Chore/githib actions ci

.Rbuildignore

@@ -25,3 +25,4 @@
 ^\.github$
 ^REFACTOR_GUIDE\.md$
 ^man-roxygen$
+^codecov\.yml$

.github/actions/setup-armadillo-with-dsbase/action.yaml

@@ -0,0 +1,140 @@
+name: Setup Armadillo with dsBase
+description: >
+ Starts a fresh Armadillo instance via docker-compose, with the "default"
+ Rock profile as a static sibling container. Installs R and system
+ dependencies, waits for readiness, uploads test datasets, and installs
+ dsBase. Assumes the caller has already checked out dsBaseClient at
+ ./dsBaseClient. Shared by the Armadillo dsbase shard workflow and the
+ Armadillo dsdanger job, so this setup only needs fixing in one place.
+
+inputs:
+ dsbase-tarball:
+ description: dsBase tarball filename to install
+ required: false
+ default: dsBase_7.0.0-permissive.tar.gz
+
+runs:
+ using: composite
+ steps:
+ - name: Write Armadillo config
+ shell: bash
+ run: |
+ mkdir -p armadillo_home/config
+
+ cat > armadillo_home/config/application.yml <<EOF
+ armadillo:
+ docker-management-enabled: false
+ docker-run-in-container: true
+ profiles:
+ - name: default
+ image: datashield/rock_citest-permissive:latest
+ host: default
+ port: 8085
+ package-whitelist:
+ - dsBase
+ - dsTidyverse
+ - resourcer
+ function-blacklist: [ ]
+ options:
+ datashield:
+ seed: 342325352
+ spring:
+ security:
+ user:
+ name: admin
+ password: admin
+ servlet:
+ multipart:
+ max-file-size: 1000MB
+ max-request-size: 1000MB
+ storage:
+ root-dir: /data
+ audit.log.path: '/logs/audit.log'
+ stdout.log.path: '/logs/armadillo.log'
+ logging:
+ level:
+ root: "warn"
+ org.molgenis: "warn"
+ EOF
+ working-directory: dsBaseClient
+
+ - name: Start Armadillo docker-compose
+ shell: bash
+ run: docker compose -f docker-compose_armadillo.yml up -d
+ working-directory: dsBaseClient
+
+ - uses: ./dsBaseClient/.github/actions/setup-r-with-dsbase-deps
+ with:
+ additional-packages: cran::covr
+
+ - name: Wait for Armadillo to be ready
+ shell: bash
+ run: |
+ for i in $(seq 1 60); do
+ if curl -fsS http://localhost:8080/actuator/health 2>/dev/null | grep -q '"status":"UP"'; then
+ echo "Armadillo is ready"
+ exit 0
+ fi
+ sleep 5
+ done
+ echo "Armadillo did not become ready in time"
+ docker compose -f docker-compose_armadillo.yml logs armadillo || true
+ exit 1
+ working-directory: dsBaseClient
+
+ - name: Install test datasets to Armadillo
+ shell: bash
+ run: R -q -f "molgenis_armadillo-upload_testing_datasets.R"
+ working-directory: dsBaseClient/tests/testthat/data_files
+
+ - name: Install dsBase to Armadillo
+ shell: bash
+ run: |
+ installed=false
+ for i in $(seq 1 30); do
+ if Rscript -e "
+ library(MolgenisArmadillo)
+ armadillo.login_basic('http://localhost:8080', 'admin', 'admin')
+ armadillo.install_packages('${{ inputs.dsbase-tarball }}', profile = 'default')
+ "; then
+ installed=true
+ break
+ fi
+ sleep 10
+ done
+ if [ "$installed" != "true" ]; then
+ echo "dsBase install via armadillo.install_packages() failed (default profile may not have started in time)"
+ exit 1
+ fi
+
+ expected_version=$(tar -xOzf ${{ inputs.dsbase-tarball }} dsBase/DESCRIPTION | sed -n 's/^Version: //p' | tr -d '\r')
+ if [ -z "$expected_version" ]; then
+ echo "Could not determine expected dsBase version from ${{ inputs.dsbase-tarball }}"
+ exit 1
+ fi
+ echo "Expected dsBase version: $expected_version"
+
+ actual_version=""
+ for i in $(seq 1 30); do
+ packages_json=$(curl -sf -u admin:admin -X GET http://localhost:8080/packages || true)
+ actual_version=$(echo "$packages_json" | jq -r '.[] | select(.name == "dsBase") | .version' 2>/dev/null || true)
+ if [ "$actual_version" == "$expected_version" ]; then
+ break
+ fi
+ sleep 10
+ done
+ echo "Installed dsBase version: $actual_version"
+ if [ "$actual_version" != "$expected_version" ]; then
+ echo "dsBase version mismatch: expected $expected_version, found '$actual_version'"
+ exit 1
+ fi
+ echo "$actual_version" > dsbase_version.txt
+
+ curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
+ working-directory: dsBaseClient
+
+ - name: Dump Armadillo server log
+ if: failure()
+ shell: bash
+ run: docker compose -f docker-compose_armadillo.yml logs armadillo | grep "Caused by:" | sort -u || true
+ working-directory: dsBaseClient

.github/actions/setup-opal-with-dsbase/action.yaml

@@ -0,0 +1,75 @@
+name: Setup Opal with dsBase
+description: >
+ Starts a fresh Opal instance via docker-compose, installs R and system
+ dependencies, uploads test datasets, and installs dsBase with disclosure
+ test options. Assumes the caller has already checked out dsBaseClient at
+ ./dsBaseClient. Shared by the Opal dsbase shard workflow and the Opal
+ dsdanger job, so this setup only needs fixing in one place.
+
+inputs:
+ dsbase-ref:
+ description: dsBase GitHub ref to install
+ required: false
+ default: v7.0-dev
+
+runs:
+ using: composite
+ steps:
+ - name: Start Opal docker-compose
+ shell: bash
+ run: docker compose -f docker-compose_opal.yml up -d --build
+ working-directory: dsBaseClient
+
+ - uses: ./dsBaseClient/.github/actions/setup-r-with-dsbase-deps
+
+ - name: Install test datasets to Opal
+ shell: bash
+ run: |
+ for i in $(seq 1 18); do
+ if curl -sf -o /dev/null http://localhost:8080/; then
+ echo "Opal is responding"
+ break
+ fi
+ sleep 5
+ done
+ R -q -f "obiba_opal-upload_testing_datasets.R"
+ working-directory: dsBaseClient/tests/testthat/data_files
+
+ - name: Install dsBase to Opal, set disclosure test options
+ shell: bash
+ run: |
+ R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'http://localhost:8080/'); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)"
+ R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '${{ inputs.dsbase-ref }}'); opal.logout(opal)"
+
+ expected_version=$(curl -sf "https://raw.githubusercontent.com/datashield/dsBase/${{ inputs.dsbase-ref }}/DESCRIPTION" | sed -n 's/^Version: //p' | tr -d '\r')
+ if [ -z "$expected_version" ]; then
+ echo "Could not determine expected dsBase version from GitHub"
+ exit 1
+ fi
+ echo "Expected dsBase version: $expected_version"
+ echo "$expected_version" > dsbase_version.txt
+
+ ok=false
+ for i in $(seq 1 18); do
+ if Rscript -e "
+ library(opalr)
+ opal <- opal.login('administrator', 'datashield_test&', url = 'http://localhost:8080/')
+ desc <- dsadmin.package_description(opal, 'dsBase')
+ opal.logout(opal)
+ installed <- desc[['Version']]
+ cat('Installed dsBase version:', if (is.null(installed)) '(none yet)' else installed, '\n')
+ quit(status = if (!is.null(installed) && installed == '$expected_version') 0 else 1)
+ "; then
+ ok=true
+ break
+ fi
+ sleep 10
+ done
+ if [ "$ok" != "true" ]; then
+ echo "dsBase version mismatch or install not detected after polling: expected $expected_version"
+ exit 1
+ fi
+
+ R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.profile_init(opal, name = 'default', packages = c('dsBase', 'dsTidyverse', 'resourcer')); opal.logout(opal)"
+ R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)"
+ working-directory: dsBaseClient/tests/testthat/data_files

.github/actions/setup-r-with-dsbase-deps/action.yaml

@@ -0,0 +1,61 @@
+name: Setup R with dsBaseClient dependencies
+description: >
+ Installs the system libraries, R, and R package dependencies shared by the
+ Opal and Armadillo setup actions. Assumes the caller has already checked
+ out dsBaseClient at ./dsBaseClient.
+
+inputs:
+ additional-packages:
+ description: Extra pak package specs (one per line) to install beyond the common set
+ required: false
+ default: ''
+
+runs:
+ using: composite
+ steps:
+ - name: Install system libraries
+ shell: bash
+ env:
+ SYSTEM_LIBRARIES: >-
+ libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev
+ libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev
+ run: |
+ sudo apt-get update -qq
+ sudo apt-get install -qq $SYSTEM_LIBRARIES -y
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ r-version: release
+ http-user-agent: release
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ env:
+ # RSPM doesn't always have a binary for every package/R-version combo; when it
+ # falls back to source, pak needs LinkingTo deps present to compile it.
+ PKG_INCLUDE_LINKINGTO: true
+ R_PACKAGES: |
+ cran::devtools
+ cran::fields
+ cran::meta
+ cran::metafor
+ cran::ggplot2
+ cran::gridExtra
+ cran::data.table
+ cran::DSI
+ cran::opalr
+ cran::DSOpal
+ cran::DSLite
+ cran::MolgenisAuth
+ cran::MolgenisArmadillo
+ cran::DSMolgenisArmadillo
+ cran::DescTools
+ cran::e1071
+ github::datashield/dsDangerClient
+ with:
+ working-directory: dsBaseClient
+ dependencies: 'c("Depends", "Imports", "LinkingTo")'
+ extra-packages: |
+ ${{ env.R_PACKAGES }}
+ ${{ inputs.additional-packages }}
+ needs: check

