diff --git a/svlt-core/requirements.yml b/svlt-core/requirements.yml
index 6d77a684b2e22a2e6557cdf5942822221453002a..dd0e6a21006fd99bb41d9c50f3ea8e6ecadf5a55 100644
--- a/svlt-core/requirements.yml
+++ b/svlt-core/requirements.yml
@@ -11,9 +11,8 @@ dependencies:
- pandas
- pillow
- pip
- - pydantic=1.10.*
+ - pydantic=2.*
- python=3.9.*
- - pytorch=1.*
- scikit-image>=0.21.0
- tifffile
- uvicorn>=0.23.0
diff --git a/svlt-core/src/svlt/api.py b/svlt-core/src/svlt/api.py
index f257069f5ffb8ede27d8262a6d4ef98180f5a6b0..ff7768b8399ce79759c5867b552851a5ac671ba6 100644
--- a/svlt-core/src/svlt/api.py
+++ b/svlt-core/src/svlt/api.py
@@ -7,7 +7,7 @@ from pydantic import BaseModel, Field
from .accessors import generate_file_accessor, generate_multiposition_file_accessors
from .models import BinaryThresholdSegmentationModel
-from .pipelines.common import PipelineRecord
+from .pipelines.common import PipelineParams, PipelineRecord
from .session import session, AccessorIdError, InvalidPathError, WriteAccessorError
app = FastAPI(debug=True)
@@ -185,12 +185,12 @@ def read_multiposition_from_file(filename: str, lazy: bool = False) -> List[str]
class TaskInfo(BaseModel):
module: str
- params: dict
+ params: PipelineParams
func_str: str
status: str
target: Union[str, None]
error: Union[str, None]
- result: Union[Dict, None]
+ result: Union[PipelineRecord, None]
@app.put('/tasks/run_all')
def run_all_tasks(write_all: bool = False) -> List[PipelineRecord]:
diff --git a/svlt-core/src/svlt/conf/testing.py b/svlt-core/src/svlt/conf/testing.py
index da11763dcf2042970e0bf6b1e62af50cfd27d1dd..a1e233acf1059cbec0c0520013e63f41275984d2 100644
--- a/svlt-core/src/svlt/conf/testing.py
+++ b/svlt-core/src/svlt/conf/testing.py
@@ -4,7 +4,10 @@ import unittest
from math import floor
from multiprocessing import Process
from pathlib import Path
+import requests
+from requests.adapters import HTTPAdapter
from shutil import copyfile
+from urllib3 import Retry
from fastapi import APIRouter
import numpy as np
@@ -98,8 +101,19 @@ class TestServerBaseClass(unittest.TestCase):
daemon=True
)
self.server_process.start()
+ sesh = requests.Session()
+ retries = Retry(
+ total=10,
+ backoff_factor=0.5,
+ )
+ sesh.mount('http://', requests.adapters.HTTPAdapter(max_retries=retries))
+ resp = sesh.get(f'http://{host}:{int(port):04d}/' + 'status')
+ assert resp.status_code == 200
+
self.client = HttpClient(host=host, port=port)
+
+
def assertGetSuccess(self, endpoint):
resp = self.client.get(endpoint)
self.assertEqual(resp.status_code, 200, resp.text)
diff --git a/svlt-core/src/svlt/pipelines/common.py b/svlt-core/src/svlt/pipelines/common.py
index 63ffb9255a87f9a2bb5accc4620a936f9c24a247..c4638266c4e7677d5563794600117fedd8038d82 100644
--- a/svlt-core/src/svlt/pipelines/common.py
+++ b/svlt-core/src/svlt/pipelines/common.py
@@ -4,7 +4,7 @@ from time import perf_counter
from typing import Dict, List, Union
from fastapi import HTTPException
-from pydantic import BaseModel, Field, root_validator
+from pydantic import ConfigDict, BaseModel, Field, model_validator
from ..accessors import GenericImageDataAccessor, InMemoryDataAccessor
from ..session import session, AccessorIdError
@@ -15,31 +15,32 @@ class PipelineParams(BaseModel):
keep_interm: bool = Field(False, description='Keep accessors to intermediate images in session')
api: bool = Field(True, description='Validate parameters against server session and map HTTP errors if True')
calling_task_id: Union[str, None] = Field(None, description='ID of the task that calls pipeline function')
+ model_config = ConfigDict(protected_namespaces = ())
- @root_validator(pre=False)
- def models_are_loaded(cls, dd):
- for k, v in dd.items():
- if dd['api'] and k.endswith('model_id') and v is not None:
+ @model_validator(mode='after')
+ def models_are_loaded(self):
+ for k, v in self.model_dump().items():
+ if self.api and k.endswith('model_id') and v is not None:
if v not in session.describe_loaded_models().keys():
raise HTTPException(status_code=409, detail=f'Model with {k} = {v} has not been loaded')
- return dd
+ return self
- @root_validator(pre=False)
- def accessors_are_loaded(cls, dd):
- for k, v in dd.items():
- if dd['api'] and k.endswith('accessor_id'):
+ @model_validator(mode='after')
+ def accessors_are_loaded(self):
+ for k, v in self.model_dump().items():
+ if self.api and k.endswith('accessor_id'):
try:
info = session.get_accessor_info(v)
except AccessorIdError as e:
raise HTTPException(status_code=409, detail=str(e))
if not session.is_accessor_loaded(v):
raise HTTPException(status_code=409, detail=f'Accessor with {k} = {v} has not been loaded')
- return dd
+ return self
class PipelineRecord(BaseModel):
output_accessor_id: str
- interm_accessor_ids: Union[Dict[str, str], None]
+ interm_accessor_ids: Union[Dict[str, str], None] = None
success: bool
timer: dict
diff --git a/svlt-ilastik/requirements.yml b/svlt-ilastik/requirements.yml
index 17b48c72bea7451e62e98aad382a3899c3cc2335..8e0705392a16c1accf348ca1ce56628c996dd192 100644
--- a/svlt-ilastik/requirements.yml
+++ b/svlt-ilastik/requirements.yml
@@ -6,7 +6,7 @@ channels:
dependencies:
- czifile
- fastapi>=0.101
- - ilastik=1.4.1b6
+ - ilastik=1.4.1b23
- imagecodecs
- matplotlib
- nd2
@@ -14,10 +14,9 @@ dependencies:
- pandas
- pillow
- pip
- - protobuf ==4.25.3
- - pydantic=1.10.*
+ - pydantic=2.*
- python=3.9.*
- - pytorch=1.*
+ - pytorch
- scikit-image>=0.21.0
- scikit-learn>=1.5.0
- tifffile
diff --git a/svlt-pheno/requirements.yml b/svlt-pheno/requirements.yml
index 5100aeeed4cf7f7bc6d6e9c6e4e970d279827a97..1b2acfb77f204b82fbf29638c873b82df8c88671 100644
--- a/svlt-pheno/requirements.yml
+++ b/svlt-pheno/requirements.yml
@@ -11,7 +11,7 @@ dependencies:
- pandas
- pillow
- pip
- - pydantic=1.10.*
+ - pydantic=2.*
- python=3.9.*
- scikit-image>=0.21.0
- scikit-learn>=1.5.0