The goal of dsROCrate is to provide functions to wrap elements from a ‘DataSHIELD’ analysis into an RO-Crate.
You can install the development version of dsROCrate from GitHub with:
# install.packages("pak")
pak::pak("FederatedMethods/dsROCrate")In this example, we will be using OBiBa’s Opal as the back-end for DataSHIELD. Another option would be MOLGENIS’ Armadillo.
For instructions on how to set up a local server for DataSHIELD, see the following vignette:
vignette("deploy-local-datashield-server-with-opal")Here we will use OBiBa’s Opal demo server: https://opal-demo.obiba.org/ which can be accessed with the following login credentials:
# define global variables
## Opal server access
USERNAME <- "administrator"
USERPASS <- "password"
SERVER <- "https://opal-demo.obiba.org"
## Credentials for `dsuser`
### NOTE: this is only used to simulate an analysis and generate logs
DSUSERPASS <- "P@ssw0rd"Next, define global variables used in generating the RO-Crate, such as project name, table references (within the project) and user identifiers.
## Five safes variables
PEOPLE <- "dsuser"
PROJECT <- "CNSIM"
TABLES <- c("CNSIM1")Once the credentials and Five Safes variables are configured,we can start a new session on the opal server with the following command:
# login to local server with `USERNAME` and `USERPASS`.
o <- opalr::opal.login(
username = USERNAME,
password = USERPASS,
url = SERVER
)
print(o)
#> url: https://opal-demo.obiba.org
#> name: opal-demo.obiba.org
#> version: 5.5.2
#> username: administratorTo create a basic RO-Crate, we will use the
{rocrateR} package.
This package can be installed with the following command:
# install.packages("pak")
pak::pak("rocrateR")Then, a basic RO-Crate can be created with the following command:
basic_rocrate <- rocrateR::rocrate_5s()Note that this RO-Crate uses the 5s-crate profile.
print(basic_rocrate)
#> {
#> "@context": "https://w3id.org/ro/crate/1.2/context",
#> "@graph": [
#> {
#> "@id": "ro-crate-metadata.json",
#> "@type": "CreativeWork",
#> "about": {
#> "@id": "./"
#> },
#> "conformsTo": {
#> "@id": "https://w3id.org/ro/crate/1.2"
#> }
#> },
#> {
#> "@id": "./",
#> "@type": "Dataset",
#> "name": "",
#> "description": "",
#> "datePublished": "2026-02-27",
#> "license": {
#> "@id": "http://spdx.org/licenses/CC-BY-4.0"
#> },
#> "conformsTo": {
#> "@id": "https://w3id.org/5s-crate/0.4"
#> }
#> },
#> {
#> "@id": "https://w3id.org/5s-crate/0.4",
#> "@type": ["CreativeWork", "Profile"],
#> "name": "Five Safes RO-Crate profile"
#> }
#> ]
#> }To add details for Safe Data, use the function dsROCrate::safe_data().
basic_rocrate <- o |>
dsROCrate::safe_data(rocrate = basic_rocrate,
project = PROJECT,
tables = TABLES)
print(basic_rocrate) # note that the output will be truncated
...
#> {
#> "@id": "#dataset:67adf2d8e106aca9b11de773758bd241",
#> "@type": "Dataset",
#> "name": "CNSIM1",
#> "dateCreated": "2026-02-27T06:29:50.731Z",
#> "dateModified": "2026-02-27T06:29:51.865Z",
#> "path": "/datasource/CNSIM/table/CNSIM1"
#> }
#> ]
#> }To add details for Safe Project, use the function
dsROCrate::safe_project().
basic_rocrate <- o |>
dsROCrate::safe_project(rocrate = basic_rocrate,
project = PROJECT)
print(basic_rocrate) # note that the output will be truncated
...
#> {
#> "@id": "#project:7ba189863f9f641196596cb28e04aa14",
#> "@type": "Project",
#> "name": "CNSIM",
#> "dateCreated": "2026-02-27T06:29:49.235Z",
#> "dateModified": "2026-02-27T06:29:54.200Z",
#> "hasPart": [
#> {
#> "@id": "#dataset:67adf2d8e106aca9b11de773758bd241"
#> }
#> ]
#> }
#> ]
#> }To add details for Safe People, use the function
dsROCrate::safe_people().
basic_rocrate <- o |>
dsROCrate::safe_people(rocrate = basic_rocrate, user = PEOPLE)
print(basic_rocrate) # note that the output will be truncated
...
#> {
#> "@id": "#person:a0af2a94926db1b49ad7a812eef509d2",
#> "@type": "Person",
#> "name": "dsuser",
#> "memberOf": [
#> {
#> "@id": "#project:7ba189863f9f641196596cb28e04aa14"
#> }
#> ]
#> }
#> ]
#> }To add details for Safe Setting, use the function
dsROCrate::safe_setting().
dsROCrate::safe_setting function requires
administrator privileges, so here, we will have to log in with
administrator credentials (if you used a non-administrator account
previously).
# close previous connection
opalr::opal.logout(o)
# open new connection as administrator
o <- opalr::opal.login(
username = "administrator",
password = "password",
url = SERVER
)Then, we can proceed as per usual:
basic_rocrate <- o |>
dsROCrate::safe_setting(rocrate = basic_rocrate)
print(basic_rocrate) # note that the output will be truncated
...
#> {
#> "@id": "_:localid:datashield.privacyLevel:5",
#> "@type": "PropertyValue",
#> "name": "datashield.privacyLevel",
#> "value": "5"
#> },
#> {
#> "@id": "_:localid:default.datashield.privacyControlLevel:banana",
#> "@type": "PropertyValue",
#> "name": "default.datashield.privacyControlLevel",
#> "value": "banana"
#> },
#> {
#> "@id": "_:localid:default.nfilter.glm:0.33",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.glm",
#> "value": "0.33"
#> },
#> {
#> "@id": "_:localid:default.nfilter.kNN:3",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.kNN",
#> "value": "3"
#> },
#> {
#> "@id": "_:localid:default.nfilter.levels.density:0.33",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.levels.density",
#> "value": "0.33"
#> },
#> {
#> "@id": "_:localid:default.nfilter.levels.max:40",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.levels.max",
#> "value": "40"
#> },
#> {
#> "@id": "_:localid:default.nfilter.noise:0.25",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.noise",
#> "value": "0.25"
#> },
#> {
#> "@id": "_:localid:default.nfilter.string:80",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.string",
#> "value": "80"
#> },
#> {
#> "@id": "_:localid:default.nfilter.stringShort:20",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.stringShort",
#> "value": "20"
#> },
#> {
#> "@id": "_:localid:default.nfilter.subset:3",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.subset",
#> "value": "3"
#> },
#> {
#> "@id": "_:localid:default.nfilter.tab:3",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.tab",
#> "value": "3"
#> },
#> {
#> "@id": "_:localid:3aaeab3631b4c9bbe7f44d60805b8f9c",
#> "@type": "SoftwareApplication",
#> "name": "dsBase",
#> "version": "6.3.5",
#> "description": "Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a software package which allows\n you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have\n been designed to only share non disclosive summary statistics, with built in automated output\n checking based on statistical disclosure control. With data sites setting the threshold values for\n the automated output checks. For more details, see 'citation(\"dsBase\")'."
#> },
#> {
#> "@id": "_:localid:e2f7c43973c40d7a6a6731da5a0aa564",
#> "@type": "SoftwareApplication",
#> "name": "dsTidyverse",
#> "version": "1.1.0",
#> "description": "Implementation of selected 'Tidyverse' functions within 'DataSHIELD', an open-source federated analysis solution in R. Currently, DataSHIELD contains very limited tools for data manipulation, so the aim of this package is to improve the researcher experience by implementing essential functions for data manipulation, including subsetting, filtering, grouping, and renaming variables. This is the serverside package which should be installed on the server holding the data, and is used in conjuncture with the clientside package 'dsTidyverseClient' which is installed in the local R environment of the analyst. For more information, see <https://tidyverse.org/> and <https://datashield.org/>."
#> },
#> {
#> "@id": "_:localid:411453e2513e6d909fe2cb8273b034dc",
#> "@type": "SoftwareApplication",
#> "name": "resourcer",
#> "version": "1.5.0",
#> "description": "A resource represents some data or a computation unit. It is \n described by a URL and credentials. This package proposes a Resource model\n with \"resolver\" and \"client\" classes to facilitate the access and the usage of the \n resources."
