def test_project_create_read(self):
"""
Tests creation by POST to /save and reading with GET of /project/:id/
"""
django_client = self.django_root_client
group = self.ctx.groupId
version = api_settings.API_VERSIONS[-1]
# Need to get the Schema url to create @type
base_url = reverse('api_base', kwargs={'api_version': version})
rsp = get_json(django_client, base_url)
schema_url = rsp['url:schema']
# specify group via query params
save_url = "%s?group=%s" % (rsp['url:save'], group)
projects_url = rsp['url:projects']
project_name = 'test_api_projects'
payload = {'Name': project_name,
'@type': schema_url + '#Project'}
rsp = post_json(django_client, save_url, payload,
status_code=201)
new_proj = rsp['data']
# We get the complete new Project returned
assert new_proj['Name'] == project_name
project_id = new_proj['@id']
# Read Project
project_url = "%s%s/" % (projects_url, project_id)
rsp = get_json(django_client, project_url)
new_proj = rsp['data']
assert new_proj['@id'] == project_id
conn = BlitzGateway(client_obj=self.root)
assert_objects(conn, [new_proj], [project_id])
def test_link_unlink_tagset_tags(self):
"""
Tests linking of tagset to tag, then unlinking
"""
tag = self.make_tag()
tagset = self.make_tag(ns=omero.constants.metadata.NSINSIGHTTAGSET)
tagId = tag.id.val
tagsetId = tagset.id.val
links_url = reverse("api_links")
# Link tagset to tag
data = {'tagset': {tagsetId: {'tag': [tagId]}}}
rsp = post_json(self.django_client, links_url, data)
assert rsp == {"success": True}
# Check that tag is listed under tagset...
tags_url = reverse("api_tags_and_tagged")
r = get_json(self.django_client, tags_url, {'id': tagsetId})
assert len(r['tags']) == 1
assert r['tags'][0]['id'] == tagId
# Unlink first Tag from Tagset
# data {} is same as for creating link above
response = delete_json(self.django_client, links_url, data)
assert response["success"]
# Since the Delete is ansync - need to check repeatedly for deletion
for i in range(10):
rsp = get_json(self.django_client, tags_url, {'id': tagsetId})
if len(rsp['tags']) == 0:
break
sleep(0.5)
# Check that link has been deleted
assert len(rsp['tags']) == 0
def test_validation_exception(self, user_A):
"""Test handling when we try to save something invalid."""
conn = get_connection(user_A)
group = conn.getEventContext().groupId
userName = conn.getUser().getName()
django_client = self.new_django_client(userName, userName)
version = api_settings.API_VERSIONS[-1]
save_url = reverse('api_save', kwargs={'api_version': version})
save_url += '?group=' + native_str(group)
# Create Tag
tag = TagAnnotationI()
tag.textValue = rstring('test_tag')
tag = conn.getUpdateService().saveAndReturnObject(tag)
tag_json = {'Value': 'test_tag',
'@id': tag.id.val,
'@type': OME_SCHEMA_URL + '#TagAnnotation'}
# Add Tag twice to Project to get Validation Exception
payload = {'Name': 'test_validation',
'@type': OME_SCHEMA_URL + '#Project',
'Annotations': [tag_json, tag_json]}
rsp = post_json(django_client, save_url, payload, status_code=400)
# NB: message contains whole stack trace
assert "ValidationException" in rsp['message']
assert rsp['stacktrace'].startswith(
'Traceback (most recent call last):')
def test_security_violation(self, group_B, user_A):
"""Test saving to incorrect group."""
