_entries.create_instrument_log_object_attachment(
instrument_log_entry_id=log_entry.id, object_id=i)
def set_up_state(user: User):
action = actions.create_action(
action_type_id=sampledb.models.ActionType.SAMPLE_CREATION,
name='Example Action',
schema={
'title': 'Example Object',
'type': 'object',
'properties': {
'name': {
'title': 'Sample Name',
'type': 'text'
}
},
'required': ['name']
},
description='',
instrument_id=None
)
actions.create_action(
action_type_id=sampledb.models.ActionType.SAMPLE_CREATION,
name='Irrelevant Action',
schema={
'title': 'Example Object',
'type': 'object',
'properties': {
'name': {
'title': 'Sample Name',
'type': 'text'
}
},
'required': ['name']
},
description='',
instrument_id=None
)
data = {'name': {'_type': 'text', 'text': 'Object'}}
object = objects.create_object(user_id=user.id, action_id=action.id, data=data)
def save_content(file): file.write("This is a test file.".encode('utf-8'))
files.create_local_file(object.id, user.id, "test.txt", save_content)
files.create_url_file(object.id, user.id, "https://example.com")
instrument = sampledb.logic.instruments.create_instrument(
name="Example Instrument",
description="Example Instrument Description",
users_can_view_log_entries=True
)
category = sampledb.logic.instrument_log_entries.create_instrument_log_category(
instrument_id=instrument.id,
title="Category",
theme=sampledb.logic.instrument_log_entries.InstrumentLogCategoryTheme.RED
)
log_entry = sampledb.logic.instrument_log_entries.create_instrument_log_entry(
instrument_id=instrument.id,
user_id=user.id,
content="Example Log Entry Text",
category_ids=[category.id]
)
sampledb.logic.instrument_log_entries.create_instrument_log_file_attachment(
instrument_log_entry_id=log_entry.id,
file_name="example.txt",
content=b'Example Content'
)
sampledb.logic.instrument_log_entries.create_instrument_log_object_attachment(
instrument_log_entry_id=log_entry.id,
object_id=object.id
)
def setup_data(app):
# TODO: replace using user management logic
admin = User(name="Administrator",
email="*****@*****.**",
type=UserType.PERSON)
admin.is_admin = True
instrument_responsible_user = User(name="Instrument Responsible User",
email="*****@*****.**",
type=UserType.PERSON)
basic_user = User(name="Basic User",
email="*****@*****.**",
type=UserType.PERSON)
for user in (admin, instrument_responsible_user, basic_user):
sampledb.db.session.add(user)
sampledb.db.session.commit()
api_user = sampledb.logic.users.create_user(name="API User",
email="*****@*****.**",
type=UserType.OTHER)
sampledb.logic.authentication.add_other_authentication(
api_user.id, 'api', 'password')
group_id = groups.create_group(
"Example Group", "This is an example group for testing purposes.",
instrument_responsible_user.id).id
project_id = projects.create_project("Example Project",
"This is an example project",
instrument_responsible_user.id).id
project_id2 = projects.create_project("Example Project 2",
"This is another example project",
instrument_responsible_user.id).id
projects.create_subproject_relationship(parent_project_id=project_id,
child_project_id=project_id2,
child_can_add_users_to_parent=True)
# Setup autologin for testing
@app.route('/users/me/autologin')
@app.route('/users/<int:user_id>/autologin')
def autologin(user_id=instrument_responsible_user.id):
user = User.query.get(user_id)
assert user is not None
flask_login.login_user(user)
return flask.redirect(
flask.url_for('frontend.new_action', previous_action_id=4))
sampledb.login_manager.login_view = 'autologin'
instrument = create_instrument(
name="OMBE I", description="This is an example instrument.")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open('sampledb/schemas/ombe_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.SAMPLE_CREATION,
"Sample Creation",
"This is an example action", schema,
instrument.id)
independent_action = create_action(ActionType.SAMPLE_CREATION,
"Alternative Process",
"This is an example action", schema)
with open('sampledb/schemas/ombe_measurement_batch.sampledb.json',
'r') as schema_file:
batch_schema = json.load(schema_file)
create_action(ActionType.SAMPLE_CREATION, "Sample Creation (Batch)",
"This is an example action", batch_schema, instrument.id)
