From 95c5c9fd4a2618c9d7642218dd7c1dfeb81019e5 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Tue, 5 Sep 2023 10:42:28 +0200
Subject: [PATCH] Reorganized default paths
---
api.py | 8 ++++++++
conf/defaults.py | 14 ++++++++++++++
conf/server.py | 21 ---------------------
model_server/ilastik.py | 4 ++--
model_server/session.py | 8 ++++----
tests/test_api.py | 11 ++++++++---
tests/test_ilastik.py | 1 -
7 files changed, 36 insertions(+), 31 deletions(-)
create mode 100644 conf/defaults.py
delete mode 100644 conf/server.py
diff --git a/api.py b/api.py
index e62758b0..ff82c044 100644
--- a/api.py
+++ b/api.py
@@ -22,6 +22,14 @@ def read_root():
def read_root(par1=None, par2=None):
return {'success': True, 'params': {'par1': par1, 'par2': par2}}
+@app.get('/paths')
+def list_session_paths():
+ pass
+
+@app.put('/paths/{path_id}')
+def set_path_id(path_id: str, abs_path: str):
+ pass
+
@app.get('/restart')
def restart_session() -> dict:
session.restart()
diff --git a/conf/defaults.py b/conf/defaults.py
new file mode 100644
index 00000000..c1761b7a
--- /dev/null
+++ b/conf/defaults.py
@@ -0,0 +1,14 @@
+from pathlib import Path
+
+root = Path('c:/Users/rhodes/projects/proj0015-model-server/resources')
+paths = {
+ 'logs': root / 'logs' / 'session',
+ 'inbound_images': root / 'images' / 'inbound',
+ 'outbound_images': root / 'images' / 'outbound',
+ 'ilastik_projects': root / 'ilastik',
+}
+
+for gk in paths.keys():
+ paths[gk].mkdir(parents=True, exist_ok=True)
+
+# TODO: consider configuring paths via API, and this just becomes a HTTP client script
\ No newline at end of file
diff --git a/conf/server.py b/conf/server.py
deleted file mode 100644
index 707b60ac..00000000
--- a/conf/server.py
+++ /dev/null
@@ -1,21 +0,0 @@
-from pathlib import Path
-
-root = Path('c:/Users/rhodes/projects/proj0015-model-server/resources')
-paths = {
- 'logs': {
- 'session': root / 'logs' / 'session',
- },
- 'images': {
- 'inbound': root / 'images' / 'inbound',
- 'outbound': root / 'images' / 'outbound',
- },
- 'ilastik': {
- 'projects': root / 'ilastik'
- }
-}
-
-for gk in paths.keys():
- for pk in paths[gk].keys():
- paths[gk][pk].mkdir(parents=True, exist_ok=True)
-
-# TODO: consider configuring paths via API, and this just becomes a HTTP client script
\ No newline at end of file
diff --git a/model_server/ilastik.py b/model_server/ilastik.py
index 54419f78..c4b876de 100644
--- a/model_server/ilastik.py
+++ b/model_server/ilastik.py
@@ -4,7 +4,7 @@ import pathlib
import numpy as np
import vigra
-import conf.server
+import conf.defaults
from model_server.image import GenericImageDataAccessor, InMemoryDataAccessor
from model_server.model import ImageToImageModel, ParameterExpectedError
@@ -14,7 +14,7 @@ class IlastikImageToImageModel(ImageToImageModel):
def __init__(self, params, autoload=True):
self.project_file = str(params['project_file'])
self.project_file_abspath = pathlib.Path(
- conf.server.paths['ilastik']['projects'] / self.project_file,
+ conf.defaults.paths['ilastik_projects'] / self.project_file,
)
if 'project_file' not in params or not self.project_file_abspath.exists():
raise ParameterExpectedError('Ilastik model expects a project (*.ilp) file')
diff --git a/model_server/session.py b/model_server/session.py
index 1a9b38b9..989fc1b3 100644
--- a/model_server/session.py
+++ b/model_server/session.py
@@ -5,7 +5,7 @@ from pathlib import Path
from time import strftime, localtime
from typing import Dict
-from conf.server import paths
+from conf.defaults import paths
from model_server.model import Model
from model_server.share import SharedImageDirectory
from model_server.workflow import WorkflowRunRecord
@@ -17,9 +17,9 @@ class Session(object):
"""
Singleton class for a server session that persists data between API calls
"""
- inbound = SharedImageDirectory(paths['images']['inbound'])
- outbound = SharedImageDirectory(paths['images']['outbound'])
- where_records = Path(paths['logs']['session'])
+ inbound = SharedImageDirectory(paths['inbound_images'])
+ outbound = SharedImageDirectory(paths['outbound_images'])
+ where_records = paths['logs']
def __new__(cls):
if not hasattr(cls, 'instance'):
diff --git a/tests/test_api.py b/tests/test_api.py
index b7835ffd..8c6c248b 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -22,11 +22,10 @@ class TestServerBaseClass(unittest.TestCase):
@staticmethod
def copy_input_file_to_server():
- import pathlib
from shutil import copyfile
- from conf.server import paths
+ from conf.defaults import paths
- outpath = pathlib.Path(paths['images']['inbound'] / czifile['filename'])
+ outpath = paths['inbound_images'] / czifile['filename']
copyfile(
czifile['path'],
@@ -47,6 +46,12 @@ class TestApiFromAutomatedClient(TestServerBaseClass):
self.assertEqual(resp.json()['params']['par1'], 'hello', resp.json())
self.assertEqual(resp.json()['params']['par2'], None, resp.json())
+ def test_default_session_paths(self):
+ import conf.defaults
+ resp = requests.get(self.uri + 'paths')
+ for p in ['inbound', 'outbound', 'logs']:
+ self.assertEqual(resp.json()['paths'][p], conf.defaults.paths[p])
+
def test_list_empty_loaded_models(self):
resp = requests.get(self.uri + 'models')
self.assertEqual(resp.status_code, 200)
diff --git a/tests/test_ilastik.py b/tests/test_ilastik.py
index 204ad237..fba595e1 100644
--- a/tests/test_ilastik.py
+++ b/tests/test_ilastik.py
@@ -6,7 +6,6 @@ import numpy as np
import conf.testing
from model_server.image import CziImageFileAccessor, InMemoryDataAccessor, write_accessor_data_to_file
from model_server.ilastik import IlastikObjectClassifierModel, IlastikPixelClassifierModel
-from model_server.model import Model
from model_server.workflow import infer_image_to_image
from tests.test_api import TestServerBaseClass
--
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