diff --git a/model_server/base/api.py b/model_server/base/api.py
index 1d51cc04fbd964e8f082aa59889dffa10f41811e..db484d0f879d4717ceb1ebe40b6920383c222520 100644
--- a/model_server/base/api.py
+++ b/model_server/base/api.py
@@ -4,18 +4,11 @@ from fastapi import FastAPI, HTTPException
from .accessors import generate_file_accessor
from .session import session, AccessorIdError, InvalidPathError, WriteAccessorError
-app = FastAPI(debug=True)
-
-# TODO: automate all this
-import model_server.extensions.ilastik.router
-app.include_router(model_server.extensions.ilastik.router.router)
-
-import model_server.base.pipelines.segment
-app.include_router(model_server.base.pipelines.segment.router)
+app = FastAPI(debug=True)
-import model_server.base.pipelines.roiset_obmap
-app.include_router(model_server.base.pipelines.roiset_obmap.router)
+from .pipelines.router import router
+app.include_router(router)
@app.on_event("startup")
diff --git a/model_server/base/pipelines/__init__.py b/model_server/base/pipelines/__init__.py
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..537a687dd8ff464c5584804da871167ef202993e 100644
--- a/model_server/base/pipelines/__init__.py
+++ b/model_server/base/pipelines/__init__.py
@@ -0,0 +1 @@
+__all__ = ['roiset_obmap', 'segment', 'segment_zproj']
\ No newline at end of file
diff --git a/model_server/base/pipelines/roiset_obmap.py b/model_server/base/pipelines/roiset_obmap.py
index 24f88601afeb3a9a969452a402da762870f7db1d..c4991aa3e6ef27382e450a44aa22b44106a728ef 100644
--- a/model_server/base/pipelines/roiset_obmap.py
+++ b/model_server/base/pipelines/roiset_obmap.py
@@ -1,11 +1,11 @@
from typing import Dict, Union
-from fastapi import APIRouter
from pydantic import BaseModel, Field
from ..accessors import GenericImageDataAccessor
-from ..pipelines.segment_zproj import segment_zproj_pipeline
-from ..pipelines.shared import call_pipeline
+from .router import router
+from .segment_zproj import segment_zproj_pipeline
+from .shared import call_pipeline
from ..roiset import get_label_ids, RoiSet, RoiSetMetaParams, RoiSetExportParams
from ..session import session
@@ -13,10 +13,6 @@ from ..pipelines.shared import PipelineTrace, PipelineParams, PipelineRecord
from ..models import Model, InstanceSegmentationModel
-router = APIRouter(
- prefix='/pipelines',
- tags=['pipelines'],
-)
class RoiSetObjectMapParams(PipelineParams):
class _SegmentationParams(BaseModel):
diff --git a/model_server/base/pipelines/router.py b/model_server/base/pipelines/router.py
new file mode 100644
index 0000000000000000000000000000000000000000..3f77fd1d86e09bfc2600bedb0452454620f519e5
--- /dev/null
+++ b/model_server/base/pipelines/router.py
@@ -0,0 +1,9 @@
+from fastapi import APIRouter
+
+router = APIRouter(
+ prefix='/pipelines',
+ tags=['pipelines'],
+)
+
+# this completes routing in individual pipeline modules
+from . import *
\ No newline at end of file
diff --git a/model_server/base/pipelines/segment.py b/model_server/base/pipelines/segment.py
index 2e34c209b857ae6f2643b0a64d951327102c9e3c..fac1835111872ab563b71d6795982e170d52e61f 100644
--- a/model_server/base/pipelines/segment.py
+++ b/model_server/base/pipelines/segment.py
@@ -1,19 +1,13 @@
from typing import Dict
-from fastapi import APIRouter
-
from .shared import call_pipeline, IncompatibleModelsError, PipelineTrace, PipelineParams, PipelineRecord
from ..accessors import GenericImageDataAccessor
from ..models import Model, SemanticSegmentationModel
from ..process import smooth
+from .router import router
from pydantic import Field
-router = APIRouter(
- prefix='/pipelines',
- tags=['pipelines'],
-)
-
class SegmentParams(PipelineParams):
accessor_id: str = Field(description='ID(s) of previously loaded accessor(s) to use as pipeline input')
diff --git a/model_server/base/pipelines/segment_zproj.py b/model_server/base/pipelines/segment_zproj.py
index 1314fbb483abf31c6f0e8d83f39850c9e5d7ca76..5f5ed9ba755433ef8445198b80885412e2161d98 100644
--- a/model_server/base/pipelines/segment_zproj.py
+++ b/model_server/base/pipelines/segment_zproj.py
@@ -1,7 +1,6 @@
from typing import Dict
-from fastapi import APIRouter
-
+from .router import router
from .segment import SegmentParams, SegmentRecord, segment_pipeline
from .shared import call_pipeline, PipelineTrace
from ..accessors import GenericImageDataAccessor
@@ -9,12 +8,6 @@ from ..models import Model
from pydantic import Field
