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https://github.com/joundso/gpas_connector
gPASconnectoR
https://github.com/joundso/gpas_connector
Last synced: about 1 month ago
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gPASconnectoR
- Host: GitHub
- URL: https://github.com/joundso/gpas_connector
- Owner: joundso
- License: gpl-3.0
- Created: 2021-04-19T10:01:09.000Z (over 3 years ago)
- Default Branch: master
- Last Pushed: 2021-06-25T10:51:21.000Z (over 3 years ago)
- Last Synced: 2023-03-04T02:03:22.221Z (almost 2 years ago)
- Language: R
- Homepage:
- Size: 45.9 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
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README
# gPASconnectoR
[](https://codecov.io/gh/joundso/gpas_connector)
[](https://git.uk-erlangen.de/mik-diz/mik-diz-tea/r-packages/gpas_connector/commits/master)
[](https://git.uk-erlangen.de/mik-diz/mik-diz-tea/r-packages/gpas_connector/commits/master)
[](https://cran.r-project.org/package=gPASconnectoR)
[](https://cran.r-project.org/web/checks/check_results_gPASconnectoR.html)
The R package `gPASconnectoR` provides utility functions used to access a running gPAS-Instance.
## Installation
The development version can be installed using
```r
install.packages("devtools")
devtools::install_github("joundso/gpas_connector", ref = "development")
```
## Basic functions
### Pseudonymize a value(set)
#### Without setting the environment variables
```R
res <- gPASconnectoR::pseudonymize(
GPAS_BASE_URL = "https://your-organization.org",
GPAS_PSEUDONYM_DOMAIN = "https://fhir.your.organization.org/identifiers/person-id",
gpas_fieldvalue = c(123, 456, "abc")
)
## Result (e.g.):
res
#> $`123`
#> [1] "psn-pid.217172DEACFA2C751515641C"
#>
#> $`456`
#> [1] "psn-pid.41A7D91C53DC2A457FBAB041"
#>
#> $abc
#> [1] "psn-pid.1FFDF5A91EA051608AC4E03A"
```
#### With setting the environment variables
Simply fill a `.env` file:
```sh
## Save this e.g. as `demo.env`:
GPAS_BASE_URL=https://your-organization.org
GPAS_PSEUDONYM_DOMAIN=https://fhir.your.organization.org/identifiers/person-id
```
Then read in the file and assign all variables to the environment:
```R
## Read in the '.env' file:
DIZutils::set_env_vars(env_file = "./demo.env")
## And use the smaller function call:
res <- gPASconnectoR::pseudonymize(c(123, 456, "abc"))
## Result (e.g.):
res
#> $`123`
#> [1] "psn-pid.217172DEACFA2C751515641C"
#>
#> $`456`
#> [1] "psn-pid.41A7D91C53DC2A457FBAB041"
#>
#> $abc
#> [1] "psn-pid.1FFDF5A91EA051608AC4E03A"
```
#### Accessing the result
```R
## Result (e.g.):
res
# 123 456 abc
# "000C30WP" "T4ECWT4Q" "Y2FAYH5D"
## The result is a named list and can be accessed like this:
## Access the element with the name "123" (and receive a single-item-list):
res["123"]
# Result:
# 123
# "000C30WP"
## Access the element with the name "123" (and receive a string):
res[["123"]]
# Result:
# "000C30WP"
## Access the first element (and receive a string):
res[[1]]
# Result:
# "000C30WP"
```
### De-Pseudonymize a value(set)
This is exactly the same like pseudonymizing, but use `gPASconnectoR::depseudonymize` instead of `gPASconnectoR::pseudonymize`.
## More Infos
* Some debugging and other examples can be found in the file [`data-raw/debugging.R`](./data-raw/debugging.R).
* About the gPAS in its [Repo](https://bitbucket.org/medicalinformatics/gPAS/src/master) or its [Wiki](https://bitbucket.org/medicalinformatics/gPAS/wiki/Home)
* About MIRACUM:
* About the Medical Informatics Initiative: