diff --git a/model_server/conf/testing.py b/model_server/conf/testing.py
index 16b656c225bcc7f1373e025c1659b8c0893a6ca7..12d93c8b884dfad672a5e7adf0f5cbe05c60eeba 100644
--- a/model_server/conf/testing.py
+++ b/model_server/conf/testing.py
@@ -3,10 +3,12 @@ import os
import unittest
from multiprocessing import Process
from pathlib import Path
+from shutil import copyfile
import requests
from urllib3 import Retry
+from ..base.accessors import generate_file_accessor
class TestServerBaseClass(unittest.TestCase):
"""
@@ -52,6 +54,22 @@ class TestServerBaseClass(unittest.TestCase):
self.server_process.terminate()
self.server_process.join()
+ def copy_input_file_to_server(self):
+ resp = self._get('paths')
+ pa = resp.json()['inbound_images']
+ copyfile(
+ self.input_data['path'],
+ Path(pa) / self.input_data['name']
+ )
+ return self.input_data['name']
+
+ def get_accessor(self, accessor_id, filename=None):
+ resp = self._put(f'/accessors/write_to_file/{accessor_id}', query={'filename': filename})
+ where_out = self._get('paths').json()['outbound_images']
+ fp_out = (Path(where_out) / resp.json())
+ self.assertTrue(fp_out.exists())
+ return generate_file_accessor(fp_out)
+
def setup_test_data():
"""
diff --git a/tests/base/test_api.py b/tests/base/test_api.py
index b60b0e4e2afc1dba04b4f4f382867ba42981f9e0..7f692af23e42651fed96b0714a9b4798f7b5c412 100644
--- a/tests/base/test_api.py
+++ b/tests/base/test_api.py
@@ -11,7 +11,6 @@ from model_server.base.session import session
from tests.base.test_model import DummyInstanceSegmentationModel, DummySemanticSegmentationModel
czifile = conf.meta['image_files']['czifile']
-cfn = czifile['name']
"""
Configure additional endpoints for testing
@@ -57,19 +56,10 @@ app.include_router(router)
Implement unit testing on extended base app
"""
+
class TestServerTestCase(conf.TestServerBaseClass):
app_name = 'tests.base.test_api:app'
-
- def copy_input_file_to_server(self):
- from shutil import copyfile
-
- resp = self._get('paths')
- pa = resp.json()['inbound_images']
- outpath = Path(pa) / cfn
- copyfile(
- czifile['path'],
- outpath
- )
+ input_data = czifile
class TestApiFromAutomatedClient(TestServerTestCase):
@@ -126,11 +116,10 @@ class TestApiFromAutomatedClient(TestServerTestCase):
)
self.assertEqual(resp.status_code, 404, resp.content.decode())
-
def test_pipeline_errors_when_ids_not_found(self):
- self.copy_input_file_to_server()
+ fname = self.copy_input_file_to_server()
model_id = self._put(f'testing/models/dummy_semantic/load').json()['model_id']
- in_acc_id = self._put(f'accessors/read_from_file/{cfn}').json()
+ in_acc_id = self._put(f'accessors/read_from_file/{fname}').json()
# respond with 409 for invalid accessor_id
self.assertEqual(
@@ -152,9 +141,9 @@ class TestApiFromAutomatedClient(TestServerTestCase):
def test_i2i_dummy_inference_by_api(self):
- self.copy_input_file_to_server()
+ fname = self.copy_input_file_to_server()
model_id = self._put(f'testing/models/dummy_semantic/load').json()['model_id']
- in_acc_id = self._put(f'accessors/read_from_file/{cfn}').json()
+ in_acc_id = self._put(f'accessors/read_from_file/{fname}').json()
# run segmentation pipeline on preloaded accessor
resp_infer = self._put(
@@ -169,14 +158,7 @@ class TestApiFromAutomatedClient(TestServerTestCase):
self.assertEqual(resp_infer.status_code, 200, resp_infer.content.decode())
out_acc_id = resp_infer.json()['output_accessor_id']
self.assertTrue(self._get(f'accessors/{out_acc_id}').json()['loaded'])
-
- # write and re-read output
- filename = 'dummy_semantic_output.tif'
- self._put(f'/accessors/write_to_file/{out_acc_id}', query={'filename': filename})
- where_out = self._get('paths').json()['outbound_images']
- fp_out = (Path(where_out) / filename)
- self.assertTrue(fp_out.exists())
- acc_out = generate_file_accessor(fp_out)
+ acc_out = self.get_accessor(out_acc_id, 'dummy_semantic_output.tif')
self.assertEqual(acc_out.shape_dict['C'], 1)
# validate intermediate data
@@ -233,11 +215,11 @@ class TestApiFromAutomatedClient(TestServerTestCase):
self.assertEqual(resp.json()[0]['message'], 'Initialized session')
def test_add_and_delete_accessor(self):
- self.copy_input_file_to_server()
+ fname = self.copy_input_file_to_server()
# add accessor to session
resp_add_acc = self._put(
- f'accessors/read_from_file/{cfn}',
+ f'accessors/read_from_file/{fname}',
)
acc_id = resp_add_acc.json()
self.assertTrue(acc_id.startswith('auto_'))
@@ -270,13 +252,5 @@ class TestApiFromAutomatedClient(TestServerTestCase):
self.assertTrue(self._get(f'accessors/{acc_id}').json()['loaded'])
sd = self._get(f'accessors/{acc_id}').json()['shape_dict']
self.assertEqual(self._get(f'accessors/{acc_id}').json()['filepath'], '')
-
- filename = 'test_output.tif'
- self._put(f'/accessors/write_to_file/{acc_id}', query={'filename': filename})
- where_out = self._get('paths').json()['outbound_images']
- fp_out = (Path(where_out) / filename)
-
- self.assertTrue(fp_out.exists())
-
- acc_out = generate_file_accessor(fp_out)
+ acc_out = self.get_accessor(accessor_id=acc_id, filename='test_output.tif')
self.assertEqual(sd, acc_out.shape_dict)
\ No newline at end of file
diff --git a/tests/test_ilastik/test_ilastik.py b/tests/test_ilastik/test_ilastik.py
index 8a68a2cdbf471e387dc2d237ef12cbdd1e23cfc6..b6a6f851f6cb674e29b904470a28b0b4100f3966 100644
--- a/tests/test_ilastik/test_ilastik.py
+++ b/tests/test_ilastik/test_ilastik.py
@@ -15,7 +15,6 @@ data = conf.meta['image_files']
output_path = conf.meta['output_path']
params = conf.meta['roiset']
czifile = conf.meta['image_files']['czifile']
-cfn = czifile['name']
ilastik_classifiers = conf.meta['ilastik_classifiers']
def _random_int(*args):
@@ -200,13 +199,7 @@ class TestIlastikPixelClassification(unittest.TestCase):
class TestIlastikOverApi(conf.TestServerBaseClass):
- def _copy_input_file_to_server(self):
- resp = self._get('paths')
- pa = resp.json()['inbound_images']
- copyfile(
- czifile['path'],
- Path(pa) / czifile['name']
- )
+ input_data = czifile
def test_httpexception_if_incorrect_project_file_loaded(self):
resp_load = self._put(
@@ -304,9 +297,9 @@ class TestIlastikOverApi(conf.TestServerBaseClass):
return model_id
def test_ilastik_infer_pixel_probability(self):
- self._copy_input_file_to_server()
+ fname = self.copy_input_file_to_server()
model_id = self.test_load_ilastik_pixel_model()
- in_acc_id = self._put(f'accessors/read_from_file/{cfn}').json()
+ in_acc_id = self._put(f'accessors/read_from_file/{fname}').json()
resp_infer = self._put(
f'pipelines/segment',
@@ -316,11 +309,11 @@ class TestIlastikOverApi(conf.TestServerBaseClass):
def test_ilastik_infer_px_then_ob(self):
- self._copy_input_file_to_server()
+ fname = self.copy_input_file_to_server()
px_model_id = self.test_load_ilastik_pixel_model()
ob_model_id = self.test_load_ilastik_pxmap_to_obj_model()
- in_acc_id = self._put(f'accessors/read_from_file/{cfn}').json()
+ in_acc_id = self._put(f'accessors/read_from_file/{fname}').json()
resp_infer = self._put(
'ilastik/pipelines/pixel_then_object_classification/infer/',
@@ -430,11 +423,7 @@ class TestIlastikOnMultichannelInputs(conf.TestServerBaseClass):
# save output object map to file and compare
obmap_id = resp_infer.json()['output_accessor_id']
- obmap_fn = self._put(f'/accessors/write_to_file/{obmap_id}').json()
- where_out = self._get('paths').json()['outbound_images']
- obmap_fp = Path(where_out) / obmap_fn
- self.assertTrue(obmap_fp.exists())
- obmap_acc = generate_file_accessor(obmap_fp)
+ obmap_acc = self.get_accessor(obmap_id)
self.assertEqual(obmap_acc.shape_dict['C'], 1)
# compare dimensions to input image