.Rbuildignore

@@ -25,3 +25,4 @@
 ^\.github$
 ^REFACTOR_GUIDE\.md$
 ^man-roxygen$
+^codecov\.yml$

.github/actions/setup-armadillo-with-dsbase/action.yaml

@@ -0,0 +1,140 @@
+name: Setup Armadillo with dsBase
+description: >
+ Starts a fresh Armadillo instance via docker-compose, with the "default"
+ Rock profile as a static sibling container. Installs R and system
+ dependencies, waits for readiness, uploads test datasets, and installs
+ dsBase. Assumes the caller has already checked out dsBaseClient at
+ ./dsBaseClient. Shared by the Armadillo dsbase shard workflow and the
+ Armadillo dsdanger job, so this setup only needs fixing in one place.
+
+inputs:
+ dsbase-tarball:
+ description: dsBase tarball filename to install
+ required: false
+ default: dsBase_7.0.0-permissive.tar.gz
+
+runs:
+ using: composite
+ steps:
+ - name: Write Armadillo config
+ shell: bash
+ run: |
+ mkdir -p armadillo_home/config
+
+ cat > armadillo_home/config/application.yml <<EOF
+ armadillo:
+ docker-management-enabled: false
+ docker-run-in-container: true
+ profiles:
+ - name: default
+ image: datashield/rock_citest-permissive:latest
+ host: default
+ port: 8085
+ package-whitelist:
+ - dsBase
+ - dsTidyverse
+ - resourcer
+ function-blacklist: [ ]
+ options:
+ datashield:
+ seed: 342325352
+ spring:
+ security:
+ user:
+ name: admin
+ password: admin
+ servlet:
+ multipart:
+ max-file-size: 1000MB
+ max-request-size: 1000MB
+ storage:
+ root-dir: /data
+ audit.log.path: '/logs/audit.log'
+ stdout.log.path: '/logs/armadillo.log'
+ logging:
+ level:
+ root: "warn"
+ org.molgenis: "warn"
+ EOF
+ working-directory: dsBaseClient
+
+ - name: Start Armadillo docker-compose
+ shell: bash
+ run: docker compose -f docker-compose_armadillo.yml up -d
+ working-directory: dsBaseClient
+
+ - uses: ./dsBaseClient/.github/actions/setup-r-with-dsbase-deps
+ with:
+ additional-packages: cran::covr
+
+ - name: Wait for Armadillo to be ready
+ shell: bash
+ run: |
+ for i in $(seq 1 60); do
+ if curl -fsS http://localhost:8080/actuator/health 2>/dev/null | grep -q '"status":"UP"'; then
+ echo "Armadillo is ready"
+ exit 0
+ fi
+ sleep 5
+ done
+ echo "Armadillo did not become ready in time"
+ docker compose -f docker-compose_armadillo.yml logs armadillo || true
+ exit 1
+ working-directory: dsBaseClient
+
+ - name: Install test datasets to Armadillo
+ shell: bash
+ run: R -q -f "molgenis_armadillo-upload_testing_datasets.R"
+ working-directory: dsBaseClient/tests/testthat/data_files
+
+ - name: Install dsBase to Armadillo
+ shell: bash
+ run: |
+ installed=false
+ for i in $(seq 1 30); do
+ if Rscript -e "
+ library(MolgenisArmadillo)
+ armadillo.login_basic('http://localhost:8080', 'admin', 'admin')
+ armadillo.install_packages('${{ inputs.dsbase-tarball }}', profile = 'default')
+ "; then
+ installed=true
+ break
+ fi
+ sleep 10
+ done
+ if [ "$installed" != "true" ]; then
+ echo "dsBase install via armadillo.install_packages() failed (default profile may not have started in time)"
+ exit 1
+ fi
+
+ expected_version=$(tar -xOzf ${{ inputs.dsbase-tarball }} dsBase/DESCRIPTION | sed -n 's/^Version: //p' | tr -d '\r')
+ if [ -z "$expected_version" ]; then
+ echo "Could not determine expected dsBase version from ${{ inputs.dsbase-tarball }}"
+ exit 1
+ fi
+ echo "Expected dsBase version: $expected_version"
+
+ actual_version=""
+ for i in $(seq 1 30); do
+ packages_json=$(curl -sf -u admin:admin -X GET http://localhost:8080/packages || true)
+ actual_version=$(echo "$packages_json" | jq -r '.[] | select(.name == "dsBase") | .version' 2>/dev/null || true)
+ if [ "$actual_version" == "$expected_version" ]; then
+ break
+ fi
+ sleep 10
+ done
+ echo "Installed dsBase version: $actual_version"
+ if [ "$actual_version" != "$expected_version" ]; then
+ echo "dsBase version mismatch: expected $expected_version, found '$actual_version'"
+ exit 1
+ fi
+ echo "$actual_version" > dsbase_version.txt
+
+ curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
+ working-directory: dsBaseClient
+
+ - name: Dump Armadillo server log
+ if: failure()
+ shell: bash
+ run: docker compose -f docker-compose_armadillo.yml logs armadillo | grep "Caused by:" | sort -u || true
+ working-directory: dsBaseClient

.github/actions/setup-opal-with-dsbase/action.yaml

@@ -0,0 +1,75 @@
+name: Setup Opal with dsBase
+description: >
+ Starts a fresh Opal instance via docker-compose, installs R and system
+ dependencies, uploads test datasets, and installs dsBase with disclosure
+ test options. Assumes the caller has already checked out dsBaseClient at
+ ./dsBaseClient. Shared by the Opal dsbase shard workflow and the Opal
+ dsdanger job, so this setup only needs fixing in one place.
+
+inputs:
+ dsbase-ref:
+ description: dsBase GitHub ref to install
+ required: false
+ default: v7.0-dev
+
+runs:
+ using: composite
+ steps:
+ - name: Start Opal docker-compose
+ shell: bash
+ run: docker compose -f docker-compose_opal.yml up -d --build
+ working-directory: dsBaseClient
+
+ - uses: ./dsBaseClient/.github/actions/setup-r-with-dsbase-deps
+
+ - name: Install test datasets to Opal
+ shell: bash
+ run: |
+ for i in $(seq 1 18); do
+ if curl -sf -o /dev/null http://localhost:8080/; then
+ echo "Opal is responding"
+ break
+ fi
+ sleep 5
+ done
+ R -q -f "obiba_opal-upload_testing_datasets.R"
+ working-directory: dsBaseClient/tests/testthat/data_files
+
+ - name: Install dsBase to Opal, set disclosure test options
+ shell: bash
+ run: |
+ R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'http://localhost:8080/'); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)"
+ R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '${{ inputs.dsbase-ref }}'); opal.logout(opal)"
+
+ expected_version=$(curl -sf "https://raw.githubusercontent.com/datashield/dsBase/${{ inputs.dsbase-ref }}/DESCRIPTION" | sed -n 's/^Version: //p' | tr -d '\r')
+ if [ -z "$expected_version" ]; then
+ echo "Could not determine expected dsBase version from GitHub"
+ exit 1
+ fi
+ echo "Expected dsBase version: $expected_version"
+ echo "$expected_version" > dsbase_version.txt
+
+ ok=false
+ for i in $(seq 1 18); do
+ if Rscript -e "
+ library(opalr)
+ opal <- opal.login('administrator', 'datashield_test&', url = 'http://localhost:8080/')
+ desc <- dsadmin.package_description(opal, 'dsBase')
+ opal.logout(opal)
+ installed <- desc[['Version']]
+ cat('Installed dsBase version:', if (is.null(installed)) '(none yet)' else installed, '\n')
+ quit(status = if (!is.null(installed) && installed == '$expected_version') 0 else 1)
+ "; then
+ ok=true
+ break
+ fi
+ sleep 10
+ done
+ if [ "$ok" != "true" ]; then
+ echo "dsBase version mismatch or install not detected after polling: expected $expected_version"
+ exit 1
+ fi
+
+ R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.profile_init(opal, name = 'default', packages = c('dsBase', 'dsTidyverse', 'resourcer')); opal.logout(opal)"
+ R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)"
+ working-directory: dsBaseClient/tests/testthat/data_files

.github/actions/setup-r-with-dsbase-deps/action.yaml

@@ -0,0 +1,61 @@
+name: Setup R with dsBaseClient dependencies
+description: >
+ Installs the system libraries, R, and R package dependencies shared by the
+ Opal and Armadillo setup actions. Assumes the caller has already checked
+ out dsBaseClient at ./dsBaseClient.
+
+inputs:
+ additional-packages:
+ description: Extra pak package specs (one per line) to install beyond the common set
+ required: false
+ default: ''
+
+runs:
+ using: composite
+ steps:
+ - name: Install system libraries
+ shell: bash
+ env:
+ SYSTEM_LIBRARIES: >-
+ libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev
+ libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev
+ run: |
+ sudo apt-get update -qq
+ sudo apt-get install -qq $SYSTEM_LIBRARIES -y
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ r-version: release
+ http-user-agent: release
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ env:
+ # RSPM doesn't always have a binary for every package/R-version combo; when it
+ # falls back to source, pak needs LinkingTo deps present to compile it.
+ PKG_INCLUDE_LINKINGTO: true
+ R_PACKAGES: |
+ cran::devtools
+ cran::fields
+ cran::meta
+ cran::metafor
+ cran::ggplot2
+ cran::gridExtra
+ cran::data.table
+ cran::DSI
+ cran::opalr
+ cran::DSOpal
+ cran::DSLite
+ cran::MolgenisAuth
+ cran::MolgenisArmadillo
+ cran::DSMolgenisArmadillo
+ cran::DescTools
+ cran::e1071
+ github::datashield/dsDangerClient
+ with:
+ working-directory: dsBaseClient
+ dependencies: 'c("Depends", "Imports", "LinkingTo")'
+ extra-packages: |
+ ${{ env.R_PACKAGES }}
+ ${{ inputs.additional-packages }}
+ needs: check

