From 35805441b980eba999f757211d563debe717bb4a Mon Sep 17 00:00:00 2001 From: SimonKonar Date: Fri, 19 Jan 2024 11:33:59 +0100 Subject: [PATCH] feat: update documentation --- README.md | 3 ++- docs/DEPLOYMENT.md | 4 +++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index c70ff62..719f952 100644 --- a/README.md +++ b/README.md @@ -15,9 +15,10 @@ part of BBMRI-ERIC. This tool should support ETL processes by providing the foll ## State -Supports syncing of patients between a [Blaze FHIR store](https://github.com/samply/blaze) and a repository of XML files +Supports syncing of patients between a [Blaze FHIR store](https://github.com/samply/blaze) and a repository of XML or CSV files stored on a regular filesystem. Currently, the XML files must have the same structure as this [test file](./test/xml_data/MMCI_1.xml). +This module cannot work with different types of files at the same time, so the records needs to be in either XML or CSV format, not both. ## Quick Start diff --git a/docs/DEPLOYMENT.md b/docs/DEPLOYMENT.md index d7ce42b..7276e59 100644 --- a/docs/DEPLOYMENT.md +++ b/docs/DEPLOYMENT.md @@ -49,7 +49,9 @@ simply specify them in `compose.yaml` in the environment section. | PARSING_MAP_PATH | /opt/fhir-module/default_map.json | Path to a JSON file containing object parsing mappings. Example [here](../util/default_map.json). | | MATERIAL_TYPE_MAP_PATH | /opt/fhir-module/default_material_type_map.json | Path to a JSON file containing mappings between organizational and FHIR material types. Example [here](../util/default_material_type_map.json). | | SAMPLE_COLLECTIONS_PATH | /opt/fhir-module/default_sample_collection.json | Path to a JSON file containing information about Sample collections. Example [here](../util/default_sample_collection.json). | - + | RECORDS_DIR_PATH | /mock_dir/ | Path to a folder containing file(s) with records. | + | RECORDS_FILE_TYPE | xml | Type of files containing the records. | + | CSV_SEPARATOR | ; | Separator used inside csv file, if the records are in a csv format. | ## Object mapping The FHIR module uses dynamically configurable maps currently stored as json files