sampledb.db.session.commit()
with open('example_data/ombe-1.sampledb.json', 'r') as data_file:
data = json.load(data_file)
instrument_object = Objects.create_object(
data=data,
schema=schema,
user_id=instrument_responsible_user.id,
action_id=instrument_action.id,
connection=sampledb.db.engine)
create_object(object_id=instrument_object.object_id,
user_id=instrument_responsible_user.id)
data['multilayer'][0]['repetitions']['magnitude_in_base_units'] = 20000
data['multilayer'][1]['films'][0]['thickness'][
'magnitude_in_base_units'] = 1
independent_object = Objects.create_object(
data=data,
schema=schema,
user_id=instrument_responsible_user.id,
action_id=independent_action.id,
connection=sampledb.db.engine)
create_object(object_id=independent_object.object_id,
user_id=instrument_responsible_user.id)
comments.create_comment(
instrument_object.id, instrument_responsible_user.id,
'This comment is very long. ' * 20 + '\n' +
'This comment has three paragraphs. ' * 20 + '\n' + '\n' +
'This comment has three paragraphs. ' * 20)
comments.create_comment(instrument_object.id,
instrument_responsible_user.id,
'This is another, shorter comment')
files.create_local_file(
instrument_object.id, instrument_responsible_user.id, 'example.txt',
lambda stream: stream.write("Dies ist ein Test".encode('utf-8')))
files.create_local_file(
instrument_object.id, instrument_responsible_user.id, 'demo.png',
lambda stream: stream.write(
open('sampledb/static/img/ghs01.png', 'rb').read()))
files.update_file_information(instrument_object.id, 1,
instrument_responsible_user.id,
'Example File',
'This is a file description.')
files.create_url_file(instrument_object.id, instrument_responsible_user.id,
'http://iffsamples.fz-juelich.de/')
with open('server_schemas/ombe_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
sampledb.logic.actions.update_action(instrument_action.id,
"Updated Sample Creation", "", schema)
object_permissions.set_group_object_permissions(
independent_object.object_id, group_id,
object_permissions.Permissions.READ)
instrument = create_instrument(name="XRR",
description="X-Ray Reflectometry")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open('sampledb/schemas/xrr_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.MEASUREMENT,
"XRR Measurement", "", schema,
instrument.id)
with open('sampledb/schemas/searchable_quantity.json', 'r') as schema_file:
schema = json.load(schema_file)
action = create_action(ActionType.SAMPLE_CREATION, "Searchable Object", "",
schema, None)
independent_object = Objects.create_object(
data={
"name": {
"_type": "text",
"text": "TEST-1"
},
"tags": {
"_type": "tags",
"tags": ["tag1", "tag2"]
},
"mass": {
"_type": "quantity",
"dimensionality": "[mass]",
"magnitude_in_base_units": 0.00001,
"units": "mg"
}
},
schema=schema,
user_id=instrument_responsible_user.id,
action_id=action.id,
connection=sampledb.db.engine)
create_object(object_id=independent_object.object_id,
user_id=instrument_responsible_user.id)
object_permissions.set_group_object_permissions(
independent_object.object_id, group_id,
object_permissions.Permissions.READ)
object_permissions.set_user_object_permissions(
independent_object.object_id, api_user.id,
object_permissions.Permissions.WRITE)
independent_object = Objects.create_object(
data={
"name": {
"_type": "text",
"text": "TEST-2"
},
"tags": {
"_type": "tags",
"tags": ["tag2", "tag3"]
},
"mass": {
"_type": "quantity",
"dimensionality": "[mass]",
"magnitude_in_base_units": 0.000005,
"units": "mg"
}
},
schema=schema,
user_id=instrument_responsible_user.id,
action_id=action.id,
connection=sampledb.db.engine)
create_object(object_id=independent_object.object_id,
user_id=instrument_responsible_user.id)
object_permissions.set_group_object_permissions(
independent_object.object_id, group_id,
object_permissions.Permissions.READ)
sampledb.db.session.commit()
instrument = create_instrument(
name="MPMS SQUID", description="MPMS SQUID Magnetometer JCNS-2")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open('server_schemas/squid_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.MEASUREMENT,
"Perform Measurement", "", schema,
instrument.id)
sampledb.db.session.commit()
instrument = create_instrument(
name="Powder Diffractometer",
description="Huber Imaging Plate Guinier Camera G670 at JCNS-2")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open('server_schemas/powder_diffractometer_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.MEASUREMENT,
"Perform Measurement", "", schema,
instrument.id)
sampledb.db.session.commit()
instrument = create_instrument(
name="GALAXI", description="Gallium Anode Low-Angle X-ray Instrument")
add_instrument_responsible_user(instrument.id,
instrument_responsible_user.id)
with open('server_schemas/galaxi_measurement.sampledb.json',
'r') as schema_file:
schema = json.load(schema_file)
instrument_action = create_action(ActionType.MEASUREMENT,
"Perform Measurement", "", schema,
instrument.id)
sampledb.db.session.commit()
with open('server_schemas/other_sample.sampledb.json', 'r') as schema_file:
schema = json.load(schema_file)
create_action(ActionType.SAMPLE_CREATION, "Other Sample", "", schema, None)
sampledb.db.session.commit()
sample_action = sampledb.logic.actions.create_action(
action_type=ActionType.SAMPLE_CREATION,
name="sample_action",
description="",
schema={
'title': 'Example Object',
'type': 'object',
'properties': {
'name': {
'title': 'Object Name',
'type': 'text'
},
'sample': {
'title': 'Sample',
'type': 'sample'
}
},
'required': ['name']
})
measurement_action = sampledb.logic.actions.create_action(
action_type=ActionType.MEASUREMENT,
name="measurement_action",
description="",
schema={
'title': 'Example Object',
'type': 'object',
'properties': {
'name': {
'title': 'Object Name',
'type': 'text'
},
'sample': {
'title': 'Sample',
'type': 'sample'
},
'comment': {
'title': 'Comment',
'type': 'text',
'multiline': True
}
},
'required': ['name']
})
data = {'name': {'_type': 'text', 'text': 'Object 1'}}
object = sampledb.logic.objects.create_object(sample_action.id, data,
user.id)
sampledb.logic.object_permissions.set_object_public(object.id, True)
data = {
'name': {
'_type': 'text',
'text': 'Object 2'
},
'sample': {
'_type': 'sample',
'object_id': object.id
}
}
sample = sampledb.logic.objects.create_object(sample_action.id, data,
user.id)
sampledb.logic.object_permissions.set_object_public(sample.id, True)
data = {
'name': {
'_type': 'text',
'text': 'Object 1'
},
'sample': {
'_type': 'sample',
'object_id': sample.id
}
}
sampledb.logic.objects.update_object(object.id, data, user.id)
data = {
'name': {
'_type': 'text',
'text': 'Measurement'
},
'sample': {
'_type': 'sample',
'object_id': object.id
},
'comment': {
'_type':
'text',
'text':
'This is a test.\nThis is a second line.\n\nThis line follows an empty line.'
}
}
measurement = sampledb.logic.objects.create_object(measurement_action.id,
data, user.id)
sampledb.logic.object_permissions.set_object_public(measurement.id, True)
data = {
'name': {
'_type': 'text',
'text': 'Measurement 2'
},
'sample': {
'_type': 'sample',
'object_id': sample.id
},
'comment': {
'_type':
'text',
'text':
'This is a test.\nThis is a second line.\n\nThis line follows an empty line.'
}
}
measurement = sampledb.logic.objects.create_object(
measurement_action.id, data, instrument_responsible_user.id)
sampledb.logic.object_permissions.set_object_public(measurement.id, True)
juelich = sampledb.logic.locations.create_location(
"FZJ", "Forschungszentrum Jülich", None,
instrument_responsible_user.id)
building_04_8 = sampledb.logic.locations.create_location(
"Building 04.8", "Building 04.8 at Forschungszentrum Jülich",
juelich.id, instrument_responsible_user.id)
room_139 = sampledb.logic.locations.create_location(
"Room 139b", "Building 04.8, Room 139", building_04_8.id,
instrument_responsible_user.id)
room_141 = sampledb.logic.locations.create_location(
"Room 141", "Building 04.8, Room 141", building_04_8.id,
instrument_responsible_user.id)
sampledb.logic.locations.assign_location_to_object(
measurement.id, room_141.id, None, instrument_responsible_user.id,
"Temporarily stored on table\n\nSome other text")
sampledb.logic.locations.assign_location_to_object(
measurement.id, room_141.id, instrument_responsible_user.id,
basic_user.id, "Stored in shelf K")
sampledb.logic.notifications.create_other_notification(
instrument_responsible_user.id, "This is a demo.")
