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doc/FORMATS.md

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+This document describes the input and output formats for the current, basic Contact Tracer program.
+
+All input and output formats are CSV.
+
+All dates are of the format "YYYY-MM-DD"
+
+Inputs in < brackets > are optional.
+
+INPUT formats
+=============
+
+Timeline
+--------
+
+Timeline files contain information about which patient was in which location at which time.
+
+	patient_native_id (Free text), move_in (Date), move_out (Date)
+
+
+Infections
+----------
+
+This file contains a list of all infections, giving the dates of beginning/ending (optional) of contagiousness, and other notes if you desire.
+The program only actually uses the first four fields at the moment, but the database stores all of this.
+
+	patient_native_id (free text), linger_days (integer, 0, 1, 2...), onset_date (Date), <cure_date> (Date, ongoing if blank), <diagnosis_date> (Date), <disease_name> (Free text), <notes> (Free text)
+
+
+It is acceptable to not have commas for later unused fields.
+So:
+	12345, 0, 2012-01-01
+
+Is an acceptable input line.
+
+
+Contaminations
+--------------
+
+	enclosure_native_id (Free text), start_date (Date), <end_date> (Date, defaults to today if not given.), <direct_or_environmental "0" or "1"> (defaults to 0 if not given, the proceeding comma is optional.)
+
+
+Basic Diagnosis
+---------------
+
+This convinience file allows the program to guess the onset and linger dates based on the diagnosis date and default parameters. (Default parameters are provided elsewhere.)
+
+	animal_native_ID (free text), DoDx (Date), <disease_name> (Free text)
+
+
+OUTPUTS
+=======
+
+
+
+Exposure
+--------
+
+	animal_native_ID (text), source_animal_native_id (text, blank if unavailable, for example exposed to an environmental contamination.), duration_in_days (integer), start_date (Date), end_date (Date), enclosure_name
+
+Contamination
+-------------
+
+This file contains all the enclosure contaminations identified by the program. It is compatible with the input Contaminations, which will ignore the extra field.
+
+	enclosure_native_id (text), start_date (date), end_date (date), direct_or_environmental (integer), source_animal_native_ID (text)