#> }
#> ]
#> }To add details for Safe Outputs, use the function
dsROCrate::safe_output(). Currently, only log files from the
operations executed by the user within a specific period. Set the period
using logs_from and logs_to. Additionally, a list of functions
executed by the user are extracted in a separate file/entity.
dsROCrate::safe_setting, the
dsROCrate::safe_output function requires of administrator rights, so
here, we will have to log in with administrator credentials:
# close previous connection
opalr::opal.logout(o)
# open new connection as administrator
o <- opalr::opal.login(
username = "administrator",
password = "password",
url = SERVER
)You will need the following packages:
pak::pak("DSI")
pak::pak("DSOpal")
pak::pak("dsBaseClient")# run some test commands with dsBaseClient
## needed to defined the OpalDriver class in the current environment
DSOpal::Opal()
#> An object of class "OpalDriver"
#> <S4 Type Object>
## create new login object, note that here we use the `dsuser`
builder <- DSI::newDSLoginBuilder()
builder$append(server = "study1",
url = SERVER,
user = "dsuser",
password = DSUSERPASS,
driver = "OpalDriver")
logindata <- builder$build()
conns <- DSI::datashield.login(logins = logindata)
#>
#> Logging into the collaborating servers## assign data
DSI::datashield.assign.table(conns["study1"],
symbol = "dsROCrate_test",
table = paste0(PROJECT, ".", TABLES[1]),
errors.print = TRUE)
dsBaseClient::ds.ls(datasources = conns["study1"])
#> $study1
#> $study1$environment.searched
#> [1] "R_GlobalEnv"
#>
#> $study1$objects.found
#> [1] "dsROCrate_test"
dsBaseClient::ds.summary("dsROCrate_test")
#> $study1
#> $study1$class
#> [1] "data.frame"
#>
#> $study1$`number of rows`
#> [1] 2163
#>
#> $study1$`number of columns`
#> [1] 11
#>
#> $study1$`variables held`
#> [1] "LAB_TSC" "LAB_TRIG" "LAB_HDL"
#> [4] "LAB_GLUC_ADJUSTED" "PM_BMI_CONTINUOUS" "DIS_CVA"
#> [7] "MEDI_LPD" "DIS_DIAB" "DIS_AMI"
#> [10] "GENDER" "PM_BMI_CATEGORICAL"Then, we can proceed as per usual:
basic_rocrate <- o |>
dsROCrate::safe_output(rocrate = basic_rocrate,
logs_from = Sys.time() - 60, # capture the last minute
logs_to = Sys.time())
#> opening file input connection.
#> Found 83 records... Imported 83 records. Simplifying...
#> closing file input connection.
#> Warning: A `path` wasn't provided! The logs will be included in the RO-Crate
#> object, under the `content` tag!print(basic_rocrate) # note that the output will be truncated
...
#> "@type": "SoftwareApplication",
#> "name": "resourcer",
#> "version": "1.5.0",
#> "description": "A resource represents some data or a computation unit. It is \n described by a URL and credentials. This package proposes a Resource model\n with \"resolver\" and \"client\" classes to facilitate the access and the usage of the \n resources."
#> },
#> {
#> "@id": "20260227T152405-dslogs-dsuser.log",
#> "@type": "File",
#> "dateModified": "2026-02-27 15:24:05",
#> "name": "20260227T152405-dslogs-dsuser.log",
#> "description": "This file contains the raw logs for the user: `dsuser` , between: 2026-02-27 15:23:05 and 2026-02-27 15:24:05",
#> "encodingFormat": "text/plain",
#> "content": [
#> ["[INFO][2026-02-27T15:24:02][OPEN] created a datashield session fc258313-6846-4a8e-93d9-4809cd794fbe", "[INFO][2026-02-27T15:24:02][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T15:24:03][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:24:04][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:24:04][PARSE] parsed 'base::exists(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][AGGREGATE] evaluated 'base::exists(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][PARSE] parsed 'dsBase::classDS(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][AGGREGATE] evaluated 'dsBase::classDS(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][PARSE] parsed 'dsBase::isValidDS(dsROCrate_test)'", "[INFO][2026-02-27T15:24:04][AGGREGATE] evaluated 'dsBase::isValidDS(dsROCrate_test)'", "[INFO][2026-02-27T15:24:04][PARSE] parsed 'dsBase::dimDS(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][AGGREGATE] evaluated 'dsBase::dimDS(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][PARSE] parsed 'dsBase::colnamesDS(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:05][AGGREGATE] evaluated 'dsBase::colnamesDS(\"dsROCrate_test\")'"]
#> ]
#> },
#> {
#> "@id": "20260227T152405-dslogs-dsuser_mappings.csv",
#> "@type": "File",
#> "dateModified": "2026-02-27 15:24:05",
#> "name": "20260227T152405-dslogs-dsuser_mappings.csv",
#> "description": "This file contains mappings and evaluated functions",
#> "encodingFormat": "text/csv",
#> "content": [
#> [
#> {
#> "timestamp": "2026-02-27T15:24:02",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "fx": "DSI::datashield.login",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:02",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:04",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:04",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "base::exists(\"dsROCrate_test\")",
#> "fx": "base::exists",
#> "symbol": "dsROCrate_test",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:04",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::classDS(\"dsROCrate_test\")",
#> "fx": "dsBase::classDS",
#> "symbol": "dsROCrate_test",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:04",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::isValidDS(dsROCrate_test)",
#> "fx": "dsBase::isValidDS",
#> "symbol": "dsROCrate_test",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:04",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::dimDS(\"dsROCrate_test\")",
#> "fx": "dsBase::dimDS",
#> "symbol": "dsROCrate_test",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:05",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::colnamesDS(\"dsROCrate_test\")",
#> "fx": "dsBase::colnamesDS",
#> "symbol": "dsROCrate_test",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> }
#> ]
#> ]
#> }
#> ]
#> }opalr::opal.logout(o)The resulting RO-Crate can be stored into an RO-Crate bag/archive with
the function rocrateR::bag_rocrate:
# create temp directory
dir.create("./rocrates", showWarnings = FALSE)NOTE: In the above example, a path to store the logs wasn’t provided
when calling dsROCrate::safe_output, before creating an RO-Crate bag,
we should save the contents of this file first. In addition, the
contents for the entity with the list of functions executed:
logs_entity <- basic_rocrate |>
rocrateR::get_entity(type = "File")
# write file using the path given by `@id`
## write raw logs
writeLines(
logs_entity[[1]]$content[[1]],
file.path("./rocrates", logs_entity[[1]]$`@id`)
)
## write CSV with mappings and executed functions
write.csv(
logs_entity[[2]]$content[[1]],
file.path("./rocrates", logs_entity[[2]]$`@id`),
row.names = FALSE
)
# remove the section `content`
logs_entity[[1]]$content <- NULL
logs_entity[[2]]$content <- NULL
# update the RO-Crate
basic_rocrate <- basic_rocrate |>
rocrateR::add_entity(logs_entity[[1]], overwrite = TRUE) |>
rocrateR::add_entity(logs_entity[[2]], overwrite = TRUE)# create RO-Crate bag
path_to_rocrate_bag <- basic_rocrate |>
rocrateR::bag_rocrate(path = "./rocrates", overwrite = TRUE)
#> RO-Crate successfully 'bagged'!
#> For details, see: ./rocrates/rocrate-200ecad114285e36b84c12cfa3be6526.zipWe can explore the contents with the following commands:
# extract files in temporary directory
path_to_rocrate_bag |>
# extract contents inside ./rocrates/ROC
rocrateR::unbag_rocrate(output = "./rocrates/ROC", quiet = TRUE) |>
# create tree with the files
fs::dir_tree()
#> ./rocrates/ROC/
#> ├── bagit.txt
#> ├── data
#> │ ├── 20260227T152405-dslogs-dsuser.log
#> │ ├── 20260227T152405-dslogs-dsuser_mappings.csv
#> │ └── ro-crate-metadata.json
#> ├── manifest-sha512.txt
#> └── tagmanifest-sha512.txtunlink("./rocrates", recursive = TRUE, force = TRUE)safe_people_crate_v1 <- opalr::opal.login(
username = USERNAME,
password = USERPASS,
url = SERVER
) |>
dsROCrate::audit_safe_people(user = "dsuser", project = "CNSIM")
#> opening file input connection.