.Rbuildignore

@@ -25,3 +25,4 @@
 ^\.github$
 ^REFACTOR_GUIDE\.md$
 ^man-roxygen$
+^codecov\.yml$

.github/actions/setup-armadillo-with-dsbase/action.yaml

@@ -0,0 +1,140 @@
+name: Setup Armadillo with dsBase
+description: >
+ Starts a fresh Armadillo instance via docker-compose, with the "default"
+ Rock profile as a static sibling container. Installs R and system
+ dependencies, waits for readiness, uploads test datasets, and installs
+ dsBase. Assumes the caller has already checked out dsBaseClient at
+ ./dsBaseClient. Shared by the Armadillo dsbase shard workflow and the
+ Armadillo dsdanger job, so this setup only needs fixing in one place.
+
+inputs:
+ dsbase-tarball:
+ description: dsBase tarball filename to install
+ required: false
+ default: dsBase_7.0.0-permissive.tar.gz
+
+runs:
+ using: composite
+ steps:
+ - name: Write Armadillo config
+ shell: bash
+ run: |
+ mkdir -p armadillo_home/config
+
+ cat > armadillo_home/config/application.yml <<EOF
+ armadillo:
+ docker-management-enabled: false
+ docker-run-in-container: true
+ profiles:
+ - name: default
+ image: datashield/rock_citest-permissive:latest
+ host: default
+ port: 8085
+ package-whitelist:
+ - dsBase
+ - dsTidyverse
+ - resourcer
+ function-blacklist: [ ]
+ options:
+ datashield:
+ seed: 342325352
+ spring:
+ security:
+ user:
+ name: admin
+ password: admin
+ servlet:
+ multipart:
+ max-file-size: 1000MB
+ max-request-size: 1000MB
+ storage:
+ root-dir: /data
+ audit.log.path: '/logs/audit.log'
+ stdout.log.path: '/logs/armadillo.log'
+ logging:
+ level:
+ root: "warn"
+ org.molgenis: "warn"
+ EOF
+ working-directory: dsBaseClient
+
+ - name: Start Armadillo docker-compose
+ shell: bash
+ run: docker compose -f docker-compose_armadillo.yml up -d
+ working-directory: dsBaseClient
+
+ - uses: ./dsBaseClient/.github/actions/setup-r-with-dsbase-deps
+ with:
+ additional-packages: cran::covr
+
+ - name: Wait for Armadillo to be ready
+ shell: bash
+ run: |
+ for i in $(seq 1 60); do
+ if curl -fsS http://localhost:8080/actuator/health 2>/dev/null | grep -q '"status":"UP"'; then
+ echo "Armadillo is ready"
+ exit 0
+ fi
+ sleep 5
+ done
+ echo "Armadillo did not become ready in time"
+ docker compose -f docker-compose_armadillo.yml logs armadillo || true
+ exit 1
+ working-directory: dsBaseClient
+
+ - name: Install test datasets to Armadillo
+ shell: bash
+ run: R -q -f "molgenis_armadillo-upload_testing_datasets.R"
+ working-directory: dsBaseClient/tests/testthat/data_files
+
+ - name: Install dsBase to Armadillo
+ shell: bash
+ run: |
+ installed=false
+ for i in $(seq 1 30); do
+ if Rscript -e "
+ library(MolgenisArmadillo)
+ armadillo.login_basic('http://localhost:8080', 'admin', 'admin')
+ armadillo.install_packages('${{ inputs.dsbase-tarball }}', profile = 'default')
+ "; then
+ installed=true
+ break
+ fi
+ sleep 10
+ done
+ if [ "$installed" != "true" ]; then
+ echo "dsBase install via armadillo.install_packages() failed (default profile may not have started in time)"
+ exit 1
+ fi
+
+ expected_version=$(tar -xOzf ${{ inputs.dsbase-tarball }} dsBase/DESCRIPTION | sed -n 's/^Version: //p' | tr -d '\r')
+ if [ -z "$expected_version" ]; then
+ echo "Could not determine expected dsBase version from ${{ inputs.dsbase-tarball }}"
+ exit 1
+ fi
+ echo "Expected dsBase version: $expected_version"
+
+ actual_version=""
+ for i in $(seq 1 30); do
+ packages_json=$(curl -sf -u admin:admin -X GET http://localhost:8080/packages || true)
+ actual_version=$(echo "$packages_json" | jq -r '.[] | select(.name == "dsBase") | .version' 2>/dev/null || true)
+ if [ "$actual_version" == "$expected_version" ]; then
+ break
+ fi
+ sleep 10
+ done
+ echo "Installed dsBase version: $actual_version"
+ if [ "$actual_version" != "$expected_version" ]; then
+ echo "dsBase version mismatch: expected $expected_version, found '$actual_version'"
+ exit 1
+ fi
+ echo "$actual_version" > dsbase_version.txt
+
+ curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
+ working-directory: dsBaseClient
+
+ - name: Dump Armadillo server log
+ if: failure()
+ shell: bash
+ run: docker compose -f docker-compose_armadillo.yml logs armadillo | grep "Caused by:" | sort -u || true
+ working-directory: dsBaseClient

.github/actions/setup-opal-with-dsbase/action.yaml

@@ -0,0 +1,75 @@
+name: Setup Opal with dsBase
+description: >
+ Starts a fresh Opal instance via docker-compose, installs R and system
+ dependencies, uploads test datasets, and installs dsBase with disclosure
+ test options. Assumes the caller has already checked out dsBaseClient at
+ ./dsBaseClient. Shared by the Opal dsbase shard workflow and the Opal
+ dsdanger job, so this setup only needs fixing in one place.
+
+inputs:
+ dsbase-ref:
+ description: dsBase GitHub ref to install
+ required: false
+ default: v7.0-dev
+
+runs:
+ using: composite
+ steps:
+ - name: Start Opal docker-compose
+ shell: bash
+ run: docker compose -f docker-compose_opal.yml up -d --build
+ working-directory: dsBaseClient
+
+ - uses: ./dsBaseClient/.github/actions/setup-r-with-dsbase-deps
+
+ - name: Install test datasets to Opal
+ shell: bash
+ run: |
+ for i in $(seq 1 18); do
+ if curl -sf -o /dev/null http://localhost:8080/; then
+ echo "Opal is responding"
+ break
+ fi
+ sleep 5
+ done
+ R -q -f "obiba_opal-upload_testing_datasets.R"
+ working-directory: dsBaseClient/tests/testthat/data_files
+
+ - name: Install dsBase to Opal, set disclosure test options
+ shell: bash
+ run: |
+ R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'http://localhost:8080/'); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)"
+ R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '${{ inputs.dsbase-ref }}'); opal.logout(opal)"
+
+ expected_version=$(curl -sf "https://raw.githubusercontent.com/datashield/dsBase/${{ inputs.dsbase-ref }}/DESCRIPTION" | sed -n 's/^Version: //p' | tr -d '\r')
+ if [ -z "$expected_version" ]; then
+ echo "Could not determine expected dsBase version from GitHub"
+ exit 1
+ fi
+ echo "Expected dsBase version: $expected_version"
+ echo "$expected_version" > dsbase_version.txt
+
+ ok=false
+ for i in $(seq 1 18); do
+ if Rscript -e "
+ library(opalr)
+ opal <- opal.login('administrator', 'datashield_test&', url = 'http://localhost:8080/')
+ desc <- dsadmin.package_description(opal, 'dsBase')
+ opal.logout(opal)
+ installed <- desc[['Version']]
+ cat('Installed dsBase version:', if (is.null(installed)) '(none yet)' else installed, '\n')
+ quit(status = if (!is.null(installed) && installed == '$expected_version') 0 else 1)
+ "; then
+ ok=true
+ break
+ fi
+ sleep 10
+ done
+ if [ "$ok" != "true" ]; then
+ echo "dsBase version mismatch or install not detected after polling: expected $expected_version"
+ exit 1
+ fi
+
+ R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.profile_init(opal, name = 'default', packages = c('dsBase', 'dsTidyverse', 'resourcer')); opal.logout(opal)"
+ R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)"
+ working-directory: dsBaseClient/tests/testthat/data_files

.github/actions/setup-r-with-dsbase-deps/action.yaml

@@ -0,0 +1,61 @@
+name: Setup R with dsBaseClient dependencies
+description: >
+ Installs the system libraries, R, and R package dependencies shared by the
+ Opal and Armadillo setup actions. Assumes the caller has already checked
+ out dsBaseClient at ./dsBaseClient.
+
+inputs:
+ additional-packages:
+ description: Extra pak package specs (one per line) to install beyond the common set
+ required: false
+ default: ''
+
+runs:
+ using: composite
+ steps:
+ - name: Install system libraries
+ shell: bash
+ env:
+ SYSTEM_LIBRARIES: >-
+ libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev
+ libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev
+ run: |
+ sudo apt-get update -qq
+ sudo apt-get install -qq $SYSTEM_LIBRARIES -y
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ r-version: release
+ http-user-agent: release
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ env:
+ # RSPM doesn't always have a binary for every package/R-version combo; when it
+ # falls back to source, pak needs LinkingTo deps present to compile it.
+ PKG_INCLUDE_LINKINGTO: true
+ R_PACKAGES: |
+ cran::devtools
+ cran::fields
+ cran::meta
+ cran::metafor
+ cran::ggplot2
+ cran::gridExtra
+ cran::data.table
+ cran::DSI
+ cran::opalr
+ cran::DSOpal
+ cran::DSLite
+ cran::MolgenisAuth
+ cran::MolgenisArmadillo
+ cran::DSMolgenisArmadillo
+ cran::DescTools
+ cran::e1071
+ github::datashield/dsDangerClient
+ with:
+ working-directory: dsBaseClient
+ dependencies: 'c("Depends", "Imports", "LinkingTo")'
+ extra-packages: |
+ ${{ env.R_PACKAGES }}
+ ${{ inputs.additional-packages }}
+ needs: check

