diff --git a/client/Makefile b/client/Makefile index 5033053f..3b36337a 100644 --- a/client/Makefile +++ b/client/Makefile @@ -1,6 +1,6 @@ include ../common.mk -ANNOTATIONS := $(if $(ANNOTATIONS),$(ANNOTATIONS),../server/test/test_datasets/pbmc3k-annotations.csv) +ANNOTATIONS := $(if $(ANNOTATIONS),$(ANNOTATIONS),../server/test/fixtures/pbmc3k-annotations.csv) ANNOTATIONS_FILENAME := $(shell basename $(ANNOTATIONS)) # Packaging diff --git a/server/test/__init__.py b/server/test/__init__.py index 44103190..e4d8d67a 100644 --- a/server/test/__init__.py +++ b/server/test/__init__.py @@ -20,16 +20,17 @@ from server.data_common.matrix_loader import MatrixDataLoader, MatrixDataType PROJECT_ROOT = popen("git rev-parse --show-toplevel").read().strip() +FIXTURES_ROOT = PROJECT_ROOT + "/server/test/fixtures" def data_with_tmp_annotations(ext: MatrixDataType, annotations_fixture=False): tmp_dir = tempfile.mkdtemp() annotations_file = path.join(tmp_dir, "test_annotations.csv") if annotations_fixture: - shutil.copyfile(f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k-annotations.csv", annotations_file) + shutil.copyfile(f"{PROJECT_ROOT}/server/test/fixtures/pbmc3k-annotations.csv", annotations_file) fname = { MatrixDataType.H5AD: f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad", - MatrixDataType.CXG: "test/test_datasets/pbmc3k.cxg", + MatrixDataType.CXG: "test/fixtures/pbmc3k.cxg", }[ext] data_locator = DataLocator(fname) config = AppConfig() diff --git a/server/test/test_datasets/fixtures.py b/server/test/fixtures/fixtures.py similarity index 100% rename from server/test/test_datasets/fixtures.py rename to server/test/fixtures/fixtures.py diff --git a/server/test/test_datasets/nan.h5ad b/server/test/fixtures/nan.h5ad similarity index 100% rename from server/test/test_datasets/nan.h5ad rename to server/test/fixtures/nan.h5ad diff --git a/server/test/test_datasets/pbmc3k-CSC-gz.h5ad b/server/test/fixtures/pbmc3k-CSC-gz.h5ad similarity index 100% rename from server/test/test_datasets/pbmc3k-CSC-gz.h5ad rename to server/test/fixtures/pbmc3k-CSC-gz.h5ad diff --git a/server/test/test_datasets/pbmc3k-CSR-gz.h5ad b/server/test/fixtures/pbmc3k-CSR-gz.h5ad similarity index 100% rename from server/test/test_datasets/pbmc3k-CSR-gz.h5ad rename to server/test/fixtures/pbmc3k-CSR-gz.h5ad diff --git a/server/test/test_datasets/pbmc3k-annotations.csv b/server/test/fixtures/pbmc3k-annotations.csv similarity index 100% rename from server/test/test_datasets/pbmc3k-annotations.csv rename to server/test/fixtures/pbmc3k-annotations.csv diff --git a/server/test/test_datasets/pbmc3k.cxg/X/__1587182255882_1587182255882_f7aa6ccb49a944f9ab9e25b11bbfab4f/__attr.tdb b/server/test/fixtures/pbmc3k.cxg/X/__1587182255882_1587182255882_f7aa6ccb49a944f9ab9e25b11bbfab4f/__attr.tdb similarity index 100% rename from server/test/test_datasets/pbmc3k.cxg/X/__1587182255882_1587182255882_f7aa6ccb49a944f9ab9e25b11bbfab4f/__attr.tdb rename to 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a/server/test/test_datasets/pbmc3k_v0.cxg/var/__meta/__1576858533966_1576858533966_1362646d804b4982b35052a367633436 b/server/test/fixtures/pbmc3k_v0.cxg/var/__meta/__1576858533966_1576858533966_1362646d804b4982b35052a367633436 similarity index 100% rename from server/test/test_datasets/pbmc3k_v0.cxg/var/__meta/__1576858533966_1576858533966_1362646d804b4982b35052a367633436 rename to server/test/fixtures/pbmc3k_v0.cxg/var/__meta/__1576858533966_1576858533966_1362646d804b4982b35052a367633436 diff --git a/server/test/schema.json b/server/test/fixtures/schema.json similarity index 100% rename from server/test/schema.json rename to server/test/fixtures/schema.json diff --git a/server/locust/README.md