grz-cli 0.6.0__tar.gz → 0.7.0__tar.gz

grz_cli-0.7.0/.gitignore

@@ -0,0 +1,195 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore

grz_cli-0.7.0/CHANGELOG.md

@@ -0,0 +1,8 @@
+# Changelog
+
+## [0.7.0](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v0.6.1...grz-cli-v0.7.0) (2025-06-11)
+
+
+### Features
+
+* migrate to monorepo configuration ([36c7360](https://github.com/BfArM-MVH/grz-tools/commit/36c736044ce09473cc664b4471117465c5cab9a3))

grz_cli-0.6.0/README.md → grz_cli-0.7.0/PKG-INFO

@@ -1,3 +1,34 @@
+Metadata-Version: 2.4
+Name: grz-cli
+Version: 0.7.0
+Summary: Tool for validation, encryption and upload of MV submissions to GDCs.
+Project-URL: Homepage, https://github.com/BfArM-MVH/grz-tools
+Project-URL: Repository, https://github.com/BfArM-MVH/grz-tools
+Project-URL: Documentation, https://github.com/BfArM-MVH/grz-tools/tree/main/packages/grz-cli
+Project-URL: Issues, https://github.com/BfArM-MVH/grz-tools/issues
+Author-email: Koray Kirli <koraykirli@gmail.com>, Mathias Lesche <mathias.lesche@tu-dresden.de>, "Florian R. Hölzlwimmer" <git.ich@frhoelzlwimmer.de>, Till Hartmann <till.hartmann@bih-charite.de>, Thomas Sell <thomas.sell@bih-charite.de>, Travis Wrightsman <travis.wrightsman@uni-tuebingen.de>
+License-Expression: MIT
+License-File: LICENSE
+Keywords: GDC,GRZ,S3
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.12
+Requires-Dist: boto3<2,>=1.36
+Requires-Dist: click<9,>=8.1.7
+Requires-Dist: crypt4gh<2,>=1.7
+Requires-Dist: grz-common
+Requires-Dist: grz-pydantic-models>=1.3.0
+Requires-Dist: jsonschema<5,>=4.23.0
+Requires-Dist: platformdirs<5,>=4.3.6
+Requires-Dist: pydantic-settings<2.10,>=2.9.0
+Requires-Dist: pydantic<2.10,>=2.9.2
+Requires-Dist: pysam==0.23.*
+Requires-Dist: pyyaml<7,>=6.0.2
+Requires-Dist: requests<3,>=2.32.3
+Requires-Dist: rich==13.*
+Requires-Dist: tqdm<5,>=4.66.5
+Description-Content-Type: text/markdown
+
 # GRZ CLI
 
 A command-line tool for validating, encrypting, uploading and downloading submissions to/from a GDC/GRZ (Genomrechenzentrum).
@@ -8,10 +39,9 @@ A command-line tool for validating, encrypting, uploading and downloading submis
 - [Features](#features)
 - [Installation](#installation)
   - [Requirements](#requirements)
-  - [End-user setup](#end-user)
+  - [End-user setup](#end-user-setup)
     - [Installation via `conda` (recommended)](#installation-via-conda-recommended)
     - [Installation via `pip` (not recommended)](#installation-via-pip-not-recommended)
-  - [Development setup](#development-setup)
 - [Usage](#usage)
   - [Configuration](#configuration)
   - [Exemplary submission procedure](#exemplary-submission-procedure)
@@ -110,18 +140,6 @@ pip upgrade grz-cli
 Docker images are available via biocontainers at [https://biocontainers.pro/tools/grz-cli](https://biocontainers.pro/tools/grz-cli).
 