#> Found 83 records... Imported 83 records. Simplifying...
#> closing file input connection.
print(safe_people_crate_v1)
#> {
#> "@context": "https://w3id.org/ro/crate/1.2/context",
#> "@graph": [
#> {
#> "@id": "ro-crate-metadata.json",
#> "@type": "CreativeWork",
#> "about": {
#> "@id": "./"
#> },
#> "conformsTo": {
#> "@id": "https://w3id.org/ro/crate/1.2"
#> }
#> },
#> {
#> "@id": "./",
#> "@type": "Dataset",
#> "name": "",
#> "description": "",
#> "datePublished": "2026-02-27",
#> "license": {
#> "@id": "http://spdx.org/licenses/CC-BY-4.0"
#> },
#> "conformsTo": {
#> "@id": "https://w3id.org/5s-crate/0.4"
#> },
#> "hasPart": [
#> {
#> "@id": "20260227T152406-dslogs-dsuser.log"
#> },
#> {
#> "@id": "20260227T152406-dslogs-dsuser_mappings.csv"
#> }
#> ]
#> },
#> {
#> "@id": "https://w3id.org/5s-crate/0.4",
#> "@type": ["CreativeWork", "Profile"],
#> "name": "Five Safes RO-Crate profile"
#> },
#> {
#> "@id": "#dataset:67adf2d8e106aca9b11de773758bd241",
#> "@type": "Dataset",
#> "name": "CNSIM1",
#> "dateCreated": "2026-02-27T06:29:50.731Z",
#> "dateModified": "2026-02-27T06:29:51.865Z",
#> "path": "/datasource/CNSIM/table/CNSIM1"
#> },
#> {
#> "@id": "#dataset:ffb1b1adcafc024743be1b0c252787c9",
#> "@type": "Dataset",
#> "name": "CNSIM2",
#> "dateCreated": "2026-02-27T06:29:51.872Z",
#> "dateModified": "2026-02-27T06:29:53.057Z",
#> "path": "/datasource/CNSIM/table/CNSIM2"
#> },
#> {
#> "@id": "#dataset:cc3061aef69ce457358815fb9d8c6492",
#> "@type": "Dataset",
#> "name": "CNSIM3",
#> "dateCreated": "2026-02-27T06:29:53.064Z",
#> "dateModified": "2026-02-27T06:29:54.200Z",
#> "path": "/datasource/CNSIM/table/CNSIM3"
#> },
#> {
#> "@id": "#project:7ba189863f9f641196596cb28e04aa14",
#> "@type": "Project",
#> "name": "CNSIM",
#> "dateCreated": "2026-02-27T06:29:49.235Z",
#> "dateModified": "2026-02-27T06:29:54.200Z",
#> "hasPart": [
#> {
#> "@id": "#dataset:67adf2d8e106aca9b11de773758bd241"
#> },
#> {
#> "@id": "#dataset:ffb1b1adcafc024743be1b0c252787c9"
#> },
#> {
#> "@id": "#dataset:cc3061aef69ce457358815fb9d8c6492"
#> }
#> ]
#> },
#> {
#> "@id": "#person:a0af2a94926db1b49ad7a812eef509d2",
#> "@type": "Person",
#> "name": "dsuser"
#> },
#> {
#> "@id": "#perm:9bf7f75b6c5b07d02830b95652cd39a0-dict-summary-read",
#> "@type": "ReadAction",
#> "agent": {
#> "@id": "#person:a0af2a94926db1b49ad7a812eef509d2"
#> },
#> "object": {
#> "@id": "#dataset:67adf2d8e106aca9b11de773758bd241"
#> },
#> "actionStatus": "PotentialActionStatus",
#> "description": "User may view table dictionary and summary statistics only; access to individual values is restricted."
#> },
#> {
#> "@id": "#perm:363eb627d1e49c08933f2e26142e6d56-dict-summary-read",
#> "@type": "ReadAction",
#> "agent": {
#> "@id": "#person:a0af2a94926db1b49ad7a812eef509d2"
#> },
#> "object": {
#> "@id": "#dataset:ffb1b1adcafc024743be1b0c252787c9"
#> },
#> "actionStatus": "PotentialActionStatus",
#> "description": "User may view table dictionary and summary statistics only; access to individual values is restricted."
#> },
#> {
#> "@id": "#perm:63b8097908f682bff1760e48d28c5855-dict-summary-read",
#> "@type": "ReadAction",
#> "agent": {
#> "@id": "#person:a0af2a94926db1b49ad7a812eef509d2"
#> },
#> "object": {
#> "@id": "#dataset:cc3061aef69ce457358815fb9d8c6492"
#> },
#> "actionStatus": "PotentialActionStatus",
#> "description": "User may view table dictionary and summary statistics only; access to individual values is restricted."
#> },
#> {
#> "@id": "_:localid:datashield.privacyLevel:5",
#> "@type": "PropertyValue",
#> "name": "datashield.privacyLevel",
#> "value": "5"
#> },
#> {
#> "@id": "_:localid:default.datashield.privacyControlLevel:banana",
#> "@type": "PropertyValue",
#> "name": "default.datashield.privacyControlLevel",
#> "value": "banana"
#> },
#> {
#> "@id": "_:localid:default.nfilter.glm:0.33",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.glm",
#> "value": "0.33"
#> },
#> {
#> "@id": "_:localid:default.nfilter.kNN:3",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.kNN",
#> "value": "3"
#> },
#> {
#> "@id": "_:localid:default.nfilter.levels.density:0.33",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.levels.density",
#> "value": "0.33"
#> },
#> {
#> "@id": "_:localid:default.nfilter.levels.max:40",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.levels.max",
#> "value": "40"
#> },
#> {
#> "@id": "_:localid:default.nfilter.noise:0.25",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.noise",
#> "value": "0.25"
#> },
#> {
#> "@id": "_:localid:default.nfilter.string:80",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.string",
#> "value": "80"
#> },
#> {
#> "@id": "_:localid:default.nfilter.stringShort:20",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.stringShort",
#> "value": "20"
#> },
#> {
#> "@id": "_:localid:default.nfilter.subset:3",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.subset",
#> "value": "3"
#> },
#> {
#> "@id": "_:localid:default.nfilter.tab:3",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.tab",
#> "value": "3"
#> },
#> {
#> "@id": "_:localid:3aaeab3631b4c9bbe7f44d60805b8f9c",
#> "@type": "SoftwareApplication",
#> "name": "dsBase",
#> "version": "6.3.5",
#> "description": "Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a software package which allows\n you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have\n been designed to only share non disclosive summary statistics, with built in automated output\n checking based on statistical disclosure control. With data sites setting the threshold values for\n the automated output checks. For more details, see 'citation(\"dsBase\")'."
#> },
#> {
#> "@id": "_:localid:e2f7c43973c40d7a6a6731da5a0aa564",
#> "@type": "SoftwareApplication",
#> "name": "dsTidyverse",
#> "version": "1.1.0",
#> "description": "Implementation of selected 'Tidyverse' functions within 'DataSHIELD', an open-source federated analysis solution in R. Currently, DataSHIELD contains very limited tools for data manipulation, so the aim of this package is to improve the researcher experience by implementing essential functions for data manipulation, including subsetting, filtering, grouping, and renaming variables. This is the serverside package which should be installed on the server holding the data, and is used in conjuncture with the clientside package 'dsTidyverseClient' which is installed in the local R environment of the analyst. For more information, see <https://tidyverse.org/> and <https://datashield.org/>."
#> },
#> {
#> "@id": "_:localid:411453e2513e6d909fe2cb8273b034dc",
#> "@type": "SoftwareApplication",
#> "name": "resourcer",
#> "version": "1.5.0",
#> "description": "A resource represents some data or a computation unit. It is \n described by a URL and credentials. This package proposes a Resource model\n with \"resolver\" and \"client\" classes to facilitate the access and the usage of the \n resources."
#> },
#> {
#> "@id": "20260227T152406-dslogs-dsuser.log",
#> "@type": "File",
#> "dateModified": "2026-02-27 15:24:06",
#> "name": "20260227T152406-dslogs-dsuser.log",
#> "description": "This file contains the raw logs for the user: `dsuser` , between: ALL and ALL",
#> "encodingFormat": "text/plain",
#> "content": [
#> ["[INFO][2026-02-27T08:56:24][OPEN] created a datashield session 622f2c74-9242-48e2-82d9-bc3250f8aa4b", "[INFO][2026-02-27T08:56:26][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T08:56:26][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T08:56:27][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T09:00:37][OPEN] created a datashield session 7925f5e8-f7b6-416e-b05b-5ac2c19f00c1", "[INFO][2026-02-27T09:00:37][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T09:00:38][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T09:00:38][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T09:20:47][OPEN] created a datashield session 08413766-4fa8-4eec-9392-ec30581fb48c", "[INFO][2026-02-27T09:20:48][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T09:20:48][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T09:20:49][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T14:08:39][OPEN] created a datashield session 88a48432-61c8-4444-bb6f-1d0174d4f177", "[INFO][2026-02-27T14:08:39][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T14:08:39][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T14:08:40][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T14:18:40][OPEN] created a datashield session e45b3573-21cc-445d-8d22-b7fc289d279a", "[INFO][2026-02-27T14:18:40][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T14:18:40][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T14:18:41][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:04:13][OPEN] created a datashield session 026b4b18-c40c-4f08-8a19-75716fee1c75", "[INFO][2026-02-27T15:04:13][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T15:04:14][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:04:14][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:13:01][OPEN] created a datashield session a3a6f257-79ef-443c-a110-393b1ff196f0", "[INFO][2026-02-27T15:13:01][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T15:13:02][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:13:03][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:24:02][OPEN] created a datashield session fc258313-6846-4a8e-93d9-4809cd794fbe", "[INFO][2026-02-27T15:24:02][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T15:24:03][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:24:04][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:24:04][PARSE] parsed 'base::exists(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][AGGREGATE] evaluated 'base::exists(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][PARSE] parsed 'dsBase::classDS(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][AGGREGATE] evaluated 'dsBase::classDS(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][PARSE] parsed 'dsBase::isValidDS(dsROCrate_test)'", "[INFO][2026-02-27T15:24:04][AGGREGATE] evaluated 'dsBase::isValidDS(dsROCrate_test)'", "[INFO][2026-02-27T15:24:04][PARSE] parsed 'dsBase::dimDS(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][AGGREGATE] evaluated 'dsBase::dimDS(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][PARSE] parsed 'dsBase::colnamesDS(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:05][AGGREGATE] evaluated 'dsBase::colnamesDS(\"dsROCrate_test\")'"]
#> ]
#> },
#> {
#> "@id": "20260227T152406-dslogs-dsuser_mappings.csv",
#> "@type": "File",
#> "dateModified": "2026-02-27 15:24:06",
#> "name": "20260227T152406-dslogs-dsuser_mappings.csv",
#> "description": "This file contains mappings and evaluated functions",
#> "encodingFormat": "text/csv",
#> "content": [
#> [
#> {
#> "timestamp": "2026-02-27T08:56:24",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: 622f2c74-9242-48e2-82d9-bc3250f8aa4b",
#> "fx": "DSI::datashield.login",
#> "session": "622f2c74-9242-48e2-82d9-bc3250f8aa4b",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T08:56:26",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "622f2c74-9242-48e2-82d9-bc3250f8aa4b",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T08:56:27",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "622f2c74-9242-48e2-82d9-bc3250f8aa4b",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T09:00:37",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: 7925f5e8-f7b6-416e-b05b-5ac2c19f00c1",
#> "fx": "DSI::datashield.login",
#> "session": "7925f5e8-f7b6-416e-b05b-5ac2c19f00c1",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T09:00:37",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "7925f5e8-f7b6-416e-b05b-5ac2c19f00c1",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T09:00:38",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "7925f5e8-f7b6-416e-b05b-5ac2c19f00c1",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T09:20:47",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: 08413766-4fa8-4eec-9392-ec30581fb48c",
#> "fx": "DSI::datashield.login",
#> "session": "08413766-4fa8-4eec-9392-ec30581fb48c",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T09:20:48",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "08413766-4fa8-4eec-9392-ec30581fb48c",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T09:20:49",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "08413766-4fa8-4eec-9392-ec30581fb48c",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T14:08:39",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: 88a48432-61c8-4444-bb6f-1d0174d4f177",
#> "fx": "DSI::datashield.login",
#> "session": "88a48432-61c8-4444-bb6f-1d0174d4f177",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T14:08:39",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "88a48432-61c8-4444-bb6f-1d0174d4f177",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T14:08:40",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "88a48432-61c8-4444-bb6f-1d0174d4f177",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T14:18:40",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: e45b3573-21cc-445d-8d22-b7fc289d279a",
#> "fx": "DSI::datashield.login",
#> "session": "e45b3573-21cc-445d-8d22-b7fc289d279a",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T14:18:40",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "e45b3573-21cc-445d-8d22-b7fc289d279a",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T14:18:41",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "e45b3573-21cc-445d-8d22-b7fc289d279a",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:04:13",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: 026b4b18-c40c-4f08-8a19-75716fee1c75",
#> "fx": "DSI::datashield.login",
#> "session": "026b4b18-c40c-4f08-8a19-75716fee1c75",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:04:13",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "026b4b18-c40c-4f08-8a19-75716fee1c75",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:04:14",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "026b4b18-c40c-4f08-8a19-75716fee1c75",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:13:01",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: a3a6f257-79ef-443c-a110-393b1ff196f0",
#> "fx": "DSI::datashield.login",
#> "session": "a3a6f257-79ef-443c-a110-393b1ff196f0",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:13:01",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "a3a6f257-79ef-443c-a110-393b1ff196f0",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:13:03",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "a3a6f257-79ef-443c-a110-393b1ff196f0",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:02",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "fx": "DSI::datashield.login",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:02",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:04",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:04",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "base::exists(\"dsROCrate_test\")",
#> "fx": "base::exists",
#> "symbol": "dsROCrate_test",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:04",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::classDS(\"dsROCrate_test\")",
#> "fx": "dsBase::classDS",
#> "symbol": "dsROCrate_test",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:04",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::isValidDS(dsROCrate_test)",
#> "fx": "dsBase::isValidDS",
#> "symbol": "dsROCrate_test",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:04",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::dimDS(\"dsROCrate_test\")",
#> "fx": "dsBase::dimDS",
#> "symbol": "dsROCrate_test",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:05",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::colnamesDS(\"dsROCrate_test\")",
#> "fx": "dsBase::colnamesDS",
#> "symbol": "dsROCrate_test",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> }
#> ]
#> ]
#> }
#> ]
#> }A markdown report can be created with an overview and details for an
RO-Crate, using the dsROCrate::rocrate_report:
Only generate .Rmd file
safe_people_crate_v1_rmd <- tempfile(fileext = ".Rmd") # temporary file
safe_people_crate_contents <- safe_people_crate_v1 |>
dsROCrate::rocrate_report(filepath = safe_people_crate_v1_rmd, render = FALSE)
#> 1 'Author' entity was found!
#> 3 'Dataset' entities were found!
#> Warning: No entities were found with @type = 'WriteAction'!
#> Warning: No entities were found with @type = 'ControlAction'!
#> 1 'Project' entity was found!
#> 14 'PropertyValue' OR 'SoftwareApplication' entities were found!
#> 2 'File' entities were found!