.Rbuildignore

@@ -25,3 +25,4 @@
 ^\.github$
 ^REFACTOR_GUIDE\.md$
 ^man-roxygen$
+^codecov\.yml$

.github/actions/setup-armadillo-with-dsbase/action.yaml

@@ -0,0 +1,140 @@
+name: Setup Armadillo with dsBase
+description: >
+ Starts a fresh Armadillo instance via docker-compose, with the "default"
+ Rock profile as a static sibling container. Installs R and system
+ dependencies, waits for readiness, uploads test datasets, and installs
+ dsBase. Assumes the caller has already checked out dsBaseClient at
+ ./dsBaseClient. Shared by the Armadillo dsbase shard workflow and the
+ Armadillo dsdanger job, so this setup only needs fixing in one place.
+
+inputs:
+ dsbase-tarball:
+ description: dsBase tarball filename to install
+ required: false
+ default: dsBase_7.0.0-permissive.tar.gz
+
+runs:
+ using: composite
+ steps:
+ - name: Write Armadillo config
+ shell: bash
+ run: |
+ mkdir -p armadillo_home/config
+
+ cat > armadillo_home/config/application.yml <<EOF
+ armadillo:
+ docker-management-enabled: false
+ docker-run-in-container: true
+ profiles:
+ - name: default
+ image: datashield/rock_citest-permissive:latest
+ host: default
+ port: 8085
+ package-whitelist:
+ - dsBase
+ - dsTidyverse
+ - resourcer
+ function-blacklist: [ ]
+ options:
+ datashield:
+ seed: 342325352
+ spring:
+ security:
+ user:
+ name: admin
+ password: admin
+ servlet:
+ multipart:
+ max-file-size: 1000MB
+ max-request-size: 1000MB
+ storage:
+ root-dir: /data
+ audit.log.path: '/logs/audit.log'
+ stdout.log.path: '/logs/armadillo.log'
+ logging:
+ level:
+ root: "warn"
+ org.molgenis: "warn"
+ EOF
+ working-directory: dsBaseClient
+
+ - name: Start Armadillo docker-compose
+ shell: bash
+ run: docker compose -f docker-compose_armadillo.yml up -d
+ working-directory: dsBaseClient
+
+ - uses: ./dsBaseClient/.github/actions/setup-r-with-dsbase-deps
+ with:
+ additional-packages: cran::covr
+
+ - name: Wait for Armadillo to be ready
+ shell: bash
+ run: |
+ for i in $(seq 1 60); do
+ if curl -fsS http://localhost:8080/actuator/health 2>/dev/null | grep -q '"status":"UP"'; then
+ echo "Armadillo is ready"
+ exit 0
+ fi
+ sleep 5
+ done
+ echo "Armadillo did not become ready in time"
+ docker compose -f docker-compose_armadillo.yml logs armadillo || true
+ exit 1
+ working-directory: dsBaseClient
+
+ - name: Install test datasets to Armadillo
+ shell: bash
+ run: R -q -f "molgenis_armadillo-upload_testing_datasets.R"
+ working-directory: dsBaseClient/tests/testthat/data_files
+
+ - name: Install dsBase to Armadillo
+ shell: bash
+ run: |
+ installed=false
+ for i in $(seq 1 30); do
+ if Rscript -e "
+ library(MolgenisArmadillo)
+ armadillo.login_basic('http://localhost:8080', 'admin', 'admin')
+ armadillo.install_packages('${{ inputs.dsbase-tarball }}', profile = 'default')
+ "; then
+ installed=true
+ break
+ fi
+ sleep 10
+ done
+ if [ "$installed" != "true" ]; then
+ echo "dsBase install via armadillo.install_packages() failed (default profile may not have started in time)"
+ exit 1
+ fi
+
+ expected_version=$(tar -xOzf ${{ inputs.dsbase-tarball }} dsBase/DESCRIPTION | sed -n 's/^Version: //p' | tr -d '\r')
+ if [ -z "$expected_version" ]; then
+ echo "Could not determine expected dsBase version from ${{ inputs.dsbase-tarball }}"
+ exit 1
+ fi
+ echo "Expected dsBase version: $expected_version"
+
+ actual_version=""
+ for i in $(seq 1 30); do
+ packages_json=$(curl -sf -u admin:admin -X GET http://localhost:8080/packages || true)
+ actual_version=$(echo "$packages_json" | jq -r '.[] | select(.name == "dsBase") | .version' 2>/dev/null || true)
+ if [ "$actual_version" == "$expected_version" ]; then
+ break
+ fi
+ sleep 10
+ done
+ echo "Installed dsBase version: $actual_version"
+ if [ "$actual_version" != "$expected_version" ]; then
+ echo "dsBase version mismatch: expected $expected_version, found '$actual_version'"
+ exit 1
+ fi
+ echo "$actual_version" > dsbase_version.txt
+
+ curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
+ working-directory: dsBaseClient
+
+ - name: Dump Armadillo server log
+ if: failure()
+ shell: bash
+ run: docker compose -f docker-compose_armadillo.yml logs armadillo | grep "Caused by:" | sort -u || true
+ working-directory: dsBaseClient

.github/actions/setup-opal-with-dsbase/action.yaml

@@ -0,0 +1,75 @@
+name: Setup Opal with dsBase
+description: >
+ Starts a fresh Opal instance via docker-compose, installs R and system
+ dependencies, uploads test datasets, and installs dsBase with disclosure
+ test options. Assumes the caller has already checked out dsBaseClient at
+ ./dsBaseClient. Shared by the Opal dsbase shard workflow and the Opal
+ dsdanger job, so this setup only needs fixing in one place.
+
+inputs:
+ dsbase-ref:
+ description: dsBase GitHub ref to install
+ required: false
+ default: v7.0-dev
+
+runs:
+ using: composite
+ steps:
+ - name: Start Opal docker-compose
+ shell: bash
+ run: docker compose -f docker-compose_opal.yml up -d --build
+ working-directory: dsBaseClient
+
+ - uses: ./dsBaseClient/.github/actions/setup-r-with-dsbase-deps
+
+ - name: Install test datasets to Opal
+ shell: bash
+ run: |
+ for i in $(seq 1 18); do
+ if curl -sf -o /dev/null http://localhost:8080/; then
+ echo "Opal is responding"
+ break
+ fi
+ sleep 5
+ done
+ R -q -f "obiba_opal-upload_testing_datasets.R"
+ working-directory: dsBaseClient/tests/testthat/data_files
+
+ - name: Install dsBase to Opal, set disclosure test options
+ shell: bash
+ run: |
+ R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'http://localhost:8080/'); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)"
+ R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '${{ inputs.dsbase-ref }}'); opal.logout(opal)"
+
+ expected_version=$(curl -sf "https://raw.githubusercontent.com/datashield/dsBase/${{ inputs.dsbase-ref }}/DESCRIPTION" | sed -n 's/^Version: //p' | tr -d '\r')
+ if [ -z "$expected_version" ]; then
+ echo "Could not determine expected dsBase version from GitHub"
+ exit 1
+ fi
+ echo "Expected dsBase version: $expected_version"
+ echo "$expected_version" > dsbase_version.txt
+
+ ok=false
+ for i in $(seq 1 18); do
+ if Rscript -e "
+ library(opalr)
+ opal <- opal.login('administrator', 'datashield_test&', url = 'http://localhost:8080/')
+ desc <- dsadmin.package_description(opal, 'dsBase')
+ opal.logout(opal)
+ installed <- desc[['Version']]
+ cat('Installed dsBase version:', if (is.null(installed)) '(none yet)' else installed, '\n')
+ quit(status = if (!is.null(installed) && installed == '$expected_version') 0 else 1)
+ "; then
+ ok=true
+ break
+ fi
+ sleep 10
+ done
+ if [ "$ok" != "true" ]; then
+ echo "dsBase version mismatch or install not detected after polling: expected $expected_version"
+ exit 1
+ fi
+
+ R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.profile_init(opal, name = 'default', packages = c('dsBase', 'dsTidyverse', 'resourcer')); opal.logout(opal)"
+ R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)"
+ working-directory: dsBaseClient/tests/testthat/data_files

.github/actions/setup-r-with-dsbase-deps/action.yaml

@@ -0,0 +1,61 @@
+name: Setup R with dsBaseClient dependencies
+description: >
+ Installs the system libraries, R, and R package dependencies shared by the
+ Opal and Armadillo setup actions. Assumes the caller has already checked
+ out dsBaseClient at ./dsBaseClient.
+
+inputs:
+ additional-packages:
+ description: Extra pak package specs (one per line) to install beyond the common set
+ required: false
+ default: ''
+
+runs:
+ using: composite
+ steps:
+ - name: Install system libraries
+ shell: bash
+ env:
+ SYSTEM_LIBRARIES: >-
+ libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev
+ libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev
+ run: |
+ sudo apt-get update -qq
+ sudo apt-get install -qq $SYSTEM_LIBRARIES -y
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ r-version: release
+ http-user-agent: release
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ env:
+ # RSPM doesn't always have a binary for every package/R-version combo; when it
+ # falls back to source, pak needs LinkingTo deps present to compile it.
+ PKG_INCLUDE_LINKINGTO: true
+ R_PACKAGES: |
+ cran::devtools
+ cran::fields
+ cran::meta
+ cran::metafor
+ cran::ggplot2
+ cran::gridExtra
+ cran::data.table
+ cran::DSI
+ cran::opalr
+ cran::DSOpal
+ cran::DSLite
+ cran::MolgenisAuth
+ cran::MolgenisArmadillo
+ cran::DSMolgenisArmadillo
+ cran::DescTools
+ cran::e1071
+ github::datashield/dsDangerClient
+ with:
+ working-directory: dsBaseClient
+ dependencies: 'c("Depends", "Imports", "LinkingTo")'
+ extra-packages: |
+ ${{ env.R_PACKAGES }}
+ ${{ inputs.additional-packages }}
+ needs: check