conn = get_connection(user_A)
group_A_id = conn.getEventContext().groupId
userName = conn.getUser().getName()
django_client = self.new_django_client(userName, userName)
version = api_settings.API_VERSIONS[-1]
group_B_id = group_B.id.val
save_url = reverse('api_save', kwargs={'api_version': version})
# Create project in group_A (default group)
payload = {'Name': 'test_security_violation',
'@type': OME_SCHEMA_URL + '#Project'}
save_url_grp_A = save_url + '?group=' + native_str(group_A_id)
rsp = post_json(django_client, save_url_grp_A, payload,
status_code=201)
pr_json = rsp['data']
projectId = pr_json['@id']
# Try to save again into group B
save_url_grp_B = save_url + '?group=' + native_str(group_B_id)
rsp = put_json(django_client, save_url_grp_B, pr_json, status_code=403)
assert 'message' in rsp
msg = "Cannot read ome.model.containers.Project:Id_%s" % projectId
assert msg in rsp['message']
assert rsp['stacktrace'].startswith(
'Traceback (most recent call last):')
def test_marshal_type(self):
"""If no decoder found for @type, get suitable message."""
django_client = self.django_root_client
version = api_settings.API_VERSIONS[-1]
save_url = reverse('api_save', kwargs={'api_version': version})
objType = 'SomeInvalidSchema#Project'
payload = {'Name': 'test_marshal_type', '@type': objType}
rsp = post_json(django_client, save_url, payload, status_code=400)
assert (rsp['message'] == 'No decoder found for type: %s' % objType)
def test_link_datasets_images(self, datasets, images):
# Link Datasets to Images
request_url = reverse("api_links")
dids = [d.id.val for d in datasets]
iids = [i.id.val for i in images]
# Link first dataset to first image,
# Second dataset linked to both images
data = {
'dataset': {
dids[0]: {
'image': [iids[0]]
},
dids[1]: {
'image': iids
}
}
}
rsp = post_json(self.django_client, request_url, data)
assert rsp == {"success": True}
# Check links
images_url = reverse("api_images")
# First Dataset has single image
rsp = get_json(self.django_client, images_url, {'id': dids[0]})
assert len(rsp['images']) == 1
assert rsp['images'][0]['id'] == iids[0]
# Second Dataset has both images
rsp = get_json(self.django_client, images_url, {'id': dids[1]})
assert len(rsp['images']) == 2
assert rsp['images'][0]['id'] == iids[0]
assert rsp['images'][1]['id'] == iids[1]
# Link BOTH images to first Dataset. Shouldn't get any
# Validation Exception, even though first image is already linked
data = {'dataset': {dids[0]: {'image': iids}}}
rsp = post_json(self.django_client, request_url, data)
assert rsp == {"success": True}
# Check first Dataset now has both images
rsp = get_json(self.django_client, images_url, {'id': dids[0]})
assert len(rsp['images']) == 2
assert rsp['images'][0]['id'] == iids[0]
assert rsp['images'][1]['id'] == iids[1]
def test_save_post_no_id(self):
"""If POST to /save/ data shouldn't contain @id."""
django_client = self.django_root_client
version = api_settings.API_VERSIONS[-1]
save_url = reverse('api_save', kwargs={'api_version': version})
payload = {'Name': 'test_save_post_no_id',
'@type': '%s#Project' % OME_SCHEMA_URL,
'@id': 1}
rsp = post_json(django_client, save_url, payload, status_code=400)
assert (rsp['message'] ==
"Object has '@id' attribute. Use PUT to update objects")
def test_project_create_other_group(self, user1, projects_user1_group2):
"""
Test saving to non-default group
"""
conn = get_connection(user1)
user_name = conn.getUser().getName()
django_client = self.new_django_client(user_name, user_name)
version = api_settings.API_VERSIONS[-1]
# We're only using projects_user1_group2 to get group2 id
group2_id = projects_user1_group2[0].getDetails().group.id.val
# This seems to be the minimum details needed to pass group ID
group2_details = {
'group': {
'@id': group2_id,
'@type': OME_SCHEMA_URL + '#ExperimenterGroup'
},
'@type': 'TBD#Details'
}
save_url = reverse('api_save', kwargs={'api_version': version})
project_name = 'test_project_create_group'
payload = {'Name': project_name, '@type': OME_SCHEMA_URL + '#Project'}
# Saving fails with NO group specified
rsp = post_json(django_client, save_url, payload, status_code=400)
assert rsp['message'] == ("Specify Group in omero:details or "
"query parameters ?group=:id")
# Add group details and try again
payload['omero:details'] = group2_details
rsp = post_json(django_client, save_url, payload, status_code=201)
new_proj = rsp['data']
new_project_id = new_proj['@id']
assert new_proj['omero:details']['group']['@id'] == group2_id
# Read Project
project_url = reverse('api_project',
kwargs={
'api_version': version,
'object_id': new_project_id
})
rsp = get_json(django_client, project_url)
assert rsp['data']['omero:details']['group']['@id'] == group2_id
def test_marshal_validation(self):
"""Test that we get expected error with invalid @type in json."""
