def marshal_objects(objects):
""" Marshal objects using omero_marshal """
expected = []
for obj in objects:
encoder = get_encoder(obj.__class__)
expected.append(encoder.encode(obj))
return expected
def get(self, request, object_id, conn=None, **kwargs):
"""Simply GET a single Object and marshal it or 404 if not found."""
opts = self.get_opts(request)
object_id = int(object_id)
query, params, wrapper = conn.buildQuery(self.OMERO_TYPE, [object_id],
opts=opts)
# Allow subclasses to access the result object
self.result = conn.getQueryService().findByQuery(
query, params, conn.SERVICE_OPTS)
if self.result is None:
raise NotFoundError("%s %s not found" %
(self.OMERO_TYPE, object_id))
encoder = get_encoder(self.result.__class__)
marshalled = encoder.encode(self.result)
# Optionally lookup child counts
child_count = request.GET.get("childCount", False) == "true"
if child_count and wrapper.LINK_CLASS:
counts = get_child_counts(conn, wrapper.LINK_CLASS, [object_id])
ch_count = counts[object_id] if object_id in counts else 0
marshalled["omero:childCount"] = ch_count
self.add_data(marshalled, request, conn, self.urls, **kwargs)
return {"data": marshalled}
def test_base_decoder(self, roi):
encoder = get_encoder(roi.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(roi)
v = decoder.decode(v)
self.assert_roi(v)
self.assert_externalInfo(v.details.externalInfo)
def test_base_decoder(self, roi):
encoder = get_encoder(roi.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(roi)
v = decoder.decode(v)
self.assert_roi(v)
self.assert_externalInfo(v.details.externalInfo)
def test_project_with_datasets_encoder(self, project_with_datasets):
encoder = get_encoder(project_with_datasets.__class__)
v = encoder.encode(project_with_datasets)
assert v == {
'@id':
1,
'@type':
'%s#Project' % OME_SCHEMA_URL,
'Name':
'the_name',
'Description':
'the_description',
'omero:details': {
'@type': 'TBD#Details'
},
'Datasets': [{
'@id': 1,
'@type': '%s#Dataset' % OME_SCHEMA_URL,
'Name': 'dataset_name_1',
'Description': 'dataset_description_1',
'omero:details': {
'@type': 'TBD#Details'
}
}, {
'@id': 2,
'@type': '%s#Dataset' % OME_SCHEMA_URL,
'Name': 'dataset_name_2',
'Description': 'dataset_description_2',
'omero:details': {
'@type': 'TBD#Details'
}
}]
}
def test_roi_with_shapes_and_annotations(self,
roi_with_shapes_and_annotations):
encoder = get_encoder(roi_with_shapes_and_annotations.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(roi_with_shapes_and_annotations)
v = decoder.decode(v)
self.assert_roi_with_shapes(v, has_annotations=True)
def test_base_encoder_with_unloaded_details_children(
self, roi_with_unloaded_details_children):
encoder = get_encoder(roi_with_unloaded_details_children.__class__)
v = encoder.encode(roi_with_unloaded_details_children)
assert v == {
'@id': 1L,
'@type': 'http://www.openmicroscopy.org/Schemas/ROI/2015-01#ROI',
'Name': 'the_name',
'Description': 'the_description',
'omero:details': {
'@type': 'TBD#Details',
'owner': {
'@id': 1L,
'@type':
'http://www.openmicroscopy.org/Schemas/OME/2015-01'
'#Experimenter'
},
'group': {
'@id': 1L,
'@type':
'http://www.openmicroscopy.org/Schemas/OME/2015-01'
'#ExperimenterGroup'
},
'permissions': {
'@type': 'TBD#Permissions',
'canAnnotate': True,
'canDelete': True,
'canEdit': True,
'canLink': True,
'perm': 'rwrwrw'
}
}
}
def test_project_decoder(self, project):
encoder = get_encoder(project.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(project)
v = decoder.decode(v)
self.assert_project(v)
assert v.sizeOfDatasetLinks() == 0
def test_encoder(self, polygon):
encoder = get_encoder(polygon.__class__)
v = encoder.encode(polygon)
self.assert_shape(v)
assert v['@id'] == 5L
assert v['@type'] == '%s#Polygon' % ROI_SCHEMA_URL
assert v['Points'] == '0,0 1,2 3,5'
def test_roi_with_shapes_and_annotations(
self, roi_with_shapes_and_annotations):
encoder = get_encoder(roi_with_shapes_and_annotations.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(roi_with_shapes_and_annotations)
v = decoder.decode(v)
self.assert_roi_with_shapes(v, has_annotations=True)
def test_decoder(self, mask):
encoder = get_encoder(mask.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(mask)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 8
def eventContextMarshal(event_context):
"""
Marshals the omero::sys::EventContext as a dict.