.Rbuildignore

@@ -25,3 +25,4 @@
 ^\.github$
 ^REFACTOR_GUIDE\.md$
 ^man-roxygen$
+^codecov\.yml$

.github/actions/setup-armadillo-with-dsbase/action.yaml

@@ -0,0 +1,140 @@
+name: Setup Armadillo with dsBase
+description: >
+ Starts a fresh Armadillo instance via docker-compose, with the "default"
+ Rock profile as a static sibling container. Installs R and system
+ dependencies, waits for readiness, uploads test datasets, and installs
+ dsBase. Assumes the caller has already checked out dsBaseClient at
+ ./dsBaseClient. Shared by the Armadillo dsbase shard workflow and the
+ Armadillo dsdanger job, so this setup only needs fixing in one place.
+
+inputs:
+ dsbase-tarball:
+ description: dsBase tarball filename to install
+ required: false
+ default: dsBase_7.0.0-permissive.tar.gz
+
+runs:
+ using: composite
+ steps:
+ - name: Write Armadillo config
+ shell: bash
+ run: |
+ mkdir -p armadillo_home/config
+
+ cat > armadillo_home/config/application.yml <<EOF
+ armadillo:
+ docker-management-enabled: false
+ docker-run-in-container: true
+ profiles:
+ - name: default
+ image: datashield/rock_citest-permissive:latest
+ host: default
+ port: 8085
+ package-whitelist:
+ - dsBase
+ - dsTidyverse
+ - resourcer
+ function-blacklist: [ ]
+ options:
+ datashield:
+ seed: 342325352
+ spring:
+ security:
+ user:
+ name: admin
+ password: admin
+ servlet:
+ multipart:
+ max-file-size: 1000MB
+ max-request-size: 1000MB
+ storage:
+ root-dir: /data
+ audit.log.path: '/logs/audit.log'
+ stdout.log.path: '/logs/armadillo.log'
+ logging:
+ level:
+ root: "warn"
+ org.molgenis: "warn"
+ EOF
+ working-directory: dsBaseClient
+
+ - name: Start Armadillo docker-compose
+ shell: bash
+ run: docker compose -f docker-compose_armadillo.yml up -d
+ working-directory: dsBaseClient
+
+ - uses: ./dsBaseClient/.github/actions/setup-r-with-dsbase-deps
+ with:
+ additional-packages: cran::covr
+
+ - name: Wait for Armadillo to be ready
+ shell: bash
+ run: |
+ for i in $(seq 1 60); do
+ if curl -fsS http://localhost:8080/actuator/health 2>/dev/null | grep -q '"status":"UP"'; then
+ echo "Armadillo is ready"
+ exit 0
+ fi
+ sleep 5
+ done
+ echo "Armadillo did not become ready in time"
+ docker compose -f docker-compose_armadillo.yml logs armadillo || true
+ exit 1
+ working-directory: dsBaseClient
+
+ - name: Install test datasets to Armadillo
+ shell: bash
+ run: R -q -f "molgenis_armadillo-upload_testing_datasets.R"
+ working-directory: dsBaseClient/tests/testthat/data_files
+
+ - name: Install dsBase to Armadillo
+ shell: bash
+ run: |
+ installed=false
+ for i in $(seq 1 30); do
+ if Rscript -e "
+ library(MolgenisArmadillo)
+ armadillo.login_basic('http://localhost:8080', 'admin', 'admin')
+ armadillo.install_packages('${{ inputs.dsbase-tarball }}', profile = 'default')
+ "; then
+ installed=true
+ break
+ fi
+ sleep 10
+ done
+ if [ "$installed" != "true" ]; then
+ echo "dsBase install via armadillo.install_packages() failed (default profile may not have started in time)"
+ exit 1
+ fi
+
+ expected_version=$(tar -xOzf ${{ inputs.dsbase-tarball }} dsBase/DESCRIPTION | sed -n 's/^Version: //p' | tr -d '\r')
+ if [ -z "$expected_version" ]; then
+ echo "Could not determine expected dsBase version from ${{ inputs.dsbase-tarball }}"
+ exit 1
+ fi
+ echo "Expected dsBase version: $expected_version"
+
+ actual_version=""
+ for i in $(seq 1 30); do
+ packages_json=$(curl -sf -u admin:admin -X GET http://localhost:8080/packages || true)
+ actual_version=$(echo "$packages_json" | jq -r '.[] | select(.name == "dsBase") | .version' 2>/dev/null || true)
+ if [ "$actual_version" == "$expected_version" ]; then
+ break
+ fi
+ sleep 10
+ done
+ echo "Installed dsBase version: $actual_version"
+ if [ "$actual_version" != "$expected_version" ]; then
+ echo "dsBase version mismatch: expected $expected_version, found '$actual_version'"
+ exit 1
+ fi
+ echo "$actual_version" > dsbase_version.txt
+
+ curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
+ working-directory: dsBaseClient
+
+ - name: Dump Armadillo server log
+ if: failure()
+ shell: bash
+ run: docker compose -f docker-compose_armadillo.yml logs armadillo | grep "Caused by:" | sort -u || true
+ working-directory: dsBaseClient

.github/actions/setup-opal-with-dsbase/action.yaml

@@ -0,0 +1,75 @@
+name: Setup Opal with dsBase
+description: >
+ Starts a fresh Opal instance via docker-compose, installs R and system
+ dependencies, uploads test datasets, and installs dsBase with disclosure
+ test options. Assumes the caller has already checked out dsBaseClient at
+ ./dsBaseClient. Shared by the Opal dsbase shard workflow and the Opal
+ dsdanger job, so this setup only needs fixing in one place.
+
+inputs:
+ dsbase-ref:
+ description: dsBase GitHub ref to install
+ required: false
+ default: v7.0-dev
+
+runs:
+ using: composite
+ steps:
+ - name: Start Opal docker-compose
+ shell: bash
+ run: docker compose -f docker-compose_opal.yml up -d --build
+ working-directory: dsBaseClient
+
+ - uses: ./dsBaseClient/.github/actions/setup-r-with-dsbase-deps
+
+ - name: Install test datasets to Opal
+ shell: bash
+ run: |
+ for i in $(seq 1 18); do
+ if curl -sf -o /dev/null http://localhost:8080/; then
+ echo "Opal is responding"
+ break
+ fi
+ sleep 5
+ done
+ R -q -f "obiba_opal-upload_testing_datasets.R"
+ working-directory: dsBaseClient/tests/testthat/data_files
+
+ - name: Install dsBase to Opal, set disclosure test options
+ shell: bash
+ run: |
+ R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'http://localhost:8080/'); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)"
+ R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '${{ inputs.dsbase-ref }}'); opal.logout(opal)"
+
+ expected_version=$(curl -sf "https://raw.githubusercontent.com/datashield/dsBase/${{ inputs.dsbase-ref }}/DESCRIPTION" | sed -n 's/^Version: //p' | tr -d '\r')
+ if [ -z "$expected_version" ]; then
+ echo "Could not determine expected dsBase version from GitHub"
+ exit 1
+ fi
+ echo "Expected dsBase version: $expected_version"
+ echo "$expected_version" > dsbase_version.txt
+
+ ok=false
+ for i in $(seq 1 18); do
+ if Rscript -e "
+ library(opalr)
+ opal <- opal.login('administrator', 'datashield_test&', url = 'http://localhost:8080/')
+ desc <- dsadmin.package_description(opal, 'dsBase')
+ opal.logout(opal)
+ installed <- desc[['Version']]
+ cat('Installed dsBase version:', if (is.null(installed)) '(none yet)' else installed, '\n')
+ quit(status = if (!is.null(installed) && installed == '$expected_version') 0 else 1)
+ "; then
+ ok=true
+ break
+ fi
+ sleep 10
+ done
+ if [ "$ok" != "true" ]; then
+ echo "dsBase version mismatch or install not detected after polling: expected $expected_version"
+ exit 1
+ fi
+
+ R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.profile_init(opal, name = 'default', packages = c('dsBase', 'dsTidyverse', 'resourcer')); opal.logout(opal)"
+ R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)"
+ working-directory: dsBaseClient/tests/testthat/data_files

.github/actions/setup-r-with-dsbase-deps/action.yaml

@@ -0,0 +1,61 @@
+name: Setup R with dsBaseClient dependencies
+description: >
+ Installs the system libraries, R, and R package dependencies shared by the
+ Opal and Armadillo setup actions. Assumes the caller has already checked
+ out dsBaseClient at ./dsBaseClient.
+
+inputs:
+ additional-packages:
+ description: Extra pak package specs (one per line) to install beyond the common set
+ required: false
+ default: ''
+
+runs:
+ using: composite
+ steps:
+ - name: Install system libraries
+ shell: bash
+ env:
+ SYSTEM_LIBRARIES: >-
+ libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev
+ libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev
+ run: |
+ sudo apt-get update -qq
+ sudo apt-get install -qq $SYSTEM_LIBRARIES -y
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ r-version: release
+ http-user-agent: release
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ env:
+ # RSPM doesn't always have a binary for every package/R-version combo; when it
+ # falls back to source, pak needs LinkingTo deps present to compile it.
+ PKG_INCLUDE_LINKINGTO: true
+ R_PACKAGES: |
+ cran::devtools
+ cran::fields
+ cran::meta
+ cran::metafor
+ cran::ggplot2
+ cran::gridExtra
+ cran::data.table
+ cran::DSI
+ cran::opalr
+ cran::DSOpal
+ cran::DSLite
+ cran::MolgenisAuth
+ cran::MolgenisArmadillo
+ cran::DSMolgenisArmadillo
+ cran::DescTools
+ cran::e1071
+ github::datashield/dsDangerClient
+ with:
+ working-directory: dsBaseClient
+ dependencies: 'c("Depends", "Imports", "LinkingTo")'
+ extra-packages: |
+ ${{ env.R_PACKAGES }}
+ ${{ inputs.additional-packages }}
+ needs: check

