Adding timeout to the http client (#54)

* template updates

* dependency updates

* add timeout to http client

* version bump

.pyproject_generation/pyproject_custom.toml

@@ -1,12 +1,12 @@
 [project]
 name = "ghga_datasteward_kit"
-version = "4.0.0"
+version = "4.0.1"
 description = "GHGA Data Steward Kit - A utils package for GHGA data stewards."
 dependencies = [
     "crypt4gh >=1.6, <2",
     "hexkit[s3] >=3, <4",
     "ghga-transpiler >=2.1.2, <3",
-    "metldata~=2.0.0",
+    "metldata~=2.1.1",
 ]
 
 [project.urls]

.template/mandatory_files.txt

@@ -23,6 +23,7 @@ lock/requirements-dev.txt
 lock/requirements.txt
 
 Dockerfile
+Dockerfile.debian
 config_schema.json
 example_config.yaml
 LICENSE

.template/static_files_ignore.txt

@@ -4,6 +4,7 @@
 .github/workflows/check_config_docs.yaml
 .github/workflows/check_openapi_spec.yaml
 .github/workflows/check_readme.yaml
+.github/workflows/ci_release.yaml
 .readme_generation/readme_template.md
 .readme_generation/README.md
 scripts/update_config_docs.py

Dockerfile.debian

@@ -0,0 +1,48 @@
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# for the German Human Genome-Phenome Archive (GHGA)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+## creating building container
+FROM python:3.12-slim-bookworm AS builder
+# update and install dependencies
+RUN apt update
+RUN apt upgrade -y
+RUN pip install build
+# copy code
+COPY . /service
+WORKDIR /service
+# build wheel
+RUN python -m build
+
+# creating running container
+FROM python:3.12-slim-bookworm
+# update and install dependencies
+RUN apt update
+RUN apt upgrade -y
+# copy and install requirements and wheel
+WORKDIR /service
+COPY --from=builder /service/lock/requirements.txt /service
+RUN pip install --no-deps -r requirements.txt
+RUN rm requirements.txt
+COPY --from=builder /service/dist/ /service
+RUN pip install --no-deps *.whl
+RUN rm *.whl
+# create new user and execute as that user
+RUN useradd --create-home appuser
+WORKDIR /home/appuser
+USER appuser
+# set environment
+ENV PYTHONUNBUFFERED=1
+# Please adapt to package name:
+ENTRYPOINT ["my-microservice"]

lock/requirements-dev.txt

@@ -518,9 +518,9 @@ hbreader==0.9.1 \
     #   jsonasobj2
     #   linkml
     #   linkml-runtime
-hexkit==3.4.0 \
-    --hash=sha256:3f87d76d746a9e506d458eb729374a8b2facc04f4b40307a2db3b970a8ee4713 \
-    --hash=sha256:a02f086de15858b8c72852d022c63ffcec555c24cd30b2f6628f0d41fd2fd88a
+hexkit==3.5.0 \
+    --hash=sha256:30a82d170630a615836d6a42116f10a2052a9ae752137419f6abe1286a113a32 \
+    --hash=sha256:b27599809b94f24e87153667afd9a72f46c46d267c06cafc595d40cdc6c53f89
     # via
     #   ghga-datasteward-kit (pyproject.toml)
     #   ghga-service-commons
@@ -760,9 +760,9 @@ mdurl==0.1.2 \
     --hash=sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8 \
     --hash=sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba
     # via markdown-it-py
-metldata==2.0.0 \
-    --hash=sha256:a89c4408681c8f798a4d252187569cc98abbe7e4104bf64092bfca4f5978217b \
-    --hash=sha256:b5bf87619ee2b7c9665c1852ad9f0190db5ac4daada97017c7b19ebad4501aa0
+metldata==2.1.1 \
+    --hash=sha256:32e0f509186aee26fee0c5b6ee6c650e4affcae6224888457a8af4a2adbf495a \
+    --hash=sha256:e1dd6be9b589dc2289ae3f9d603738c42092e243ad108f1007f17441ff89e990
     # via ghga-datasteward-kit (pyproject.toml)
 motor==3.5.1 \
     --hash=sha256:1622bd7b39c3e6375607c14736f6e1d498128eadf6f5f93f8786cf17d37062ac \

