def get_opts(self, request, **kwargs):
"""Add extra parameters to the opts dict."""
opts = super(ScreensView, self).get_opts(request, **kwargs)
opts["order_by"] = "lower(obj.name)"
# at /plate/:plate_id/screens/ we have 'plate_id' in kwargs
if "plate_id" in kwargs:
opts["plate"] = int(kwargs["plate_id"])
else:
# filter by query /screens/?plate=:id
plate = getIntOrDefault(request, "plate", None)
if plate is not None:
opts["plate"] = plate
return opts
def get_opts(self, request, **kwargs):
"""Add extra parameters to the opts dict."""
opts = super(ProjectsView, self).get_opts(request, **kwargs)
opts["order_by"] = "lower(obj.name)"
# at /datasets/:dataset_id/projects/ we have 'dataset_id' in kwargs
if "dataset_id" in kwargs:
opts["dataset"] = int(kwargs["dataset_id"])
else:
# Filter Projects by child 'dataset'
dataset = getIntOrDefault(request, "dataset", None)
if dataset is not None:
opts["dataset"] = dataset
return opts
def get_opts(self, request, **kwargs):
"""Add extra parameters to the opts dict."""
opts = super(ScreensView, self).get_opts(request, **kwargs)
opts['order_by'] = 'lower(obj.name)'
# at /plate/:plate_id/screens/ we have 'plate_id' in kwargs
if 'plate_id' in kwargs:
opts['plate'] = long(kwargs['plate_id'])
else:
# filter by query /screens/?plate=:id
plate = getIntOrDefault(request, 'plate', None)
if plate is not None:
opts['plate'] = plate
return opts
def get_opts(self, request, **kwargs):
"""Add extra parameters to the opts dict."""
opts = super(ProjectsView, self).get_opts(request, **kwargs)
opts['order_by'] = 'lower(obj.name)'
# at /datasets/:dataset_id/projects/ we have 'dataset_id' in kwargs
if 'dataset_id' in kwargs:
opts['dataset'] = long(kwargs['dataset_id'])
else:
# Filter Projects by child 'dataset'
dataset = getIntOrDefault(request, 'dataset', None)
if dataset is not None:
opts['dataset'] = dataset
return opts
def get_opts(self, request, **kwargs):
"""Add extra parameters to the opts dict."""
opts = super(ImagesView, self).get_opts(request, **kwargs)
opts["order_by"] = "lower(obj.name)"
# at /datasets/:dataset_id/images/ we have 'dataset_id' in kwargs
if "dataset_id" in kwargs:
opts["dataset"] = int(kwargs["dataset_id"])
else:
# filter by query /images/?dataset=:id
dataset = getIntOrDefault(request, "dataset", None)
if dataset is not None:
opts["dataset"] = dataset
# When listing images, always load pixels by default
opts["load_pixels"] = True
return opts
def _save_object(self, request, conn, object_json, **kwargs):
"""Here we handle the saving for PUT and POST."""
# Try to get group from request, OR from details below...
group = getIntOrDefault(request, 'group', None)
decoder = None
objType = object_json['@type']
decoder = get_decoder(objType)
# If we are passed incomplete object, or decoder couldn't be found...
if decoder is None:
raise BadRequestError('No decoder found for type: %s' % objType)
# Any marshal errors most likely due to invalid input. status=400
try:
obj = decoder.decode(object_json)
except Exception:
msg = 'Error in decode of json data by omero_marshal'
raise BadRequestError(msg, traceback.format_exc())
if group is None:
try:
# group might be None or unloaded
group = obj.getDetails().group.id.val
except AttributeError:
# Instead of default stack trace, give nicer message:
msg = ("Specify Group in omero:details or "
"query parameters ?group=:id")
raise BadRequestError(msg)
# If owner was unloaded (E.g. from get() above) or if missing
# ome.model.meta.Experimenter.ldap (not supported by omero_marshal)
# then saveObject() will give ValidationException.
# Therefore we ignore any details for now:
obj.unloadDetails()
# TODO: Unlink children for Projects, Datasets and Screens to avoid
# breaking links. See PR #4930
if hasattr(obj, 'unloadDatasetLinks'):
obj.unloadDatasetLinks()
if hasattr(obj, 'unloadImageLinks'):
obj.unloadImageLinks()
if hasattr(obj, 'unloadPlateLinks'):
obj.unloadPlateLinks()
conn.SERVICE_OPTS.setOmeroGroup(group)
obj = conn.getUpdateService().saveAndReturnObject(
obj, conn.SERVICE_OPTS)
encoder = get_encoder(obj.__class__)
return {'data': encoder.encode(obj)}
def get_opts(self, request, **kwargs):
"""Add extra parameters to the opts dict."""
