def test_create_sample(self):
sample_name = base.random_string(5)
sample_tags = base.random_string(4)
ef1 = inv.ExtraField("f1", inv.ExtraFieldType.TEXT, "hello")
ef2 = inv.ExtraField("f2", inv.ExtraFieldType.NUMBER, 123)
minTemp = inv.StorageTemperature(1, inv.TemperatureUnit.KELVIN)
maxTemp = inv.StorageTemperature(4, inv.TemperatureUnit.KELVIN)
expiry_date = dt.date(2024, 12, 25)
amount = inv.Quantity(5, qu.QuantityUnit.of("ml"))
sample = self.invapi.create_sample(
name=sample_name,
tags=sample_tags,
extra_fields=[ef1, ef2],
storage_temperature_min=minTemp,
storage_temperature_max=maxTemp,
expiry_date=expiry_date,
total_quantity=amount,
subsample_count=12,
attachments=[open(base.get_any_datafile(), "rb")],
)
self.assertEqual(sample_name, sample["name"])
self.assertEqual(2, len(sample["extraFields"]))
self.assertEqual(4, sample["storageTempMax"]["numericValue"])
self.assertEqual(1, sample["storageTempMin"]["numericValue"])
self.assertEqual(12, sample["subSamplesCount"])
self.assertEqual(expiry_date.isoformat(), sample["expiryDate"])
self.assertEqual(1, len(sample["attachments"]))
s_ob = inv.Sample(sample)
def test_move_container_to_list_container(self):
name = base.random_string() + "_to_move"
toMove = self.invapi.create_list_container(name)
name_target = base.random_string() + "_target"
target = self.invapi.create_list_container(name_target)
moved = self.invapi.add_items_to_list_container(
target["id"], toMove["globalId"])
self.assertTrue(moved.is_ok())
def test_move_subsamples_to_list_container(self):
name = base.random_string() + "_to_move"
toMove = self.invapi.create_sample(name, subsample_count=2)
name_target = base.random_string() + "_target"
target = self.invapi.create_list_container(name_target)
## get the 2 subsample ids ad move to container
subsample_ids = [ss["globalId"] for ss in toMove["subSamples"]]
moved = self.invapi.add_items_to_list_container(
target["id"], *subsample_ids)
self.assertTrue(moved.is_ok())
def test_upload_file(self):
sample = self.invapi.create_sample(base.random_string())
data_file = base.get_any_datafile()
with open(data_file, "rb") as f:
resp = self.invapi.uploadAttachment(sample["globalId"], f)
self.assertIsNotNone(resp["id"])
self.assertTrue(resp["globalId"][0:2] == "IF")
def test_add_note_to_subsample(self):
note = " a note about a subsample " + base.random_string()
sample = self.invapi.create_sample("with_note", subsample_count=1)
ss = sample["subSamples"][0]
updated = self.invapi.add_note_to_subsample(ss, note)
self.assertEqual(1, len(updated["notes"]))
self.assertEqual(note, updated["notes"][0]["content"])
def test_equal_split(self):
name = base.random_string()
sample = self.invapi.create_sample(name)
ss = sample["subSamples"][0]
splits = self.invapi.split_subsample(ss, num_new_subsamples=3)
self.assertEqual(3, len(splits))
self.assertAlmostEqual(
750, sum([x["quantity"]["numericValue"] for x in splits]))
def test_paginated_containers(self):
pag = inv.Pagination(page_number=0, page_size=1)
name = base.random_string()
c = self.invapi.create_list_container(name)
c = self.invapi.set_as_top_level_container(c)
containers = self.invapi.list_top_level_containers(pag)
self.assertEqual(0, containers["pageNumber"])
self.assertEqual(1, len(containers["containers"]))
def test_add_extra_fields(self):
sample = self.invapi.create_sample(base.random_string())
ef1 = inv.ExtraField(name="ef1", content="ef1 content")
ef2 = inv.ExtraField(name="ef2", content="ef2 content")
updatedS = self.invapi.add_extra_fields(sample["globalId"], ef1, ef2)
self.assertEqual(2, len(updatedS["extraFields"]))
container = self.invapi.create_list_container("any list container")
updatedC = self.invapi.add_extra_fields(container, ef2)
self.assertEqual(1, len(updatedC["extraFields"]))
def test_search_sample(self):
name = base.random_string()
tags = base.random_string()
sample = self.invapi.create_sample(name, tags=tags)
results = self.invapi.search(query=name)
## sample and its subsample
self.assertEqual(2, results["totalHits"])