@param event_context: omero::sys::EventContext
@return: Dict
"""
ctx = {}
for a in [
"shareId",
"sessionId",
"sessionUuid",
"userId",
"userName",
"sudoerId",
"sudoerName",
"groupId",
"groupName",
"isAdmin",
"eventId",
"eventType",
"memberOfGroups",
"leaderOfGroups",
"adminPrivileges",
]:
if hasattr(event_context, a):
ctx[a] = unwrap(getattr(event_context, a))
perms = event_context.groupPermissions
encoder = get_encoder(perms.__class__)
ctx["groupPermissions"] = encoder.encode(perms)
return ctx
def test_well_color_decoder(self, color, well):
"""Test different combinations of r, g, b, a."""
well.red = rint(color[0])
well.green = rint(color[1])
well.blue = rint(color[2])
well.alpha = rint(color[3])
encoder = get_encoder(well.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(well)
# Check we get the expected Integer
assert v.get('Color') == color[4]
v = decoder.decode(v)
# If red is None, all are None
if color[0] is None:
assert v.red is None
assert v.green is None
assert v.blue is None
assert v.alpha is None
elif color[3] is None:
# alpha None -> 255 by default
assert v.red.val == color[0]
assert v.green.val == color[1]
assert v.blue.val == color[2]
assert v.alpha.val == 255
else:
# Otherwise, all preserved
assert v.red.val == color[0]
assert v.green.val == color[1]
assert v.blue.val == color[2]
assert v.alpha.val == color[3]
def test_project_decoder(self, project):
encoder = get_encoder(project.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(project)
v = decoder.decode(v)
self.assert_project(v)
assert v.sizeOfDatasetLinks() == 0
def test_screen_decoder(self, screen):
encoder = get_encoder(screen.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(screen)
v = decoder.decode(v)
self.assert_screen(v)
assert v.sizeOfPlateLinks() == 0
def test_project_validation(self, user_A):
"""
Test to demonstrate details bug on encode->decode.
Test illustrates the ValidationException we see when
Project is encoded to dict then decoded back to Project
and saved.
No exception is seen if the original Project is simply
saved without encode & decode OR if the details are unloaded
before saving
"""
conn = get_connection(user_A)
project = ProjectI()
project.name = rstring('test_project_validation')
project = conn.getUpdateService().saveAndReturnObject(project)
# Saving original Project again is OK
conn.getUpdateService().saveObject(project)
# encode and decode before Save raises Validation Exception
project_json = get_encoder(project.__class__).encode(project)
decoder = get_decoder(project_json['@type'])
p = decoder.decode(project_json)
with pytest.raises(ValidationException):
conn.getUpdateService().saveObject(p)
p = decoder.decode(project_json)
# Unloading details allows Save without exception
p.unloadDetails()
conn.getUpdateService().saveObject(p)
def test_project_with_datasets_encoder(self, project_with_datasets):
encoder = get_encoder(project_with_datasets.__class__)
v = encoder.encode(project_with_datasets)
assert v == {
"@id": 1L,
"@type": "%s#Project" % OME_SCHEMA_URL,
"Name": "the_name",
"Description": "the_description",
"omero:details": {"@type": "TBD#Details"},
"Datasets": [
{
"@id": 1L,
"@type": "%s#Dataset" % OME_SCHEMA_URL,
"Name": "dataset_name_1",
