From d8661a0d6a03197bb5671e01d9e2f9f926c20526 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 5 Jul 2024 15:42:47 +0200
Subject: [PATCH] Moved test configuration to its own module
---
model_server/base/util.py | 86 -----------------------
model_server/conf/testing.py | 109 +++++++++++++++++++++++++++++
tests/base/conf.py | 83 ----------------------
tests/base/test_accessors.py | 4 +-
tests/base/test_api.py | 5 +-
tests/base/test_model.py | 3 +-
tests/base/test_roiset.py | 5 +-
tests/base/test_workflow.py | 4 +-
tests/test_ilastik/_conf.py | 12 ----
tests/test_ilastik/test_ilastik.py | 2 +-
10 files changed, 120 insertions(+), 193 deletions(-)
create mode 100644 model_server/conf/testing.py
delete mode 100644 tests/base/conf.py
delete mode 100644 tests/test_ilastik/_conf.py
diff --git a/model_server/base/util.py b/model_server/base/util.py
index 6185ae21..9b95edca 100644
--- a/model_server/base/util.py
+++ b/model_server/base/util.py
@@ -1,16 +1,10 @@
-import json
-import unittest
from math import ceil
-from multiprocessing import Process
from pathlib import Path
-import os
import re
from time import localtime, strftime
from typing import List
import pandas as pd
-import requests
-from urllib3 import Retry
from .accessors import InMemoryDataAccessor, write_accessor_data_to_file
from .models import Model
@@ -170,83 +164,3 @@ def loop_workflow(
if len(failures) > 0:
pd.DataFrame(failures).to_csv(Path(output_folder_path) / 'failures.csv')
-
-
-class TestServerBaseClass(unittest.TestCase):
- """
- Base class for unittests of API functionality. Implements both server and clients for testing.
- """
-
- app_name = 'model_server.base.api:app'
-
- def setUp(self) -> None:
- import uvicorn
- host = '127.0.0.1'
- port = 5001
-
- self.server_process = Process(
- target=uvicorn.run,
- args=(self.app_name, ),
- kwargs={'host': host, 'port': port, 'log_level': 'critical'},
- daemon=True
- )
- self.uri = f'http://{host}:{port}/'
- self.server_process.start()
-
- def _get_sesh(self):
- sesh = requests.Session()
- retries = Retry(
- total=5,
- backoff_factor=0.1,
- )
- sesh.mount('http://', requests.adapters.HTTPAdapter(max_retries=retries))
- return sesh
-
- def _get(self, endpoint):
- return self._get_sesh().get(self.uri + endpoint)
-
- def _put(self, endpoint, query=None, body=None):
- return self._get_sesh().put(
- self.uri + endpoint,
- params=query,
- data=json.dumps(body)
- )
-
- def tearDown(self) -> None:
- self.server_process.terminate()
- self.server_process.join()
-
-def setup_test_data():
- """
- Look for test data, create test output directory, parse and return meta information
- :return:
- meta (dict) of test data and paths
- """
- # places to look for test data
- data_paths = [
- os.environ.get('UNITTEST_DATA_ROOT'),
- Path.home() / 'model_server' / 'testing',
- os.getcwd(),
- ]
- root = None
-
- # look for first instance of summary.json
- for dp in data_paths:
- if dp is None:
- continue
- sf = (Path(dp) / 'summary.json')
- if sf.exists():
- with open(sf, 'r') as fh:
- meta = json.load(fh)
- root = Path(dp)
- break
-
- if root is None:
- raise Exception('Could not find test data, try setting environmental variable UNITTEST_DATA_ROOT.')
-
- op_ev = os.environ.get('UNITTEST_OUTPUT', (root / 'test_output').__str__())
- output_path = Path(op_ev)
- output_path.mkdir(parents=True, exist_ok=True)
- meta['root'] = root.__str__()
- meta['output_path'] = output_path.__str__()
- return meta
\ No newline at end of file
diff --git a/model_server/conf/testing.py b/model_server/conf/testing.py
new file mode 100644
index 00000000..f982ec8b
--- /dev/null
+++ b/model_server/conf/testing.py
@@ -0,0 +1,109 @@
+import json
+import os
+import unittest
+from multiprocessing import Process
+from pathlib import Path
+
+import requests
+from urllib3 import Retry
+
+
+class TestServerBaseClass(unittest.TestCase):
+ """
+ Base class for unittests of API functionality. Implements both server and clients for testing.
