def test_admin_images(config, database, fastapi, caplog):
caplog.set_level(logging.ERROR)
from tests.test_import import test_import_uvp6
prj_id = test_import_uvp6(config, database, caplog, "Test Project Admin")
url = PROJECT_DIGEST_URL.format(project_id=prj_id)
# Simple user cannot
rsp = fastapi.get(url, headers=USER_AUTH)
assert rsp.status_code == status.HTTP_403_FORBIDDEN
# Admin can
rsp = fastapi.get(url, headers=ADMIN_AUTH)
assert rsp.status_code == status.HTTP_200_OK
assert rsp.json() == "Digest for 30 images done."
# TODO: some common error cases
# md5 is persisted
rsp = fastapi.get(url, headers=ADMIN_AUTH)
assert rsp.status_code == status.HTTP_200_OK
assert rsp.json() == "Digest for 0 images done."
def test_subentities(config, database, fastapi, caplog):
caplog.set_level(logging.ERROR)
from tests.test_import import test_import_uvp6
prj_id = test_import_uvp6(config, database, caplog, "Test Subset Merge")
check_project(prj_id)
# Pick the first object
qry_rsp, _total = ObjectManager().query(ADMIN_USER_ID, prj_id, filters={})
first_obj = qry_rsp[0]
first_objid = first_obj[0] # obj id
# Wrong ID
url = OBJECT_QUERY_URL.format(object_id=-1)
response = fastapi.get(url, headers=ADMIN_AUTH)
assert response.status_code == status.HTTP_404_NOT_FOUND
# OK ID
url = OBJECT_QUERY_URL.format(object_id=first_objid)
response = fastapi.get(url, headers=ADMIN_AUTH)
assert response.status_code == status.HTTP_200_OK
obj = response.json()
assert obj is not None
# Move up in hierarchy
sample_id = first_obj[2]
# Wrong ID
url = SAMPLE_QUERY_URL.format(sample_id=-1)
response = fastapi.get(url, headers=ADMIN_AUTH)
assert response.status_code == status.HTTP_404_NOT_FOUND
# OK ID
url = SAMPLE_QUERY_URL.format(sample_id=sample_id)
response = fastapi.get(url, headers=ADMIN_AUTH)
assert response.status_code == status.HTTP_200_OK
sample = response.json()
assert sample is not None
acquis_id = first_obj[1]
# Wrong ID
url = ACQUISITION_QUERY_URL.format(acquisition_id=-1)
response = fastapi.get(url, headers=ADMIN_AUTH)
assert response.status_code == status.HTTP_404_NOT_FOUND
# OK ID
url = ACQUISITION_QUERY_URL.format(acquisition_id=acquis_id)
response = fastapi.get(url, headers=ADMIN_AUTH)
assert response.status_code == status.HTTP_200_OK
acquisition = response.json()
assert acquisition is not None
process_id = acquis_id
# Wrong ID
url = PROCESS_QUERY_URL.format(process_id=-1)
response = fastapi.get(url, headers=ADMIN_AUTH)
assert response.status_code == status.HTTP_404_NOT_FOUND
# OK ID
url = PROCESS_QUERY_URL.format(process_id=process_id)
response = fastapi.get(url, headers=ADMIN_AUTH)
assert response.status_code == status.HTTP_200_OK
process = response.json()
assert process is not None
# Wrong ID
url = OBJECT_HISTORY_QUERY_URL.format(object_id=-1)
response = fastapi.get(url)