# display Overview diagram
safe_people_crate_contents$overview_diagram
# display Overview data (Safe People, Safe Projects and Safe Data)
safe_people_crate_contents$overview_data |>
knitr::kable()| Project | Data | Access Level | People | Function | Timestamp |
|---|---|---|---|---|---|
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T08:56:26 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T08:56:27 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T09:00:37 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T09:00:38 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T09:20:48 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T09:20:49 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T14:08:39 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T14:08:40 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T14:18:40 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T14:18:41 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T15:04:13 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T15:04:14 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T15:13:01 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T15:13:03 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T15:24:02 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T15:24:04 |
| CNSIM | CNSIM1 | read | dsuser | base::exists | 2026-02-27T15:24:04 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::classDS | 2026-02-27T15:24:04 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::isValidDS | 2026-02-27T15:24:04 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::dimDS | 2026-02-27T15:24:04 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::colnamesDS | 2026-02-27T15:24:05 |
| CNSIM | CNSIM2 | read | dsuser | ||
| CNSIM | CNSIM3 | read | dsuser |
Render and display report (HTML)
safe_people_crate_v1 |>
dsROCrate::rocrate_report(filepath = safe_people_crate_v1_rmd,
title = "DataSHIELD Safe People - Audit Report",
render = TRUE,
overwrite = TRUE)safe_people_crate_v2 <- opalr::opal.login(
username = USERNAME,
password = USERPASS,
url = SERVER
) |>
dsROCrate::audit_safe_people(user = "dsuser")
#> opening file input connection.
#> Found 83 records... Imported 83 records. Simplifying...
#> closing file input connection.
safe_people_crate_v2_rmd <- tempfile(fileext = ".Rmd") # temporary file
safe_people_crate_contents_v2 <- safe_people_crate_v2 |>
dsROCrate::rocrate_report(filepath = safe_people_crate_v2_rmd, render = FALSE)
#> 1 'Author' entity was found!
#> 30 'Dataset' entities were found!
#> 11 'Project' entities were found!
#> 14 'PropertyValue' OR 'SoftwareApplication' entities were found!
#> 2 'File' entities were found!
# display Overview diagram
safe_people_crate_contents_v2$overview_diagram
# display Overview data (Safe People, Safe Projects and Safe Data)
safe_people_crate_contents_v2$overview_data |>
knitr::kable()| Project | Data | Access Level | People | Function | Timestamp |
|---|---|---|---|---|---|
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T08:56:26 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T08:56:27 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T09:00:37 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T09:00:38 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T09:20:48 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T09:20:49 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T14:08:39 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T14:08:40 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T14:18:40 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T14:18:41 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T15:04:13 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T15:04:14 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T15:13:01 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T15:13:03 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T15:24:02 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T15:24:04 |
| CNSIM | CNSIM1 | read | dsuser | base::exists | 2026-02-27T15:24:04 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::classDS | 2026-02-27T15:24:04 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::isValidDS | 2026-02-27T15:24:04 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::dimDS | 2026-02-27T15:24:04 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::colnamesDS | 2026-02-27T15:24:05 |
| CNSIM | CNSIM2 | read | dsuser | ||
| CNSIM | CNSIM3 | read | dsuser | ||
| DASIM | DASIM1 | read | dsuser | ||
| DASIM | DASIM2 | read | dsuser | ||
| DASIM | DASIM3 | read | dsuser | ||
| DISCORDANT | DISCORDANT_STUDY1 | read | dsuser | ||
| DISCORDANT | DISCORDANT_STUDY2 | read | dsuser | ||
| DISCORDANT | DISCORDANT_STUDY3 | read | dsuser | ||
| GREENSPACE | Cohort1_exposome | read | dsuser | ||
| GREENSPACE | Cohort2_exposome | read | dsuser | ||
| GREENSPACE | Cohort3_exposome | read | dsuser | ||
| GWAS | ega_phenotypes | read | dsuser | ||
| GWAS | ega_phenotypes_1 | read | dsuser | ||
| GWAS | ega_phenotypes_2 | read | dsuser | ||
| GWAS | ega_phenotypes_3 | read | dsuser | ||
| MEDIATION | UPBdata1 | read | dsuser | ||
| MEDIATION | UPBdata2 | read | dsuser | ||
| MEDIATION | UPBdata3 | read | dsuser | ||
| SURVIVAL | EXPAND_WITH_MISSING1 | read | dsuser | ||
| SURVIVAL | EXPAND_WITH_MISSING2 | read | dsuser | ||
| SURVIVAL | EXPAND_WITH_MISSING3 | read | dsuser | ||
| TESTING | TESTING1 | read | dsuser | ||
| TESTING | TESTING2 | read | dsuser | ||
| TESTING | TESTING3 | read | dsuser | ||
| TITANIC_NEWCOMERS_WORKSHOP | titanic_server_1 | read | dsuser | ||
| TITANIC_NEWCOMERS_WORKSHOP | titanic_server_2 | read | dsuser | ||
| depression | growth_1 | read | dsuser | ||
| depression | growth_2 | read | dsuser | ||
| serverDataKey | myKey | read | dsuser |
safe_project_crate_v1 <- opalr::opal.login(
username = USERNAME,
password = USERPASS,
url = SERVER
) |>
dsROCrate::audit_safe_project(project = "CNSIM")
#> opening file input connection.
#> Found 83 records... Imported 83 records. Simplifying...
#> closing file input connection.
print(safe_project_crate_v1)
#> {
#> "@context": "https://w3id.org/ro/crate/1.2/context",
#> "@graph": [
#> {
#> "@id": "ro-crate-metadata.json",
#> "@type": "CreativeWork",
#> "about": {
#> "@id": "./"
#> },
#> "conformsTo": {
#> "@id": "https://w3id.org/ro/crate/1.2"
#> }
#> },
#> {
#> "@id": "./",
#> "@type": "Dataset",
#> "name": "",
#> "description": "",
#> "datePublished": "2026-02-27",
#> "license": {
#> "@id": "http://spdx.org/licenses/CC-BY-4.0"
#> },
#> "conformsTo": {
#> "@id": "https://w3id.org/5s-crate/0.4"
#> },
#> "hasPart": [
#> {
#> "@id": "20260227T152439-dslogs-dsuser.log"
#> },
#> {
#> "@id": "20260227T152439-dslogs-dsuser_mappings.csv"
#> }
#> ]
#> },
#> {
#> "@id": "https://w3id.org/5s-crate/0.4",
#> "@type": ["CreativeWork", "Profile"],
#> "name": "Five Safes RO-Crate profile"
#> },
#> {
#> "@id": "#dataset:67adf2d8e106aca9b11de773758bd241",
#> "@type": "Dataset",
#> "name": "CNSIM1",
#> "dateCreated": "2026-02-27T06:29:50.731Z",
#> "dateModified": "2026-02-27T06:29:51.865Z",
#> "path": "/datasource/CNSIM/table/CNSIM1"
#> },
#> {
#> "@id": "#dataset:ffb1b1adcafc024743be1b0c252787c9",
#> "@type": "Dataset",
#> "name": "CNSIM2",
#> "dateCreated": "2026-02-27T06:29:51.872Z",
#> "dateModified": "2026-02-27T06:29:53.057Z",
#> "path": "/datasource/CNSIM/table/CNSIM2"
#> },
#> {
#> "@id": "#dataset:cc3061aef69ce457358815fb9d8c6492",
#> "@type": "Dataset",
#> "name": "CNSIM3",
#> "dateCreated": "2026-02-27T06:29:53.064Z",
#> "dateModified": "2026-02-27T06:29:54.200Z",
#> "path": "/datasource/CNSIM/table/CNSIM3"
#> },
#> {
#> "@id": "#project:7ba189863f9f641196596cb28e04aa14",
#> "@type": "Project",
#> "name": "CNSIM",
#> "dateCreated": "2026-02-27T06:29:49.235Z",
#> "dateModified": "2026-02-27T06:29:54.200Z",
#> "hasPart": [
#> {
#> "@id": "#dataset:67adf2d8e106aca9b11de773758bd241"
#> },
#> {
#> "@id": "#dataset:ffb1b1adcafc024743be1b0c252787c9"
#> },
#> {
#> "@id": "#dataset:cc3061aef69ce457358815fb9d8c6492"
#> }
#> ]
#> },
#> {
#> "@id": "#person:a0af2a94926db1b49ad7a812eef509d2",
#> "@type": "Person",
#> "name": "dsuser"
#> },
#> {
#> "@id": "#perm:9bf7f75b6c5b07d02830b95652cd39a0-dict-summary-read",
#> "@type": "ReadAction",
#> "agent": {
#> "@id": "#person:a0af2a94926db1b49ad7a812eef509d2"
#> },
#> "object": {
#> "@id": "#dataset:67adf2d8e106aca9b11de773758bd241"
#> },
#> "actionStatus": "PotentialActionStatus",
#> "description": "User may view table dictionary and summary statistics only; access to individual values is restricted."