 
-### Development setup
-For development purposes, you can clone the repository and install the package in editable mode:
-
-```bash
-git clone https://codebase.helmholtz.cloud/grz-mv-genomseq/grz-cli
-# create conda environment and activate it
-conda env create -f grz-cli/environment-dev.yaml -n grz-tools-dev
-conda activate grz-tools-dev
-# install the grz-cli tool
-pip install -e grz-cli/
-```
-
 ## Usage
 
 ### Configuration
@@ -165,8 +183,6 @@ Example usage:
 grz_cli validate --submission-dir foo
 ```
 
-Option is for the usage at a hospital (Leistungserbringer) and GDC/GRZ.
-
 ### encrypt
 
 If a working directory is not provided, then the current directory is used automatically. The log-files are going to be stored in the sub-folder of the working directory.
@@ -179,21 +195,6 @@ Files are stored in a folder named `encrypted_files` as a sub-folder of the work
 grz-cli encrypt --submission-dir foo
 ```
 
-Option is for the usage at a hospital (Leistungserbringer). Please approach your GDC/GRZ for a valid config file.
-
-### decrypt
-
-Decrypt a submission using the GRZ private key.
-
-- `-s, --submission-dir`: Path to the submission directory containing both 'metadata/' and 'encrypted_files/' directories  [**Required**]
-- `-c,--config-file`: Path to config file [_optional_]
-
-```bash
-grz-cli decrypt --submission-dir foo
-```
-
-Option is for the usage at a GDC/GRZ.
-
 ### upload
 
 Upload the submission into a S3 structure of a GRZ.
@@ -207,24 +208,6 @@ Example usage:
 grz-cli upload --submission-dir foo
 ```
 
-Option is for the usage at a hospital (Leistungserbringer). Please approach your GDC/GRZ for a valid config file.
-
-### download
-
-Download a submission from a GRZ
-
-- `-s, --submission-id`: S3 submission prefix [**Required**]
-- `-o, --output-dir`: Path to the target submission output directory [**Required**]
-- `-c, --config-file`: Path to config file [_optional_]
-
-Example usage:
-
-```bash
-grz-cli download --submission-id foo --output-dir bar
-```
-
-Option is for the usage at a GDC/GRZ.
-
 ## Testing
 
 Please note that binary files used for testing are managed with [Git LFS](https://git-lfs.com), which will be needed to clone them locally with the git repository.
@@ -238,9 +221,9 @@ Alternatively, install `uv` and `tox` and run `uv run tox`.
 
 ## License
 
-This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+This project is licensed under the MIT License — see the [LICENSE](LICENSE) file for details.
 
 ## Acknowledgements
 
-Parts of `cryp4gh` code is used in modified form
+Parts of `crypt4gh` code is used in modified form
 

grz_cli-0.6.0/src/grz_cli.egg-info/PKG-INFO → grz_cli-0.7.0/README.md

@@ -1,40 +1,3 @@
-Metadata-Version: 2.4
-Name: grz-cli
-Version: 0.6.0
-Summary: Tool for validation, encryption and upload of MV submissions to GDCs.
-Author-email: Koray Kirli <koraykirli@gmail.com>, Mathias Lesche <mathias.lesche@tu-dresden.de>, "Florian R. Hölzlwimmer" <git.ich@frhoelzlwimmer.de>, Till Hartmann <till.hartmann@bih-charite.de>, Thomas Sell <thomas.sell@bih-charite.de>
-License-Expression: MIT
-Project-URL: Homepage, https://codebase.helmholtz.cloud/grz-mv-genomseq/grz-cli
-Keywords: GRZ,GDC,S3
-Classifier: Programming Language :: Python :: 3
-Classifier: Operating System :: OS Independent
-Requires-Python: >=3.12
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: boto3<2,>=1.36
-Requires-Dist: click<9,>=8.1.7
-Requires-Dist: crypt4gh<2,>=1.7
-Requires-Dist: jsonschema<5,>=4.23.0
-Requires-Dist: pyyaml<7,>=6.0.2
-Requires-Dist: tqdm<5,>=4.66.5
-Requires-Dist: pydantic<2.10,>=2.9.2
-Requires-Dist: pydantic-settings<2.10,>=2.9.0
-Requires-Dist: platformdirs<5,>=4.3.6
-Requires-Dist: grz-pydantic-models>=1.3.0
-Requires-Dist: pysam==0.23.*
-Requires-Dist: rich==13.*
-Requires-Dist: requests<3,>=2.32.3
-Provides-Extra: test
-Requires-Dist: pytest<9,>=8.3.3; extra == "test"
-Requires-Dist: pytest-cov<6,>=5.0.0; extra == "test"
-Requires-Dist: pytest-mock<4,>=3.14.0; extra == "test"
-Requires-Dist: moto[s3]<6,>=5.0.16; extra == "test"
-Requires-Dist: pytest-sugar<2,>=1.0.0; extra == "test"
-Requires-Dist: ruff<1,>=0.9.6; extra == "test"
-Requires-Dist: numpy<3,>=2.1.2; extra == "test"
-Requires-Dist: responses==0.25.*; extra == "test"
-Dynamic: license-file
-
 # GRZ CLI
 
 A command-line tool for validating, encrypting, uploading and downloading submissions to/from a GDC/GRZ (Genomrechenzentrum).
@@ -45,10 +8,9 @@ A command-line tool for validating, encrypting, uploading and downloading submis
 - [Features](#features)
 - [Installation](#installation)
   - [Requirements](#requirements)
-  - [End-user setup](#end-user)
+  - [End-user setup](#end-user-setup)
     - [Installation via `conda` (recommended)](#installation-via-conda-recommended)
     - [Installation via `pip` (not recommended)](#installation-via-pip-not-recommended)
-  - [Development setup](#development-setup)
 - [Usage](#usage)
   - [Configuration](#configuration)
   - [Exemplary submission procedure](#exemplary-submission-procedure)
@@ -147,18 +109,6 @@ pip upgrade grz-cli
 Docker images are available via biocontainers at [https://biocontainers.pro/tools/grz-cli](https://biocontainers.pro/tools/grz-cli).
 
 
-### Development setup
-For development purposes, you can clone the repository and install the package in editable mode:
-
-```bash
-git clone https://codebase.helmholtz.cloud/grz-mv-genomseq/grz-cli
-# create conda environment and activate it
-conda env create -f grz-cli/environment-dev.yaml -n grz-tools-dev
-conda activate grz-tools-dev
-# install the grz-cli tool
-pip install -e grz-cli/
-```
-
 ## Usage
 
 ### Configuration
@@ -202,8 +152,6 @@ Example usage:
 grz_cli validate --submission-dir foo
 ```
 