# TODO: A 0-len history should be a not found ?
# assert response.status_code == status.HTTP_404_NOT_FOUND
# OK ID
url = OBJECT_HISTORY_QUERY_URL.format(object_id=first_objid)
response = fastapi.get(
url
) # The entry point is public and project as well, no need for: , headers=ADMIN_AUTH)
assert response.status_code == status.HTTP_200_OK
classif = response.json()
assert classif is not None
assert len(classif) == 0
def test_update_prj(config, database, fastapi, caplog):
caplog.set_level(logging.ERROR)
from tests.test_import import test_import_uvp6
prj_id = test_import_uvp6(config, database, caplog, "Test Project Updates")
# Do like in legacy app, i.e. fetch/modify/resend
url = PROJECT_QUERY_URL.format(project_id=prj_id, manage=True)
rsp = fastapi.get(url, headers=ADMIN_AUTH)
ref_json = {'acquisition_free_cols': {'aa': 't03',
'exp': 't04',
'gain': 't06',
'pixel': 't05',
'ratio': 't10',
'smbase': 't08',
'smzoo': 't09',
'sn': 't01',
'threshold': 't07',
'volimage': 't02'},
'annotators': [],
'highest_right': 'Manage',
'classiffieldlist': None,
'classifsettings': None,
'cnn_network_id': None,
'comments': None,
'contact': None,
'instrument': 'uvp6',
'init_classif_list': [],
'license': '',
'managers': [{'active': True,
'country': None,
'email': 'admin',
'id': 1,
'name': 'Application Administrator',
'organisation': None,
'usercreationdate': '2020-05-12T08:59:48.701060',
'usercreationreason': None}],
'obj_free_cols': {'%area': 'n23',
'angle': 'n16',
'area': 'n01',
'area_exc': 'n24',
'circ.': 'n17',
'circex': 'n51',
'convarea': 'n39',
'convarea_area': 'n55',
'convperim': 'n38',
'convperim_perim': 'n54',
'cv': 'n45',
'elongation': 'n42',
'fcons': 'n40',
'feret': 'n18',
'feretareaexc': 'n48',
'fractal': 'n25',
'height': 'n13',
'histcum1': 'n28',
'histcum2': 'n29',
'histcum3': 'n30',
'intden': 'n19',
'kurt': 'n22',
'kurt_mean': 'n52',
'major': 'n14',
'max': 'n06',
'mean': 'n02',
'meanpos': 'n44',
'median': 'n20',
'median_mean': 'n64',
'median_mean_range': 'n65',
'min': 'n05',
'minor': 'n15',
'mode': 'n04',
'nb1': 'n31',
'nb1_area': 'n58',
'nb1_range': 'n61',
'nb2': 'n32',
'nb2_area': 'n59',
'nb2_range': 'n62',
'nb3': 'n33',
'nb3_area': 'n60',
'nb3_range': 'n63',
'perim.': 'n11',
'perimareaexc': 'n47',
'perimferet': 'n49',
'perimmajor': 'n50',
'range': 'n43',
'skelarea': 'n26',
'skeleton_area': 'n66',
'skew': 'n21',
'skew_mean': 'n53',
'slope': 'n27',
'sr': 'n46',
'stddev': 'n03',
'symetrieh': 'n34',
'symetrieh_area': 'n56',
'symetriehc': 'n36',
'symetriev': 'n35',
'symetriev_area': 'n57',
'symetrievc': 'n37',
'thickr': 'n41',
'width': 'n12',
'x': 'n07',
'xm': 'n09',
'y': 'n08',
'ym': 'n10'},
'objcount': 15.0,
# 'owner': {'active': True,
# 'country': None,
# 'email': 'admin',
# 'id': 1,
# 'name': 'Application Administrator',
# 'organisation': None,
# 'usercreationdate': '2020-05-12T08:59:48.701060',
# 'usercreationreason': None},
# 'owner_id': 0,
'pctclassified': None,
'pctvalidated': 0.0,
'popoverfieldlist': None,
'process_free_cols': {'date': 't02',
'first_img': 't04',
'fontcolor': 't10',
'fontheight_px': 't11',
'footerheight_px': 't12',
'gamma': 't06',
'invert': 't07',
'keeporiginal': 't09',
'last_img': 't05',
'scale': 't13',
'scalebarsize_mm': 't08',
'software': 't01',
'time': 't03'},
'projid': prj_id,
'projtype': None,
'rf_models_used': None,
'sample_free_cols': {'argoid': 't17',
'barcode': 't14',
'bottomdepth': 't05',
'comment': 't13',
'cruise': 't02',
'ctdrosettefilename': 't06',
'dn': 't07',
'integrationtime': 't16',
'nebuloussness': 't11',
'profileid': 't01',
'sampledatetime': 't18',
'sampletype': 't15',
'seastate': 't10',
