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‎Makefile‎

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## testcov : run the ${MODULE} test suite and collect coverage
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testcov: $(PYSOURCES)
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python setup.py test --addopts "--cov" ${PYTEST_EXTRA}
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pytest --cov ${PYTEST_EXTRA}
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sloccount.sc: $(PYSOURCES) Makefile
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sloccount --duplicates --wide --details $^ > $@

‎README.rst‎

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# cwl-utils
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A collection of scripts to demonstrate the use of the new Python classes for
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loading and parsing [CWL v1.0 ](https://github.com/common-workflow-language/cwl-utils/blob/main/cwl_utils/parser/v1_0.py),
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[CWL v1.1](https://github.com/common-workflow-language/cwl-utils/blob/main/cwl_utils/parser/v1_1.py),
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and [CWL v1.2](https://github.com/common-workflow-language/cwl-utils/blob/main/cwl_utils/parser/v1_2.py)
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|Linux Build Status| |Code coverage| |Documentation Status|
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.. |Linux Build Status| image:: https://github.com/common-workflow-language/cwl-utils/actions/workflows/ci-tests.yml/badge.svg?branch=main
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:target: https://github.com/common-workflow-language/cwl-utils/actions/workflows/ci-tests.yml
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.. |Code coverage| image:: https://codecov.io/gh/common-workflow-language/cwl-utils/branch/main/graph/badge.svg
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:target: https://codecov.io/gh/common-workflow-language/cwl-utils
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.. |Documentation Status| image:: https://readthedocs.org/projects/cwl-utils/badge/?version=latest
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:target: https://cwl-utils.readthedocs.io/en/latest/?badge=latest
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:alt: Documentation Status
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cwl-utils
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---------
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A collection of scripts to demonstrate the use of the new Python classes
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for loading and parsing `CWL
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v1.0 <https://github.com/common-workflow-language/cwl-utils/blob/main/cwl_utils/parser/v1_0.py>`__,
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`CWL
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v1.1 <https://github.com/common-workflow-language/cwl-utils/blob/main/cwl_utils/parser/v1_1.py>`__,
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and `CWL
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v1.2 <https://github.com/common-workflow-language/cwl-utils/blob/main/cwl_utils/parser/v1_2.py>`__
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documents.
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## Install
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Requires Python 3.6+
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``` bash
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virtualenv -p python3.6 venv3.6 # Python 3.7, 3.8, or 3.9 would also work
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source venv3.6/bin/activate
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pip install cwl-utils
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```
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or install the latest development version of `cwl-utils`
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Installation
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------------
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::
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pip3 install cwl-utils
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``` bash
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git clone https://github.com/common-workflow-language/cwl-utils.git
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cd cwl-utils
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virtualenv -p python3.6 venv3.6 # Python 3.7, 3.8, or 3.9 would also work
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source venv3.6/bin/activate
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pip install .
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```
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(If you want to edit the sources from the development version, then run
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`pip install -e .`)
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To install from source::
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## Usage
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git clone https://github.com/common-workflow-language/cwl-utils.git
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cd cwl-utils
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pip3 install .
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### Pull the all referenced software container images
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Usage
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-----
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`docker_extract.py` is useful to cache or pre-pull all software container images
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referenced in a CWL CommandLineTool or CWL Workflow (including all referenced
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CommandLineTools and sub-Workflows and so on).
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Pull the all referenced software container images
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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The default behaviour is to use the Docker engine to download and save the software
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container images in Docker format.
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``docker_extract.py`` is useful to cache or pre-pull all software
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container images referenced in a CWL CommandLineTool or CWL Workflow
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(including all referenced CommandLineTools and sub-Workflows and so on).
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```bash
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docker_extract.py DIRECTORY path_to_my_workflow.cwl
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```
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The default behaviour is to use the Docker engine to download and save
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the software container images in Docker format.
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Or you can use the Singularity software container engine to download and save the
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software container images and convert them to the Singularity format at the same
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time.
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.. code:: bash
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```bash
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docker_extract.py --singularity DIRECTORY path_to_my_workflow.cwl
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```
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docker_extract.py DIRECTORY path_to_my_workflow.cwl
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### Using the CWL Parsers
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Or you can use the Singularity software container engine to download and
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save the software container images and convert them to the Singularity
