Metadata-Version: 2.1
Name: claml2transmart
Version: 0.1.4
Summary: Example ClaML to TranSMART loader
Home-page: https://github.com/thehyve/python_claml2transmart
Author: Gijs Kant
Author-email: gijs@thehyve.nl
License: MIT
Description: ################################################################################
        ClaML ontology to TranSMART loader
        ################################################################################
        
        |Build status| |codecov| |pypi| |downloads|
        
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        This package contains a mapper that reads ontologies in Classification Markup Language (ClaML) format
        and translates them to the data model of the TranSMART_ platform,
        an open source data sharing and analytics platform for translational biomedical research.
        
        It also provides a utility that applies the mapper and writes the translated data,
        using transmart-loader_, to tab-separated files
        that can be loaded into a TranSMART database using the transmart-copy_ tool.
        
        The packages uses the python-claml_ package for reading ClaML files.
        
        ⚠️ Note: this is a very preliminary version, still under development.
        Issues can be reported at https://github.com/thehyve/python_claml2transmart/issues.
        
        .. _python-claml: https://pypi.org/project/python-claml/
        .. _TranSMART: https://github.com/thehyve/transmart_core
        .. _transmart-copy: https://github.com/thehyve/transmart-core/tree/dev/transmart-copy
        .. _transmart-loader: https://pypi.org/project/transmart-loader
        
        
        Installation
        ------------
        
        The package requires Python 3.6.
        
        To install ``claml2transmart``, do:
        
        .. code-block:: bash
        
          pip install claml2transmart
        
        Or from source:
        
        .. code-block:: bash
        
          git clone https://github.com/thehyve/python_claml2transmart.git
          cd python_claml2transmart
          pip install .
        
        
        Run tests (including coverage) with:
        
        .. code-block:: bash
        
          python setup.py test
        
        
        Usage
        -----
        
        Read ontology from an XML file in ClaML format and write the output in transmart-copy
        format to ``/path/to/output``. The output directory should be
        empty of not existing (then it will be created).
        
        .. code-block:: bash
        
          claml2transmart [--code-prefix] <system> <input.xml> /path/to/output
        
        With ``--code_prefix``, the concept code is used as prefix for the concept label.
        
        
        Example: the ICD-10-GM (German modification of ICD-10) is available at icd10gm2019syst-claml.zip_.
        
        .. _icd10gm2019syst-claml.zip: https://www.dimdi.de/dynamic/.downloads/klassifikationen/icd-10-gm/version2019/icd10gm2019syst-claml.zip
        
        .. code-block:: bash
        
          # Unzip and navigate to the classification directory
          mkdir icd10gm2019syst-claml
          cd icd10gm2019sys-claml
          unzip ../icd10gm2019syst-claml.zip
          # create an output directory
          mkdir output
          # apply the mapping
          claml2transmart http://dimdi.de/icd10gm2019 Klassifikationsdateien/icd10gm2019syst_claml_20180921.xml output
        
        This generates the directories ``i2b2metadata`` and ``i2b2demodata`` in the ``output`` directory.
        The generated data can be loaded using transmart-copy_:
        
        .. code-block:: console
        
          # Download transmart-copy:
          curl -f -L https://repo.thehyve.nl/service/local/repositories/releases/content/org/transmartproject/transmart-copy/17.1-HYVE-5.9-RC3/transmart-copy-17.1-HYVE-5.9-RC3.jar -o transmart-copy.jar
          # Load data
          PGUSER=tm_cz PGPASSWORD=tm_cz java -jar transmart-copy.jar -d output
        
        
        License
        -------
        
        Copyright (c) 2019 The Hyve B.V.
        
        The ClaML ontology to TranSMART loader is licensed under the MIT License. See the file `<LICENSE>`_.
        
        
        
Keywords: claml2transmart
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Requires-Python: >=3.6.0
Provides-Extra: dev
