From ef31604c4d986dd8d9550490236979e92a13b945 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 25 Oct 2024 11:02:09 +0200
Subject: [PATCH] ilastik and pipeline tests now all use TestServer request
assertions
---
tests/test_ilastik/test_ilastik.py | 108 ++++++++-------------
tests/test_ilastik/test_roiset_workflow.py | 33 +++----
2 files changed, 57 insertions(+), 84 deletions(-)
diff --git a/tests/test_ilastik/test_ilastik.py b/tests/test_ilastik/test_ilastik.py
index 4e45dfb7..40ba7e0b 100644
--- a/tests/test_ilastik/test_ilastik.py
+++ b/tests/test_ilastik/test_ilastik.py
@@ -209,11 +209,11 @@ class TestServerTestCase(conf.TestServerBaseClass):
class TestIlastikOverApi(TestServerTestCase):
def test_httpexception_if_incorrect_project_file_loaded(self):
- resp_load = self.assertPutSuccess(
+ self.assertPutFailure(
'ilastik/seg/load/',
+ 500,
body={'project_file': 'improper.ilp'},
)
- self.assertEqual(resp_load.status_code, 500)
def test_load_ilastik_pixel_model(self):
@@ -226,21 +226,18 @@ class TestIlastikOverApi(TestServerTestCase):
return mid
def test_load_another_ilastik_pixel_model(self):
- model_id = self.test_load_ilastik_pixel_model()
- resp_list_1st = self.assertGetSuccess('models').json()
- self.assertEqual(len(resp_list_1st), 1, resp_list_1st)
- resp_load_2nd = self.assertPutSuccess(
+ self.test_load_ilastik_pixel_model()
+ self.assertEqual(len(self.assertGetSuccess('models')), 1)
+ self.assertPutSuccess(
'ilastik/seg/load/',
body={'project_file': str(ilastik_classifiers['px']['path']), 'duplicate': True},
)
- resp_list_2nd = self.assertGetSuccess('models').json()
- self.assertEqual(len(resp_list_2nd), 2, resp_list_2nd)
- resp_load_3rd = self.assertPutSuccess(
+ self.assertEqual(len(self.assertGetSuccess('models')), 2)
+ self.assertPutSuccess(
'ilastik/seg/load/',
body={'project_file': str(ilastik_classifiers['px']['path']), 'duplicate': False},
)
- resp_list_3rd = self.assertGetSuccess('models').json()
- self.assertEqual(len(resp_list_3rd), 2, resp_list_3rd)
+ self.assertEqual(len(self.assertGetSuccess('models')), 2)
def test_load_ilastik_pixel_model_with_params(self):
params = {
@@ -248,67 +245,55 @@ class TestIlastikOverApi(TestServerTestCase):
'px_class': 0,
'px_prob_threshold': 0.5
}
- resp_load = self.assertPutSuccess(
+ mid = self.assertPutSuccess(
'ilastik/seg/load/',
body=params,
- )
- self.assertEqual(resp_load.status_code, 200, resp_load.json())
- model_id = resp_load.json()['model_id']
- mods = self.assertGetSuccess('models').json()
+ )['model_id']
+ mods = self.assertGetSuccess('models')
self.assertEqual(len(mods), 1)
- self.assertEqual(mods[model_id]['params']['px_prob_threshold'], 0.5)
+ self.assertEqual(mods[mid]['params']['px_prob_threshold'], 0.5)
def test_load_ilastik_pxmap_to_obj_model(self):
- resp_load = self.assertPutSuccess(
+ mid = self.assertPutSuccess(
'ilastik/pxmap_to_obj/load/',
body={'project_file': str(ilastik_classifiers['pxmap_to_obj']['path'])},
- )
- model_id = resp_load.json()['model_id']
-
- self.assertEqual(resp_load.status_code, 200, resp_load.json())
- resp_list = self.assertGetSuccess('models')
- self.assertEqual(resp_list.status_code, 200)
- rj = resp_list.json()
- self.assertEqual(rj[model_id]['class'], 'IlastikObjectClassifierFromPixelPredictionsModel')
- return model_id
+ )['model_id']
+ rl = self.assertGetSuccess('models')
+ self.assertEqual(rl[mid]['class'], 'IlastikObjectClassifierFromPixelPredictionsModel')
+ return mid
def test_load_ilastik_model_with_model_id(self):
- mid = 'new_model_id'
- resp_load = self.assertPutSuccess(
+ nmid = 'new_model_id'
+ rmid = self.assertPutSuccess(
'ilastik/pxmap_to_obj/load/',
+ query={
+ 'model_id': nmid,
+ },
body={
'project_file': str(ilastik_classifiers['pxmap_to_obj']['path']),
- 'model_id': mid,
},
- )
- res_mid = resp_load.json()['model_id']
- self.assertEqual(res_mid, mid)
+ )['model_id']
+ self.assertEqual(rmid, nmid)
def test_load_ilastik_seg_to_obj_model(self):
- resp_load = self.assertPutSuccess(
+ mid = self.assertPutSuccess(
'ilastik/seg_to_obj/load/',
body={'project_file': str(ilastik_classifiers['seg_to_obj']['path'])},
- )
- model_id = resp_load.json()['model_id']
-
- self.assertEqual(resp_load.status_code, 200, resp_load.json())
- resp_list = self.assertGetSuccess('models')
- self.assertEqual(resp_list.status_code, 200)
- rj = resp_list.json()
- self.assertEqual(rj[model_id]['class'], 'IlastikObjectClassifierFromSegmentationModel')
- return model_id
+ )['model_id']
+ rl = self.assertGetSuccess('models')
+ self.assertEqual(rl[mid]['class'], 'IlastikObjectClassifierFromSegmentationModel')
+ return mid
def test_ilastik_infer_pixel_probability(self):
fname = self.copy_input_file_to_server()
- model_id = self.test_load_ilastik_pixel_model()
- in_acc_id = self.assertPutSuccess(f'accessors/read_from_file/{fname}').json()
+ mid = self.test_load_ilastik_pixel_model()
+ acc_id = self.assertPutSuccess(f'accessors/read_from_file/{fname}')
- resp_infer = self.assertPutSuccess(
+ self.assertPutSuccess(
f'pipelines/segment',
- body={'model_id': model_id, 'accessor_id': in_acc_id, 'channel': 0},
+ body={'model_id': mid, 'accessor_id': acc_id, 'channel': 0},
)
- self.assertEqual(resp_infer.status_code, 200, resp_infer.content.decode())
def test_ilastik_infer_px_then_ob(self):
@@ -316,9 +301,9 @@ class TestIlastikOverApi(TestServerTestCase):
px_model_id = self.test_load_ilastik_pixel_model()
ob_model_id = self.test_load_ilastik_pxmap_to_obj_model()
- in_acc_id = self.assertPutSuccess(f'accessors/read_from_file/{fname}').json()
+ in_acc_id = self.assertPutSuccess(f'accessors/read_from_file/{fname}')
- resp_infer = self.assertPutSuccess(
+ self.assertPutSuccess(
'ilastik/pipelines/pixel_then_object_classification/infer/',
body={
'px_model_id': px_model_id,
@@ -327,7 +312,6 @@ class TestIlastikOverApi(TestServerTestCase):
'channel': 0,
}
)
- self.assertEqual(resp_infer.status_code, 200, resp_infer.content.decode())
class TestIlastikOnMultichannelInputs(TestServerTestCase):
@@ -394,38 +378,32 @@ class TestIlastikOnMultichannelInputs(TestServerTestCase):
"""
copyfile(
self.pa_input_image,
- Path(self.assertGetSuccess('paths').json()['inbound_images']) / self.pa_input_image.name
+ Path(self.assertGetSuccess('paths')['inbound_images']) / self.pa_input_image.name
)
- in_acc_id = self.assertPutSuccess(f'accessors/read_from_file/{self.pa_input_image.name}').json()
+ in_acc_id = self.assertPutSuccess(f'accessors/read_from_file/{self.pa_input_image.name}')
- resp_load_px = self.assertPutSuccess(
+ px_model_id = self.assertPutSuccess(
'ilastik/seg/load/',
body={'project_file': str(self.pa_px_classifier)},
- )
- self.assertEqual(resp_load_px.status_code, 200, resp_load_px.json())
- px_model_id = resp_load_px.json()['model_id']
+ )['model_id']
- resp_load_ob = self.assertPutSuccess(
+ ob_model_id = self.assertPutSuccess(
'ilastik/pxmap_to_obj/load/',
body={'project_file': str(self.pa_ob_pxmap_classifier)},
- )
- self.assertEqual(resp_load_ob.status_code, 200, resp_load_ob.json())
- ob_model_id = resp_load_ob.json()['model_id']
+ )['model_id']
# run the pipeline
- resp_infer = self.assertPutSuccess(
+ obmap_id = self.assertPutSuccess(
'ilastik/pipelines/pixel_then_object_classification/infer/',
body={
'accessor_id': in_acc_id,
'px_model_id': px_model_id,
'ob_model_id': ob_model_id,
}
- )
- self.assertEqual(resp_infer.status_code, 200, resp_infer.content.decode())
+ )['output_accessor_id']
# save output object map to file and compare
- obmap_id = resp_infer.json()['output_accessor_id']
obmap_acc = self.get_accessor(obmap_id)
self.assertEqual(obmap_acc.shape_dict['C'], 1)
diff --git a/tests/test_ilastik/test_roiset_workflow.py b/tests/test_ilastik/test_roiset_workflow.py
index 1b824fee..5f799089 100644
--- a/tests/test_ilastik/test_roiset_workflow.py
+++ b/tests/test_ilastik/test_roiset_workflow.py
@@ -136,33 +136,30 @@ class TestRoiSetWorkflowOverApi(conf.TestServerBaseClass, BaseTestRoiSetMonoProd
return conf.TestServerBaseClass.setUp(self)
def test_trivial_api_response(self):
- resp = self.assertGetSuccess('')
- self.assertEqual(resp.status_code, 200)
+ self.assertGetSuccess('')
def test_load_input_accessor(self):
fname = self.copy_input_file_to_server()
- return self.assertPutSuccess(f'accessors/read_from_file/{fname}').json()
+ return self.assertPutSuccess(f'accessors/read_from_file/{fname}')
def test_load_pixel_classifier(self):
- resp = self.assertPutSuccess(
+ mid = self.assertPutSuccess(
'ilastik/seg/load/',
body={'project_file': self._get_models()['pixel_classifier_segmentation']['project_file']},
- )
- model_id = resp.json()['model_id']
- self.assertTrue(model_id.startswith('IlastikPixelClassifierModel'))
- return model_id
+ )['model_id']
+ self.assertTrue(mid.startswith('IlastikPixelClassifierModel'))
+ return mid
def test_load_object_classifier(self):
- resp = self.assertPutSuccess(
+ mid = self.assertPutSuccess(
'ilastik/seg_to_obj/load/',
body={'project_file': self._get_models()['object_classifier']['project_file']},
- )
- model_id = resp.json()['model_id']
- self.assertTrue(model_id.startswith('IlastikObjectClassifierFromSegmentationModel'))
- return model_id
+ )['model_id']
+ self.assertTrue(mid.startswith('IlastikObjectClassifierFromSegmentationModel'))
+ return mid
def _object_map_workflow(self, ob_classifer_id):
- resp = self.assertPutSuccess(
+ oid = self.assertPutSuccess(
'pipelines/roiset_to_obmap/infer',
body={
'accessor_id': self.test_load_input_accessor(),
@@ -173,11 +170,9 @@ class TestRoiSetWorkflowOverApi(conf.TestServerBaseClass, BaseTestRoiSetMonoProd
'roi_params': self._get_roi_params(),
'export_params': self._get_export_params(),
},
- )
- self.assertEqual(resp.status_code, 200, resp.json())
- oid = resp.json()['output_accessor_id']
- obmap_fn = self.assertPutSuccess(f'/accessors/write_to_file/{oid}').json()
- where_out = self.assertGetSuccess('paths').json()['outbound_images']
+ )['output_accessor_id']
+ obmap_fn = self.assertPutSuccess(f'/accessors/write_to_file/{oid}')
+ where_out = self.assertGetSuccess('paths')['outbound_images']
obmap_fp = Path(where_out) / obmap_fn
self.assertTrue(obmap_fp.exists())
return generate_file_accessor(obmap_fp)
--
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