.Rbuildignore

@@ -25,3 +25,4 @@
 ^\.github$
 ^REFACTOR_GUIDE\.md$
 ^man-roxygen$
+^codecov\.yml$

.github/actions/setup-armadillo-with-dsbase/action.yaml

@@ -0,0 +1,140 @@
+name: Setup Armadillo with dsBase
+description: >
+ Starts a fresh Armadillo instance via docker-compose, with the "default"
+ Rock profile as a static sibling container. Installs R and system
+ dependencies, waits for readiness, uploads test datasets, and installs
+ dsBase. Assumes the caller has already checked out dsBaseClient at
+ ./dsBaseClient. Shared by the Armadillo dsbase shard workflow and the
+ Armadillo dsdanger job, so this setup only needs fixing in one place.
+
+inputs:
+ dsbase-tarball:
+ description: dsBase tarball filename to install
+ required: false
+ default: dsBase_7.0.0-permissive.tar.gz
+
+runs:
+ using: composite
+ steps:
+ - name: Write Armadillo config
+ shell: bash
+ run: |
+ mkdir -p armadillo_home/config
+
+ cat > armadillo_home/config/application.yml <<EOF
+ armadillo:
+ docker-management-enabled: false
+ docker-run-in-container: true
+ profiles:
+ - name: default
+ image: datashield/rock_citest-permissive:latest
+ host: default
+ port: 8085
+ package-whitelist:
+ - dsBase
+ - dsTidyverse
+ - resourcer
+ function-blacklist: [ ]
+ options:
+ datashield:
+ seed: 342325352
+ spring:
+ security:
+ user:
+ name: admin
+ password: admin
+ servlet:
+ multipart:
+ max-file-size: 1000MB
+ max-request-size: 1000MB
+ storage:
+ root-dir: /data
+ audit.log.path: '/logs/audit.log'
+ stdout.log.path: '/logs/armadillo.log'
+ logging:
+ level:
+ root: "warn"
+ org.molgenis: "warn"
+ EOF
+ working-directory: dsBaseClient
+
+ - name: Start Armadillo docker-compose
+ shell: bash
+ run: docker compose -f docker-compose_armadillo.yml up -d
+ working-directory: dsBaseClient
+
+ - uses: ./dsBaseClient/.github/actions/setup-r-with-dsbase-deps
+ with:
+ additional-packages: cran::covr
+
+ - name: Wait for Armadillo to be ready
+ shell: bash
+ run: |
+ for i in $(seq 1 60); do
+ if curl -fsS http://localhost:8080/actuator/health 2>/dev/null | grep -q '"status":"UP"'; then
+ echo "Armadillo is ready"
+ exit 0
+ fi
+ sleep 5
+ done
+ echo "Armadillo did not become ready in time"
+ docker compose -f docker-compose_armadillo.yml logs armadillo || true
+ exit 1
+ working-directory: dsBaseClient
+
+ - name: Install test datasets to Armadillo
+ shell: bash
+ run: R -q -f "molgenis_armadillo-upload_testing_datasets.R"
+ working-directory: dsBaseClient/tests/testthat/data_files
+
+ - name: Install dsBase to Armadillo
+ shell: bash
+ run: |
+ installed=false
+ for i in $(seq 1 30); do
+ if Rscript -e "
+ library(MolgenisArmadillo)
+ armadillo.login_basic('http://localhost:8080', 'admin', 'admin')
+ armadillo.install_packages('${{ inputs.dsbase-tarball }}', profile = 'default')
+ "; then
+ installed=true
+ break
+ fi
+ sleep 10
+ done
+ if [ "$installed" != "true" ]; then
+ echo "dsBase install via armadillo.install_packages() failed (default profile may not have started in time)"
+ exit 1
+ fi
+
+ expected_version=$(tar -xOzf ${{ inputs.dsbase-tarball }} dsBase/DESCRIPTION | sed -n 's/^Version: //p' | tr -d '\r')
+ if [ -z "$expected_version" ]; then
+ echo "Could not determine expected dsBase version from ${{ inputs.dsbase-tarball }}"
+ exit 1
+ fi
+ echo "Expected dsBase version: $expected_version"
+
+ actual_version=""
+ for i in $(seq 1 30); do
+ packages_json=$(curl -sf -u admin:admin -X GET http://localhost:8080/packages || true)
+ actual_version=$(echo "$packages_json" | jq -r '.[] | select(.name == "dsBase") | .version' 2>/dev/null || true)
+ if [ "$actual_version" == "$expected_version" ]; then
+ break
+ fi
+ sleep 10
+ done
+ echo "Installed dsBase version: $actual_version"
+ if [ "$actual_version" != "$expected_version" ]; then
+ echo "dsBase version mismatch: expected $expected_version, found '$actual_version'"
+ exit 1
+ fi
+ echo "$actual_version" > dsbase_version.txt
+
+ curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
+ working-directory: dsBaseClient
+
+ - name: Dump Armadillo server log
+ if: failure()
+ shell: bash
+ run: docker compose -f docker-compose_armadillo.yml logs armadillo | grep "Caused by:" | sort -u || true
+ working-directory: dsBaseClient

.github/actions/setup-opal-with-dsbase/action.yaml

@@ -0,0 +1,75 @@
+name: Setup Opal with dsBase
+description: >
+ Starts a fresh Opal instance via docker-compose, installs R and system
+ dependencies, uploads test datasets, and installs dsBase with disclosure
+ test options. Assumes the caller has already checked out dsBaseClient at
+ ./dsBaseClient. Shared by the Opal dsbase shard workflow and the Opal
+ dsdanger job, so this setup only needs fixing in one place.
+
+inputs:
+ dsbase-ref:
+ description: dsBase GitHub ref to install
+ required: false
+ default: v7.0-dev
+
+runs:
+ using: composite
+ steps:
+ - name: Start Opal docker-compose
+ shell: bash
+ run: docker compose -f docker-compose_opal.yml up -d --build
+ working-directory: dsBaseClient
+
+ - uses: ./dsBaseClient/.github/actions/setup-r-with-dsbase-deps
+
+ - name: Install test datasets to Opal
+ shell: bash
+ run: |
+ for i in $(seq 1 18); do
+ if curl -sf -o /dev/null http://localhost:8080/; then
+ echo "Opal is responding"
+ break
+ fi
+ sleep 5
+ done
+ R -q -f "obiba_opal-upload_testing_datasets.R"
+ working-directory: dsBaseClient/tests/testthat/data_files
+
+ - name: Install dsBase to Opal, set disclosure test options
+ shell: bash
+ run: |
+ R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'http://localhost:8080/'); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)"
+ R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '${{ inputs.dsbase-ref }}'); opal.logout(opal)"
+
+ expected_version=$(curl -sf "https://raw.githubusercontent.com/datashield/dsBase/${{ inputs.dsbase-ref }}/DESCRIPTION" | sed -n 's/^Version: //p' | tr -d '\r')
+ if [ -z "$expected_version" ]; then
+ echo "Could not determine expected dsBase version from GitHub"
+ exit 1
+ fi
+ echo "Expected dsBase version: $expected_version"
+ echo "$expected_version" > dsbase_version.txt
+
+ ok=false
+ for i in $(seq 1 18); do
+ if Rscript -e "
+ library(opalr)
+ opal <- opal.login('administrator', 'datashield_test&', url = 'http://localhost:8080/')
+ desc <- dsadmin.package_description(opal, 'dsBase')
+ opal.logout(opal)
+ installed <- desc[['Version']]
+ cat('Installed dsBase version:', if (is.null(installed)) '(none yet)' else installed, '\n')
+ quit(status = if (!is.null(installed) && installed == '$expected_version') 0 else 1)
+ "; then
+ ok=true
+ break
+ fi
+ sleep 10
+ done
+ if [ "$ok" != "true" ]; then
+ echo "dsBase version mismatch or install not detected after polling: expected $expected_version"
+ exit 1
+ fi
+
+ R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.profile_init(opal, name = 'default', packages = c('dsBase', 'dsTidyverse', 'resourcer')); opal.logout(opal)"
+ R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)"
+ working-directory: dsBaseClient/tests/testthat/data_files

.github/actions/setup-r-with-dsbase-deps/action.yaml

@@ -0,0 +1,61 @@
+name: Setup R with dsBaseClient dependencies
+description: >
+ Installs the system libraries, R, and R package dependencies shared by the
+ Opal and Armadillo setup actions. Assumes the caller has already checked
+ out dsBaseClient at ./dsBaseClient.
+
+inputs:
+ additional-packages:
+ description: Extra pak package specs (one per line) to install beyond the common set
+ required: false
+ default: ''
+
+runs:
+ using: composite
+ steps:
+ - name: Install system libraries
+ shell: bash
+ env:
+ SYSTEM_LIBRARIES: >-
+ libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev
+ libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev
+ run: |
+ sudo apt-get update -qq
+ sudo apt-get install -qq $SYSTEM_LIBRARIES -y
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ r-version: release
+ http-user-agent: release
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ env:
+ # RSPM doesn't always have a binary for every package/R-version combo; when it
+ # falls back to source, pak needs LinkingTo deps present to compile it.
+ PKG_INCLUDE_LINKINGTO: true
+ R_PACKAGES: |
+ cran::devtools
+ cran::fields
+ cran::meta
+ cran::metafor
+ cran::ggplot2
+ cran::gridExtra
+ cran::data.table
+ cran::DSI
+ cran::opalr
+ cran::DSOpal
+ cran::DSLite
+ cran::MolgenisAuth
+ cran::MolgenisArmadillo
+ cran::DSMolgenisArmadillo
+ cran::DescTools
+ cran::e1071
+ github::datashield/dsDangerClient
+ with:
+ working-directory: dsBaseClient
+ dependencies: 'c("Depends", "Imports", "LinkingTo")'
+ extra-packages: |
+ ${{ env.R_PACKAGES }}
+ ${{ inputs.additional-packages }}
+ needs: check