-Option is for the usage at a hospital (Leistungserbringer) and GDC/GRZ.
-
 ### encrypt
 
 If a working directory is not provided, then the current directory is used automatically. The log-files are going to be stored in the sub-folder of the working directory.
@@ -216,21 +164,6 @@ Files are stored in a folder named `encrypted_files` as a sub-folder of the work
 grz-cli encrypt --submission-dir foo
 ```
 
-Option is for the usage at a hospital (Leistungserbringer). Please approach your GDC/GRZ for a valid config file.
-
-### decrypt
-
-Decrypt a submission using the GRZ private key.
-
-- `-s, --submission-dir`: Path to the submission directory containing both 'metadata/' and 'encrypted_files/' directories  [**Required**]
-- `-c,--config-file`: Path to config file [_optional_]
-
-```bash
-grz-cli decrypt --submission-dir foo
-```
-
-Option is for the usage at a GDC/GRZ.
-
 ### upload
 
 Upload the submission into a S3 structure of a GRZ.
@@ -244,24 +177,6 @@ Example usage:
 grz-cli upload --submission-dir foo
 ```
 
-Option is for the usage at a hospital (Leistungserbringer). Please approach your GDC/GRZ for a valid config file.
-
-### download
-
-Download a submission from a GRZ
-
-- `-s, --submission-id`: S3 submission prefix [**Required**]
-- `-o, --output-dir`: Path to the target submission output directory [**Required**]
-- `-c, --config-file`: Path to config file [_optional_]
-
-Example usage:
-
-```bash
-grz-cli download --submission-id foo --output-dir bar
-```
-
-Option is for the usage at a GDC/GRZ.
-
 ## Testing
 
 Please note that binary files used for testing are managed with [Git LFS](https://git-lfs.com), which will be needed to clone them locally with the git repository.
@@ -275,9 +190,9 @@ Alternatively, install `uv` and `tox` and run `uv run tox`.
 
