def test_get_file(user: User, object: Object, tmpdir):
files.FILE_STORAGE_PATH = tmpdir
assert files.get_file_for_object(object_id=object.object_id, file_id=0) is None
assert len(files.get_files_for_object(object_id=object.object_id)) == 0
files.create_local_file(object_id=object.object_id, user_id=user.id, file_name="test.png", save_content=lambda stream: None)
assert len(files.get_files_for_object(object_id=object.object_id)) == 1
assert files.get_file_for_object(object_id=object.object_id, file_id=0) is not None
def test_files(user: User, object: Object, tmpdir):
files.FILE_STORAGE_PATH = tmpdir
start_datetime = datetime.datetime.utcnow()
assert len(files.get_files_for_object(object_id=object.object_id)) == 0
files.create_local_file(object_id=object.object_id,
user_id=user.id,
file_name="test.png",
save_content=lambda stream: stream.write(b"1"))
assert len(files.get_files_for_object(object_id=object.object_id)) == 1
file = files.get_files_for_object(object_id=object.object_id)[0]
assert file.id == 0
assert file.user_id == user.id
assert file.uploader == user
assert file.object_id == object.object_id
assert file.original_file_name == "test.png"
assert file.utc_datetime >= start_datetime
assert file.utc_datetime <= datetime.datetime.utcnow()
assert file.real_file_name == tmpdir.join(str(object.action_id)).join(
str(object.id)).join("0000_test.png")
assert file.open().read() == b"1"
files.create_local_file(object_id=object.object_id,
user_id=user.id,
file_name="example.txt",
save_content=lambda stream: None)
assert len(files.get_files_for_object(object_id=object.object_id)) == 2
file2, file1 = files.get_files_for_object(object_id=object.object_id)
assert file1.original_file_name == "example.txt"
assert file2.original_file_name == "test.png"
assert file1.id == 1
assert file2.id == 0
assert file2.utc_datetime >= start_datetime
assert file2.utc_datetime <= datetime.datetime.utcnow()
def test_same_file_name(user: User, object: Object, tmpdir):
files.FILE_STORAGE_PATH = tmpdir
files.create_local_file(object_id=object.object_id, user_id=user.id, file_name="test.png", save_content=lambda stream: None)
files.create_local_file(object_id=object.object_id, user_id=user.id, file_name="test.png", save_content=lambda stream: None)
file1, file2 = files.get_files_for_object(object_id=object.object_id)
assert file1.original_file_name == file2.original_file_name
assert file1.real_file_name != file2.real_file_name
def test_file_information(user: User, object: Object, tmpdir):
files.FILE_STORAGE_PATH = tmpdir
assert len(files.get_files_for_object(object_id=object.object_id)) == 0
files.create_local_file(object_id=object.object_id,
user_id=user.id,
file_name="test.png",
save_content=lambda stream: stream.write(b"1"))
file = files.get_file_for_object(object.object_id, 0)
assert file.title == file.original_file_name
assert file.description is None
files.update_file_information(object_id=object.object_id,
file_id=file.id,
user_id=user.id,
title='Title',
description='')
file = files.get_file_for_object(object.object_id, 0)
assert file.title == 'Title'
assert file.description is None
assert len(file.log_entries) == 1
log_entry = file.log_entries[0]
assert log_entry.type == files.FileLogEntryType.EDIT_TITLE
assert log_entry.data == {'title': 'Title'}
files.update_file_information(object_id=object.object_id,
file_id=file.id,
user_id=user.id,
title='Title',
description='Description')
file = files.get_file_for_object(object.object_id, 0)
assert file.title == 'Title'
assert file.description == 'Description'
assert len(file.log_entries) == 2
log_entry = file.log_entries[1]
assert log_entry.type == files.FileLogEntryType.EDIT_DESCRIPTION
assert log_entry.data == {'description': 'Description'}
files.update_file_information(object_id=object.object_id,
file_id=file.id,
user_id=user.id,
title='',
description='Description')
file = files.get_file_for_object(object.object_id, 0)
assert file.title == file.original_file_name
assert file.description == 'Description'
assert len(file.log_entries) == 3
log_entry = file.log_entries[2]
assert log_entry.type == files.FileLogEntryType.EDIT_TITLE
assert log_entry.data == {'title': file.original_file_name}