#> },
#> {
#> "@id": "#perm:363eb627d1e49c08933f2e26142e6d56-dict-summary-read",
#> "@type": "ReadAction",
#> "agent": {
#> "@id": "#person:a0af2a94926db1b49ad7a812eef509d2"
#> },
#> "object": {
#> "@id": "#dataset:ffb1b1adcafc024743be1b0c252787c9"
#> },
#> "actionStatus": "PotentialActionStatus",
#> "description": "User may view table dictionary and summary statistics only; access to individual values is restricted."
#> },
#> {
#> "@id": "#perm:63b8097908f682bff1760e48d28c5855-dict-summary-read",
#> "@type": "ReadAction",
#> "agent": {
#> "@id": "#person:a0af2a94926db1b49ad7a812eef509d2"
#> },
#> "object": {
#> "@id": "#dataset:cc3061aef69ce457358815fb9d8c6492"
#> },
#> "actionStatus": "PotentialActionStatus",
#> "description": "User may view table dictionary and summary statistics only; access to individual values is restricted."
#> },
#> {
#> "@id": "_:localid:datashield.privacyLevel:5",
#> "@type": "PropertyValue",
#> "name": "datashield.privacyLevel",
#> "value": "5"
#> },
#> {
#> "@id": "_:localid:default.datashield.privacyControlLevel:banana",
#> "@type": "PropertyValue",
#> "name": "default.datashield.privacyControlLevel",
#> "value": "banana"
#> },
#> {
#> "@id": "_:localid:default.nfilter.glm:0.33",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.glm",
#> "value": "0.33"
#> },
#> {
#> "@id": "_:localid:default.nfilter.kNN:3",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.kNN",
#> "value": "3"
#> },
#> {
#> "@id": "_:localid:default.nfilter.levels.density:0.33",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.levels.density",
#> "value": "0.33"
#> },
#> {
#> "@id": "_:localid:default.nfilter.levels.max:40",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.levels.max",
#> "value": "40"
#> },
#> {
#> "@id": "_:localid:default.nfilter.noise:0.25",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.noise",
#> "value": "0.25"
#> },
#> {
#> "@id": "_:localid:default.nfilter.string:80",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.string",
#> "value": "80"
#> },
#> {
#> "@id": "_:localid:default.nfilter.stringShort:20",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.stringShort",
#> "value": "20"
#> },
#> {
#> "@id": "_:localid:default.nfilter.subset:3",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.subset",
#> "value": "3"
#> },
#> {
#> "@id": "_:localid:default.nfilter.tab:3",
#> "@type": "PropertyValue",
#> "name": "default.nfilter.tab",
#> "value": "3"
#> },
#> {
#> "@id": "_:localid:3aaeab3631b4c9bbe7f44d60805b8f9c",
#> "@type": "SoftwareApplication",
#> "name": "dsBase",
#> "version": "6.3.5",
#> "description": "Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a software package which allows\n you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have\n been designed to only share non disclosive summary statistics, with built in automated output\n checking based on statistical disclosure control. With data sites setting the threshold values for\n the automated output checks. For more details, see 'citation(\"dsBase\")'."
#> },
#> {
#> "@id": "_:localid:e2f7c43973c40d7a6a6731da5a0aa564",
#> "@type": "SoftwareApplication",
#> "name": "dsTidyverse",
#> "version": "1.1.0",
#> "description": "Implementation of selected 'Tidyverse' functions within 'DataSHIELD', an open-source federated analysis solution in R. Currently, DataSHIELD contains very limited tools for data manipulation, so the aim of this package is to improve the researcher experience by implementing essential functions for data manipulation, including subsetting, filtering, grouping, and renaming variables. This is the serverside package which should be installed on the server holding the data, and is used in conjuncture with the clientside package 'dsTidyverseClient' which is installed in the local R environment of the analyst. For more information, see <https://tidyverse.org/> and <https://datashield.org/>."
#> },
#> {
#> "@id": "_:localid:411453e2513e6d909fe2cb8273b034dc",
#> "@type": "SoftwareApplication",
#> "name": "resourcer",
#> "version": "1.5.0",
#> "description": "A resource represents some data or a computation unit. It is \n described by a URL and credentials. This package proposes a Resource model\n with \"resolver\" and \"client\" classes to facilitate the access and the usage of the \n resources."
#> },
#> {
#> "@id": "20260227T152439-dslogs-dsuser.log",
#> "@type": "File",
#> "dateModified": "2026-02-27 15:24:39",
#> "name": "20260227T152439-dslogs-dsuser.log",
#> "description": "This file contains the raw logs for the user: `dsuser` , between: ALL and ALL",
#> "encodingFormat": "text/plain",
#> "content": [
#> ["[INFO][2026-02-27T08:56:24][OPEN] created a datashield session 622f2c74-9242-48e2-82d9-bc3250f8aa4b", "[INFO][2026-02-27T08:56:26][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T08:56:26][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T08:56:27][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T09:00:37][OPEN] created a datashield session 7925f5e8-f7b6-416e-b05b-5ac2c19f00c1", "[INFO][2026-02-27T09:00:37][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T09:00:38][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T09:00:38][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T09:20:47][OPEN] created a datashield session 08413766-4fa8-4eec-9392-ec30581fb48c", "[INFO][2026-02-27T09:20:48][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T09:20:48][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T09:20:49][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T14:08:39][OPEN] created a datashield session 88a48432-61c8-4444-bb6f-1d0174d4f177", "[INFO][2026-02-27T14:08:39][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T14:08:39][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T14:08:40][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T14:18:40][OPEN] created a datashield session e45b3573-21cc-445d-8d22-b7fc289d279a", "[INFO][2026-02-27T14:18:40][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T14:18:40][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T14:18:41][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:04:13][OPEN] created a datashield session 026b4b18-c40c-4f08-8a19-75716fee1c75", "[INFO][2026-02-27T15:04:13][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T15:04:14][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:04:14][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:13:01][OPEN] created a datashield session a3a6f257-79ef-443c-a110-393b1ff196f0", "[INFO][2026-02-27T15:13:01][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T15:13:02][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:13:03][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:24:02][OPEN] created a datashield session fc258313-6846-4a8e-93d9-4809cd794fbe", "[INFO][2026-02-27T15:24:02][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T15:24:03][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:24:04][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:24:04][PARSE] parsed 'base::exists(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][AGGREGATE] evaluated 'base::exists(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][PARSE] parsed 'dsBase::classDS(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][AGGREGATE] evaluated 'dsBase::classDS(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][PARSE] parsed 'dsBase::isValidDS(dsROCrate_test)'", "[INFO][2026-02-27T15:24:04][AGGREGATE] evaluated 'dsBase::isValidDS(dsROCrate_test)'", "[INFO][2026-02-27T15:24:04][PARSE] parsed 'dsBase::dimDS(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][AGGREGATE] evaluated 'dsBase::dimDS(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][PARSE] parsed 'dsBase::colnamesDS(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:05][AGGREGATE] evaluated 'dsBase::colnamesDS(\"dsROCrate_test\")'"]
#> ]
#> },
#> {
#> "@id": "20260227T152439-dslogs-dsuser_mappings.csv",
#> "@type": "File",
#> "dateModified": "2026-02-27 15:24:39",
#> "name": "20260227T152439-dslogs-dsuser_mappings.csv",
#> "description": "This file contains mappings and evaluated functions",
#> "encodingFormat": "text/csv",
#> "content": [
#> [
#> {
#> "timestamp": "2026-02-27T08:56:24",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: 622f2c74-9242-48e2-82d9-bc3250f8aa4b",
#> "fx": "DSI::datashield.login",
#> "session": "622f2c74-9242-48e2-82d9-bc3250f8aa4b",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T08:56:26",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "622f2c74-9242-48e2-82d9-bc3250f8aa4b",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T08:56:27",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "622f2c74-9242-48e2-82d9-bc3250f8aa4b",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T09:00:37",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: 7925f5e8-f7b6-416e-b05b-5ac2c19f00c1",
#> "fx": "DSI::datashield.login",
#> "session": "7925f5e8-f7b6-416e-b05b-5ac2c19f00c1",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T09:00:37",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "7925f5e8-f7b6-416e-b05b-5ac2c19f00c1",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T09:00:38",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "7925f5e8-f7b6-416e-b05b-5ac2c19f00c1",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T09:20:47",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: 08413766-4fa8-4eec-9392-ec30581fb48c",
#> "fx": "DSI::datashield.login",
#> "session": "08413766-4fa8-4eec-9392-ec30581fb48c",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T09:20:48",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "08413766-4fa8-4eec-9392-ec30581fb48c",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T09:20:49",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "08413766-4fa8-4eec-9392-ec30581fb48c",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T14:08:39",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: 88a48432-61c8-4444-bb6f-1d0174d4f177",