 ## License
 
-This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+This project is licensed under the MIT License — see the [LICENSE](LICENSE) file for details.
 
 ## Acknowledgements
 
-Parts of `cryp4gh` code is used in modified form
+Parts of `crypt4gh` code is used in modified form
 

grz_cli-0.7.0/pyproject.toml

@@ -0,0 +1,58 @@
+[project]
+name = "grz-cli"
+description = "Tool for validation, encryption and upload of MV submissions to GDCs."
+readme = "README.md"
+license = "MIT"
+authors = [
+    { name = "Koray Kirli", email = "koraykirli@gmail.com" },
+    { name = "Mathias Lesche", email = "mathias.lesche@tu-dresden.de" },
+    { name = "Florian R. Hölzlwimmer", email = "git.ich@frhoelzlwimmer.de" },
+    { name = "Till Hartmann", email = "till.hartmann@bih-charite.de" },
+    { name = "Thomas Sell", email = "thomas.sell@bih-charite.de" },
+    { name = "Travis Wrightsman", email = "travis.wrightsman@uni-tuebingen.de" }
+]
+dynamic = ["version"]
+dependencies = [
+    "boto3 >=1.36,<2",
+    "click >=8.1.7,<9",
+    "crypt4gh >=1.7,<2",
+    "jsonschema >=4.23.0,<5",
+    "pyyaml >=6.0.2,<7",
+    "tqdm >=4.66.5,<5",
+    "pydantic >=2.9.2,<2.10",
+    "pydantic-settings >=2.9.0,<2.10",
+    "platformdirs >=4.3.6,<5",
+    "grz-pydantic-models >=1.3.0",
+    "pysam ==0.23.*",
+    "rich ==13.*",
+    "requests >=2.32.3,<3",
+    "grz-common",
+]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent"
+]
+requires-python = ">=3.12"
+keywords = ["GRZ", "GDC", "S3"]
+
+[tool.uv.sources]
+grz-common = { workspace = true }
+
+[project.urls]
+Homepage = "https://github.com/BfArM-MVH/grz-tools"
+Repository = "https://github.com/BfArM-MVH/grz-tools"
+Documentation = "https://github.com/BfArM-MVH/grz-tools/tree/main/packages/grz-cli"
+Issues = "https://github.com/BfArM-MVH/grz-tools/issues"
+
+[project.scripts]
+grz-cli = "grz_cli.cli:main"
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.version]
+path = "src/grz_cli/__init__.py"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/grz_cli"]

grz_cli-0.7.0/src/grz_cli/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.7.0"

{grz_cli-0.6.0 → grz_cli-0.7.0}/src/grz_cli/cli.py

@@ -4,20 +4,12 @@ CLI module for handling command-line interface operations.
 
 import logging
 import logging.config
-import os
 from importlib.metadata import version
 
 import click
 import grz_pydantic_models.submission.metadata
 
-from .commands.archive import archive
-from .commands.clean import clean
-from .commands.consent import consent
-from .commands.decrypt import decrypt
-from .commands.download import download
 from .commands.encrypt import encrypt
-from .commands.list_submissions import list_submissions
-from .commands.pruefbericht import pruefbericht
 from .commands.submit import submit
 from .commands.upload import upload
 from .commands.validate import validate
@@ -37,7 +29,7 @@ class OrderedGroup(click.Group):
         return list(self.commands.keys())
 
 
-def build_cli(grz_mode=False):
+def build_cli():
     """
     Factory for building the CLI application.
     """
@@ -87,15 +79,6 @@ def build_cli(grz_mode=False):
     cli.add_command(upload)
     cli.add_command(submit)
 
