V6.3.4 dev#605

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Merged
StuartWheater merged 4 commits into from
Aug 4, 2025
Merged

V6.3.4 dev #605

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805a6a2
Switch to 'rock-omicron-karma-permissive:latest'
StuartWheater Aug 4, 2025
e03d3c6
Update profile and server images
StuartWheater Aug 4, 2025
bb5d234
Updated
StuartWheater Aug 4, 2025
52ca585
Update packages
StuartWheater Aug 4, 2025
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10 changes: 5 additions & 5 deletions armadillo_azure-pipelines.yml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
- master
always: true
- cron: "0 2 * * *"
displayName: Nightly build - v6.3.2-dev
displayName: Nightly build - v6.3.4-dev
branches:
include:
- v6.3.2-dev
- v6.3.4-dev
always: true

#########################################################################################
Expand DownExpand Up@@ -139,7 +139,7 @@ jobs:
sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

# XML grep for coverage report merging
sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:

curl -u admin:admin -X GET http://localhost:8080/packages

curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.2-permissive.tar.gz" -X POST http://localhost:8080/install-package
curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.4-permissive.tar.gz" -X POST http://localhost:8080/install-package
sleep 60

docker container restart dsbaseclient_armadillo_1
Expand DownExpand Up@@ -364,7 +364,7 @@ jobs:
- bash: |
curl -u admin:admin http://localhost:8080/whitelist

curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.2.tar.gz" -X POST http://localhost:8080/install-package
curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.4.tar.gz" -X POST http://localhost:8080/install-package

docker container restart dsbaseclient_armadillo_1
sleep 60
Expand Down
12 changes: 6 additions & 6 deletions azure-pipelines.yml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
- master
always: true
- cron: "0 2 * * *"
displayName: Nightly build - v6.3.2-dev
displayName: Nightly build - v6.3.4-dev
branches:
include:
- v6.3.2-dev
- v6.3.4-dev
always: true

#########################################################################################
Expand DownExpand Up@@ -132,15 +132,15 @@ jobs:
sudo apt-get upgrade -y

sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev -y
sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y
sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')"
sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')"
sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.2', dependencies = TRUE)"
sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

# XML grep for coverage report merging
sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:
- bash: |
R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)"
R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

sleep 60

Expand DownExpand Up@@ -363,7 +363,7 @@ jobs:

R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)"
R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsDanger package on Opal server'
Expand Down
7 changes: 3 additions & 4 deletions docker-compose_armadillo.yml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@ services:
hostname: armadillo
ports:
- 8080:8080
image: datashield/armadillo_citest:5.1.4
image: datashield/armadillo_citest:latest
environment:
LOGGING_CONFIG: 'classpath:logback-file.xml'
AUDIT_LOG_PATH: '/app/logs/audit.log'
Expand All@@ -16,7 +16,6 @@ services:

default:
hostname: default
# image: datashield/rock-margin-joule-permissive:latest
image: datashield/rserver-neutron-gypsum-permissive:latest
image: datashield/rock-omicron-karma-permissive:latest
environment:
DEBUG: "TRUE"
DEBUG: "FALSE"
6 changes: 4 additions & 2 deletions docker-compose_opal.yml
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Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
services:
opal:
image: obiba/opal:5.1.4
image: datashield/opal_citest:latest
ports:
- "8443:8443"
- 8443:8443
links:
- mongo
- rock
Expand All@@ -21,3 +21,5 @@ services:
- MONGO_INITDB_ROOT_PASSWORD=foobar
rock:
image: datashield/rock-omicron-karma-permissive:latest
environment:
DEBUG: "FALSE"
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10 changes: 5 additions & 5 deletions opal_azure-pipelines.yml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
- master
always: true
- cron: "0 2 * * *"
displayName: Nightly build - v6.3.2-dev
displayName: Nightly build - v6.3.4-dev
branches:
include:
- v6.3.2-dev
- v6.3.4-dev
always: true

#########################################################################################
Expand DownExpand Up@@ -140,7 +140,7 @@ jobs:
sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

# XML grep for coverage report merging
sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:
- bash: |
R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)"
R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

sleep 60

Expand DownExpand Up@@ -363,7 +363,7 @@ jobs:

R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)"
R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsDanger package on Opal server'
Expand Down
6 changes: 3 additions & 3 deletions tests/docker/armadillo/standard/config/application.yml
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Expand Up@@ -14,10 +14,10 @@ armadillo:
# oidc-admin-user: user@yourdomain.org
profiles:
- name: default
image: datashield/rserver-neutron-gypsum-permissive:latest
port: 6311
image: datashield/rock-omicron-karma:latest
port: 8080
host: default
package-whitelist: # Packages for 'gypsum-permissive'
package-whitelist: # Packages for 'permissive'
- dsBase
- dsMediation
- dsMTLBase
Expand Down
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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V6.3.4 dev#605

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privacy statement. We’ll occasionally send you account related emails.

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to your account

 Merged

StuartWheater
merged 4 commits into

from

Aug 4, 2025
 Merged


V6.3.4 dev
#605
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805a6a2

Switch to 'rock-omicron-karma-permissive:latest'


StuartWheater Aug 4, 2025
e03d3c6

Update profile and server images


StuartWheater Aug 4, 2025
bb5d234

Updated


StuartWheater Aug 4, 2025
52ca585

Update packages


StuartWheater Aug 4, 2025

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10 changes: 5 additions & 5 deletions
armadillo_azure-pipelines.yml

View file


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Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -139,7 +139,7 @@ jobs:
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:

 curl -u admin:admin -X GET http://localhost:8080/packages

 curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.2-permissive.tar.gz" -X POST http://localhost:8080/install-package
 curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.4-permissive.tar.gz" -X POST http://localhost:8080/install-package
 sleep 60

 docker container restart dsbaseclient_armadillo_1
Expand DownExpand Up@@ -364,7 +364,7 @@ jobs:
 - bash: |
 curl -u admin:admin http://localhost:8080/whitelist

 curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.2.tar.gz" -X POST http://localhost:8080/install-package
 curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.4.tar.gz" -X POST http://localhost:8080/install-package

 docker container restart dsbaseclient_armadillo_1
 sleep 60
Expand Down

12 changes: 6 additions & 6 deletions
azure-pipelines.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -132,15 +132,15 @@ jobs:
 sudo apt-get upgrade -y

 sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
 sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev -y
 sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y
 sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.2', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:
 - bash: |
 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 sleep 60

Expand DownExpand Up@@ -363,7 +363,7 @@ jobs:

 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 workingDirectory: $(Pipeline.Workspace)/dsBaseClient
 displayName: 'Install dsDanger package on Opal server'
Expand Down

7 changes: 3 additions & 4 deletions
docker-compose_armadillo.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@ services:
 hostname: armadillo
 ports:
 - 8080:8080
 image: datashield/armadillo_citest:5.1.4
 image: datashield/armadillo_citest:latest
 environment:
 LOGGING_CONFIG: 'classpath:logback-file.xml'
 AUDIT_LOG_PATH: '/app/logs/audit.log'
Expand All@@ -16,7 +16,6 @@ services:

 default:
 hostname: default
# image: datashield/rock-margin-joule-permissive:latest
 image: datashield/rserver-neutron-gypsum-permissive:latest
 image: datashield/rock-omicron-karma-permissive:latest
 environment:
 DEBUG: "TRUE"
 DEBUG: "FALSE"

6 changes: 4 additions & 2 deletions
docker-compose_opal.yml

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Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
services:
 opal:
 image: obiba/opal:5.1.4
 image: datashield/opal_citest:latest
 ports:
 - "8443:8443"
 - 8443:8443
 links:
 - mongo
 - rock
Expand All@@ -21,3 +21,5 @@ services:
 - MONGO_INITDB_ROOT_PASSWORD=foobar
 rock:
 image: datashield/rock-omicron-karma-permissive:latest
 environment:
 DEBUG: "FALSE"
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10 changes: 5 additions & 5 deletions
opal_azure-pipelines.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -140,7 +140,7 @@ jobs:
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:
 - bash: |
 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 sleep 60

Expand DownExpand Up@@ -363,7 +363,7 @@ jobs:

 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 workingDirectory: $(Pipeline.Workspace)/dsBaseClient
 displayName: 'Install dsDanger package on Opal server'
Expand Down

6 changes: 3 additions & 3 deletions
tests/docker/armadillo/standard/config/application.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -14,10 +14,10 @@ armadillo:
 # oidc-admin-user: user@yourdomain.org
 profiles:
 - name: default
 image: datashield/rserver-neutron-gypsum-permissive:latest
 port: 6311
 image: datashield/rock-omicron-karma:latest
 port: 8080
 host: default
 package-whitelist: # Packages for 'gypsum-permissive'
 package-whitelist: # Packages for 'permissive'
 - dsBase
 - dsMediation
 - dsMTLBase
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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V6.3.4 dev#605

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 Merged

StuartWheater
merged 4 commits into

from

Aug 4, 2025
 Merged


V6.3.4 dev
#605
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805a6a2

Switch to 'rock-omicron-karma-permissive:latest'