lock/requirements.txt

@@ -503,9 +503,9 @@ hbreader==0.9.1 \
     #   jsonasobj2
     #   linkml
     #   linkml-runtime
-hexkit==3.4.0 \
-    --hash=sha256:3f87d76d746a9e506d458eb729374a8b2facc04f4b40307a2db3b970a8ee4713 \
-    --hash=sha256:a02f086de15858b8c72852d022c63ffcec555c24cd30b2f6628f0d41fd2fd88a
+hexkit==3.5.0 \
+    --hash=sha256:30a82d170630a615836d6a42116f10a2052a9ae752137419f6abe1286a113a32 \
+    --hash=sha256:b27599809b94f24e87153667afd9a72f46c46d267c06cafc595d40cdc6c53f89
     # via
     #   -c lock/requirements-dev.txt
     #   ghga-datasteward-kit (pyproject.toml)
@@ -771,9 +771,9 @@ mdurl==0.1.2 \
     # via
     #   -c lock/requirements-dev.txt
     #   markdown-it-py
-metldata==2.0.0 \
-    --hash=sha256:a89c4408681c8f798a4d252187569cc98abbe7e4104bf64092bfca4f5978217b \
-    --hash=sha256:b5bf87619ee2b7c9665c1852ad9f0190db5ac4daada97017c7b19ebad4501aa0
+metldata==2.1.1 \
+    --hash=sha256:32e0f509186aee26fee0c5b6ee6c650e4affcae6224888457a8af4a2adbf495a \
+    --hash=sha256:e1dd6be9b589dc2289ae3f9d603738c42092e243ad108f1007f17441ff89e990
     # via
     #   -c lock/requirements-dev.txt
     #   ghga-datasteward-kit (pyproject.toml)

pyproject.toml

@@ -21,13 +21,13 @@ classifiers = [
     "Intended Audience :: Developers",
 ]
 name = "ghga_datasteward_kit"
-version = "4.0.0"
+version = "4.0.1"
 description = "GHGA Data Steward Kit - A utils package for GHGA data stewards."
 dependencies = [
     "crypt4gh >=1.6, <2",
     "hexkit[s3] >=3, <4",
     "ghga-transpiler >=2.1.2, <3",
-    "metldata~=2.0.0",
+    "metldata~=2.1.1",
 ]
 
 [project.license]

src/ghga_datasteward_kit/s3_upload/downloader.py

@@ -63,7 +63,7 @@ def _download_parts(self, download_url):
             LOG.debug("Downloading part number %i. %s", part_no, headers)
             try:
                 with httpx_client() as client:
-                    response = client.get(download_url, timeout=60, headers=headers)
+                    response = client.get(download_url, headers=headers)
                     yield response.content
             except (
                 Exception,

src/ghga_datasteward_kit/s3_upload/entrypoint.py

@@ -110,10 +110,7 @@ async def exchange_secret_for_id(
     with httpx_client() as client:
         headers = {"Authorization": f"Bearer {token}"}
         response = client.post(
-            url=endpoint_url,
-            json=encrypted_secret.model_dump(),
-            headers=headers,
-            timeout=60,
+            url=endpoint_url, json=encrypted_secret.model_dump(), headers=headers
         )
 
         if response.status_code != 200:

src/ghga_datasteward_kit/s3_upload/utils.py

@@ -31,14 +31,15 @@
 LOG = logging.getLogger("s3_upload")
 NUM_RETRIES = 5
 PART_SIZE = 16 * 1024**2
+TIMEOUT = 60
 
 
 @contextmanager
 def httpx_client():
     """Yields a context manager httpx client and closes it afterward"""
     transport = httpx.HTTPTransport(retries=NUM_RETRIES)
 
-    with httpx.Client(transport=transport) as client:
+    with httpx.Client(transport=transport, timeout=TIMEOUT) as client:
         yield client