-    if grz_mode:
-        cli.add_command(list_submissions, name="list")
-        cli.add_command(download)
-        cli.add_command(decrypt)
-        cli.add_command(archive)
-        cli.add_command(clean)
-        cli.add_command(consent)
-        cli.add_command(pruefbericht)
-
     return cli
 
 
@@ -103,9 +86,7 @@ def main():
     """
     Main entry point for the CLI application.
     """
-    grz_mode = os.environ.get("GRZ_MODE", "false").lower() in {"true", "yes", "1"}
-
-    cli = build_cli(grz_mode=grz_mode)
+    cli = build_cli()
     cli()
 
 

{grz_cli-0.6.0 → grz_cli-0.7.0}/src/grz_cli/commands/encrypt.py

@@ -6,10 +6,10 @@ from pathlib import Path
 from tempfile import NamedTemporaryFile
 
 import click
+from grz_common.cli import config_file, force, submission_dir
+from grz_common.workers.worker import Worker
 
-from ..utils.config import read_config
-from ..workers.worker import Worker
-from .common import config_file, force, submission_dir
+from ..models.config import EncryptConfig
 
 log = logging.getLogger(__name__)
 
@@ -25,9 +25,9 @@ def encrypt(submission_dir, config_file, force):
     Encryption is done with the recipient's public key.
     Sub-folders 'encrypted_files' and 'logs' are created within the submission directory.
     """
-    config = read_config(config_file)
+    config = EncryptConfig.from_path(config_file)
 
-    submitter_privkey_path = config.submitter_private_key_path
+    submitter_privkey_path = config.keys.submitter_private_key_path
     if submitter_privkey_path == "":
         submitter_privkey_path = None
 
@@ -41,15 +41,19 @@ def encrypt(submission_dir, config_file, force):
         log_dir=submission_dir / "logs",
         encrypted_files_dir=submission_dir / "encrypted_files",
     )
-    if config.grz_public_key:
+    if pubkey := config.keys.grz_public_key:
         with NamedTemporaryFile("w") as f:
-            f.write(config.grz_public_key)
+            f.write(pubkey)
             f.flush()
             worker_inst.encrypt(f.name, submitter_private_key_path=submitter_privkey_path, force=force)
     else:
         # This case cannot occur here, but an explicit check is needed for type-checking.
-        if config.grz_public_key_path is None:
+        if config.keys.grz_public_key_path is None:
             sys.exit("GRZ public key path is required for encryption.")
-        worker_inst.encrypt(config.grz_public_key_path, submitter_private_key_path=submitter_privkey_path, force=force)
+        worker_inst.encrypt(
+            config.keys.grz_public_key_path,
+            submitter_private_key_path=submitter_privkey_path,
+            force=force,
+        )
 
     log.info("Encryption successful!")

{grz_cli-0.6.0 → grz_cli-0.7.0}/src/grz_cli/commands/submit.py

@@ -10,7 +10,7 @@ from .validate import validate
 
 log = logging.getLogger(__name__)
 
-from .common import config_file, force, submission_dir, threads
+from grz_common.cli import config_file, force, submission_dir, threads
 
 
 @click.command("submit")

{grz_cli-0.6.0 → grz_cli-0.7.0}/src/grz_cli/commands/upload.py

@@ -4,13 +4,13 @@ import logging
 from pathlib import Path
 
 import click
-
-from ..workers.worker import Worker
+from grz_common.workers.worker import Worker
 
 log = logging.getLogger(__name__)
 
-from ..utils.config import read_config
-from .common import config_file, submission_dir, threads
+from grz_common.cli import config_file, submission_dir, threads
+
+from ..models.config import UploadConfig
 
 
 @click.command()
@@ -25,7 +25,7 @@ def upload(
     """
     Upload a submission to a GRZ/GDC.
     """
-    config = read_config(config_file)
+    config = UploadConfig.from_path(config_file)
 
     log.info("Starting upload...")
 
@@ -39,6 +39,6 @@ def upload(
         threads=threads,
     )
     # output the generated submission ID
-    print(worker_inst.upload(config))
+    print(worker_inst.upload(config.s3))
 
     log.info("Upload finished!")