b/server/test/locust/README.md similarity index 100% rename from server/locust/README.md rename to server/test/locust/README.md diff --git a/server/test/locust/__init__.py b/server/test/locust/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/server/locust/config.py b/server/test/locust/config.py similarity index 100% rename from server/locust/config.py rename to server/test/locust/config.py diff --git a/server/locust/locustfile.py b/server/test/locust/locustfile.py similarity index 99% rename from server/locust/locustfile.py rename to server/test/locust/locustfile.py index 092f35f5..2e6a796f 100644 --- a/server/locust/locustfile.py +++ b/server/test/locust/locustfile.py @@ -4,7 +4,7 @@ import random import json from gevent.pool import Group -import server.test.decode_fbs as decode_fbs +import server.test.unit.decode_fbs as decode_fbs from config import DataSets diff --git a/server/locust/requirements-locust.txt b/server/test/locust/requirements-locust.txt similarity index 100% rename from server/locust/requirements-locust.txt rename to server/test/locust/requirements-locust.txt diff --git a/server/test/performance/__init__.py b/server/test/performance/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/server/test/create_test_matrix.py b/server/test/performance/create_test_matrix.py similarity index 100% rename from server/test/create_test_matrix.py rename to server/test/performance/create_test_matrix.py diff --git a/server/test/run_diffexp.py b/server/test/performance/run_diffexp.py similarity index 100% rename from server/test/run_diffexp.py rename to server/test/performance/run_diffexp.py diff --git a/server/test/unit/__init__.py b/server/test/unit/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/server/test/unit/auth/__init__.py b/server/test/unit/auth/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/server/test/test_auth.py b/server/test/unit/auth/test_auth.py similarity index 92% rename from server/test/test_auth.py rename to server/test/unit/auth/test_auth.py index bd4c776e..5d6eb748 100644 --- a/server/test/test_auth.py +++ b/server/test/unit/auth/test_auth.py @@ -1,14 +1,19 @@ import unittest -from server.common.app_config import AppConfig -from server.test import PROJECT_ROOT, test_server + import requests +from server.common.app_config import AppConfig +from server.test import FIXTURES_ROOT, test_server + class AuthTest(unittest.TestCase): + def setUp(self): + self.dataset_dataroot = FIXTURES_ROOT + def test_auth_none(self): c = AppConfig() c.update_server_config( - authentication__type=None, multi_dataset__dataroot=f"{PROJECT_ROOT}/server/test/test_datasets" + authentication__type=None, multi_dataset__dataroot=self.dataset_dataroot ) c.update_default_dataset_config(user_annotations__enable=False) @@ -23,7 +28,7 @@ class AuthTest(unittest.TestCase): def test_auth_session(self): c = AppConfig() c.update_server_config( - authentication__type="session", multi_dataset__dataroot=f"{PROJECT_ROOT}/server/test/test_datasets" + authentication__type="session", multi_dataset__dataroot=self.dataset_dataroot ) c.update_default_dataset_config(user_annotations__enable=True) c.complete_config() @@ -41,8 +46,8 @@ class AuthTest(unittest.TestCase): c.update_server_config(authentication__type="test") c.update_server_config( multi_dataset__dataroot=dict( - a1=dict(dataroot=f"{PROJECT_ROOT}/server/test/test_datasets", base_url="auth"), - a2=dict(dataroot=f"{PROJECT_ROOT}/server/test/test_datasets", base_url="no-auth"), + a1=dict(dataroot=self.dataset_dataroot, base_url="auth"), + a2=dict(dataroot=self.dataset_dataroot, base_url="no-auth"), ) ) @@ -100,7 +105,7 @@ class AuthTest(unittest.TestCase): c = AppConfig() c.update_server_config( authentication__type="test", - single_dataset__datapath=f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k.cxg") + single_dataset__datapath=f"{self.dataset_dataroot}/pbmc3k.cxg") c.complete_config() diff --git a/server/test/unit/cli/__init__.py b/server/test/unit/cli/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/server/test/test_cli_prepare.py b/server/test/unit/cli/test_prepare.py similarity index 100% rename from server/test/test_cli_prepare.py rename to server/test/unit/cli/test_prepare.py diff --git a/server/test/test_cli_upgrade.py b/server/test/unit/cli/test_upgrade.py similarity index 100% rename from server/test/test_cli_upgrade.py rename to server/test/unit/cli/test_upgrade.py diff --git a/server/test/unit/common/__init__.py b/server/test/unit/common/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/server/test/test_api.py b/server/test/unit/common/test_api.py similarity index 98% rename from server/test/test_api.py rename to server/test/unit/common/test_api.py index 7b50c426..3e2c79b9 100644 --- a/server/test/test_api.py +++ b/server/test/unit/common/test_api.py @@ -6,15 +6,15 @@ from http import HTTPStatus import pandas as pd import requests -import server.test.decode_fbs as decode_fbs +import server.test.unit.decode_fbs as decode_fbs from server.data_common.matrix_loader import MatrixDataType -from server.test import data_with_tmp_annotations, make_fbs, PROJECT_ROOT -from server.test.test_datasets.fixtures import pbmc3k_colors -from server.test import start_test_server, stop_test_server - +from server.test import (data_with_tmp_annotations, make_fbs, PROJECT_ROOT, FIXTURES_ROOT, start_test_server, + stop_test_server) +from server.test.fixtures.fixtures import pbmc3k_colors BAD_FILTER = {"filter": {"obs": {"annotation_value": [{"name": "xyz"}]}}} + # TODO (mweiden): remove ANNOTATIONS_ENABLED and Annotation subclasses when annotations are no longer experimental @@ -404,7 +404,7 @@ class EndPointsCxg(unittest.TestCase, EndPoints): @classmethod def setUpClass(cls): cls._setupClass(cls, [ - f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k.cxg", + f"{FIXTURES_ROOT}/pbmc3k.cxg", "--disable-annotations", ]) diff --git a/server/test/test_app_config.py b/server/test/unit/common/test_app_config.py similarity index 94% rename from server/test/test_app_config.py rename to server/test/unit/common/test_app_config.py index c55f927a..d1cc9496 100644 --- a/server/test/test_app_config.py +++ b/server/test/unit/common/test_app_config.py @@ -1,7 +1,7 @@ import unittest from server.common.app_config import AppConfig from server.common.errors import ConfigurationError -from server.test import PROJECT_ROOT, test_server +from server.test import PROJECT_ROOT, test_server, FIXTURES_ROOT import requests # NOTE, there are more tests that should be written for AppConfig. @@ -52,8 +52,8 @@ class AppConfigTest(unittest.TestCase): c.update_server_config( multi_dataset__dataroot=dict( s1=dict(dataroot=f"{PROJECT_ROOT}/example-dataset", base_url="set1/1/2"), - s2=dict(dataroot=f"{PROJECT_ROOT}/server/test/test_datasets", base_url="set2"), - s3=dict(dataroot=f"{PROJECT_ROOT}/server/test/test_datasets", base_url="set3"), + s2=dict(dataroot=f"{FIXTURES_ROOT}", base_url="set2"), + s3=dict(dataroot=f"{FIXTURES_ROOT}", base_url="set3"), ) ) diff --git a/server/test/test_colors.py b/server/test/unit/common/test_colors.py similarity index 96% rename from server/test/test_colors.py rename to server/test/unit/common/test_colors.py index 2970587c..efef25ec 100644 --- a/server/test/test_colors.py +++ b/server/test/unit/common/test_colors.py @@ -4,7 +4,7 @@ import anndata from server.common.colors import convert_color_to_hex_format, convert_anndata_category_colors_to_cxg_category_colors