opts = super(RoisView, self).get_opts(request, **kwargs)
opts["load_shapes"] = True
# order_by ID simply for consistency & paging
opts["order_by"] = "obj.id"
# at /images/:image_id/rois/ we have 'image_id' in kwargs
if "image_id" in kwargs:
opts["image"] = int(kwargs["image_id"])
else:
# filter by query /rois/?image=:id
image = getIntOrDefault(request, "image", None)
if image is not None:
opts["image"] = image
return opts
def get_opts(self, request, **kwargs):
"""Add extra parameters to the opts dict."""
opts = super(WellsView, self).get_opts(request, **kwargs)
opts["order_by"] = "obj.column, obj.row"
# at /plates/:plate_id/wells/ we have 'plate_id' in kwargs
if "plate_id" in kwargs:
opts["plate"] = int(kwargs["plate_id"])
elif "plateacquisition_id" in kwargs:
opts["plateacquisition"] = int(kwargs["plateacquisition_id"])
else:
# filter by query /wells/?plate=:id
plate = getIntOrDefault(request, "plate", None)
if plate is not None:
opts["plate"] = plate
# When filtering by plate or plateacquisition, can filter by ws index
if "index" in kwargs:
opts["wellsample_index"] = int(kwargs["index"])
# Listing Wells, load Images
opts["load_images"] = True
return opts
def get_opts(self, request, **kwargs):
"""Add extra parameters to the opts dict."""
opts = super(WellsView, self).get_opts(request, **kwargs)
opts['order_by'] = 'obj.column, obj.row'
# at /plates/:plate_id/wells/ we have 'plate_id' in kwargs
if 'plate_id' in kwargs:
opts['plate'] = long(kwargs['plate_id'])
elif 'plateacquisition_id' in kwargs:
opts['plateacquisition'] = long(kwargs['plateacquisition_id'])
else:
# filter by query /wells/?plate=:id
plate = getIntOrDefault(request, 'plate', None)
if plate is not None:
opts['plate'] = plate
# When filtering by plate or plateacquisition, can filter by ws index
if 'index' in kwargs:
opts['wellsample_index'] = int(kwargs['index'])
# Listing Wells, load Images
opts['load_images'] = True
return opts
def get_opts(self, request, **kwargs):
"""
Add extra parameters to the opts dict.
Query will order Groups by name
"""
opts = super(ExperimenterGroupsView, self).get_opts(request, **kwargs)
# Default 'load_experimenters' = True, but we don't want them
opts["load_experimenters"] = False
# order_by group name
opts["order_by"] = "lower(obj.name)"
# handle /experimenters/:experimenter_id/experimentergroups/
if "experimenter_id" in kwargs:
opts["experimenter"] = int(kwargs["experimenter_id"])
else:
# filter by query /experimentergroups/?experimenter=:id
group = getIntOrDefault(request, "experimenter", None)
if group is not None:
opts["experimenter"] = group
return opts
def get_opts(self, request, **kwargs):
"""
Add extra parameters to the opts dict for GET /experimenters/.
Query will order by lastName, firstName
Includes option to filter by group
"""
opts = super(ExperimentersView, self).get_opts(request, **kwargs)
# Default 'load_experimentergroups' is True, but we don't need groups
opts["load_experimentergroups"] = False
# order_by lastName, firstName
opts["order_by"] = "lower(obj.lastName), lower(obj.firstName)"
# at /experimentergroups/:group_id/experimenters/
# we have 'group_id' in kwargs
if "group_id" in kwargs:
opts["experimentergroup"] = int(kwargs["group_id"])
else:
# filter by query /experimenters/?experimentergroup=:id
group = getIntOrDefault(request, "experimentergroup", None)
if group is not None:
opts["experimentergroup"] = group
return opts
