Merge pull request #289 from AIM-Harvard/#270

IDC supports local download
AIM-Harvard · Mar 8, 2024 · 469d455 · 469d455
2 parents 15dec3b + 70d745f
commit 469d455
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Showing 4 changed files with 25 additions and 18 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -1,13 +1,19 @@
 name: build
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
 
 jobs:
   build:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9"]
+        python-version: ["3.9", "3.10"]
 
     steps:
     - uses: actions/checkout@v2

diff --git a/fmcib/utils/idc_helper.py b/fmcib/utils/idc_helper.py
@@ -95,7 +95,7 @@ def download_from_manifest(df, save_dir, samples):
         None
     """
     # Instantiates a client
-    storage_client = storage.Client()
+    storage_client = storage.Client.create_anonymous_client()
     logger.info("Downloading DICOM data from IDC (Imaging Data Commons) ...")
     (save_dir / "dicom").mkdir(exist_ok=True, parents=True)
 

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -59,7 +59,7 @@ mpmath = "1.3.0"
 
 [tool.poetry.group.dev.dependencies]
 black = "^23.7.0"
-bandit = "^1.7.1"
+bandit = "^1.7.7"
 isort = {extras = ["colors"], version = "^5.10.1"}
 mypy = "^0.910"
 mypy-extensions = "^0.4.3"
@@ -73,6 +73,7 @@ coverage = "^6.1.2"
 coverage-badge = "^1.1.0"
 pytest-html = "^3.1.1"
 pytest-cov = "^3.0.0"
+aiohttp = "^3.9.3"
 
 [tool.black]
 # https://github.com/psf/black