"Description": "dataset_description_1",
"omero:details": {"@type": "TBD#Details"},
},
{
"@id": 2L,
"@type": "%s#Dataset" % OME_SCHEMA_URL,
"Name": "dataset_name_2",
"Description": "dataset_description_2",
"omero:details": {"@type": "TBD#Details"},
},
],
}
def encode_well(self, obj):
obj.details.owner.unloadDetails()
obj.details.group.unloadDetails()
obj.details.creationEvent.unloadDetails()
obj.details.creationEvent.type.unloadDetails()
obj.details.updateEvent.unloadDetails()
obj.details.updateEvent.type.unloadDetails()
if obj.isWellSamplesLoaded() and obj.sizeOfWellSamples() > 0:
for wellsample in obj.copyWellSamples():
wellsample.unloadDetails()
image = wellsample.image
if image is not None and image.isLoaded():
image.unloadDetails()
self.unload_annotation_details(image)
if image.isPixelsLoaded():
pixels = image.getPrimaryPixels()
pixels.unloadDetails()
if pixels.isChannelsLoaded():
for channel in pixels.copyChannels():
channel.unloadDetails()
self.unload_annotation_details(channel)
self.unload_annotation_details(obj)
encoder = get_encoder(obj.__class__)
v = encoder.encode(obj)
return v
def test_encoder(self, polygon):
encoder = get_encoder(polygon.__class__)
v = encoder.encode(polygon)
self.assert_shape(v)
assert v['@id'] == 5
assert v['@type'] == '%s#Polygon' % ROI_SCHEMA_URL
assert v['Points'] == '0,0 1,2 3,5'
def test_project_with_dataset_encoder(self, project_with_datasets):
encoder = get_encoder(project_with_datasets.__class__)
v = encoder.encode(project_with_datasets)
assert v == {
'@id': 1L,
'@type':
'http://www.openmicroscopy.org/Schemas/OME/2015-01#Project',
'Name': 'the_name',
'Description': 'the_description',
'omero:details': {'@type': 'TBD#Details'},
'Datasets': [{
'@id': 1L,
'@type':
'http://www.openmicroscopy.org/Schemas/OME/2015-01'
'#Dataset',
'Name': 'dataset_name_1',
'Description': 'dataset_description_1',
'omero:details': {'@type': 'TBD#Details'}
}, {
'@id': 2L,
'@type':
'http://www.openmicroscopy.org/Schemas/OME/2015-01'
'#Dataset',
'Name': 'dataset_name_2',
'Description': 'dataset_description_2',
'omero:details': {'@type': 'TBD#Details'}
}]
}
def rois_by_plane(request, image_id, the_z, the_t, z_end=None, t_end=None,
conn=None, **kwargs):
"""
Get ROIs with all Shapes where any Shapes are on the given Z and T plane.
Includes Shapes where Z or T are null.
If z_end or t_end are not None, we filter by any shape within the
range (inclusive of z/t_end)
"""
query_service = conn.getQueryService()
params = omero.sys.ParametersI()
params.addId(image_id)
filter = omero.sys.Filter()
filter.offset = rint(request.GET.get("offset", 0))
limit = min(MAX_LIMIT, long(request.GET.get("limit", MAX_LIMIT)))
filter.limit = rint(limit)
params.theFilter = filter
where_z = "shapes.theZ = %s or shapes.theZ is null" % the_z
where_t = "shapes.theT = %s or shapes.theT is null" % the_t
if z_end is not None:
where_z = """(shapes.theZ >= %s and shapes.theZ <= %s)
or shapes.theZ is null""" % (the_z, z_end)
if t_end is not None:
where_t = """(shapes.theT >= %s and shapes.theT <= %s)
or shapes.theT is null""" % (the_t, t_end)
filter_query = """
select distinct(roi) from Roi roi
join roi.shapes as shapes
where (%s) and (%s)
and roi.image.id = :id
""" % (where_z, where_t)