results_from_tag = self.invapi.search(query=tags)
self.assertEqual(1, results_from_tag["totalHits"])
results2 = self.invapi.search(query=name,
result_type=inv.ResultType.SAMPLE)
self.assertEqual(1, results2["totalHits"])
results3 = self.invapi.search(query=name,
result_type=inv.ResultType.SUBSAMPLE)
self.assertEqual(1, results3["totalHits"])
results4 = self.invapi.search(query=name,
result_type=inv.ResultType.CONTAINER)
self.assertEqual(0, results4["totalHits"])
def test_stream_samples(self):
onePerPage = inv.Pagination(page_size=1)
gen = self.invapi.stream_samples(onePerPage)
# get 2 items
s1 = next(gen)
s2 = next(gen)
self.assertNotEqual(s1["id"], s2["id"])
unknown_user = base.random_string(15)
sample_filter = inv.SearchFilter(owned_by=unknown_user)
gen = self.invapi.stream_samples(onePerPage, sample_filter)
result_count = 0
for sample in gen:
result_count += 1
self.assertEqual(0, result_count)
def test_duplicate(self):
name = base.random_string()
container = self.invapi.create_list_container("c_to_dup")
container_dup = self.invapi.duplicate(container, f"{name}-newfromtest")
self.assertNotEqual(container["id"], container_dup["id"])
self.assertEqual(f"{name}-newfromtest", container_dup["name"])
sample = self.invapi.create_sample(name)
sample_dup = self.invapi.duplicate(sample)
self.assertNotEqual(sample["id"], sample_dup["id"])
ss = sample["subSamples"][0]
ss_dup = self.invapi.duplicate(ss)
self.assertNotEqual(ss["id"], ss_dup["id"])
def test_create_list_container(self):
name = base.random_string()
ct = self.invapi.create_list_container(name, tags="ab,cd,ef")
self.assertTrue(ct["cType"] == "LIST")
self.assertEqual(0, len(ct["parentContainers"]))
## create in workbench
ct_in_wb = self.invapi.create_list_container(name,
tags="ab,cd,ef",
location="w")
self.assertEqual("BE",
ct_in_wb["parentContainers"][0]["globalId"][0:2])
## create in parent list container
ct_sub_container = self.invapi.create_list_container(name,
tags="ab,cd,ef",
location=ct["id"])
self.assertEqual(ct["globalId"],
ct_sub_container["parentContainers"][0]["globalId"])
def test_partial_split(self):
name = base.random_string()
sample_total = inv.Quantity(5, qu.QuantityUnit.of("ml"))
## create 1 sample with 1 ss of 5ml
sample = self.invapi.create_sample(name, total_quantity=sample_total)
ss = sample["subSamples"][0]
bulk_result = self.invapi.split_subsample(ss,
num_new_subsamples=3,
quantity_per_subsample=1.2)
self.assertTrue(bulk_result.is_ok())
results = bulk_result.data["results"]
## should result in original with (5 - (3 *1.2) = 1.4, new ones with 1.2
ss_to_amount = {}
for updated_ss in results:
ss_to_amount[updated_ss["record"]["id"]] = updated_ss["record"][
"quantity"]["numericValue"]
self.assertAlmostEqual(1.4, ss_to_amount[ss["id"]])
ss_to_amount.pop(ss["id"])
for v in ss_to_amount.values():
self.assertAlmostEqual(1.2, v)
def test_create_document(self):
nameStr = random_string(10)
tag_str = random_string(5)
resp = self.api.create_document(name=nameStr, tags=tag_str)
self.assertEqual(nameStr, resp["name"])
self.assertEqual(tag_str, resp["tags"])
def test_rename_item(self):
sample = self.invapi.create_sample(base.random_string(5))
new_name = base.random_string()
updated = self.invapi.rename(sample["globalId"], new_name)
self.assertEqual(new_name, updated["name"])
def test_get_single_sample(self):
sample = self.invapi.create_sample(base.random_string(5))
sample2 = self.invapi.get_sample_by_id(sample["id"])
sample3 = self.invapi.get_sample_by_id(sample["globalId"])
self.assertEqual(sample["name"], sample2["name"])
self.assertEqual(sample["name"], sample3["name"])
def test_transfer_sample_owner(self):
sample = self.invapi.create_sample(base.random_string(5))
updated = self.invapi.transfer_sample_owner(sample["id"], "user2b")
self.assertEqual("user2b", updated["owner"]["username"])
def test_create_sample_name_only(self):
sample = self.invapi.create_sample(base.random_string(5))
self.assertIsNotNone(sample)