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Adds verify SSL option #10

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merged 3 commits into from
Jun 12, 2024
Merged

Adds verify SSL option #10

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0593655
deleted transfer command
tclose Jun 12, 2024
5b951d1
added verify-ssl option to upload tool
tclose Jun 12, 2024
9881ea4
strip 'v' from docker tag in ci-cd
tclose Jun 12, 2024
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1 change: 1 addition & 0 deletions .github/workflows/ci-cd.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -103,6 +103,7 @@ jobs:
id: versions
run: |
VERSION=$(git describe --tags --abbrev=0)
VERSION=${VERSION#v}
IMAGE=${{ env.REGISTRY }}/$(echo "${{ env.IMAGE_NAME }}" | awk '{print tolower($0)}')
echo "IMAGE=$IMAGE" >> $GITHUB_OUTPUT
echo "TAG=$IMAGE:$VERSION" >> $GITHUB_OUTPUT
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4 changes: 2 additions & 2 deletions pyproject.toml
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Expand Up @@ -17,7 +17,7 @@ dependencies = [
"paramiko",
"xnat",
"arcana",
"arcana-xnat",
"arcana-xnat >=0.4.1",
]
license = { file = "LICENSE" }
authors = [{ name = "Thomas G. Close", email = "[email protected]" }]
Expand Down Expand Up @@ -47,7 +47,7 @@ dev = ["black", "pre-commit", "codespell", "flake8", "flake8-pyproject"]
test = [
"pytest >=6.2.5",
"pytest-env>=0.6.2",
"pytest-cov>=2.12.1",
"pytest-cov>=2.12.1",
"xnat4tests >=0.3",
"medimages4tests >=0.3.1",
"PyYAML",
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1 change: 0 additions & 1 deletion xnat_ingest/cli/__init__.py
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@@ -1,4 +1,3 @@
from .base import cli
from .upload import upload
from .stage import stage
from .transfer import transfer
273 changes: 0 additions & 273 deletions xnat_ingest/cli/transfer.py
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14 changes: 13 additions & 1 deletion xnat_ingest/cli/upload.py
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Expand Up @@ -154,6 +154,13 @@
default=0,
help="The number of days to keep files in the remote store for",
)
@click.option(
"--verify-ssl/--dont-verify-ssl",
type=bool,
default=False,
envvar="XNAT_INGEST_UPLOAD_VERIFY_SSL",
help="Whether to verify the SSL certificate of the XNAT server",
)
def upload(
staged: str,
server: str,
Expand All @@ -170,6 +177,7 @@ def upload(
temp_dir: ty.Optional[Path],
use_manifest: bool,
clean_up_older_than: int,
verify_ssl: bool,
):

set_logger_handling(
Expand All @@ -182,7 +190,11 @@ def upload(
tempfile.tempdir = str(temp_dir)

xnat_repo = Xnat(
server=server, user=user, password=password, cache_dir=Path(tempfile.mkdtemp())
server=server,
user=user,
password=password,
cache_dir=Path(tempfile.mkdtemp()),
verify_ssl=verify_ssl,
)

with xnat_repo.connection:
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