omero-download-tool

utils/omero-download-tool/.bumpversion.cfg

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+[bumpversion]
+current_version = 0.1.0-dev0
+commit = True
+tag = False
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
+serialize = 
+	{major}.{minor}.{patch}-{release}{dev}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = _
+first_value = dev
+values = 
+	dev
+	_
+
+[bumpversion:part:dev]
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:plugin.json]
+
+[bumpversion:file:VERSION]
+
+[bumpversion:file:src/polus/images/utils/omero_download/__init__.py]

utils/omero-download-tool/.gitignore

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+ #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
+
+ # 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.lock
+
+ # 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/#use-with-ide
+ .pdm.toml
+
+ # 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/
+
+ # vscode
+ .vscode
+
+ # test data directory
+ data
+ # yaml file
+ .pre-commit-config.yaml
+
+ # hidden files
+ .DS_Store
+ .ds_store
+ # flake8
+ .flake8

utils/omero-download-tool/Dockerfile

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+FROM continuumio/miniconda3
+
+# environment variables defined in polusai/bfio
+ENV EXEC_DIR="/opt/executables"
+ENV POLUS_IMG_EXT=".ome.tif"
+ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
+
+ARG OMERO_USERNAME
+ARG OMERO_PASSWORD
+ENV OMERO_USERNAME=$OMERO_USERNAME
+ENV OMERO_PASSWORD=$OMERO_PASSWORD
+
+
+ARG conda_env=project_env
+
+# Work directory defined in the base container
+WORKDIR ${EXEC_DIR}
+
+COPY pyproject.toml ${EXEC_DIR}
+COPY environment.yml ${EXEC_DIR}
+COPY VERSION ${EXEC_DIR}
+COPY README.md ${EXEC_DIR}
+COPY src ${EXEC_DIR}/src
+
+RUN conda env create -f environment.yml
+
+ENV PATH /opt/conda/envs/myenv/bin:$PATH
+RUN /bin/bash -c "source activate project_env"
+
+RUN pip3 install ${EXEC_DIR} --no-cache-dir
+
+ENTRYPOINT ["python3", "-m", "polus.images.utils.omero_download"]
+CMD ["--help"]

utils/omero-download-tool/README.md

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+# Omero Download (v0.1.0-dev0)
+
+This tool enables the retrieval of data from the Omero NCATS server.  [omero_plus](http://165.112.226.159/omero_plus/login/?url=%2Fwebclient%2F).
+
+## Note
+To access data from the Omero NCATS server, user must have to be connection to `NIHVPN`
+1. Specify environmental variables for a server's username and password using the command prompt
+
+   export `OMERO_USERNAME=XXXX` \
+   export `OMERO_PASSWORD=XXXX`
+
+
+Conda is employed to install all dependencies because one of the critical packages, `omero-py`, encountered installation issues with pip
+
+Currently, the supported object types in a tool include:  `project`, `dataset`, `screen`, `plate`, `well`
+
+
+## Building
+
+To build the Docker image for the download plugin, run
+`bash build-docker.sh`.
+
+## Run the Docker image
+
+To execute the built docker image for the download plugin, run
+`bash run-plugin.sh`.
+
+## Options
+
+This plugin takes 2 input arguments and
+1 output argument:
+
+| Name            | Description                                                  | I/O    | Type        |
+| --------------- | ------------------------------------------------------------ | ------ | ----------- |
+| `--dataType`      | Object types to be retreived from Omero Server                    | Input  | String      |
+| `--name  `      | Name of an object                   | Input  | String      |
+| `--objectId  `      |  Identification of an object of an object                 | Input  | Integer      |
+| `--outDir`      | Directory to store the downloaded data                  | Output | genericData |
+| `--preview`      | Generate a JSON file with outputs                  | Output | JSON |
+
+
+
+## Sample docker command:
+```bash
+docker run -e OMERO_USERNAME=$OMERO_USERNAME -e OMERO_PASSWORD=$OMERO_PASSWORD -v /home/ec2-user/data/:/home/ec2-user/data/ polusai/omero-download-tool:0.1.0-dev0 --dataType="plate" --objectId=108 --outDir=/home/ec2-user/data/output```

utils/omero-download-tool/VERSION

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+0.1.0-dev0

utils/omero-download-tool/build-docker.sh

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+#!/bin/bash
+
+version=$(<VERSION)
+docker build . -t polusai/omero-download-tool:${version}

utils/omero-download-tool/environment.yml

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+name: project_env
+channels:
+  - defaults
+  - conda-forge
+dependencies:
+  - python==3.9.18
+  - numpy==1.21.0
+  - bfio=*
+  - ome:omero-py
+  - pydantic=*
+  - pip

utils/omero-download-tool/ict.yml

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+author:
+- Hamdah Shafqat
+contact: [email protected]
+container: polusai/omero-download-tool:0.1.0-dev0
+description: This plugin allows to retrieve the microscopy image data from the OMERO
+  NCATS server.
+entrypoint: python3 -m polus.images.utils.omero_download
+inputs:
+- description: The supported object types to be retreived.
+  format:
+  - dataType
+  name: dataType
+  required: true
+  type: string
+- description: Name of the object to be downloaded.
+  format:
+  - name
+  name: name
+  required: false
+  type: string
+- description: Identifier of the object to be downloaded.
+  format:
+  - objectId
+  name: objectId
+  required: false
+  type: number
+- description: Generate an output preview.
+  format:
+  - preview
+  name: preview
+  required: false
+  type: boolean
+name: polusai/OmeroDownload
+outputs:
+- description: Output collection.
+  format:
+  - outDir
+  name: outDir
+  required: true
+  type: path
+repository: https://github.com/PolusAI/image-tools
+specVersion: 1.0.0
+title: Omero Download
+ui:
+- description: The supported object types to be retreived.
+  fields:
+  - project
+  - dataset
+  - screen
+  - plate
+  - well
+  - default
+  key: inputs.dataType
+  title: dataType
+  type: select
+- description: Name of the object to be downloaded.
+  key: inputs.name
+  title: name
+  type: text
+- description: Identifier of the object to be downloaded.
+  key: inputs.objectId
+  title: objectId
+  type: number
+- description: Generate an output preview.
+  key: inputs.preview
+  title: Preview example output of this plugin
+  type: checkbox
+version: 0.1.0-dev0