Metadata-Version: 2.1
Name: globus-pilot
Version: 0.5.0.dev0
Summary: A CLI tool for cataloging pilot 1 data
Home-page: https://github.com/globusonline/pilot1-tools/tree/master
Maintainer: globus
Maintainer-email: support@globus.org
License: UNKNOWN
Description: pilot1-tools
        ------------
        .. image:: https://anaconda.org/nickolaussaint/pilot1-tools/badges/version.svg
          :target: https://anaconda.org/nickolaussaint/pilot1-tools
        
        
        A Command Line tool for managing data in Globus Search as well as transferring corresponding data to and from a Globus Endpoint.
        
        
        Installation
        ------------
        
        These tools are available on Conda for Python 3.6, you can install them with the following:
        
        .. code-block:: bash
        
            conda create -n pilot1-env -c conda-forge -c nickolaussaint pilot1-tools
        
        
        You can see the `Developer Guide Installation
        <https://github.com/globusonline/pilot1-tools/blob/master/docs/developer-guide.rst>`_ for more options.
        
        
        Setting Your Local
        ^^^^^^^^^^^^^^^^^^
        
        The first time you run `pilot`, you may encounter an error an error like the one below:
        
        .. code-block::
        
            RuntimeError: Click will abort further execution because Python 3 was
              configured to use ASCII as encoding for the environment.
        
        
        This can happen if on systems with custom configured UTF-8 settings. You should
        see a list of encodings your system supports, simply choose one and set it.
        For example:
        
        .. code-block::
        
            export LC_ALL=en_US.utf-8
            export LANG=en_US.utf-8
        
        
        Replace ``en_US.utf-8`` with an encoding your system supports.
        
        
        Quick Start
        -----------
        
        For a full walkthrough, see the `User Guide
        <https://github.com/globusonline/pilot1-tools/blob/master/docs/user-guide.rst>`_.
        Administrators can also view the `Admin Guide
        <https://github.com/globusonline/pilot1-tools/blob/master/docs/project-admin.rst>`_.
        
        A quick walkthrough is below.
        
        First, login using Globus:
        
        .. code-block:: bash
        
            pilot login
        
        Then choose your project. See ``pilot project info`` for info on any listed project:
        
        .. code-block:: bash
        
            pilot project
            pilot project set <myproject>
        
        You can use ``list`` to get a high level overview of the data:
        
        .. code-block:: bash
        
            pilot list
        
        If you want more detail about a specific search record, you can use ``describe`` to view details:
        
        .. code-block:: bash
        
            pilot describe dose_response/rescaled_combined_single_drug_growth
        
        You can also download the data associated with the search record:
        
        .. code-block:: bash
        
            pilot download dose_response/rescaled_combined_single_drug_growth
        
        
        When you want to add more data to the collection, you can use the ``upload`` command. This will upload the
        data in addition to creating a record in Globus Search to track it.
        
        
        .. code-block:: bash
        
            touch my_data.tsv
            pilot upload my_data.tsv test_dir --dry-run --verbose -j my_metadata.json
        
        The two flags '--dry-run --verbose' are optional but handy for testing. '-j my_metadata.json'
        is for providing any extra metadata the pilot tool can't automatically determine. Here is an example of the metadata:
        
        .. code-block:: json
        
            {
                "title": "Drug Identifiers",
                "description": "Drug identifiers, including InChIKey, SMILES, and PubChem.",
                "data_type": "Drug Response",
                "dataframe_type": "List",
                "source": [
                    "InChIKey",
                    "SMILES",
                    "PubChem"
                ]
            }
        
        
        Running Tests
        -------------
        
        Ensure packages in test-requirements.txt are installed, then run:
        
        .. code-block:: bash
        
            pytest
        
        And for coverage:
        
        .. code-block:: bash
        
            pytest --cov pilot
        
        
        Building for Conda
        ------------------
        
        Currently, the tableschema package has not been built for python 3.7, so this only
        lists instructions for python 3.6. Two channels must be used, nickolaussaint and
        conda-forge. The nickolaussaint channel contains fair-research-login, and conda-forge
        contains various other packages we need including the globus-sdk.
        
        
        .. code-block:: bash
        
            conda build -c nickolaussaint -c conda-forge --python 3.6 .
        
        
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Description-Content-Type: text/x-rst