django_client = self.django_root_client
version = api_settings.API_VERSIONS[-1]
save_url = reverse('api_save', kwargs={'api_version': version})
payload = {'Name': 'test_marshal_validation',
'@type': OME_SCHEMA_URL + '#Project',
'omero:details': {'@type': 'foo'}}
rsp = post_json(django_client, save_url, payload, status_code=400)
assert (rsp['message'] ==
"Error in decode of json data by omero_marshal")
assert rsp['stacktrace'].startswith(
'Traceback (most recent call last):')
def test_container_crud(self, dtype):
"""
Test create, read, update and delete of Containers.
Create with POST to /save
Read with GET of /m/dtype/:id/
Update with PUT to /m/dtype/:id/
Delete with DELETE to /m/dtype/:id/
"""
django_client = self.django_root_client
group = self.ctx.groupId
version = api_settings.API_VERSIONS[-1]
# Need to get the Schema url to create @type
base_url = reverse('api_base', kwargs={'api_version': version})
rsp = get_json(django_client, base_url)
schema_url = rsp['url:schema']
# specify group via query params
save_url = "%s?group=%s" % (rsp['url:save'], group)
project_name = 'test_container_create_read'
payload = {
'Name': project_name,
'@type': '%s#%s' % (schema_url, dtype)
}
rsp = post_json(django_client, save_url, payload, status_code=201)
new_obj = rsp['data']
# We get the complete new Object returned
assert new_obj['Name'] == project_name
object_id = new_obj['@id']
# Read Object
object_url = "%sm/%ss/%s/" % (base_url, dtype.lower(), object_id)
rsp = get_json(django_client, object_url)
object_json = rsp['data']
assert object_json['@id'] == object_id
conn = BlitzGateway(client_obj=self.root)
assert_objects(conn, [object_json], [object_id], dtype=dtype)
# Update Object...
object_json['Name'] = 'new name'
rsp = put_json(django_client, save_url, object_json)
# ...and read again to check
rsp = get_json(django_client, object_url)
updated_json = rsp['data']
assert updated_json['Name'] == 'new name'
# Delete
delete_json(django_client, object_url, {})
# Get should now return 404
rsp = get_json(django_client, object_url, status_code=404)
def test_paste_move_remove_deletamany_image(self):
# Add dataset
request_url = reverse("manage_action_containers",
args=["addnewcontainer"])
data = {'folder_type': 'dataset', 'name': 'foobar'}
response = post(self.django_client, request_url, data)
did = json.loads(response.content).get("id")
img = self.make_image()
print img
# Link image to Dataset
request_url = reverse("api_links")
data = {'dataset': {did: {'image': [img.id.val]}}}
post_json(self.django_client, request_url, data)
# Unlink image from Dataset
request_url = reverse("api_links")
data = {'dataset': {did: {'image': [img.id.val]}}}
response = delete_json(self.django_client, request_url, data)
# Response will contain remaining links from image (see test_links.py)
assert response == {"success": True}
def test_link_project_datasets(self, project, datasets):
# Link Project to Datasets
request_url = reverse("api_links")
pid = project.id.val
dids = [d.id.val for d in datasets]
data = {'project': {pid: {'dataset': dids}}}
rsp = post_json(self.django_client, request_url, data)
assert rsp == {"success": True}
# Check links
request_url = reverse("api_datasets")
rsp = get_json(self.django_client, request_url, {'id': pid})
# Expect a single Dataset with correct id
assert len(rsp['datasets']) == 2
assert rsp['datasets'][0]['id'] == dids[0]
assert rsp['datasets'][1]['id'] == dids[1]
def test_unlink_screen_plate(self, screens, plates):
# Link both plates to both screens
request_url = reverse("api_links")
sids = [s.id.val for s in screens]
pids = [p.id.val for p in plates]
data = {
'screen': {sids[0]: {'plate': pids},
sids[1]: {'plate': pids}}
}
rsp = post_json(self.django_client, request_url, data)
assert rsp == {"success": True}
# Confirm that first Screen linked to 2 Plates
plates_url = reverse("api_plates")
rsp = get_json(self.django_client, plates_url, {'id': sids[0]})
assert len(rsp['plates']) == 2
# Unlink first Plate from first Screen
request_url = reverse("api_links")
data = {
'screen': {sids[0]: {'plate': pids[:1]}}
}
response = delete_json(self.django_client, request_url, data)