sampledb.logic.object_permissions.set_user_object_permissions(
independent_object.id, instrument_responsible_user.id,
sampledb.models.Permissions.GRANT)
sampledb.logic.notifications.create_notification_for_having_received_an_objects_permissions_request(
instrument_responsible_user.id, independent_object.id, admin.id)
def test_generate_rdf(flask_server, user, other_user):
action = actions.create_action(
action_type=ActionType.SAMPLE_CREATION,
name='Example Action',
schema={
'title': 'Example Object',
'type': 'object',
'properties': {
'name': {
'title': 'Sample Name',
'type': 'text'
}
},
'required': ['name']
},
description='',
instrument_id=None
)
data = {'name': {'_type': 'text', 'text': 'Example Object'}}
object = objects.create_object(user_id=user.id, action_id=action.id, data=data)
comments.create_comment(object.id, other_user.id, 'Example Comment')
objects.update_object(object.id, data, user.id)
objects.update_object(object.id, data, other_user.id)
flask_server.app.config['SERVER_NAME'] = urlparse(flask_server.base_url).netloc
with flask_server.app.app_context():
rdf_document = rdf.generate_rdf(user.id, object.id)
etree.register_namespace('dcterms', 'http://purl.org/dc/terms/')
et = etree.fromstring(rdf_document)
assert next(et.iter('{*}title')).text == 'Example Object'
assert next(et.iter('{*}identifier')).text == f'{flask_server.base_url}objects/{object.id}'
creators = list(et.iter('{*}creator'))
assert len(creators) == 2
assert creators[0][0].get('{http://www.w3.org/1999/02/22-rdf-syntax-ns#}about') == f'{flask_server.base_url}users/{user.id}'
assert creators[0][0][0].text == user.name
assert creators[1][0].get('{http://www.w3.org/1999/02/22-rdf-syntax-ns#}about') == f'{flask_server.base_url}users/{other_user.id}'
assert creators[1][0][0].text == other_user.name
contributors = list(et.iter('{*}contributor'))
assert len(contributors) == 0
versions = list(et.iter('{*}hasVersion'))
assert len(versions) == 3
assert versions[0].get('{http://www.w3.org/1999/02/22-rdf-syntax-ns#}resource') == f'{flask_server.base_url}objects/{object.id}/versions/0'
assert versions[1].get('{http://www.w3.org/1999/02/22-rdf-syntax-ns#}resource') == f'{flask_server.base_url}objects/{object.id}/versions/1'
assert versions[2].get('{http://www.w3.org/1999/02/22-rdf-syntax-ns#}resource') == f'{flask_server.base_url}objects/{object.id}/versions/2'
is_version_of = list(et.iter('{*}isVersionOf'))
assert len(is_version_of) == 0
flask_server.app.config['SERVER_NAME'] = urlparse(flask_server.base_url).netloc
with flask_server.app.app_context():
rdf_document = rdf.generate_rdf(user.id, object.id, 1)
etree.register_namespace('dcterms', 'http://purl.org/dc/terms/')
et = etree.fromstring(rdf_document)
assert next(et.iter('{*}title')).text == 'Example Object'
assert next(et.iter('{*}identifier')).text == f'{flask_server.base_url}objects/{object.id}/versions/1'
creators = list(et.iter('{*}creator'))
assert len(creators) == 1
assert creators[0][0].get('{http://www.w3.org/1999/02/22-rdf-syntax-ns#}about') == f'{flask_server.base_url}users/{user.id}'
assert creators[0][0][0].text == user.name
contributors = list(et.iter('{*}contributor'))
assert len(contributors) == 1
assert contributors[0][0].get('{http://www.w3.org/1999/02/22-rdf-syntax-ns#}about') == f'{flask_server.base_url}users/{other_user.id}'
assert contributors[0][0][0].text == other_user.name
versions = list(et.iter('{*}hasVersion'))
assert len(versions) == 0
is_version_of = list(et.iter('{*}isVersionOf'))
assert len(is_version_of) == 1
assert is_version_of[0].get('{http://www.w3.org/1999/02/22-rdf-syntax-ns#}resource') == f'{flask_server.base_url}objects/{object.id}'