#> "fx": "DSI::datashield.login",
#> "session": "88a48432-61c8-4444-bb6f-1d0174d4f177",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T14:08:39",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "88a48432-61c8-4444-bb6f-1d0174d4f177",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T14:08:40",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "88a48432-61c8-4444-bb6f-1d0174d4f177",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T14:18:40",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: e45b3573-21cc-445d-8d22-b7fc289d279a",
#> "fx": "DSI::datashield.login",
#> "session": "e45b3573-21cc-445d-8d22-b7fc289d279a",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T14:18:40",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "e45b3573-21cc-445d-8d22-b7fc289d279a",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T14:18:41",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "e45b3573-21cc-445d-8d22-b7fc289d279a",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:04:13",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: 026b4b18-c40c-4f08-8a19-75716fee1c75",
#> "fx": "DSI::datashield.login",
#> "session": "026b4b18-c40c-4f08-8a19-75716fee1c75",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:04:13",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "026b4b18-c40c-4f08-8a19-75716fee1c75",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:04:14",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "026b4b18-c40c-4f08-8a19-75716fee1c75",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:13:01",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: a3a6f257-79ef-443c-a110-393b1ff196f0",
#> "fx": "DSI::datashield.login",
#> "session": "a3a6f257-79ef-443c-a110-393b1ff196f0",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:13:01",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "a3a6f257-79ef-443c-a110-393b1ff196f0",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:13:03",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "a3a6f257-79ef-443c-a110-393b1ff196f0",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:02",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "fx": "DSI::datashield.login",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:02",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:04",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:04",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "base::exists(\"dsROCrate_test\")",
#> "fx": "base::exists",
#> "symbol": "dsROCrate_test",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:04",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::classDS(\"dsROCrate_test\")",
#> "fx": "dsBase::classDS",
#> "symbol": "dsROCrate_test",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:04",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::isValidDS(dsROCrate_test)",
#> "fx": "dsBase::isValidDS",
#> "symbol": "dsROCrate_test",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:04",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::dimDS(\"dsROCrate_test\")",
#> "fx": "dsBase::dimDS",
#> "symbol": "dsROCrate_test",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:05",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::colnamesDS(\"dsROCrate_test\")",
#> "fx": "dsBase::colnamesDS",
#> "symbol": "dsROCrate_test",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> }
#> ]
#> ]
#> }
#> ]
#> }A markdown report can be created with an overview and details for an
RO-Crate, using the dsROCrate::rocrate_report:
Only generate .Rmd file
safe_project_crate_v1_rmd <- tempfile(fileext = ".Rmd") # temporary file
safe_project_crate_contents <- safe_project_crate_v1 |>
dsROCrate::rocrate_report(filepath = safe_project_crate_v1_rmd, render = FALSE)
#> 1 'Author' entity was found!
#> 3 'Dataset' entities were found!
#> Warning: No entities were found with @type = 'WriteAction'!
#> Warning: No entities were found with @type = 'ControlAction'!
#> 1 'Project' entity was found!
#> 14 'PropertyValue' OR 'SoftwareApplication' entities were found!
#> 2 'File' entities were found!
# display Overview diagram
safe_project_crate_contents$overview_diagram
# display Overview data (Safe People, Safe Projects and Safe Data)
safe_project_crate_contents$overview_data |>
knitr::kable()| Project | Data | Access Level | People | Function | Timestamp |
|---|---|---|---|---|---|
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T08:56:26 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T08:56:27 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T09:00:37 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T09:00:38 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T09:20:48 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T09:20:49 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T14:08:39 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T14:08:40 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T14:18:40 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T14:18:41 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T15:04:13 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T15:04:14 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T15:13:01 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T15:13:03 |
| CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T15:24:02 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T15:24:04 |
| CNSIM | CNSIM1 | read | dsuser | base::exists | 2026-02-27T15:24:04 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::classDS | 2026-02-27T15:24:04 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::isValidDS | 2026-02-27T15:24:04 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::dimDS | 2026-02-27T15:24:04 |
| CNSIM | CNSIM1 | read | dsuser | dsBase::colnamesDS | 2026-02-27T15:24:05 |
| CNSIM | CNSIM2 | read | dsuser | ||
| CNSIM | CNSIM3 | read | dsuser |
Render and display report (HTML)
safe_project_crate_v1 |>
dsROCrate::rocrate_report(filepath = safe_project_crate_v1_rmd,
title = "DataSHIELD Safe Project - Audit Report",
render = TRUE,
overwrite = TRUE)study_crate_v1 <-
list(
"opal_test" = opalr::opal.login(
username = USERNAME,
password = USERPASS,
url = "https://opal-test.obiba.org"
),
"opal_demo" = opalr::opal.login(
username = USERNAME,
password = USERPASS,
url = "https://opal-demo.obiba.org"
)
) |>
dsROCrate::audit_study(project = "CNSIM")
print(study_crate_v1)
#> $opal_test
#> {
#> "@context": "https://w3id.org/ro/crate/1.2/context",
#> "@graph": [
#> {
#> "@id": "ro-crate-metadata.json",
#> "@type": "CreativeWork",
#> "about": {
#> "@id": "./"
#> },
#> "conformsTo": {
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#> "name": "20260227T152444-dslogs-dsuser.log",
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#> ["[INFO][2026-02-27T08:56:24][OPEN] created a datashield session 622f2c74-9242-48e2-82d9-bc3250f8aa4b", "[INFO][2026-02-27T08:56:26][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T08:56:26][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T08:56:27][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T09:00:37][OPEN] created a datashield session 7925f5e8-f7b6-416e-b05b-5ac2c19f00c1", "[INFO][2026-02-27T09:00:37][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T09:00:38][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T09:00:38][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T09:20:47][OPEN] created a datashield session 08413766-4fa8-4eec-9392-ec30581fb48c", "[INFO][2026-02-27T09:20:48][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T09:20:48][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T09:20:49][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T14:08:39][OPEN] created a datashield session 88a48432-61c8-4444-bb6f-1d0174d4f177", "[INFO][2026-02-27T14:08:39][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T14:08:39][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T14:08:40][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T14:18:40][OPEN] created a datashield session e45b3573-21cc-445d-8d22-b7fc289d279a", "[INFO][2026-02-27T14:18:40][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T14:18:40][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T14:18:41][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:04:13][OPEN] created a datashield session 026b4b18-c40c-4f08-8a19-75716fee1c75", "[INFO][2026-02-27T15:04:13][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T15:04:14][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:04:14][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:13:01][OPEN] created a datashield session a3a6f257-79ef-443c-a110-393b1ff196f0", "[INFO][2026-02-27T15:13:01][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T15:13:02][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:13:03][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:24:02][OPEN] created a datashield session fc258313-6846-4a8e-93d9-4809cd794fbe", "[INFO][2026-02-27T15:24:02][ASSIGN] created symbol 'dsROCrate_test' from: 'dsROCrate_test <- opal[CNSIM.CNSIM1]'", "[INFO][2026-02-27T15:24:03][PARSE] parsed 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:24:04][AGGREGATE] evaluated 'dsBase::lsDS(search.filter = NULL, 1L)'", "[INFO][2026-02-27T15:24:04][PARSE] parsed 'base::exists(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][AGGREGATE] evaluated 'base::exists(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][PARSE] parsed 'dsBase::classDS(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][AGGREGATE] evaluated 'dsBase::classDS(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][PARSE] parsed 'dsBase::isValidDS(dsROCrate_test)'", "[INFO][2026-02-27T15:24:04][AGGREGATE] evaluated 'dsBase::isValidDS(dsROCrate_test)'", "[INFO][2026-02-27T15:24:04][PARSE] parsed 'dsBase::dimDS(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][AGGREGATE] evaluated 'dsBase::dimDS(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:04][PARSE] parsed 'dsBase::colnamesDS(\"dsROCrate_test\")'", "[INFO][2026-02-27T15:24:05][AGGREGATE] evaluated 'dsBase::colnamesDS(\"dsROCrate_test\")'"]
