Public-Health-Bioinformatics / LexMapr / 474
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Apply punctuation treatment to ontology terms (#87)

* Empty commit

* Simplify and generalize ``punctuation_treatment``

* Replace unnecessary parameter with in-function variable

* Simplify code with simple regex expression

  * Slightly alter logic: consecutive whitespaces no longer possible

* Adjust tests accordingly

* More consistent samples and resource terms

* Clean-up ``punctuation_treatment``

* Apply punctuation_treatment when standardizing resource terms

* Eliminate unnecessary ``resource_bracketed_permutation_terms``, and
  accompanying code

* Modify tests accordingly

* wip

* Added ``,`` to ``punctuation_treatment``

* Attempting to map samples to punctuation-treated resource terms,
  while continuing to report non-punctuation-treated resource terms

  * This makes the output less confusing

  * For now, ``resource_terms_id_based`` has non-punctuation-treated
    resource terms, while ``resource_terms`` has punctuation-treated
    resource terms

* Removes punctuation from ``suffixes.csv`` for improved mapping

* Modified tests accordingly

* More informative lookup table labels

* ``resource_terms_id_based`` is now ``non_standard_resource_ids``

* ``resource_terms`` is now ``standard_resource_labels``

* ``resource_permutation_terms`` is now ``standard_resource_label_permutations``

* Other changes

  * Removed stale lookup table keys ``processes`` and ``collocations``,
    and associated resource files

  * Better in-code documentation of ``create_lookup_table_skeleton``

* Updated tests

  * Renamed a lot of variables to reflect new lookup table labels

* Meat no longer classified alongside food

* Better meat-food mutual exclusion

* Make non-standardized resources lowercase

* To avoid changes in functionality

  * Standardized will be lowercase AND punctuation-treated

* Remove now-unnecessary call to ``str.lower`` when printing output

* Remove unnecessary... (continued)

935 of 1086 relevant lines covered (86.1%)

1.72 hits per line

Jobs
ID Job ID Ran Files Coverage
1 474.1 (PYTHONHASHSEED=0) 0
86.1
 Travis Job 474.1
2 474.2 (PYTHONHASHSEED=0) 0
86.1
 Travis Job 474.2
Source Files on build 474
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