with pytest.raises(files.FileDoesNotExistError):
files.update_file_information(object_id=object.object_id,
file_id=file.id + 1,
user_id=user.id,
title='Title',
description='Description')
assert len(file.log_entries) == 3
def test_invalid_file_name(user: User, object: Object, tmpdir):
files.FILE_STORAGE_PATH = tmpdir
assert len(files.get_files_for_object(object_id=object.object_id)) == 0
files.create_local_file(object_id=object.object_id, user_id=user.id, file_name="t" * 146 + ".png", save_content=lambda stream: None)
assert len(files.get_files_for_object(object_id=object.object_id)) == 1
with pytest.raises(errors.FileNameTooLongError):
files.create_local_file(object_id=object.object_id, user_id=user.id, file_name="t" * 147 + ".png", save_content=lambda stream: None)
assert len(files.get_files_for_object(object_id=object.object_id)) == 1
def test_file_exists(user: User, object: Object, tmpdir):
files.FILE_STORAGE_PATH = tmpdir
assert len(files.get_files_for_object(object_id=object.object_id)) == 0
tmpdir.join(str(object.action_id)).join(str(object.id)).join("0000_test.png").write("", ensure=True)
with pytest.raises(FileExistsError):
files.create_local_file(object_id=object.object_id, user_id=user.id, file_name="test.png", save_content=lambda stream: None)
assert len(files.get_files_for_object(object_id=object.object_id)) == 0
def test_too_many_files(user: User, object: Object, tmpdir):
files.FILE_STORAGE_PATH = tmpdir
files.MAX_NUM_FILES = 1
assert len(files.get_files_for_object(object_id=object.object_id)) == 0
files.create_local_file(object_id=object.object_id, user_id=user.id, file_name="test.png", save_content=lambda stream: None)
assert len(files.get_files_for_object(object_id=object.object_id)) == 1
with pytest.raises(errors.TooManyFilesForObjectError):
files.create_local_file(object_id=object.object_id, user_id=user.id, file_name="test.png", save_content=lambda stream: None)
assert len(files.get_files_for_object(object_id=object.object_id)) == 1
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 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)
# 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 post(self, object_id: int):
request_json = flask.request.get_json(force=True)
if not isinstance(request_json, dict):
return {"message": "JSON object body required"}, 400
object = get_object(object_id=object_id)
if 'object_id' in request_json:
if request_json['object_id'] != object.object_id:
return {
"message": "object_id must be {}".format(object.object_id)
}, 400
if 'storage' not in request_json:
return {"message": "storage must be set"}, 400
storage = request_json['storage']
if storage not in ('local', 'url'):
return {"message": "storage must be 'local' or 'url'"}, 400
if storage == 'local':
for key in request_json:
if key not in {
'object_id', 'storage', 'original_file_name',
'base64_content'
}:
return {"message": "invalid key '{}'".format(key)}, 400
if 'original_file_name' not in request_json or not request_json[
'original_file_name']:
return {
"message":
"original_file_name must be set for files with local storage"
}, 400
original_file_name = request_json['original_file_name']
if 'base64_content' not in request_json:
return {
"message":
"base64_content must be set for files with local storage"
}, 400
base64_content = request_json['base64_content']
try:
content = base64.b64decode(base64_content.encode('utf-8'),
validate=True)
except Exception:
return {
"message": "base64_content must be base64 encoded"
}, 400
file = create_local_file(
object_id=object_id,
user_id=flask.g.user.id,
file_name=original_file_name,
save_content=lambda stream: stream.write(content))
if storage == 'url':
for key in request_json:
if key not in {'object_id', 'storage', 'url'}:
return {"message": "invalid key '{}'".format(key)}, 400
if 'url' not in request_json:
return {
"message": "url must be set for files with url storage"
}, 400
url = request_json['url']
if not _validate_url(url):
return {"message": "url must be a valid url"}, 400
file = create_url_file(object_id=object_id,
user_id=flask.g.user.id,
url=url)
file_url = flask.url_for('api.object_file',
object_id=file.object_id,
file_id=file.id)
return flask.redirect(file_url, code=201)
