From b0133570fedfff2a38488ca974a36bd20e929999 Mon Sep 17 00:00:00 2001
From: David Lougheed <david.lougheed@gmail.com>
Date: Wed, 10 Apr 2024 14:52:33 -0400
Subject: [PATCH 1/4] fix: write temp file uploads (during upload) to ingest
 tmp dir

---
 chord_drs/app.py     |  2 ++
 chord_drs/request.py | 18 ++++++++++++++++++
 2 files changed, 20 insertions(+)
 create mode 100644 chord_drs/request.py

diff --git a/chord_drs/app.py b/chord_drs/app.py
index e41bad7..1e2c112 100644
--- a/chord_drs/app.py
+++ b/chord_drs/app.py
@@ -13,6 +13,7 @@
 from .constants import SERVICE_NAME
 from .db import db
 from .metrics import metrics
+from .request import DrsRequest
 from .routes import drs_service
 
 
@@ -20,6 +21,7 @@
 
 application = Flask(__name__)
 application.config.from_object(Config)
+application.request_class = DrsRequest
 
 # Set up CORS
 CORS(
diff --git a/chord_drs/request.py b/chord_drs/request.py
new file mode 100644
index 0000000..e6e7cc4
--- /dev/null
+++ b/chord_drs/request.py
@@ -0,0 +1,18 @@
+from flask import Request, current_app
+from tempfile import SpooledTemporaryFile
+from typing import Optional
+
+__all__ = ["DrsRequest"]
+
+MAX_IN_MEMORY_SIZE = 1024 * 1024  # 1 MB
+
+
+class DrsRequest(Request):
+    def _get_file_stream(
+        self,
+        total_content_length: Optional[int],
+        content_type: Optional[str],
+        filename: Optional[str] = None,
+        content_length: Optional[int] = None,
+    ):
+        return SpooledTemporaryFile(max_size=MAX_IN_MEMORY_SIZE, dir=current_app.config["DRS_INGEST_TMP_DIR"])

From d3e16d5bf17ed2f2f37ffe0243d6cccbcaac8fab Mon Sep 17 00:00:00 2001
From: David Lougheed <david.lougheed@gmail.com>
Date: Wed, 10 Apr 2024 14:52:50 -0400
Subject: [PATCH 2/4] chore: bump version to 0.16.1 and update mako in lockfile

---
 poetry.lock    | 6 +++---
 pyproject.toml | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 711999c..9cde784 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1000,13 +1000,13 @@ referencing = ">=0.31.0"
 
 [[package]]
 name = "mako"
-version = "1.3.2"
+version = "1.3.3"
 description = "A super-fast templating language that borrows the best ideas from the existing templating languages."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "Mako-1.3.2-py3-none-any.whl", hash = "sha256:32a99d70754dfce237019d17ffe4a282d2d3351b9c476e90d8a60e63f133b80c"},
-    {file = "Mako-1.3.2.tar.gz", hash = "sha256:2a0c8ad7f6274271b3bb7467dd37cf9cc6dab4bc19cb69a4ef10669402de698e"},
+    {file = "Mako-1.3.3-py3-none-any.whl", hash = "sha256:5324b88089a8978bf76d1629774fcc2f1c07b82acdf00f4c5dd8ceadfffc4b40"},
+    {file = "Mako-1.3.3.tar.gz", hash = "sha256:e16c01d9ab9c11f7290eef1cfefc093fb5a45ee4a3da09e2fec2e4d1bae54e73"},
 ]
 
 [package.dependencies]
diff --git a/pyproject.toml b/pyproject.toml
index 14e20ea..a9a4dc5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "chord-drs"
-version = "0.16.0"
+version = "0.16.1"
 description = "An implementation of a data repository system (as per GA4GH's specs) for the Bento platform."
 authors = ["David Lougheed <david.lougheed@mail.mcgill.ca>"]
 license = "LGPL-3.0"

From 0fb274450eeac3588415abc89d99a82eff32643b Mon Sep 17 00:00:00 2001
From: David Lougheed <david.lougheed@gmail.com>
Date: Fri, 12 Apr 2024 11:39:01 -0400
Subject: [PATCH 3/4] lint: type hint

---
 chord_drs/request.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/chord_drs/request.py b/chord_drs/request.py
index e6e7cc4..7a5e88c 100644
--- a/chord_drs/request.py
+++ b/chord_drs/request.py
@@ -1,6 +1,6 @@
 from flask import Request, current_app
 from tempfile import SpooledTemporaryFile
-from typing import Optional
+from typing import IO, Optional
 
 __all__ = ["DrsRequest"]
 
@@ -14,5 +14,5 @@ def _get_file_stream(
         content_type: Optional[str],
         filename: Optional[str] = None,
         content_length: Optional[int] = None,
-    ):
+    ) -> IO[bytes]:
         return SpooledTemporaryFile(max_size=MAX_IN_MEMORY_SIZE, dir=current_app.config["DRS_INGEST_TMP_DIR"])

From e362895381fb43502e8018779d038fe6fb12b421 Mon Sep 17 00:00:00 2001
From: David Lougheed <david.lougheed@gmail.com>
Date: Fri, 12 Apr 2024 11:39:10 -0400
Subject: [PATCH 4/4] chore: add ingest debug log for temp path

---
 chord_drs/routes.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/chord_drs/routes.py b/chord_drs/routes.py
index ef7b97c..5bdfa03 100644
--- a/chord_drs/routes.py
+++ b/chord_drs/routes.py
@@ -449,6 +449,7 @@ def object_ingest():
         filename: str | None = None  # no override, use path filename if path is specified instead of a file upload
         if file is not None:
             logger.debug(f"ingest - received file object: {file}")
+            logger.debug(f"ingest - writing to temporary path: {t_obj_path}")
             file.save(t_obj_path)
             obj_path = t_obj_path
             filename = file.filename  # still may be none, in which case the temporary filename will be used