from server.common.errors import ColorFormatException from server.test import PROJECT_ROOT -from server.test.test_datasets.fixtures import pbmc3k_colors +from server.test.fixtures.fixtures import pbmc3k_colors class ColorsTest(unittest.TestCase): diff --git a/server/test/test_corpora.py b/server/test/unit/common/test_corpora.py similarity index 100% rename from server/test/test_corpora.py rename to server/test/unit/common/test_corpora.py diff --git a/server/test/test_nan_rest.py b/server/test/unit/common/test_nan_rest.py similarity index 94% rename from server/test/test_nan_rest.py rename to server/test/unit/common/test_nan_rest.py index 00c072e5..1dd28a54 100644 --- a/server/test/test_nan_rest.py +++ b/server/test/unit/common/test_nan_rest.py @@ -3,7 +3,7 @@ import unittest import math from server.test import start_test_server, stop_test_server -import server.test.decode_fbs as decode_fbs +import server.test.unit.decode_fbs as decode_fbs import requests @@ -16,7 +16,7 @@ class WithNaNs(unittest.TestCase): @classmethod def setUpClass(cls): - cls.ps, cls.server = start_test_server(["test/test_datasets/nan.h5ad"]) + cls.ps, cls.server = start_test_server(["test/fixtures/nan.h5ad"]) @classmethod def tearDownClass(cls): diff --git a/server/test/test_filter.py b/server/test/unit/common/test_rest.py similarity index 100% rename from server/test/test_filter.py rename to server/test/unit/common/test_rest.py diff --git a/server/test/test_plugins.py b/server/test/unit/common/test_utils.py similarity index 100% rename from server/test/test_plugins.py rename to server/test/unit/common/test_utils.py diff --git a/server/test/test_writable_annotation.py b/server/test/unit/common/test_writable_annotation.py similarity index 99% rename from server/test/test_writable_annotation.py rename to server/test/unit/common/test_writable_annotation.py index 6ca0419d..3178f64c 100644 --- a/server/test/test_writable_annotation.py +++ b/server/test/unit/common/test_writable_annotation.py @@ -1,7 +1,7 @@ import json from os import path, listdir import unittest -import server.test.decode_fbs as decode_fbs +import server.test.unit.decode_fbs as decode_fbs import shutil import numpy as np diff --git a/server/test/unit/compute/__init__.py b/server/test/unit/compute/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/server/test/test_diffexp.py b/server/test/unit/compute/test_diffexp_cxg.py similarity index 96% rename from server/test/test_diffexp.py rename to server/test/unit/compute/test_diffexp_cxg.py index ee49681f..7a6aabdd 100644 --- a/server/test/test_diffexp.py +++ b/server/test/unit/compute/test_diffexp_cxg.py @@ -1,10 +1,10 @@ import unittest from server.data_common.matrix_loader import MatrixDataLoader -from server.test import PROJECT_ROOT, app_config +from server.test import PROJECT_ROOT, app_config, FIXTURES_ROOT import server.compute.diffexp_cxg as diffexp_cxg import server.compute.diffexp_generic as diffexp_generic from server.converters.cxgtool import write_cxg, create_cxg_group_metadata -from server.test.create_test_matrix import create_test_h5ad +from server.test.performance.create_test_matrix import create_test_h5ad from server.data_common.fbs.matrix import encode_matrix_fbs, decode_matrix_fbs import numpy as np import tempfile @@ -68,7 +68,7 @@ class DiffExpTest(unittest.TestCase): def test_cxg_default(self): """Test a cxg adaptor with its default diffexp algorithm (diffexp_cxg)""" - adaptor = self.load_dataset(f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k.cxg") + adaptor = self.load_dataset(f"{FIXTURES_ROOT}/pbmc3k.cxg") maskA = self.get_mask(adaptor, 1, 10) maskB = self.get_mask(adaptor, 2, 10) @@ -82,7 +82,7 @@ class DiffExpTest(unittest.TestCase): def