#> ]
#> },
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#> "@type": "File",
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#> [
#> {
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#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: 622f2c74-9242-48e2-82d9-bc3250f8aa4b",
#> "fx": "DSI::datashield.login",
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#> {
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#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
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#> {
#> "timestamp": "2026-02-27T09:00:37",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: 7925f5e8-f7b6-416e-b05b-5ac2c19f00c1",
#> "fx": "DSI::datashield.login",
#> "session": "7925f5e8-f7b6-416e-b05b-5ac2c19f00c1",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T09:00:37",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "7925f5e8-f7b6-416e-b05b-5ac2c19f00c1",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T09:00:38",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "7925f5e8-f7b6-416e-b05b-5ac2c19f00c1",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T09:20:47",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: 08413766-4fa8-4eec-9392-ec30581fb48c",
#> "fx": "DSI::datashield.login",
#> "session": "08413766-4fa8-4eec-9392-ec30581fb48c",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T09:20:48",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "08413766-4fa8-4eec-9392-ec30581fb48c",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T09:20:49",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "08413766-4fa8-4eec-9392-ec30581fb48c",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T14:08:39",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: 88a48432-61c8-4444-bb6f-1d0174d4f177",
#> "fx": "DSI::datashield.login",
#> "session": "88a48432-61c8-4444-bb6f-1d0174d4f177",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T14:08:39",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "88a48432-61c8-4444-bb6f-1d0174d4f177",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T14:08:40",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "88a48432-61c8-4444-bb6f-1d0174d4f177",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T14:18:40",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: e45b3573-21cc-445d-8d22-b7fc289d279a",
#> "fx": "DSI::datashield.login",
#> "session": "e45b3573-21cc-445d-8d22-b7fc289d279a",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T14:18:40",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "e45b3573-21cc-445d-8d22-b7fc289d279a",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T14:18:41",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "e45b3573-21cc-445d-8d22-b7fc289d279a",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:04:13",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: 026b4b18-c40c-4f08-8a19-75716fee1c75",
#> "fx": "DSI::datashield.login",
#> "session": "026b4b18-c40c-4f08-8a19-75716fee1c75",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:04:13",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "026b4b18-c40c-4f08-8a19-75716fee1c75",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:04:14",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "026b4b18-c40c-4f08-8a19-75716fee1c75",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:13:01",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: a3a6f257-79ef-443c-a110-393b1ff196f0",
#> "fx": "DSI::datashield.login",
#> "session": "a3a6f257-79ef-443c-a110-393b1ff196f0",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:13:01",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "a3a6f257-79ef-443c-a110-393b1ff196f0",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:13:03",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "a3a6f257-79ef-443c-a110-393b1ff196f0",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:02",
#> "action": "OPEN",
#> "user": "dsuser",
#> "r_cmd": "Open session: fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "fx": "DSI::datashield.login",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:02",
#> "action": "ASSIGN",
#> "user": "dsuser",
#> "r_cmd": "dsROCrate_test <- opal[CNSIM.CNSIM1]",
#> "fx": "base::assign",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:04",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::lsDS(search.filter = NULL, 1L)",
#> "fx": "dsBase::lsDS",
#> "symbol": "search.filter = NULL, 1L",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:04",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "base::exists(\"dsROCrate_test\")",
#> "fx": "base::exists",
#> "symbol": "dsROCrate_test",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:04",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::classDS(\"dsROCrate_test\")",
#> "fx": "dsBase::classDS",
#> "symbol": "dsROCrate_test",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:04",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::isValidDS(dsROCrate_test)",
#> "fx": "dsBase::isValidDS",
#> "symbol": "dsROCrate_test",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:04",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::dimDS(\"dsROCrate_test\")",
#> "fx": "dsBase::dimDS",
#> "symbol": "dsROCrate_test",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> },
#> {
#> "timestamp": "2026-02-27T15:24:05",
#> "action": "AGGREGATE",
#> "user": "dsuser",
#> "r_cmd": "dsBase::colnamesDS(\"dsROCrate_test\")",
#> "fx": "dsBase::colnamesDS",
#> "symbol": "dsROCrate_test",
#> "table": "CNSIM.CNSIM1",
#> "session": "fc258313-6846-4a8e-93d9-4809cd794fbe",
#> "backend": "OBiBa's Opal"
#> }
#> ]
#> ]
#> }
#> ]
#> }
#>
#> attr(,"audit_type")
#> [1] "Study"
#> attr(,"project")
#> [1] "CNSIM"A markdown report can be created with an overview and details for an
RO-Crate, using the dsROCrate::rocrate_report:
Only generate .Rmd file
study_crate_v1_rmd <- tempfile(fileext = ".Rmd") # temporary file
safe_project_crate_contents <- study_crate_v1 |>
dsROCrate::rocrate_report(filepath = study_crate_v1_rmd, render = FALSE)
#> 1 'Author' entity was found!
#> 3 'Dataset' entities were found!
#> Warning: No entities were found with @type = 'WriteAction'!
#> Warning: No entities were found with @type = 'ControlAction'!
#> 1 'Project' entity was found!
#> 14 'PropertyValue' OR 'SoftwareApplication' entities were found!
#> Warning: No entities were found with @type = 'File'!
#> 1 'Author' entity was found!
#> 3 'Dataset' entities were found!
#> Warning: No entities were found with @type = 'WriteAction'!
#> Warning: No entities were found with @type = 'ControlAction'!
#> 1 'Project' entity was found!
#> 14 'PropertyValue' OR 'SoftwareApplication' entities were found!
#> 2 'File' entities were found!
# display Overview diagram
safe_project_crate_contents$overview_diagram
# display Overview data (Safe People, Safe Projects and Safe Data)
safe_project_crate_contents$overview_data |>
knitr::kable()| Server | Project | Data | Access Level | People | Function | Timestamp |
|---|---|---|---|---|---|---|
| opal_demo | CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T08:56:26 |
| opal_demo | CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T08:56:27 |
| opal_demo | CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T09:00:37 |
| opal_demo | CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T09:00:38 |
| opal_demo | CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T09:20:48 |
| opal_demo | CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T09:20:49 |
| opal_demo | CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T14:08:39 |
| opal_demo | CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T14:08:40 |
| opal_demo | CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T14:18:40 |
| opal_demo | CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T14:18:41 |
| opal_demo | CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T15:04:13 |
| opal_demo | CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T15:04:14 |
| opal_demo | CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T15:13:01 |
| opal_demo | CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T15:13:03 |
| opal_demo | CNSIM | CNSIM1 | read | dsuser | base::assign | 2026-02-27T15:24:02 |
| opal_demo | CNSIM | CNSIM1 | read | dsuser | dsBase::lsDS | 2026-02-27T15:24:04 |
| opal_demo | CNSIM | CNSIM1 | read | dsuser | base::exists | 2026-02-27T15:24:04 |
| opal_demo | CNSIM | CNSIM1 | read | dsuser | dsBase::classDS | 2026-02-27T15:24:04 |
| opal_demo | CNSIM | CNSIM1 | read | dsuser | dsBase::isValidDS | 2026-02-27T15:24:04 |
| opal_demo | CNSIM | CNSIM1 | read | dsuser | dsBase::dimDS | 2026-02-27T15:24:04 |
| opal_demo | CNSIM | CNSIM1 | read | dsuser | dsBase::colnamesDS | 2026-02-27T15:24:05 |
| opal_demo | CNSIM | CNSIM2 | read | dsuser | ||
| opal_demo | CNSIM | CNSIM3 | read | dsuser | ||
| opal_test | CNSIM | CNSIM1 | read | dsuser |
Render and display report (HTML)
study_crate_v1 |>
dsROCrate::rocrate_report(filepath = study_crate_v1_rmd,
title = "DataSHIELD Study audit",
render = TRUE,
overwrite = TRUE)You are welcome to use any of the following hex codes when referencing
{dsROCrate}:
