From dd38b096c9588f8b249684e0c5c8507361ec52a6 Mon Sep 17 00:00:00 2001 From: Karim-Mane Date: Mon, 9 Sep 2024 14:38:20 +0000 Subject: [PATCH] add note for memory --- vignettes/query_parameters.Rmd | 51 ++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/vignettes/query_parameters.Rmd b/vignettes/query_parameters.Rmd index 58702bb3..82080f33 100644 --- a/vignettes/query_parameters.Rmd +++ b/vignettes/query_parameters.Rmd @@ -52,4 +52,55 @@ Note that the syntax in the SQL query depends on the server type. The example ab ## APIs query parameters +### SORMAS + +SORMAS (Surveillance Outbreak Response Management and Analysis System) aims at optimizing **the processes** used in monitoring the spread of infectious diseases and responding to outbreak situations. + +what are these processes? + +```{bash eval=FALSE, include=FALSE} +# copy the content of this file: /Users/karimmane/Documents/Karim/LSHTM/TRACE_dev/deploy\ 2/openapi/sormas-rest.yaml + +# paste it in https://editor.swagger.io/ to visualize the ReST API documentation +``` + +access to the SORMAS data + +Questions: + +1. How does OIDC/OAUTH2/Bearer authentication work? +2. what is the difference between clinical, laboratory and epidemiological + confirmations? Which one defines whether a person is infected or not? +3. Is directionality captured in contact tracing? i.e can I generate 'from' and + 'to' columns from the contact data? +4. 'lastContactDate' is captured in the contact data, but not 'firstContactDate' + Is this correct? or I am missing something? +5. How to fetch multiple cases using a vector of cases (without having to fetch all cases and subset the ones of interest)? +6. What is the base URL to the live server? can we have a user to test our + functionality. +7. From what endpoint can I get the Ct (viral load/shedding) values of infected cases? +8. Currently logging multiple times. Can a user have access a endpoit and not have access to another? for example: can a user have access to cases data but not the persons or contact data? + +TODO: + +1. automate the process of fetching the list of disease name from sormas (done) +2. automate the process of fetching the data dictionary from sormas and extract + the relevant part for the final data +3. complete the request queries with more details +4. replace with the base url of the live server +5. If access is given to a user across all endpoints, we could just authenticate once and use that object in other requests. + + + +External Visit API: + +* uses basic auth +* only users with the role REST_EXTERNAL_VISITS_USER are authorised +* enable communication between SORMAS and other symptom journals +* Visits hold information about symptoms at a specific time point + * Visits can be created for cases and contacts +* ??? need clarification around **person, cases, contacts** in the visits API + + +