test_cxg_generic(self): """Test a cxg adaptor with the generic adaptor""" - adaptor = self.load_dataset(f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k.cxg") + adaptor = self.load_dataset(f"{FIXTURES_ROOT}/pbmc3k.cxg") maskA = self.get_mask(adaptor, 1, 10) maskB = self.get_mask(adaptor, 2, 10) # run it directly diff --git a/server/test/unit/converters/__init__.py b/server/test/unit/converters/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/server/test/test_cxgtool.py b/server/test/unit/converters/test_cxgtool.py similarity index 96% rename from server/test/test_cxgtool.py rename to server/test/unit/converters/test_cxgtool.py index 91ab8605..46e26b48 100644 --- a/server/test/test_cxgtool.py +++ b/server/test/unit/converters/test_cxgtool.py @@ -7,7 +7,7 @@ from server.common.data_locator import DataLocator from server.converters.cxgtool import write_cxg, create_cxg_group_metadata from server.data_cxg.cxg_adaptor import CxgAdaptor from server.test import PROJECT_ROOT, app_config, random_string -from server.test.test_datasets.fixtures import pbmc3k_colors +from server.test.fixtures.fixtures import pbmc3k_colors class TestCxgAdaptor(unittest.TestCase): diff --git a/server/test/unit/data_anndata/__init__.py b/server/test/unit/data_anndata/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/server/test/test_anndata_adaptor.py b/server/test/unit/data_anndata/test_anndata_adaptor.py similarity index 94% rename from server/test/test_anndata_adaptor.py rename to server/test/unit/data_anndata/test_anndata_adaptor.py index 440e9b82..d4a3a778 100644 --- a/server/test/test_anndata_adaptor.py +++ b/server/test/unit/data_anndata/test_anndata_adaptor.py @@ -1,20 +1,19 @@ import json -from os import path -import pytest +import sys import time import unittest -import sys -import server.test.decode_fbs as decode_fbs -from parameterized import parameterized_class import numpy as np import pandas as pd +import pytest +from parameterized import parameterized_class +import server.test.unit.decode_fbs as decode_fbs from server.common.data_locator import DataLocator from server.common.errors import FilterError from server.data_anndata.anndata_adaptor import AnndataAdaptor -from server.test import PROJECT_ROOT, app_config -from server.test.test_datasets.fixtures import pbmc3k_colors +from server.test import PROJECT_ROOT, app_config, FIXTURES_ROOT +from server.test.fixtures.fixtures import pbmc3k_colors """ Test the anndata adaptor using the pbmc3k data set. @@ -25,11 +24,11 @@ Test the anndata adaptor using the pbmc3k data set. ("data_locator", "backed"), [ (f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad", False), - (f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k-CSC-gz.h5ad", False), - (f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k-CSR-gz.h5ad", False), + (f"{FIXTURES_ROOT}/pbmc3k-CSC-gz.h5ad", False), + (f"{FIXTURES_ROOT}/pbmc3k-CSR-gz.h5ad", False), (f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad", True), - (f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k-CSC-gz.h5ad", True), - (f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k-CSR-gz.h5ad", True), + (f"{FIXTURES_ROOT}/pbmc3k-CSC-gz.h5ad", True), + (f"{FIXTURES_ROOT}/pbmc3k-CSR-gz.h5ad", True), ], ) class AdaptorTest(unittest.TestCase): @@ -84,7 +83,7 @@ class AdaptorTest(unittest.TestCase): self.assertEqual(self.data.get_colors(), pbmc3k_colors) def test_get_schema(self): - with open(path.join(path.dirname(__file__), "schema.json")) as fh: + with open(f"{FIXTURES_ROOT}/schema.json") as fh: schema = json.load(fh) self.assertDictEqual(self.data.get_schema(), schema) diff --git a/server/test/test_anndata_adaptor_data_load.py b/server/test/unit/data_anndata/test_anndata_adaptor_data_load.py similarity index 100% rename from server/test/test_anndata_adaptor_data_load.py rename to server/test/unit/data_anndata/test_anndata_adaptor_data_load.py diff --git a/server/test/test_nan_anndata_adaptor.py b/server/test/unit/data_anndata/test_nan_anndata_adaptor.py similarity index 93% rename from server/test/test_nan_anndata_adaptor.py rename to server/test/unit/data_anndata/test_nan_anndata_adaptor.py index 6471dd8b..29ca178f 100644 --- a/server/test/test_nan_anndata_adaptor.py +++ b/server/test/unit/data_anndata/test_nan_anndata_adaptor.py @@ -1,19 +1,19 @@ -import pytest +import math import unittest import warnings -import math -import server.test.decode_fbs as decode_fbs +import pytest -from server.data_anndata.anndata_adaptor import AnndataAdaptor -from server.common.errors import FilterError +import server.test.unit.decode_fbs as decode_fbs from server.common.data_locator import DataLocator -from server.test import PROJECT_ROOT, app_config +from server.common.errors import FilterError +from server.data_anndata.anndata_adaptor import AnndataAdaptor +from server.test import app_config, FIXTURES_ROOT class NaNTest(unittest.TestCase): def setUp(self): - self.data_locator = DataLocator(f"{PROJECT_ROOT}/server/test/test_datasets/nan.h5ad") + self.data_locator = DataLocator(f"{FIXTURES_ROOT}/nan.h5ad") self.config = app_config(self.data_locator.path) with warnings.catch_warnings(): diff --git a/server/test/unit/data_common/__init__.py b/server/test/unit/data_common/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/server/test/unit/data_common/fbs/__init__.py b/server/test/unit/data_common/fbs/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/server/test/test_fbs.py b/server/test/unit/data_common/fbs/test_matrix.py similarity index 98% rename from server/test/test_fbs.py rename to server/test/unit/data_common/fbs/test_matrix.py index 59ad989a..1e23cb6b 100644 --- a/server/test/test_fbs.py +++ b/server/test/unit/data_common/fbs/test_matrix.py @@ -3,7 +3,7 @@ import pandas as pd import numpy as np from scipy import sparse -import server.test.decode_fbs as decode_fbs +import server.test.unit.decode_fbs as decode_fbs from server.data_common.fbs.matrix import encode_matrix_fbs, decode_matrix_fbs diff --git a/server/test/test_matrixcache.py b/server/test/unit/data_common/test_matrix_loader.py similarity index 96% rename from server/test/test_matrixcache.py rename to server/test/unit/data_common/test_matrix_loader.py index 6c68cfc3..d365b001 100644 --- a/server/test/test_matrixcache.py +++ b/server/test/unit/data_common/test_matrix_loader.py @@ -1,13 +1,13 @@ +import os +import shutil +import tempfile +import time import unittest -from server.data_common.matrix_loader import MatrixDataCacheManager + from server.common.app_config import AppConfig from server.common.errors import DatasetAccessError -import tempfile -import shutil -import os -import time - -from server.test import PROJECT_ROOT +from server.data_common.matrix_loader import MatrixDataCacheManager +from server.test import FIXTURES_ROOT class MatrixCacheTest(unittest.TestCase): @@ -15,7 +15,7 @@ class MatrixCacheTest(unittest.TestCase): pass def make_temporay_datasets(self, dirname, num): - source = f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k.cxg" + source = f"{FIXTURES_ROOT}/pbmc3k.cxg" for i in range(num): target = os.path.join(dirname, str(i) + ".cxg") shutil.copytree(source, target) @@ -38,7 +38,7 @@ class MatrixCacheTest(unittest.TestCase): result = {} for k, v in datasets.items(): # filter out the dirname and the .cxg from the name - newk = int(k[1][len(dirname) + 1 : -4]) + newk = int(k[1][len(dirname) + 1: -4]) result[newk] = v return result diff --git a/server/test/unit/data_cxg/__init__.py b/server/test/unit/data_cxg/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/server/test/test_cxg_adaptor.py b/server/test/unit/data_cxg/test_cxg_adaptor.py similarity index 74% rename from server/test/test_cxg_adaptor.py rename to server/test/unit/data_cxg/test_cxg_adaptor.py index 205ce24b..3544138c 100644 --- a/server/test/test_cxg_adaptor.py +++ b/server/test/unit/data_cxg/test_cxg_adaptor.py @@ -2,8 +2,8 @@ import unittest from server.common.data_locator import DataLocator from server.data_cxg.cxg_adaptor import CxgAdaptor -from server.test import PROJECT_ROOT, app_config -from server.test.test_datasets.fixtures import pbmc3k_colors +from server.test import FIXTURES_ROOT, app_config +from server.test.fixtures.fixtures import pbmc3k_colors class TestCxgAdaptor(unittest.TestCase): @@ -14,6 +14,6 @@ class TestCxgAdaptor(unittest.TestCase): self.assertDictEqual(data.get_colors(), dict()) def get_data(self, fixture): - data_locator = f"{PROJECT_ROOT}/server/test/test_datasets/{fixture}" + data_locator = f"{FIXTURES_ROOT}/{fixture}" config = app_config(data_locator) return CxgAdaptor(DataLocator(data_locator), config) diff --git a/server/test/decode_fbs.py b/server/test/unit/decode_fbs.py similarity index 99% rename from server/test/decode_fbs.py rename to server/test/unit/decode_fbs.py index 5debe7ae..477ce189 100644 --- a/server/test/decode_fbs.py +++ b/server/test/unit/decode_fbs.py @@ -1,18 +1,17 @@ """ Code to decode, for testing purposes, the flatbuffer encoded blobs. This code will need to be updated if fbs/matrix.fbs changes. - For more information, see fbs/matrix.fbs and server/data_common/fbs/ """ import json -import server.data_common.fbs.NetEncoding.TypedArray as TypedArray -import server.data_common.fbs.NetEncoding.Matrix as Matrix -import server.data_common.fbs.NetEncoding.Int32Array as Int32Array -import server.data_common.fbs.NetEncoding.Uint32Array as Uint32Array import server.data_common.fbs.NetEncoding.Float32Array as Float32Array import server.data_common.fbs.NetEncoding.Float64Array as Float64Array +import server.data_common.fbs.NetEncoding.Int32Array as Int32Array import server.data_common.fbs.NetEncoding.JSONEncodedArray as JSONEncodedArray +import server.data_common.fbs.NetEncoding.Matrix as Matrix +import server.data_common.fbs.NetEncoding.TypedArray as TypedArray +import server.data_common.fbs.NetEncoding.Uint32Array as Uint32Array def decode_typed_array(tarr): @@ -42,7 +41,6 @@ def decode_matrix_FBS(buf): """ Given a FBS Matrix, return an decoded Python dict containing same info in native format. - NOTE / TODO: row_idx not currently implemented """ df = Matrix.Matrix.GetRootAsMatrix(buf, 0) diff --git a/server/test/unit/eb/__init__.py b/server/test/unit/eb/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/server/test/test_eb.py b/server/test/unit/eb/test_eb.py similarity index 90% rename from server/test/test_eb.py rename to server/test/unit/eb/test_eb.py index f1e1ef9d..b43fda24 100644 --- a/server/test/test_eb.py +++ b/server/test/unit/eb/test_eb.py @@ -2,7 +2,7 @@ import unittest import tempfile import requests import subprocess -from server.test import PROJECT_ROOT +from server.test import PROJECT_ROOT, FIXTURES_ROOT from server.common.app_config import AppConfig from contextlib import contextmanager import time @@ -37,7 +37,7 @@ class Elastic_Beanstalk_Test(unittest.TestCase): c = AppConfig() # test that eb works c.update_server_config( - multi_dataset__dataroot=f"{PROJECT_ROOT}/server/test/test_datasets", app__flask_secret_key="open sesame" + multi_dataset__dataroot=f"{FIXTURES_ROOT}", app__flask_secret_key="open sesame" ) c.complete_config()