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format at the same time.
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[//]: # "Please keep the below synchronized with load_cwl_by_path.py"
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```python
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from pathlib import Path
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from ruamel import yaml
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import sys
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.. code:: bash
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from cwl_utils.parser import load_document_by_path, save
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docker_extract.py --singularity DIRECTORY path_to_my_workflow.cwl
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# File Input - This is the only thing you will need to adjust or take in as an input to your function:
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cwl_file = Path("testdata/md5sum.cwl") # or a plain string works as well
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Using the CWL Parsers
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~~~~~~~~~~~~~~~~~~~~~
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# Import CWL Object
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cwl_obj = load_document_by_path(cwl_file)
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.. code:: python
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# View CWL Object
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print("List of object attributes:\n{}".format("\n".join(map(str, dir(cwl_obj)))))
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from pathlib import Path
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from ruamel import yaml
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import sys
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# Export CWL Object into a built-in typed object
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saved_obj = save(cwl_obj)
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print(f"Export of the loaded CWL object: {saved_obj}.")
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```
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from cwl_utils.parser import load_document_by_path, save
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## Development
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# File Input - This is the only thing you will need to adjust or take in as an input to your function:
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cwl_file = Path("testdata/md5sum.cwl") # or a plain string works as well
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### Regenerate parsers
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# Import CWL Object
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cwl_obj = load_document_by_path(cwl_file)
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To regenerate install the `schema_salad` package and run:
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# View CWL Object
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print("List of object attributes:\n{}".format("\n".join(map(str, dir(cwl_obj)))))
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`cwl_utils/parser/cwl_v1_0.py` was created via
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`schema-salad-tool --codegen python https://github.com/common-workflow-language/common-workflow-language/raw/main/v1.0/CommonWorkflowLanguage.yml`
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# Export CWL Object into a built-in typed object
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saved_obj = save(cwl_obj)
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print(f"Export of the loaded CWL object: {saved_obj}.")
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`cwl_utils/parser/cwl_v1_1.py` was created via
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`schema-salad-tool --codegen python https://github.com/common-workflow-language/cwl-v1.1/raw/main/CommonWorkflowLanguage.yml`
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Development
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-----------
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`cwl_utils/parser/cwl_v1_2.py` was created via
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`schema-salad-tool --codegen python https://github.com/common-workflow-language/cwl-v1.2/raw/1.2.1_proposed/CommonWorkflowLanguage.yml`
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Regenerate parsers
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~~~~~~~~~~~~~~~~~~
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To regenerate install the ``schema_salad`` package and run:
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### Release
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``cwl_utils/parser/cwl_v1_0.py`` was created via
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``schema-salad-tool --codegen python https://github.com/common-workflow-language/common-workflow-language/raw/main/v1.0/CommonWorkflowLanguage.yml``
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To release CWLUtils, bump the version in `cwl_utils/__meta__.py`, and tag that
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commit with the new version. The [gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish)
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``cwl_utils/parser/cwl_v1_1.py`` was created via
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``schema-salad-tool --codegen python https://github.com/common-workflow-language/cwl-v1.1/raw/main/CommonWorkflowLanguage.yml``
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``cwl_utils/parser/cwl_v1_2.py`` was created via
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``schema-salad-tool --codegen python https://github.com/common-workflow-language/cwl-v1.2/raw/1.2.1_proposed/CommonWorkflowLanguage.yml``
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Release
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~~~~~~~
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To release CWLUtils, bump the version in ``cwl_utils/__meta__.py``, and
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tag that commit with the new version. The
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`gh-action-pypi-publish <https://github.com/pypa/gh-action-pypi-publish>`__
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should release that tag.
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‎tox.ini‎

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py{36,37,38,39,310}-unit,
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py{36,37,38,39,310}-bandit,
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py{36,37,38,39,310}-mypy,
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py39-lint-readme,
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py310-lint-readme,
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py39-pydocstyle
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skip_missing_interpreters = True
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py{36,37,38,39,310}-bandit: Search for common security issues
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py{36,37,38,39,310}-mypy: Check for type safety
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py39-pydocstyle: docstring style checker
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py39-lint-readme: Lint the README.rst->.md conversion
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py310-lint-readme: Lint the README.rst->.md conversion
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passenv =
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CI
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diff-cover
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skip_install = true
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[testenv:py39-lint-readme]
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[testenv:py310-lint-readme]
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description = Lint the README.rst->.md conversion
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commands =
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python setup.py sdist

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