+ """
+
+ app_name = 'model_server.base.api:app'
+
+ def setUp(self) -> None:
+ import uvicorn
+ host = '127.0.0.1'
+ port = 5001
+
+ self.server_process = Process(
+ target=uvicorn.run,
+ args=(self.app_name, ),
+ kwargs={'host': host, 'port': port, 'log_level': 'critical'},
+ daemon=True
+ )
+ self.uri = f'http://{host}:{port}/'
+ self.server_process.start()
+
+ def _get_sesh(self):
+ sesh = requests.Session()
+ retries = Retry(
+ total=5,
+ backoff_factor=0.1,
+ )
+ sesh.mount('http://', requests.adapters.HTTPAdapter(max_retries=retries))
+ return sesh
+
+ def _get(self, endpoint):
+ return self._get_sesh().get(self.uri + endpoint)
+
+ def _put(self, endpoint, query=None, body=None):
+ return self._get_sesh().put(
+ self.uri + endpoint,
+ params=query,
+ data=json.dumps(body)
+ )
+
+ def tearDown(self) -> None:
+ self.server_process.terminate()
+ self.server_process.join()
+
+
+def setup_test_data():
+ """
+ Look for test data, create test output directory, parse and return meta information
+ :return:
+ meta (dict) of test data and paths
+ """
+ # places to look for test data
+ data_paths = [
+ os.environ.get('UNITTEST_DATA_ROOT'),
+ Path.home() / 'model_server' / 'testing',
+ os.getcwd(),
+ ]
+ root = None
+
+ # look for first instance of summary.json
+ for dp in data_paths:
+ if dp is None:
+ continue
+ sf = (Path(dp) / 'summary.json')
+ if sf.exists():
+ with open(sf, 'r') as fh:
+ meta = json.load(fh)
+ root = dp
+ break
+
+ if root is None:
+ raise Exception('Could not find test data, try setting environmental variable UNITTEST_DATA_ROOT.')
+
+ op_ev = os.environ.get('UNITTEST_OUTPUT', (root / 'test_output'))
+ meta['output_path'] = Path(op_ev)
+ meta['root'] = Path(root)
+ meta['output_path'].mkdir(parents=True, exist_ok=True)
+
+
+ # resolve relative paths
+ def _resolve_paths(d):
+ keys = list(d.keys())
+ for k in keys:
+ if k == 'name':
+ d['path'] = root / d['name']
+ elif isinstance(d[k], dict):
+ _resolve_paths(d[k])
+ _resolve_paths(meta)
+
+ return meta
+
+meta = setup_test_data()
+# root = Path(meta['root'])
+# output_path = Path(meta['output_path'])
+
+# # resolve paths in test image files
+# imgs = meta['image_files']
+# for k in imgs.keys():
+# imgs[k]['path'] = root / imgs[k]['name']
\ No newline at end of file
diff --git a/tests/base/conf.py b/tests/base/conf.py
deleted file mode 100644
index 18d49871..00000000
--- a/tests/base/conf.py
+++ /dev/null
@@ -1,83 +0,0 @@
-from pathlib import Path
-from model_server.base.util import setup_test_data
-
-meta = setup_test_data()
-
-root = Path(meta['root'])
-output_path = Path(meta['output_path'])
-
-# resolve paths in test image files
-imgs = meta['image_files']
-for k in imgs.keys():
- imgs[k]['path'] = root / imgs[k]['name']
-
-# filename = 'D3-selection-01.czi'
-# czifile = {
-# 'filename': filename,
-# 'path': root / filename,
-# 'w': 1274,
-# 'h': 1274,
-# 'c': 5,
-# 'z': 1,
-# 'um_per_pixel': 1/3.9881,
-# }
-#
-# filename = 'rgb.png'
-# rgbpngfile = {
-# 'filename': filename,
-# 'path': root / filename,
-# 'w': 64,
-# 'h': 128,
-# 'c': 3,
-# 'z': 1
-# }
-#
-# filename = 'mono.png'
-# monopngfile = {
-# 'filename': filename,
-# 'path': root / filename,
-# 'w': 64,
-# 'h': 128,
-# 'c': 1,
-# 'z': 1
-# }
-#
-# filename = 'zmask-test-stack.tif'
-# tifffile = {
-# 'filename': filename,
-# 'path': root / filename,
-# 'w': 512,
-# 'h': 512,
-# 'c': 2,
-# 'z': 7,
-# }
-#
-# filename = 'mono_zstack_mask.tif'
-# monozstackmask = {
-# 'filename': filename,
-# 'path': root / filename,
-# 'w': 256,
-# 'h': 256,
-# 'c': 1,
-# 'z': 85
-# }
-#
-# roiset_test_data = {
-# 'multichannel_zstack': {
-# 'path': root / 'zmask-test-stack-chlorophyl.tif',
-# 'w': 512,
-# 'h': 512,
-# 'c': 5,
-# 'z': 7,
-# 'mask_path': root / 'zmask-test-stack-mask.tif',
-# 'mask_path_3d': root / 'zmask-test-stack-mask-3d.tif',
-# },
-# 'pipeline_params': {
-# 'segmentation_channel': 0,
-# 'patches_channel': 4,
-# 'pxmap_channel': 0,
-# 'pxmap_threshold': 0.6,
-# },
-# 'pixel_classifier': root / 'zmask' / 'AF405-bodies_boundaries.ilp',
-# }
-
diff --git a/tests/base/test_accessors.py b/tests/base/test_accessors.py
index 540f2121..a8a879f2 100644
--- a/tests/base/test_accessors.py
+++ b/tests/base/test_accessors.py
@@ -4,11 +4,11 @@ import numpy as np
from model_server.base.accessors import PatchStack, make_patch_stack_from_file, FileNotFoundError
-from tests.base import conf
from model_server.base.accessors import CziImageFileAccessor, DataShapeError, generate_file_accessor, InMemoryDataAccessor, PngFileAccessor, write_accessor_data_to_file, TifSingleSeriesFileAccessor
+import model_server.conf.testing as conf
data = conf.meta['image_files']
-output_path = conf.output_path
+output_path = conf.meta['output_path']
def _random_int(*args):
return np.random.randint(0, 2 ** 8, size=args, dtype='uint8')
diff --git a/tests/base/test_api.py b/tests/base/test_api.py
index b8d406e8..46f614be 100644
--- a/tests/base/test_api.py
+++ b/tests/base/test_api.py
@@ -1,11 +1,10 @@
from pathlib import Path
-from base.util import TestServerBaseClass
-from tests.base import conf
+import model_server.conf.testing as conf
czifile = conf.meta['image_files']['czifile']
-class TestApiFromAutomatedClient(TestServerBaseClass):
+class TestApiFromAutomatedClient(conf.TestServerBaseClass):
def copy_input_file_to_server(self):
from shutil import copyfile
diff --git a/tests/base/test_model.py b/tests/base/test_model.py
index ce0159e7..d5b25c17 100644
--- a/tests/base/test_model.py
+++ b/tests/base/test_model.py
@@ -1,7 +1,8 @@
import unittest
-from tests.base import conf
+
from model_server.base.accessors import CziImageFileAccessor
from model_server.base.models import DummySemanticSegmentationModel, DummyInstanceSegmentationModel, CouldNotLoadModelError
+import model_server.conf.testing as conf
czifile = conf.meta['image_files']['czifile']
diff --git a/tests/base/test_roiset.py b/tests/base/test_roiset.py
index c7bf2752..f993d2a0 100644
--- a/tests/base/test_roiset.py
+++ b/tests/base/test_roiset.py
@@ -6,15 +6,14 @@ from pathlib import Path
import pandas as pd
-from tests.base import conf
-
from model_server.base.roiset import RoiSetExportParams, RoiSetMetaParams
from model_server.base.roiset import RoiSet
from model_server.base.accessors import generate_file_accessor, InMemoryDataAccessor, write_accessor_data_to_file, PatchStack
from model_server.base.models import DummyInstanceSegmentationModel
+import model_server.conf.testing as conf
data = conf.meta['image_files']
-output_path = conf.output_path
+output_path = conf.meta['output_path']
params = conf.meta['roiset']
class BaseTestRoiSetMonoProducts(object):
diff --git a/tests/base/test_workflow.py b/tests/base/test_workflow.py
index c0f857ef..54b83268 100644
--- a/tests/base/test_workflow.py
+++ b/tests/base/test_workflow.py
@@ -1,11 +1,11 @@
import unittest
-from tests.base import conf
from model_server.base.models import DummySemanticSegmentationModel
from model_server.base.workflows import classify_pixels
+import model_server.conf.testing as conf
czifile = conf.meta['image_files']['czifile']
-output_path = conf.output_path
+output_path = conf.meta['output_path']
class TestGetSessionObject(unittest.TestCase):
def setUp(self) -> None:
diff --git a/tests/test_ilastik/_conf.py b/tests/test_ilastik/_conf.py
deleted file mode 100644
index 8fb8fc5e..00000000
--- a/tests/test_ilastik/_conf.py
+++ /dev/null
@@ -1,12 +0,0 @@
-from tests.base import _conf
-root = _conf.root / 'ilastik'
-
-
-ilastik_classifiers = {
- 'px': root / 'demo_px.ilp',
- 'pxmap_to_obj': root / 'demo_obj.ilp',
- 'seg_to_obj': root / 'demo_obj_seg.ilp',
- 'px_color_zstack': root / 'px-3d-color.ilp',
- 'ob_pxmap_color_zstack': root / 'ob-pxmap-color-zstack.ilp',
- 'ob_seg_color_zstack': root / 'ob-seg-color-zstack.ilp',
-}
\ No newline at end of file
diff --git a/tests/test_ilastik/test_ilastik.py b/tests/test_ilastik/test_ilastik.py
index 5153e854..3214d04f 100644
--- a/tests/test_ilastik/test_ilastik.py
+++ b/tests/test_ilastik/test_ilastik.py
@@ -7,7 +7,7 @@ from model_server.extensions.ilastik import models as ilm
from model_server.extensions.ilastik.workflows import infer_px_then_ob_model
from model_server.base.roiset import _get_label_ids, RoiSet, RoiSetMetaParams
from model_server.base.workflows import classify_pixels
-from model_server.base.util import TestServerBaseClass
+from conf.testing import TestServerBaseClass
from tests.test_ilastik import conf
--
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