Download `Gene_full_name` and `Protein_RefSeq_ID` from
https://mygene.info/ using the mygene package.

Remove rows that have both Gene_full_name and Protein_RefSeq_ID values
missing.

Write NA for missing values rather than "NA" or "", in order to be
consistent with the data release.

Print messages after done running shell scripts.

mygene API may return results in different orders, so sorting the values
before output is necessary to reproduce previous results.

Add long-format-table-utils module.

Describe how to update
annotator/annotation-data/oncokb-cancer-gene-list.tsv.

Update OncoKB annotation table source to
analyses/long-format-table-utils/annotator/annotation-data/oncokb-cancer-gene-list.tsv

Co-authored-by: Jo Lynne Rokita <jharenza@gmail.com>

Co-authored-by: Jo Lynne Rokita <jharenza@gmail.com>

Co-authored-by: Jo Lynne Rokita <jharenza@gmail.com>

…ble-utils.sh

README.md is also updated accordingly.

This is suggested by @jharenza at
d3b-center#55 (comment)
, in order to follow the shell script name convention of analysis
modules.

Add annotation data versions and data of the last update in the "Update
downloaded data that are used in this module" section, as suggested by
@jharenza at
d3b-center#55 (comment)

Combine gene and disease (/cancer_group) annotations into one table.

Add additional notes on annotation data versions to the "Implementation
of long-format table annotator" section.

Change the date of the last update of
annotator/annotation-data/oncokb-cancer-gene-list.tsv to 07/16/2021.

The 07/16/2021 annotator/annotation-data/oncokb-cancer-gene-list.tsv is
identical to the previous 06/16/2021 version, even though the website at
https://www.oncokb.org/cancerGenes has changed last update from
06/16/2021 to 07/16/2021.

As suggested by @jharenza at
<d3b-center#55 (comment)>,
test cases should be removed from the source code file.

Run `bash run-tests.sh` to run all tests.

In order to import a funciton for testing from an R file without running
the whole file, a helper function import_function is defined at
tests/helper_import_function.R, and the import_function is also tested
in the tests/test_helper_import_function.R file.

Suggested by @NHJohnson at
d3b-center#55 (review)

Add "Unit testing for long-format table annotator" section to descript
how to use the unit testing framework.

Edit.