.Rbuildignore

@@ -25,3 +25,4 @@
 ^\.github$
 ^REFACTOR_GUIDE\.md$
 ^man-roxygen$
+^codecov\.yml$

.github/actions/setup-armadillo-with-dsbase/action.yaml

@@ -0,0 +1,140 @@
+name: Setup Armadillo with dsBase
+description: >
+ Starts a fresh Armadillo instance via docker-compose, with the "default"
+ Rock profile as a static sibling container. Installs R and system
+ dependencies, waits for readiness, uploads test datasets, and installs
+ dsBase. Assumes the caller has already checked out dsBaseClient at
+ ./dsBaseClient. Shared by the Armadillo dsbase shard workflow and the
+ Armadillo dsdanger job, so this setup only needs fixing in one place.
+
+inputs:
+ dsbase-tarball:
+ description: dsBase tarball filename to install
+ required: false
+ default: dsBase_7.0.0-permissive.tar.gz
+
+runs:
+ using: composite
+ steps:
+ - name: Write Armadillo config
+ shell: bash
+ run: |
+ mkdir -p armadillo_home/config
+
+ cat > armadillo_home/config/application.yml <<EOF
+ armadillo:
+ docker-management-enabled: false
+ docker-run-in-container: true
+ profiles:
+ - name: default
+ image: datashield/rock_citest-permissive:latest
+ host: default
+ port: 8085
+ package-whitelist:
+ - dsBase
+ - dsTidyverse
+ - resourcer
+ function-blacklist: [ ]
+ options:
+ datashield:
+ seed: 342325352
+ spring:
+ security:
+ user:
+ name: admin
+ password: admin
+ servlet:
+ multipart:
+ max-file-size: 1000MB
+ max-request-size: 1000MB
+ storage:
+ root-dir: /data
+ audit.log.path: '/logs/audit.log'
+ stdout.log.path: '/logs/armadillo.log'
+ logging:
+ level:
+ root: "warn"
+ org.molgenis: "warn"
+ EOF
+ working-directory: dsBaseClient
+
+ - name: Start Armadillo docker-compose
+ shell: bash
+ run: docker compose -f docker-compose_armadillo.yml up -d
+ working-directory: dsBaseClient
+
+ - uses: ./dsBaseClient/.github/actions/setup-r-with-dsbase-deps
+ with:
+ additional-packages: cran::covr
+
+ - name: Wait for Armadillo to be ready
+ shell: bash
+ run: |
+ for i in $(seq 1 60); do
+ if curl -fsS http://localhost:8080/actuator/health 2>/dev/null | grep -q '"status":"UP"'; then
+ echo "Armadillo is ready"
+ exit 0
+ fi
+ sleep 5
+ done
+ echo "Armadillo did not become ready in time"
+ docker compose -f docker-compose_armadillo.yml logs armadillo || true
+ exit 1
+ working-directory: dsBaseClient
+
+ - name: Install test datasets to Armadillo
+ shell: bash
+ run: R -q -f "molgenis_armadillo-upload_testing_datasets.R"
+ working-directory: dsBaseClient/tests/testthat/data_files
+
+ - name: Install dsBase to Armadillo
+ shell: bash
+ run: |
+ installed=false
+ for i in $(seq 1 30); do
+ if Rscript -e "
+ library(MolgenisArmadillo)
+ armadillo.login_basic('http://localhost:8080', 'admin', 'admin')
+ armadillo.install_packages('${{ inputs.dsbase-tarball }}', profile = 'default')
+ "; then
+ installed=true
+ break
+ fi
+ sleep 10
+ done
+ if [ "$installed" != "true" ]; then
+ echo "dsBase install via armadillo.install_packages() failed (default profile may not have started in time)"
+ exit 1
+ fi
+
+ expected_version=$(tar -xOzf ${{ inputs.dsbase-tarball }} dsBase/DESCRIPTION | sed -n 's/^Version: //p' | tr -d '\r')
+ if [ -z "$expected_version" ]; then
+ echo "Could not determine expected dsBase version from ${{ inputs.dsbase-tarball }}"
+ exit 1
+ fi
+ echo "Expected dsBase version: $expected_version"
+
+ actual_version=""
+ for i in $(seq 1 30); do
+ packages_json=$(curl -sf -u admin:admin -X GET http://localhost:8080/packages || true)
+ actual_version=$(echo "$packages_json" | jq -r '.[] | select(.name == "dsBase") | .version' 2>/dev/null || true)
+ if [ "$actual_version" == "$expected_version" ]; then
+ break
+ fi
+ sleep 10
+ done
+ echo "Installed dsBase version: $actual_version"
+ if [ "$actual_version" != "$expected_version" ]; then
+ echo "dsBase version mismatch: expected $expected_version, found '$actual_version'"
+ exit 1
+ fi
+ echo "$actual_version" > dsbase_version.txt
+
+ curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
+ working-directory: dsBaseClient
+
+ - name: Dump Armadillo server log
+ if: failure()
+ shell: bash
+ run: docker compose -f docker-compose_armadillo.yml logs armadillo | grep "Caused by:" | sort -u || true
+ working-directory: dsBaseClient

.github/actions/setup-opal-with-dsbase/action.yaml

@@ -0,0 +1,75 @@
+name: Setup Opal with dsBase
+description: >
+ Starts a fresh Opal instance via docker-compose, installs R and system
+ dependencies, uploads test datasets, and installs dsBase with disclosure
+ test options. Assumes the caller has already checked out dsBaseClient at
+ ./dsBaseClient. Shared by the Opal dsbase shard workflow and the Opal
+ dsdanger job, so this setup only needs fixing in one place.
+
+inputs:
+ dsbase-ref:
+ description: dsBase GitHub ref to install
+ required: false
+ default: v7.0-dev
+
+runs:
+ using: composite
+ steps:
+ - name: Start Opal docker-compose
+ shell: bash
+ run: docker compose -f docker-compose_opal.yml up -d --build
+ working-directory: dsBaseClient
+
+ - uses: ./dsBaseClient/.github/actions/setup-r-with-dsbase-deps
+
+ - name: Install test datasets to Opal
+ shell: bash
+ run: |
+ for i in $(seq 1 18); do
+ if curl -sf -o /dev/null http://localhost:8080/; then
+ echo "Opal is responding"
+ break
+ fi
+ sleep 5
+ done
+ R -q -f "obiba_opal-upload_testing_datasets.R"
+ working-directory: dsBaseClient/tests/testthat/data_files
+
+ - name: Install dsBase to Opal, set disclosure test options
+ shell: bash
+ run: |
+ R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'http://localhost:8080/'); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)"
+ R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '${{ inputs.dsbase-ref }}'); opal.logout(opal)"
+
+ expected_version=$(curl -sf "https://raw.githubusercontent.com/datashield/dsBase/${{ inputs.dsbase-ref }}/DESCRIPTION" | sed -n 's/^Version: //p' | tr -d '\r')
+ if [ -z "$expected_version" ]; then
+ echo "Could not determine expected dsBase version from GitHub"
+ exit 1
+ fi
+ echo "Expected dsBase version: $expected_version"
+ echo "$expected_version" > dsbase_version.txt
+
+ ok=false
+ for i in $(seq 1 18); do
+ if Rscript -e "
+ library(opalr)
+ opal <- opal.login('administrator', 'datashield_test&', url = 'http://localhost:8080/')
+ desc <- dsadmin.package_description(opal, 'dsBase')
+ opal.logout(opal)
+ installed <- desc[['Version']]
+ cat('Installed dsBase version:', if (is.null(installed)) '(none yet)' else installed, '\n')
+ quit(status = if (!is.null(installed) && installed == '$expected_version') 0 else 1)
+ "; then
+ ok=true
+ break
+ fi
+ sleep 10
+ done
+ if [ "$ok" != "true" ]; then
+ echo "dsBase version mismatch or install not detected after polling: expected $expected_version"
+ exit 1
+ fi
+
+ R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.profile_init(opal, name = 'default', packages = c('dsBase', 'dsTidyverse', 'resourcer')); opal.logout(opal)"
+ R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)"
+ working-directory: dsBaseClient/tests/testthat/data_files

.github/actions/setup-r-with-dsbase-deps/action.yaml

@@ -0,0 +1,61 @@
+name: Setup R with dsBaseClient dependencies
+description: >
+ Installs the system libraries, R, and R package dependencies shared by the
+ Opal and Armadillo setup actions. Assumes the caller has already checked
+ out dsBaseClient at ./dsBaseClient.
+
+inputs:
+ additional-packages:
+ description: Extra pak package specs (one per line) to install beyond the common set
+ required: false
+ default: ''
+
+runs:
+ using: composite
+ steps:
+ - name: Install system libraries
+ shell: bash
+ env:
+ SYSTEM_LIBRARIES: >-
+ libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev
+ libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev
+ run: |
+ sudo apt-get update -qq
+ sudo apt-get install -qq $SYSTEM_LIBRARIES -y
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ r-version: release
+ http-user-agent: release
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ env:
+ # RSPM doesn't always have a binary for every package/R-version combo; when it
+ # falls back to source, pak needs LinkingTo deps present to compile it.
+ PKG_INCLUDE_LINKINGTO: true
+ R_PACKAGES: |
+ cran::devtools
+ cran::fields
+ cran::meta
+ cran::metafor
+ cran::ggplot2
+ cran::gridExtra
+ cran::data.table
+ cran::DSI
+ cran::opalr
+ cran::DSOpal
+ cran::DSLite
+ cran::MolgenisAuth
+ cran::MolgenisArmadillo
+ cran::DSMolgenisArmadillo
+ cran::DescTools
+ cran::e1071
+ github::datashield/dsDangerClient
+ with:
+ working-directory: dsBaseClient
+ dependencies: 'c("Depends", "Imports", "LinkingTo")'
+ extra-packages: |
+ ${{ env.R_PACKAGES }}
+ ${{ inputs.additional-packages }}
+ needs: check