-router = APIRouter(
- prefix='/pipelines',
- tags=['pipelines'],
-)
-
-
class SegmentZStackParams(SegmentParams):
zi: int = Field(None, description='z coordinate to use on input stack; apply MIP if empty')
diff --git a/tests/base/test_api.py b/tests/base/test_api.py
index 7f692af23e42651fed96b0714a9b4798f7b5c412..a6aad378e4f8a875573afbcc88308f55a0f8573c 100644
--- a/tests/base/test_api.py
+++ b/tests/base/test_api.py
@@ -1,11 +1,11 @@
from pathlib import Path
-from fastapi import APIRouter
+from fastapi import APIRouter, FastAPI
import numpy as np
from pydantic import BaseModel
import model_server.conf.testing as conf
-from model_server.base.accessors import InMemoryDataAccessor, generate_file_accessor
+from model_server.base.accessors import InMemoryDataAccessor
from model_server.base.api import app
from model_server.base.session import session
from tests.base.test_model import DummyInstanceSegmentationModel, DummySemanticSegmentationModel
@@ -15,18 +15,17 @@ czifile = conf.meta['image_files']['czifile']
"""
Configure additional endpoints for testing
"""
-testing_app = app
-router = APIRouter(prefix='/testing', tags=['testing'])
+test_router = APIRouter(prefix='/testing', tags=['testing'])
class BounceBackParams(BaseModel):
par1: str
par2: list
-@router.put('/bounce_back')
+@test_router.put('/bounce_back')
def list_bounce_back(params: BounceBackParams):
return {'success': True, 'params': {'par1': params.par1, 'par2': params.par2}}
-@router.put('/accessors/dummy_accessor/load')
+@test_router.put('/accessors/dummy_accessor/load')
def load_dummy_accessor() -> str:
acc = InMemoryDataAccessor(
np.random.randint(
@@ -38,19 +37,19 @@ def load_dummy_accessor() -> str:
)
return session.add_accessor(acc)
-@router.put('/models/dummy_semantic/load/')
+@test_router.put('/models/dummy_semantic/load/')
def load_dummy_model() -> dict:
mid = session.load_model(DummySemanticSegmentationModel)
session.log_info(f'Loaded model {mid}')
return {'model_id': mid}
-@router.put('/models/dummy_instance/load/')
+@test_router.put('/models/dummy_instance/load/')
def load_dummy_model() -> dict:
mid = session.load_model(DummyInstanceSegmentationModel)
session.log_info(f'Loaded model {mid}')
return {'model_id': mid}
-app.include_router(router)
+app.include_router(test_router)
"""
Implement unit testing on extended base app
diff --git a/tests/test_ilastik/test_ilastik.py b/tests/test_ilastik/test_ilastik.py
index 9e2bbd3d42a4a0fdbf65b553852aa4b26cb94e91..e7744acb0c53e02353654602e7916b69de61679e 100644
--- a/tests/test_ilastik/test_ilastik.py
+++ b/tests/test_ilastik/test_ilastik.py
@@ -5,9 +5,11 @@ import unittest
import numpy as np
from model_server.base.accessors import CziImageFileAccessor, generate_file_accessor, InMemoryDataAccessor, PatchStack, write_accessor_data_to_file
+from model_server.base.api import app
from model_server.extensions.ilastik import models as ilm
from model_server.extensions.ilastik.pipelines import px_then_ob
-from model_server.base.roiset import get_label_ids, RoiSet, RoiSetMetaParams
+from model_server.extensions.ilastik.router import router
+from model_server.base.roiset import RoiSet, RoiSetMetaParams
from model_server.base.pipelines import segment
import model_server.conf.testing as conf
@@ -17,6 +19,8 @@ params = conf.meta['roiset']
czifile = conf.meta['image_files']['czifile']
ilastik_classifiers = conf.meta['ilastik_classifiers']
+app.include_router(router)
+
def _random_int(*args):
return np.random.randint(0, 2 ** 8, size=args, dtype='uint8')
@@ -197,10 +201,13 @@ class TestIlastikPixelClassification(unittest.TestCase):
)
self.assertGreater(res.times['inference'], 0.1)
-class TestIlastikOverApi(conf.TestServerBaseClass):
+class TestServerTestCase(conf.TestServerBaseClass):
+ app_name = 'tests.test_ilastik.test_ilastik:app'
input_data = czifile
+
+class TestIlastikOverApi(TestServerTestCase):
def test_httpexception_if_incorrect_project_file_loaded(self):
resp_load = self._put(
'ilastik/seg/load/',
@@ -327,7 +334,7 @@ class TestIlastikOverApi(conf.TestServerBaseClass):
self.assertEqual(resp_infer.status_code, 200, resp_infer.content.decode())
-class TestIlastikOnMultichannelInputs(conf.TestServerBaseClass):
+class TestIlastikOnMultichannelInputs(TestServerTestCase):
def setUp(self) -> None:
super(TestIlastikOnMultichannelInputs, self).setUp()
self.pa_px_classifier = ilastik_classifiers['px_color_zstack']['path']