# We want to load ALL shapes for the ROIs (omero-marshal fails if
# any shapes are None) but we want to filter by Shape so we use an inner
# query to get the ROI IDs filtered by Shape.
query = """
select roi from Roi roi
join fetch roi.details.owner join fetch roi.details.creationEvent
left outer join fetch roi.shapes
where roi.id in (%s) order by roi.id
""" % (filter_query)
rois = query_service.findAllByQuery(query, params, conn.SERVICE_OPTS)
marshalled = []
for r in rois:
encoder = omero_marshal.get_encoder(r.__class__)
if encoder is not None:
marshalled.append(encoder.encode(r))
# Modify query to only select count() and NOT paginate
query = filter_query.replace("distinct(roi)", "count(distinct roi)")
params = omero.sys.ParametersI()
params.addId(image_id)
result = query_service.projection(query, params, conn.SERVICE_OPTS)
meta = {"totalCount": result[0][0].val}
return JsonResponse({'data': marshalled, 'meta': meta})
def test_base_encoder_with_unloaded_details_children(
self, roi_with_unloaded_details_children):
encoder = get_encoder(roi_with_unloaded_details_children.__class__)
v = encoder.encode(roi_with_unloaded_details_children)
assert v == {
'@id': 1L,
'@type': 'http://www.openmicroscopy.org/Schemas/ROI/2015-01#ROI',
'Name': 'the_name',
'Description': 'the_description',
'omero:details': {
'@type': 'TBD#Details',
'owner': {
'@id':
1L,
'@type':
'http://www.openmicroscopy.org/Schemas/OME/2015-01'
'#Experimenter'
},
'group': {
'@id':
1L,
'@type':
'http://www.openmicroscopy.org/Schemas/OME/2015-01'
'#ExperimenterGroup'
},
'permissions': {
'@type': 'TBD#Permissions',
'canAnnotate': True,
'canDelete': True,
'canEdit': True,
'canLink': True,
'perm': 'rwrwrw'
}
}
}
def test_screen_decoder(self, screen):
encoder = get_encoder(screen.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(screen)
v = decoder.decode(v)
self.assert_screen(v)
assert v.sizeOfPlateLinks() == 0
def test_base_encoder(self, roi):
encoder = get_encoder(roi.__class__)
v = encoder.encode(roi)
assert v == {
'@id': 1L,
'@type': '%s#ROI' % ROI_SCHEMA_URL,
'Name': 'the_name',
'Description': 'the_description',
'omero:details': {
'@type': 'TBD#Details',
'group': {
'@id': 1L,
'@type': '%s#ExperimenterGroup' % OME_SCHEMA_URL,
'Description': 'the_description',
'Name': 'the_name',
'omero:details': {
'@type': 'TBD#Details'
}
},
'owner': {
'@id': 1L,
'@type': '%s#Experimenter' % OME_SCHEMA_URL,
'Email': 'the_email',
'FirstName': 'the_firstName',
'Institution': 'the_institution',
'LastName': 'the_lastName',
'MiddleName': 'the_middleName',
'UserName': '******',
'omero:details': {
'@type': 'TBD#Details'
}
},
'permissions': {
'@type': 'TBD#Permissions',
'canAnnotate': True,
'canDelete': True,
'canEdit': True,
'canLink': True,
'perm': 'rwrwrw',
'isGroupAnnotate': True,
'isGroupRead': True,
'isGroupWrite': True,
'isUserRead': True,
'isUserWrite': True,
'isWorldRead': True,
'isWorldWrite': True
},
'externalInfo': {
'@type': 'TBD#ExternalInfo',
'EntityId': 123,
'EntityType': 'test',
'Lsid': 'ABCDEF',
'Uuid': 'f90a1fd5-275c-4d14-82b3-87b5ef0f07de',
'omero:details': {
'@type': 'TBD#Details'
},
},
}
}
def test_encoder(self, label):
encoder = get_encoder(label.__class__)
v = encoder.encode(label)
self.assert_shape(v)
assert v['@id'] == 7
assert v['@type'] == '%s#Label' % ROI_SCHEMA_URL
assert v['X'] == 1.0
assert v['Y'] == 2.0
def test_encoder(self, point):
encoder = get_encoder(point.__class__)
v = encoder.encode(point)
self.assert_shape(v)
assert v['@id'] == 3
assert v['@type'] == '%s#Point' % ROI_SCHEMA_URL
assert v['X'] == 1.0
assert v['Y'] == 2.0
def test_decoder(self, polygon):
encoder = get_encoder(polygon.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(polygon)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 5L
assert v.points.val == '0,0 1,2 3,5'
def test_encoder(self, polygon):
encoder = get_encoder(polygon.__class__)
v = encoder.encode(polygon)
self.assert_shape(v)