.Rbuildignore

@@ -25,3 +25,4 @@
 ^\.github$
 ^REFACTOR_GUIDE\.md$
 ^man-roxygen$
+^codecov\.yml$

.github/actions/setup-armadillo-with-dsbase/action.yaml

@@ -0,0 +1,140 @@
+name: Setup Armadillo with dsBase
+description: >
+ Starts a fresh Armadillo instance via docker-compose, with the "default"
+ Rock profile as a static sibling container. Installs R and system
+ dependencies, waits for readiness, uploads test datasets, and installs
+ dsBase. Assumes the caller has already checked out dsBaseClient at
+ ./dsBaseClient. Shared by the Armadillo dsbase shard workflow and the
+ Armadillo dsdanger job, so this setup only needs fixing in one place.
+
+inputs:
+ dsbase-tarball:
+ description: dsBase tarball filename to install
+ required: false
+ default: dsBase_7.0.0-permissive.tar.gz
+
+runs:
+ using: composite
+ steps:
+ - name: Write Armadillo config
+ shell: bash
+ run: |
+ mkdir -p armadillo_home/config
+
+ cat > armadillo_home/config/application.yml <<EOF
+ armadillo:
+ docker-management-enabled: false
+ docker-run-in-container: true
+ profiles:
+ - name: default
+ image: datashield/rock_citest-permissive:latest
+ host: default
+ port: 8085
+ package-whitelist:
+ - dsBase
+ - dsTidyverse
+ - resourcer
+ function-blacklist: [ ]
+ options:
+ datashield:
+ seed: 342325352
+ spring:
+ security:
+ user:
+ name: admin
+ password: admin
+ servlet:
+ multipart:
+ max-file-size: 1000MB
+ max-request-size: 1000MB
+ storage:
+ root-dir: /data
+ audit.log.path: '/logs/audit.log'
+ stdout.log.path: '/logs/armadillo.log'
+ logging:
+ level:
+ root: "warn"
+ org.molgenis: "warn"
+ EOF
+ working-directory: dsBaseClient
+
+ - name: Start Armadillo docker-compose
+ shell: bash
+ run: docker compose -f docker-compose_armadillo.yml up -d
+ working-directory: dsBaseClient
+
+ - uses: ./dsBaseClient/.github/actions/setup-r-with-dsbase-deps
+ with:
+ additional-packages: cran::covr
+
+ - name: Wait for Armadillo to be ready
+ shell: bash
+ run: |
+ for i in $(seq 1 60); do
+ if curl -fsS http://localhost:8080/actuator/health 2>/dev/null | grep -q '"status":"UP"'; then
+ echo "Armadillo is ready"
+ exit 0
+ fi
+ sleep 5
+ done
+ echo "Armadillo did not become ready in time"
+ docker compose -f docker-compose_armadillo.yml logs armadillo || true
+ exit 1
+ working-directory: dsBaseClient
+
+ - name: Install test datasets to Armadillo
+ shell: bash
+ run: R -q -f "molgenis_armadillo-upload_testing_datasets.R"
+ working-directory: dsBaseClient/tests/testthat/data_files
+
+ - name: Install dsBase to Armadillo
+ shell: bash
+ run: |
+ installed=false
+ for i in $(seq 1 30); do
+ if Rscript -e "
+ library(MolgenisArmadillo)
+ armadillo.login_basic('http://localhost:8080', 'admin', 'admin')
+ armadillo.install_packages('${{ inputs.dsbase-tarball }}', profile = 'default')
+ "; then
+ installed=true
+ break
+ fi
+ sleep 10
+ done
+ if [ "$installed" != "true" ]; then
+ echo "dsBase install via armadillo.install_packages() failed (default profile may not have started in time)"
+ exit 1
+ fi
+
+ expected_version=$(tar -xOzf ${{ inputs.dsbase-tarball }} dsBase/DESCRIPTION | sed -n 's/^Version: //p' | tr -d '\r')
+ if [ -z "$expected_version" ]; then
+ echo "Could not determine expected dsBase version from ${{ inputs.dsbase-tarball }}"
+ exit 1
+ fi
+ echo "Expected dsBase version: $expected_version"
+
+ actual_version=""
+ for i in $(seq 1 30); do
+ packages_json=$(curl -sf -u admin:admin -X GET http://localhost:8080/packages || true)
+ actual_version=$(echo "$packages_json" | jq -r '.[] | select(.name == "dsBase") | .version' 2>/dev/null || true)
+ if [ "$actual_version" == "$expected_version" ]; then
+ break
+ fi
+ sleep 10
+ done
+ echo "Installed dsBase version: $actual_version"
+ if [ "$actual_version" != "$expected_version" ]; then
+ echo "dsBase version mismatch: expected $expected_version, found '$actual_version'"
+ exit 1
+ fi
+ echo "$actual_version" > dsbase_version.txt
+
+ curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
+ working-directory: dsBaseClient
+
+ - name: Dump Armadillo server log
+ if: failure()
+ shell: bash
+ run: docker compose -f docker-compose_armadillo.yml logs armadillo | grep "Caused by:" | sort -u || true
+ working-directory: dsBaseClient

.github/actions/setup-opal-with-dsbase/action.yaml

@@ -0,0 +1,75 @@
+name: Setup Opal with dsBase
+description: >
+ Starts a fresh Opal instance via docker-compose, installs R and system
+ dependencies, uploads test datasets, and installs dsBase with disclosure
+ test options. Assumes the caller has already checked out dsBaseClient at
+ ./dsBaseClient. Shared by the Opal dsbase shard workflow and the Opal
+ dsdanger job, so this setup only needs fixing in one place.
+
+inputs:
+ dsbase-ref:
+ description: dsBase GitHub ref to install
+ required: false
+ default: v7.0-dev
+
+runs:
+ using: composite
+ steps:
+ - name: Start Opal docker-compose
+ shell: bash
+ run: docker compose -f docker-compose_opal.yml up -d --build
+ working-directory: dsBaseClient
+
+ - uses: ./dsBaseClient/.github/actions/setup-r-with-dsbase-deps
+
+ - name: Install test datasets to Opal
+ shell: bash
+ run: |
+ for i in $(seq 1 18); do
+ if curl -sf -o /dev/null http://localhost:8080/; then
+ echo "Opal is responding"
+ break
+ fi
+ sleep 5
+ done
+ R -q -f "obiba_opal-upload_testing_datasets.R"
+ working-directory: dsBaseClient/tests/testthat/data_files
+
+ - name: Install dsBase to Opal, set disclosure test options
+ shell: bash
+ run: |
+ R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'http://localhost:8080/'); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)"
+ R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '${{ inputs.dsbase-ref }}'); opal.logout(opal)"
+
+ expected_version=$(curl -sf "https://raw.githubusercontent.com/datashield/dsBase/${{ inputs.dsbase-ref }}/DESCRIPTION" | sed -n 's/^Version: //p' | tr -d '\r')
+ if [ -z "$expected_version" ]; then
+ echo "Could not determine expected dsBase version from GitHub"
+ exit 1
+ fi
+ echo "Expected dsBase version: $expected_version"
+ echo "$expected_version" > dsbase_version.txt
+
+ ok=false
+ for i in $(seq 1 18); do
+ if Rscript -e "
+ library(opalr)
+ opal <- opal.login('administrator', 'datashield_test&', url = 'http://localhost:8080/')
+ desc <- dsadmin.package_description(opal, 'dsBase')
+ opal.logout(opal)
+ installed <- desc[['Version']]
+ cat('Installed dsBase version:', if (is.null(installed)) '(none yet)' else installed, '\n')
+ quit(status = if (!is.null(installed) && installed == '$expected_version') 0 else 1)
+ "; then
+ ok=true
+ break
+ fi
+ sleep 10
+ done
+ if [ "$ok" != "true" ]; then
+ echo "dsBase version mismatch or install not detected after polling: expected $expected_version"
+ exit 1
+ fi
+
+ R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.profile_init(opal, name = 'default', packages = c('dsBase', 'dsTidyverse', 'resourcer')); opal.logout(opal)"
+ R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)"
+ working-directory: dsBaseClient/tests/testthat/data_files

.github/actions/setup-r-with-dsbase-deps/action.yaml

@@ -0,0 +1,61 @@
+name: Setup R with dsBaseClient dependencies
+description: >
+ Installs the system libraries, R, and R package dependencies shared by the
+ Opal and Armadillo setup actions. Assumes the caller has already checked
+ out dsBaseClient at ./dsBaseClient.
+
+inputs:
+ additional-packages:
+ description: Extra pak package specs (one per line) to install beyond the common set
+ required: false
+ default: ''
+
+runs:
+ using: composite
+ steps:
+ - name: Install system libraries
+ shell: bash
+ env:
+ SYSTEM_LIBRARIES: >-
+ libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev
+ libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev
+ run: |
+ sudo apt-get update -qq
+ sudo apt-get install -qq $SYSTEM_LIBRARIES -y
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ r-version: release
+ http-user-agent: release
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ env:
+ # RSPM doesn't always have a binary for every package/R-version combo; when it
+ # falls back to source, pak needs LinkingTo deps present to compile it.
+ PKG_INCLUDE_LINKINGTO: true
+ R_PACKAGES: |
+ cran::devtools
+ cran::fields
+ cran::meta
+ cran::metafor
+ cran::ggplot2
+ cran::gridExtra
+ cran::data.table
+ cran::DSI
+ cran::opalr
+ cran::DSOpal
+ cran::DSLite
+ cran::MolgenisAuth
+ cran::MolgenisArmadillo
+ cran::DSMolgenisArmadillo
+ cran::DescTools
+ cran::e1071
+ github::datashield/dsDangerClient
+ with:
+ working-directory: dsBaseClient
+ dependencies: 'c("Depends", "Imports", "LinkingTo")'
+ extra-packages: |
+ ${{ env.R_PACKAGES }}
+ ${{ inputs.additional-packages }}
+ needs: check