TODO This README needs work. And we should make sure all our ETL scripts have the same README format.
Repo containing the Epi/HAI ETL for a alert file uploaded to the raw Epi/HAI data bucket in CAPE.
The ETL script will extract the tabular data and convert it to a common format that will then be written into the clean data bucket for later query.
This file is given as a .pdf containing various text and two tables that will be
processed by this ETL script.
The script assumes the 4th line of the pdf contains only the date of the report.
The script assumes the format of the two tables; if the tables do not have the
correct format, the script will fail.
The script filters for only the following genes and their subtypes: NDM, KPC, IMP, OXA, VIM, CMY
Table 1: Columns: WGS_ID, Accession_ID, MLST_ST Table 2: Columns: <WGS_IDs...> Rows: <Genes...>
Results in a table with the columns: Accession_ID, WGS_ID, MLST_ST, <Genes...>
The script will fail if the tables do not have the specified columns and rows.