'ship': 't03',
'stationid': 't04',
'winddir': 't08',
'windspeed': 't09',
'yoyo': 't12'},
'status': 'Annotate',
'title': 'Test Project Updates',
'viewers': [],
'visible': True}
read_json = rsp.json()
assert read_json == ref_json
upd_json = deepcopy(read_json)
contact_usr = upd_json["managers"][0]
# Attempt to reproduce ecotaxa/ecotaxa_dev#596
del contact_usr['usercreationdate']
contact_usr['usercreationdate'] = None
del contact_usr['usercreationreason']
url = PROJECT_UPDATE_URL.format(project_id=prj_id)
upd_json["comments"] = "New comment"
upd_json["contact"] = contact_usr
upd_json["visible"] = False
rsp = fastapi.put(url, headers=ADMIN_AUTH, json=upd_json)
assert rsp.status_code == status.HTTP_200_OK
# Re-read
url = PROJECT_QUERY_URL.format(project_id=prj_id, manage=False)
rsp = fastapi.get(url, headers=ADMIN_AUTH)
assert rsp.json() != ref_json
assert rsp.json()["comments"] == "New comment"
assert rsp.json()["visible"] is False
# For ecotaxa/ecotaxa_dev#602
# Set no contact at all
no_contact_upd = deepcopy(read_json)
no_contact_upd["contact"] = None
url = PROJECT_UPDATE_URL.format(project_id=prj_id)
rsp = fastapi.put(url, headers=ADMIN_AUTH, json=no_contact_upd)
assert rsp.status_code == status.HTTP_422_UNPROCESSABLE_ENTITY
assert rsp.text == '{"detail":"A valid Contact is needed."}'
# Set a contact with wrong id
wrong_contact_upd = deepcopy(read_json)
wrong_contact_upd["contact"] = {"id": ORDINARY_USER2_USER_ID,
"name": "name",
"email": "*****@*****.**"}
url = PROJECT_UPDATE_URL.format(project_id=prj_id)
rsp = fastapi.put(url, headers=ADMIN_AUTH, json=wrong_contact_upd)
assert rsp.status_code == status.HTTP_422_UNPROCESSABLE_ENTITY
assert rsp.text == '{"detail":"Could not set Contact, the designated user is not in Managers list."}'
def test_updates(config, database, caplog):
caplog.set_level(logging.ERROR)
prj_id = test_import_uvp6(config, database, caplog, "Test Updates")
check_project(prj_id)
acquis_id, process_id, sample_id = _get_ids(prj_id)
# Typo in column name
with SamplesService() as sce:
nb_upd = sce.update_set(ADMIN_USER_ID, [sample_id],
ColUpdateList([upd("chip", "sagitta4")]))
assert nb_upd == 0
# Update ship in the only sample, and a date to see
upds = ColUpdateList(
[upd("ship", "sagitta4"),
upd("sampledatetime", "20200208-111218")])
with SamplesService() as sce:
nb_upd = sce.update_set(ADMIN_USER_ID, [sample_id, sample_id], upds)
assert nb_upd == 1
# Update 1st acquisition, and a float, to see
upds = ColUpdateList([upd("orig_id", "aid5"), upd("exp", "0.6")])
with AcquisitionsService() as sce:
nb_upd = sce.update_set(ADMIN_USER_ID, [acquis_id], upds)
assert nb_upd == 1
# Update 1st process
upds = ColUpdateList([upd("date", "20200325"), upd("invert", "n")])
with ProcessesService() as sce:
nb_upd = sce.update_set(ADMIN_USER_ID, [process_id], upds)
assert nb_upd == 1
# Update all objects
with ObjectManager() as sce:
objs, _details, total = sce.query(ADMIN_USER_ID,
prj_id, {},
order_field='objid')
objs = [an_obj[0] for an_obj in objs]
assert len(objs) == 15
# Wrong column
with ObjectManager() as sce:
nb_upd = sce.update_set(ADMIN_USER_ID, objs,
ColUpdateList([upd("chip", "sagitta4")]))
assert nb_upd == 0
# Free column
with ObjectManager() as sce:
nb_upd = sce.update_set(ADMIN_USER_ID, objs,
ColUpdateList([upd("area", "10")]))
assert nb_upd == 15
# Plain column
with ObjectManager() as sce:
nb_upd = sce.update_set(ADMIN_USER_ID, objs,
ColUpdateList([upd("depth_min", "10")]))
assert nb_upd == 15
# Dump the project after changes
with open(OUT_JSON_MODIF, "w") as fd:
dump_project(ADMIN_USER_ID, prj_id, fd)
