Merge pull request #87 from girder/upload-left-atrium

MedVIC-Lab · Jun 7, 2021 · 9378e7d · 9378e7d
2 parents e3f052c + 76d7a1c
commit 9378e7d
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Showing 3 changed files with 1,146 additions and 167 deletions.
diff --git a/swcc/swcc/api.py b/swcc/swcc/api.py
@@ -6,6 +6,7 @@
 import requests
 from requests_toolbelt.sessions import BaseUrlSession
 from s3_file_field_client import S3FileFieldClient
+from urllib3.util.retry import Retry
 
 from . import __version__
 
@@ -41,6 +42,10 @@ def __init__(
         base_url = f'{base_url.rstrip("/")}/'  # tolerate input with or without trailing slash
         super().__init__(base_url=base_url, **kwargs)
 
+        retry = Retry()
+        adapter = requests.adapters.HTTPAdapter(max_retries=retry)
+        self.mount(base_url, adapter)
+
         self.headers.update(
             {
                 'User-agent': f'swcc/{__version__}',

diff --git a/swcc/swcc/models.py b/swcc/swcc/models.py
@@ -2,6 +2,7 @@
 
 from pathlib import Path
 from typing import Any, Dict, Generic, Iterator, Literal, Optional, Type, TypeVar, Union, get_args
+from urllib.parse import unquote
 
 from pydantic import (
     AnyHttpUrl,
@@ -98,8 +99,6 @@ def upload(self):
         return self.field_value
 
     def download(self, path: Union[Path, str]) -> Path:
-        session = current_session()
-
         if self.url is None:
             raise Exception('Cannot download a local file')
 
@@ -114,14 +113,24 @@ def download(self, path: Union[Path, str]) -> Path:
             path.mkdir(parents=True, exist_ok=True)
 
         path = path / self.url.path.split('/')[-1]
-        r = session.get(self.url, stream=True)
+        r = requests.get(self.url, stream=True)
         raise_for_status(r)
 
         with path.open('wb') as f:
             for chunk in r.iter_content(chunk_size=8192):
                 f.write(chunk)
         return path
 
+    @property
+    def name(self) -> str:
+        if self.path:
+            return self.path.name
+        elif self.url:
+            if self.url.path is None:
+                raise Exception('Invalid file url')
+            return unquote(self.url.path.split('/')[-1])
+        raise Exception('Invalid file object')
+
 
 ModelType = TypeVar('ModelType', bound='ApiModel')
 
@@ -285,16 +294,16 @@ def add_groomed_segmentation(
         self,
         file: Path,
         segmentation: Segmentation,
-        pre_cropping: Optional[Path],
-        pre_alignment: Optional[Path],
+        pre_cropping: Optional[Path] = None,
+        pre_alignment: Optional[Path] = None,
     ) -> GroomedSegmentation:
         return GroomedSegmentation(
             file=file,
             segmentation=segmentation,
             project=self,
             pre_cropping=pre_cropping,
             pre_alignment=pre_alignment,
-        )
+        ).create()
 
     @property
     def shape_models(self) -> Iterator[OptimizedShapeModel]:
@@ -312,8 +321,8 @@ class GroomedSegmentation(ApiModel):
     _endpoint = 'groomed-segmentations'
 
     file: FileType[Literal['core.GroomedSegmentation.file']]
-    pre_cropping: Optional[FileType[Literal['core.GroomedSegmentation.pre_cropping']]]
-    pre_alignment: Optional[FileType[Literal['core.GroomedSegmentation.pre_alignment']]]
+    pre_cropping: Optional[FileType[Literal['core.GroomedSegmentation.pre_cropping']]] = None
+    pre_alignment: Optional[FileType[Literal['core.GroomedSegmentation.pre_alignment']]] = None
 
     segmentation: Segmentation
     project: Project