assert v['@id'] == 5L
assert v['@type'] == \
'http://www.openmicroscopy.org/Schemas/ROI/2015-01#Polygon'
assert v['Points'] == '0,0 1,2 3,5'
def test_encoder(self, label):
encoder = get_encoder(label.__class__)
v = encoder.encode(label)
self.assert_shape(v)
assert v['@id'] == 7L
assert v['@type'] == '%s#Label' % ROI_SCHEMA_URL
assert v['X'] == 1.0
assert v['Y'] == 2.0
def test_encoder(self, polygon):
encoder = get_encoder(polygon.__class__)
v = encoder.encode(polygon)
self.assert_shape(v)
assert v['@id'] == 5L
assert v['@type'] == \
'http://www.openmicroscopy.org/Schemas/ROI/2015-01#Polygon'
assert v['Points'] == '0,0 1,2 3,5'
def test_decoder(self, polygon):
encoder = get_encoder(polygon.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(polygon)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 5L
assert v.points.val == '0,0 1,2 3,5'
def test_encoder(self, point):
encoder = get_encoder(point.__class__)
v = encoder.encode(point)
self.assert_shape(v)
assert v['@id'] == 3L
assert v['@type'] == '%s#Point' % ROI_SCHEMA_URL
assert v['X'] == 1.0
assert v['Y'] == 2.0
def test_encoder(self, label):
encoder = get_encoder(label.__class__)
v = encoder.encode(label)
self.assert_shape(v)
assert v['@id'] == 7L
assert v['@type'] == \
'http://www.openmicroscopy.org/Schemas/ROI/2015-01#Label'
assert v['X'] == 1.0
assert v['Y'] == 2.0
def test_encoder(self, point):
encoder = get_encoder(point.__class__)
v = encoder.encode(point)
self.assert_shape(v)
assert v['@id'] == 3L
assert v['@type'] == \
'http://www.openmicroscopy.org/Schemas/ROI/2015-01#Point'
assert v['X'] == 1.0
assert v['Y'] == 2.0
def test_details_encoder(self, details):
encoder = get_encoder(details.__class__)
v = encoder.encode(details)
assert v == {
'@type': 'TBD#Details',
'permissions': self.permissions_json(),
'owner': self.experimenter_json(),
'group': self.experimenter_group_json()
}
def test_encoder(self, point):
encoder = get_encoder(point.__class__)
v = encoder.encode(point)
self.assert_shape(v)
assert v['@id'] == 3L
assert v['@type'] == \
'http://www.openmicroscopy.org/Schemas/ROI/2015-01#Point'
assert v['X'] == 1.0
assert v['Y'] == 2.0
def test_details_encoder(self, details):
encoder = get_encoder(details.__class__)
v = encoder.encode(details)
assert v == {
'@type': 'TBD#Details',
'permissions': self.permissions_json(),
'owner': self.experimenter_json(),
'group': self.experimenter_group_json()
}
def test_permissions_cannot_delete(self, permissions_cannot_delete):
encoder = get_encoder(permissions_cannot_delete.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(permissions_cannot_delete)
v = decoder.decode(v)
assert v.canLink()
assert v.canEdit()
assert not v.canDelete()
assert v.canAnnotate()
def test_encoder(self, label):
encoder = get_encoder(label.__class__)
v = encoder.encode(label)
self.assert_shape(v)
assert v['@id'] == 7L
assert v['@type'] == \
'http://www.openmicroscopy.org/Schemas/ROI/2015-01#Label'
assert v['X'] == 1.0
assert v['Y'] == 2.0
def test_permissions_cannot_delete(self, permissions_cannot_delete):
encoder = get_encoder(permissions_cannot_delete.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(permissions_cannot_delete)
v = decoder.decode(v)
assert v.canLink()
assert v.canEdit()
assert not v.canDelete()
assert v.canAnnotate()
def test_encoder(self, polyline):
encoder = get_encoder(polyline.__class__)
v = encoder.encode(polyline)
self.assert_shape(v)
assert v['@id'] == 4L
assert v['@type'] == '%s#Polyline' % ROI_SCHEMA_URL
assert v['Points'] == '0,0 1,2 3,5'
if SCHEMA_VERSION != '2015-01':
assert v['MarkerStart'] == 'Arrow'
assert v['MarkerEnd'] == 'Arrow'
def test_base_encoder_unloaded_details(self, roi):
roi.unloadDetails()
encoder = get_encoder(roi.__class__)
v = encoder.encode(roi)
assert v == {
'@id': 1L,
'@type': '%s#ROI' % ROI_SCHEMA_URL,
'Name': 'the_name',
'Description': 'the_description'
}
def test_base_encoder_unloaded_details(self, roi):