# Special column
# TODO: Avoiding diff on purpose, it's just to cover code.
with ObjectManager() as sce:
nb_upd = sce.update_set(ADMIN_USER_ID, objs,
ColUpdateList([upd("classif_id", "100")]))
assert nb_upd == 15
# Json diff
with open(OUT_JSON_REF) as fd1:
json_src = json.load(fd1)
with open(OUT_JSON_MODIF) as fd2:
json_subset = json.load(fd2)
diffs = DeepDiff(json_src, json_subset)
# Validate by removing all know differences b/w source and subset
assert 'iterable_item_added' not in diffs
assert 'iterable_item_removed' not in diffs
assert 'dictionary_item_added' not in diffs
assert 'dictionary_item_removed' not in diffs
changed_values = diffs['values_changed']
assert changed_values == {
"root['samples'][0]['acquisitions'][0]['aid']": {
'new_value': 'aid5',
'old_value': 'b_da_19'
},
"root['samples'][0]['acquisitions'][0]['exp']": {
'new_value': '0.6',
'old_value': '1.257'
},
"root['samples'][0]['acquisitions'][0]['processings'][0]['date']": {
'new_value': '20200325',
'old_value': '20200317'
},
"root['samples'][0]['acquisitions'][0]['processings'][0]['invert']": {
'new_value': 'n',
'old_value': 'y'
},
"root['samples'][0]['acquisitions'][0]['objects'][0]['area']": {
'new_value': 10.0,
'old_value': 207.0
},
"root['samples'][0]['acquisitions'][0]['objects'][0]['depth_min']": {
'new_value': 10.0,
'old_value': 194.63
},
"root['samples'][0]['acquisitions'][0]['objects'][10]['area']": {
'new_value': 10.0,
'old_value': 119.0
},
"root['samples'][0]['acquisitions'][0]['objects'][10]['depth_min']": {
'new_value': 10.0,
'old_value': 215.76
},
"root['samples'][0]['acquisitions'][0]['objects'][11]['area']": {
'new_value': 10.0,
'old_value': 137.0
},
"root['samples'][0]['acquisitions'][0]['objects'][11]['depth_min']": {
'new_value': 10.0,
'old_value': 224.44
},
"root['samples'][0]['acquisitions'][0]['objects'][12]['area']": {
'new_value': 10.0,
'old_value': 93.0
},
"root['samples'][0]['acquisitions'][0]['objects'][12]['depth_min']": {
'new_value': 10.0,
'old_value': 252.235
},
"root['samples'][0]['acquisitions'][0]['objects'][13]['area']": {
'new_value': 10.0,
'old_value': 165.0
},
"root['samples'][0]['acquisitions'][0]['objects'][13]['depth_min']": {
'new_value': 10.0,
'old_value': 253.615
},
"root['samples'][0]['acquisitions'][0]['objects'][14]['area']": {
'new_value': 10.0,
'old_value': 360.0
},
"root['samples'][0]['acquisitions'][0]['objects'][14]['depth_min']": {
'new_value': 10.0,
'old_value': 255.44
},
"root['samples'][0]['acquisitions'][0]['objects'][1]['area']": {
'new_value': 10.0,
'old_value': 107.0
},
"root['samples'][0]['acquisitions'][0]['objects'][1]['depth_min']": {
'new_value': 10.0,
'old_value': 195.36
},
"root['samples'][0]['acquisitions'][0]['objects'][2]['area']": {
'new_value': 10.0,
'old_value': 122.0
},
"root['samples'][0]['acquisitions'][0]['objects'][2]['depth_min']": {
'new_value': 10.0,
'old_value': 195.68
},
"root['samples'][0]['acquisitions'][0]['objects'][3]['area']": {
'new_value': 10.0,
'old_value': 94.0
},
"root['samples'][0]['acquisitions'][0]['objects'][3]['depth_min']": {
'new_value': 10.0,
'old_value': 195.68
},
"root['samples'][0]['acquisitions'][0]['objects'][4]['area']": {
'new_value': 10.0,
'old_value': 199.0
},
"root['samples'][0]['acquisitions'][0]['objects'][4]['depth_min']": {
'new_value': 10.0,
'old_value': 195.68
},
"root['samples'][0]['acquisitions'][0]['objects'][5]['area']": {
'new_value': 10.0,
'old_value': 176.0
},
"root['samples'][0]['acquisitions'][0]['objects'][5]['depth_min']": {
'new_value': 10.0,
'old_value': 212.62
},
"root['samples'][0]['acquisitions'][0]['objects'][6]['area']": {
'new_value': 10.0,
'old_value': 151.0
},
"root['samples'][0]['acquisitions'][0]['objects'][6]['depth_min']": {
'new_value': 10.0,
'old_value': 213.525
},
"root['samples'][0]['acquisitions'][0]['objects'][7]['area']": {
'new_value': 10.0,
'old_value': 90.0
},
"root['samples'][0]['acquisitions'][0]['objects'][7]['depth_min']": {
'new_value': 10.0,
'old_value': 214.165
},
"root['samples'][0]['acquisitions'][0]['objects'][8]['area']": {
'new_value': 10.0,
'old_value': 158.0
},
"root['samples'][0]['acquisitions'][0]['objects'][8]['depth_min']": {
'new_value': 10.0,
'old_value': 215.415
},
"root['samples'][0]['acquisitions'][0]['objects'][9]['area']": {
'new_value': 10.0,
'old_value': 163.0
},
"root['samples'][0]['acquisitions'][0]['objects'][9]['depth_min']": {
'new_value': 10.0,
'old_value': 215.76
},
"root['samples'][0]['sampledatetime']": {
'new_value': '20200208-111218',
'old_value': '20200205-111218'
},
"root['samples'][0]['ship']": {
'new_value': 'sagitta4',
'old_value': 'sagitta3'
}
}