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Adding full text true rate estimator#8

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Commits on Oct 16, 2017

• Added Conda environment list, created using 'conda env export > environment.yml' (and then manually removing the prefix and name, which are specific to my system).

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  Jacob Levernier

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• Renamed files, and added __init.py__ file.

  

  Jacob Levernier

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• Re-added config. file template.

  

  Jacob Levernier

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• Implemented two-table solution for DOI, allowing repeat measurement of fulltext at different timepoints.

  

  Jacob Levernier

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• Wrote example for re-joining the dois and XML tables using SQLAlchemy object-oriented syntax.

  

  Jacob Levernier

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• Separated code for inserting into database into its own function.

  

  Jacob Levernier

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• Started work to filter down existing DOIs in list, but will likely abandon some of this work in next commit.

  

  Jacob Levernier

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• Replaced print() with logging.info, as it seems to be working now in Spyder's iPython console. Also created function re: whether doi is already in database, and the loop over DOIs.

  

  Jacob Levernier

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• Manually pared down Conda environment list.

  

  Jacob Levernier

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• Added state-of-oa-dois dataset file.

  

  Jacob Levernier

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• Added example database of 10 DOI results.

  

  Jacob Levernier

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• Made minor PEP8 indentation change.

  

  Jacob Levernier

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• Switched from using % method of string formation to using f-strings.

  

  Jacob Levernier

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• Added channels explicitly to Conda environment YAML file.

  

  Jacob Levernier

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• Further refined f-strings implementation.

  

  Jacob Levernier

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• Set custom user header more sensibly.

  

  Jacob Levernier

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Commits on Oct 17, 2017

• Moved ErrorWithAPI placeholder out of function definition, and used .copy() for copying a dictionary.

  

  Jacob Levernier

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• Added .gitignore file.

  

  Jacob Levernier

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Commits on Oct 18, 2017

• Specified channels line-by-line in environment.yml.

  

  Jacob Levernier

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• Made dataset variable name clearer.

  

  Jacob Levernier

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• Changed input datset in config. template file to use relative path.

  

  Jacob Levernier

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• Created unittests from examples for fulltext_indication(), and fixed a bug in that function whereby lacking a DOI in the XML would cause an error.

  

  Jacob Levernier

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• Changed multi-line comment to a triple-quoted comment.

  

  Jacob Levernier

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• Made PEP8 change to separate builtin and local imports.

  

  Jacob Levernier

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• Added clearer comment re: backoff settings.

  

  Jacob Levernier

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• Expanded ErrorWithAPI error with actual API response text.

  

  Jacob Levernier

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• Removed superfluous 'is True' in if statement.

  

  Jacob Levernier

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• Removed whitespace for PEP8.

  

  Jacob Levernier

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Commits on Oct 19, 2017

• Added in-progress proof-of-concept bayesian estimator using randomly-generated data. The next step is to hook this into our actual datset.

  

  Jacob Levernier

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• Hooked up (and tested) the Bayesian estimator to our dataset, as it is (currently split across the original tsv file and an sqlite database).

  

  Jacob Levernier

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• Added whitespace to make code easier to read.

  

  Jacob Levernier

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• Replaced tab charaters with two spaces.

  

  Jacob Levernier

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• Added whitespace in front of a comment, following Google's R style guide.

  

  Jacob Levernier

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