roi.unloadDetails()
encoder = get_encoder(roi.__class__)
v = encoder.encode(roi)
assert v == {
'@id': 1L,
'@type': '%s#ROI' % ROI_SCHEMA_URL,
'Name': 'the_name',
'Description': 'the_description'
}
def test_encoder(self, mask):
encoder = get_encoder(mask.__class__)
v = encoder.encode(mask)
self.assert_shape(v)
assert v['@id'] == 8
assert v['@type'] == '%s#Mask' % ROI_SCHEMA_URL
assert v['X'] == 0.0
assert v['Y'] == 0.0
assert v['Width'] == 1.0
assert v['Height'] == 2.0
def test_project_encoder(self, project):
encoder = get_encoder(project.__class__)
v = encoder.encode(project)
assert v == {
"@id": 1L,
"@type": "%s#Project" % OME_SCHEMA_URL,
"Name": "the_name",
"Description": "the_description",
"omero:details": {"@type": "TBD#Details"},
}
def test_project_encoder(self, project):
encoder = get_encoder(project.__class__)
v = encoder.encode(project)
assert v == {
'@id': 1L,
'@type': '%s#Project' % OME_SCHEMA_URL,
'Name': 'the_name',
'Description': 'the_description',
'omero:details': {'@type': 'TBD#Details'}
}
def test_encoder(self, polyline):
encoder = get_encoder(polyline.__class__)
v = encoder.encode(polyline)
self.assert_shape(v)
assert v['@id'] == 4
assert v['@type'] == '%s#Polyline' % ROI_SCHEMA_URL
assert v['Points'] == '0,0 1,2 3,5'
if SCHEMA_VERSION != '2015-01':
assert v['MarkerStart'] == 'Arrow'
assert v['MarkerEnd'] == 'Arrow'
def test_base_encoder(self, roi):
encoder = get_encoder(roi.__class__)
v = encoder.encode(roi)
assert v == {
'@id': 1L,
'@type': '%s#ROI' % ROI_SCHEMA_URL,
'Name': 'the_name',
'Description': 'the_description',
'omero:details': {
'@type': 'TBD#Details',
'group': {
'@id': 1L,
'@type': '%s#ExperimenterGroup' % OME_SCHEMA_URL,
'Description': 'the_description',
'Name': 'the_name',
'omero:details': {'@type': 'TBD#Details'}
},
'owner': {
'@id': 1L,
'@type': '%s#Experimenter' % OME_SCHEMA_URL,
'Email': 'the_email',
'FirstName': 'the_firstName',
'Institution': 'the_institution',
'LastName': 'the_lastName',
'MiddleName': 'the_middleName',
'UserName': '******',
'omero:details': {'@type': 'TBD#Details'}
},
'permissions': {
'@type': 'TBD#Permissions',
'canAnnotate': True,
'canDelete': True,
'canEdit': True,
'canLink': True,
'perm': 'rwrwrw',
'isGroupAnnotate': True,
'isGroupRead': True,
'isGroupWrite': True,
'isUserRead': True,
'isUserWrite': True,
'isWorldRead': True,
'isWorldWrite': True
},
'externalInfo': {
'@type': 'TBD#ExternalInfo',
'EntityId': 123,
'EntityType': 'test',
'Lsid': 'ABCDEF',
'Uuid': 'f90a1fd5-275c-4d14-82b3-87b5ef0f07de',
'omero:details': {
'@type': 'TBD#Details'
},
},
}
}
def test_decoder(self, point):
encoder = get_encoder(point.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(point)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 3L
assert v.cx.__class__ is RDoubleI
assert v.cx.val == 1.0
assert v.cy.__class__ is RDoubleI
assert v.cy.val == 2.0
def test_project_with_datasets_and_images_decoder(
self, project_with_datasets_and_images):
encoder = get_encoder(project_with_datasets_and_images.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(project_with_datasets_and_images)
v = decoder.decode(v)
assert v.id.val == 1L
assert v.name.val == 'the_name'
assert v.description.val == 'the_description'
assert v.sizeOfDatasetLinks() == 2
dataset_1, dataset_2 = v.linkedDatasetList()
assert dataset_1.id.val == 1L
assert dataset_1.name.val == 'dataset_name_1'
assert dataset_1.description.val == 'dataset_description_1'
image_1, image_2 = dataset_1.linkedImageList()
assert image_1.id.val == 1L
assert image_1.acquisitionDate.val == 1L
assert image_1.archived.val is False
assert image_1.description.val == 'image_description_1'
assert image_1.name.val == 'image_name_1'
assert image_1.partial.val is False
assert image_1.format.id.val == 1L
assert image_1.format.value.val == 'PNG'
assert image_2.id.val == 2L
assert image_2.acquisitionDate.val == 1L
assert image_2.archived.val is False