# Returns remaining link from 2nd Screen to first Plate
assert response == {"success": True,
"screen": {str(sids[1]): {"plate": pids[:1]}}
}
# Since the Delete is ansync - need to check repeatedly for deletion
# by counting plates under screen...
plates_url = reverse("api_plates")
for i in range(10):
rsp = get_json(self.django_client, plates_url, {'id': sids[0]})
if len(rsp['plates']) == 1:
break
sleep(0.5)
# Check that link has been deleted, leaving 2nd plate under 1st screen
assert len(rsp['plates']) == 1
assert rsp['plates'][0]['id'] == pids[1]
def test_save_rois(self, conn, django_client):
"""Save new ROIs to an Image"""
image = self.make_image(client=conn.c)
roi = RoiI()
roi.name = rstring("roi_name")
roi.setImage(ImageI(image.id.val, False))
point = PointI()
point.x = rdouble(1)
point.y = rdouble(2)
encoder = get_encoder(point.__class__)
point_json = encoder.encode(point)
unsaved_id = "-1:-1"
point_json['oldId'] = unsaved_id
persist_url = reverse('omero_iviewer_persist_rois')
data = {
'imageId': image.id.val,
'rois': {
'count': 1,
'new': [point_json]
}
}
rsp = post_json(django_client, persist_url, data)
print('rsp', rsp)
# {"ids": {"-1:-1": "225504:416603"}}
assert "ids" in rsp
new_ids = rsp["ids"].values()
assert len(new_ids) == 1
new_id = rsp["ids"][unsaved_id]
roi_id = int(new_id.split(':')[0])
shape_id = int(new_id.split(':')[1])
# Add Tag to ROI and Shape
tag = TagAnnotationWrapper(conn)
tag.setValue("ROI/Shape Tag")
tag.save()
roi = conn.getObject("Roi", roi_id)
roi.linkAnnotation(tag)
shape = conn.getObject("Shape", shape_id)
shape.linkAnnotation(tag)
# check...
assert len(list(conn.getAnnotationLinks(
"Shape", parent_ids=[shape_id]))) == 1
# Load Shape
rois_url = reverse('api_rois', kwargs={'api_version': 0})
rois_url += '?image=%s' % image.id.val
rsp = get_json(django_client, rois_url)
assert len(rsp['data']) == 1
# Edit Shape
point_json = rsp['data'][0]['shapes'][0]
point_json["X"] = 100
point_json["Y"] = 200
# iviewer wants to know ROI:Shape ID
point_json["oldId"] = new_id
# Unload details
del point_json["omero:details"]
data = {
'imageId': image.id.val,
'rois': {
'count': 1,
'modified': [point_json]
}
}
rsp = post_json(django_client, persist_url, data)
# IDs shouldn't have changed, e.g.
# {"ids": {"225504:416603": "225504:416603"}}
print('post rsp', rsp)
assert rsp["ids"][new_id] == new_id
# Check annotations not lost
roi = conn.getObject("Roi", roi_id)
assert len(list(roi.listAnnotations())) == 1
assert len(list(conn.getAnnotationLinks(
"Shape", parent_ids=[shape_id]))) == 1
