Public-Health-Bioinformatics / LexMapr / 425
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LAST BUILD BRANCH: v0.7.0
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Implement ``--profile`` command (#79)

* Moved cache logic to new ``pipeline_caching.py``

* Population of ``lookup_table``, ``ontology_lookup_table`` and
  ``classification_lookup_table`` moved to ``pipeline_caching.py``

  * New functions functions ``get_predefined_resources``,
    ``get_config_resources`` and ``get_classification_resources``
    respectively

  * Moved in following functions from ``pipeline_helpers.py``:

    * ``get_resource_dict``

    * ``create_lookup_table_skeleton``

    * ``add_predefined_resources_to_lookup_table``

    * ``get_resource_permutation_terms``

    * ``get_resource_bracketed_permutation_terms``

    * ``add_fetched_ontology_to_lookup_table``

  * Moved in ``add_classification_resources_to_lookup_table`` from
    ``pipeline_classification.py``

* Removed last, stale use of ``pkg_resources`` as opposed to using path
  from ``lexmapr.definitions.ROOT``

* Improved in-code documentation in some places

* Modifies tests and imports accordingly

* Docstrings for new functions

* Stylistic improvements in ``bin/lexmapr``

* Change single quotes to double quotes

* Added new lines to make PEP 8 adherent

* Improve ``bin/lexmapr`` some more

* Remove unnecessary ``if-else`` conditions by cleaning up
  ``input_file`` and ``-v, --version`` arguments somewhat

* Renamed ``lexmapr.resources``, ``lexmapr.cache``

* ``lexmapr.resources`` is now ``lexmapr.predefined_resources``

* ``lexmapr.cache`` is now ``lexmapr.resources``

* Once we started committing lookup and classification table to
  ``lexmapr.cache``, (and when we eventually commit profiles`), it
  ceases to be a cache

* Renamed ``pipeline_caching.py`` to ``pipeline_resources.py``

* Updated comments accordingly

* Implement ``-p, --profile`` functionality

* User can specify profile they want to use via ``-p, --profile`` flag,
  which will contain a pre-defined set of command-line arguments and
  onlin... (continued)

977 of 1135 relevant lines covered (86.08%)

0.86 hits per line

Jobs
ID Job ID Ran Files Coverage
1 425.1 (PYTHONHASHSEED=0) 0
86.08
 Travis Job 425.1
Source Files on build 425
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