Totalnum processing (SCILHS Central)

Prerequisites

1. Obtain totalnum_[label].csv from sites, with c_fullname,c_basecode,c_totalnum.

2. Generate list of paths (make view and datasource for pristine ontology first):

   sql2csv --db "mssql://pcori_dev" --query "select distinct c_fullname, c_name from pcornet_master_vw where c_synonym_cd!='Y' and c_visualattributes like '%A%'" -v >totalnums_allpaths.csv

3. On mac:

   pip install --user setuptools --upgrade pip install --user csvkit --upgrade

4. Other packages you'll need:

   conda install --channel https://conda.anaconda.org/etetoolkit ete3