assert image_2.description.val == 'image_description_2'
assert image_2.name.val == 'image_name_2'
assert image_2.partial.val is False
assert image_2.format.id.val == 1L
assert image_2.format.value.val == 'PNG'
assert dataset_2.id.val == 2L
assert dataset_2.name.val == 'dataset_name_2'
assert dataset_2.description.val == 'dataset_description_2'
image_3, image_4 = dataset_2.linkedImageList()
assert image_3.id.val == 3L
assert image_3.acquisitionDate.val == 1L
assert image_3.archived.val is False
assert image_3.description.val == 'image_description_3'
assert image_3.name.val == 'image_name_3'
assert image_3.partial.val is False
assert image_3.format.id.val == 1L
assert image_3.format.value.val == 'PNG'
assert image_4.id.val == 4L
assert image_4.acquisitionDate.val == 1L
assert image_4.archived.val is False
assert image_4.description.val == 'image_description_4'
assert image_4.name.val == 'image_name_4'
assert image_4.partial.val is False
assert image_4.format.id.val == 1L
assert image_4.format.value.val == 'PNG'
def test_decoder(self, polyline):
encoder = get_encoder(polyline.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(polyline)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 4L
assert v.points.val == '0,0 1,2 3,5'
if SCHEMA_VERSION != '2015-01':
assert v.markerStart.val == 'Arrow'
assert v.markerEnd.val == 'Arrow'
def test_decoder(self, label):
encoder = get_encoder(label.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(label)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 7L
assert v.x.__class__ is RDoubleI
assert v.x.val == 1.0
assert v.y.__class__ is RDoubleI
assert v.y.val == 2.0
def test_decoder(self, point):
encoder = get_encoder(point.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(point)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 3L
assert v.cx.__class__ is RDoubleI
assert v.cx.val == 1.0
assert v.cy.__class__ is RDoubleI
assert v.cy.val == 2.0
def test_decoder(self, opt_unit_label):
encoder = get_encoder(opt_unit_label.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(opt_unit_label)
v = decoder.decode(v)
self.assert_shape(v, has_unit_information=False)
assert v.id.val == 7L
assert v.x.__class__ is RDoubleI
assert v.x.val == 1.0
assert v.y.__class__ is RDoubleI
assert v.y.val == 2.0
def test_screen_with_plates_decoder(self, screen_with_plates):
encoder = get_encoder(screen_with_plates.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(screen_with_plates)
v = decoder.decode(v)
self.assert_screen(v)
assert v.id.val == 4L
assert v.sizeOfPlateLinks() == 2
plate_1, plate_2 = v.linkedPlateList()
self.assert_plate(plate_1, 5L)
self.assert_plate(plate_2, 6L)
def test_decoder(self, opt_unit_label):
encoder = get_encoder(opt_unit_label.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(opt_unit_label)
v = decoder.decode(v)
self.assert_shape(v, has_unit_information=False)
assert v.id.val == 7L
assert v.x.__class__ is RDoubleI
assert v.x.val == 1.0
assert v.y.__class__ is RDoubleI
assert v.y.val == 2.0
def test_project_encoder(self, project):
encoder = get_encoder(project.__class__)
v = encoder.encode(project)
assert v == {
'@id': 1L,
'@type':
'http://www.openmicroscopy.org/Schemas/OME/2015-01#Project',
'Name': 'the_name',
'Description': 'the_description',
'omero:details': {'@type': 'TBD#Details'}
}
def test_encoder(self, line):
encoder = get_encoder(line.__class__)
v = encoder.encode(line)
self.assert_shape(v)
assert v['@id'] == 6L
assert v['@type'] == \
'http://www.openmicroscopy.org/Schemas/ROI/2015-01#Line'
assert v['X1'] == 0.0
assert v['Y1'] == 0.0
assert v['X2'] == 1.0
assert v['Y2'] == 2.0
def test_decoder(self, label):
encoder = get_encoder(label.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(label)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 7L
assert v.x.__class__ is RDoubleI
assert v.x.val == 1.0
assert v.y.__class__ is RDoubleI
assert v.y.val == 2.0