StuartWheater Aug 4, 2025
e03d3c6

Update profile and server images


StuartWheater Aug 4, 2025
bb5d234

Updated


StuartWheater Aug 4, 2025
52ca585

Update packages


StuartWheater Aug 4, 2025

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10 changes: 5 additions & 5 deletions
armadillo_azure-pipelines.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -139,7 +139,7 @@ jobs:
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:

 curl -u admin:admin -X GET http://localhost:8080/packages

 curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.2-permissive.tar.gz" -X POST http://localhost:8080/install-package
 curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.4-permissive.tar.gz" -X POST http://localhost:8080/install-package
 sleep 60

 docker container restart dsbaseclient_armadillo_1
Expand DownExpand Up@@ -364,7 +364,7 @@ jobs:
 - bash: |
 curl -u admin:admin http://localhost:8080/whitelist

 curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.2.tar.gz" -X POST http://localhost:8080/install-package
 curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.4.tar.gz" -X POST http://localhost:8080/install-package

 docker container restart dsbaseclient_armadillo_1
 sleep 60
Expand Down

12 changes: 6 additions & 6 deletions
azure-pipelines.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -132,15 +132,15 @@ jobs:
 sudo apt-get upgrade -y

 sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
 sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev -y
 sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y
 sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.2', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:
 - bash: |
 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 sleep 60

Expand DownExpand Up@@ -363,7 +363,7 @@ jobs:

 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 workingDirectory: $(Pipeline.Workspace)/dsBaseClient
 displayName: 'Install dsDanger package on Opal server'
Expand Down

7 changes: 3 additions & 4 deletions
docker-compose_armadillo.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@ services:
 hostname: armadillo
 ports:
 - 8080:8080
 image: datashield/armadillo_citest:5.1.4
 image: datashield/armadillo_citest:latest
 environment:
 LOGGING_CONFIG: 'classpath:logback-file.xml'
 AUDIT_LOG_PATH: '/app/logs/audit.log'
Expand All@@ -16,7 +16,6 @@ services:

 default:
 hostname: default
# image: datashield/rock-margin-joule-permissive:latest
 image: datashield/rserver-neutron-gypsum-permissive:latest
 image: datashield/rock-omicron-karma-permissive:latest
 environment:
 DEBUG: "TRUE"
 DEBUG: "FALSE"

6 changes: 4 additions & 2 deletions
docker-compose_opal.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
services:
 opal:
 image: obiba/opal:5.1.4
 image: datashield/opal_citest:latest
 ports:
 - "8443:8443"
 - 8443:8443
 links:
 - mongo
 - rock
Expand All@@ -21,3 +21,5 @@ services:
 - MONGO_INITDB_ROOT_PASSWORD=foobar
 rock:
 image: datashield/rock-omicron-karma-permissive:latest
 environment:
 DEBUG: "FALSE"
Binary file removeddsBase_6.3.2-permissive.tar.gz

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Binary file not shown.

Binary file removeddsBase_6.3.2.tar.gz

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Binary file addeddsBase_6.3.4-permissive.tar.gz

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Binary file not shown.

Binary file addeddsBase_6.3.4.tar.gz

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Binary file not shown.

Binary file removeddsDanger_6.3.1.tar.gz

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Binary file addeddsDanger_6.3.4.tar.gz

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Binary file not shown.


10 changes: 5 additions & 5 deletions
opal_azure-pipelines.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -140,7 +140,7 @@ jobs:
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:
 - bash: |
 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 sleep 60

Expand DownExpand Up@@ -363,7 +363,7 @@ jobs:

 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 workingDirectory: $(Pipeline.Workspace)/dsBaseClient
 displayName: 'Install dsDanger package on Opal server'
Expand Down

6 changes: 3 additions & 3 deletions
tests/docker/armadillo/standard/config/application.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -14,10 +14,10 @@ armadillo:
 # oidc-admin-user: user@yourdomain.org
 profiles:
 - name: default
 image: datashield/rserver-neutron-gypsum-permissive:latest
 port: 6311
 image: datashield/rock-omicron-karma:latest
 port: 8080
 host: default
 package-whitelist: # Packages for 'gypsum-permissive'
 package-whitelist: # Packages for 'permissive'
 - dsBase
 - dsMediation
 - dsMTLBase
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
V6.3.4 dev#605

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 Merged

StuartWheater
merged 4 commits into

from

Aug 4, 2025
 Merged


V6.3.4 dev
#605
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805a6a2

Switch to 'rock-omicron-karma-permissive:latest'


StuartWheater Aug 4, 2025
e03d3c6

Update profile and server images


StuartWheater Aug 4, 2025
bb5d234

Updated


StuartWheater Aug 4, 2025
52ca585

Update packages


StuartWheater Aug 4, 2025

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10 changes: 5 additions & 5 deletions
armadillo_azure-pipelines.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -139,7 +139,7 @@ jobs:
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:

 curl -u admin:admin -X GET http://localhost:8080/packages

 curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.2-permissive.tar.gz" -X POST http://localhost:8080/install-package
 curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.4-permissive.tar.gz" -X POST http://localhost:8080/install-package
 sleep 60

 docker container restart dsbaseclient_armadillo_1
Expand DownExpand Up@@ -364,7 +364,7 @@ jobs:
 - bash: |
 curl -u admin:admin http://localhost:8080/whitelist

 curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.2.tar.gz" -X POST http://localhost:8080/install-package
 curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.4.tar.gz" -X POST http://localhost:8080/install-package

 docker container restart dsbaseclient_armadillo_1
 sleep 60
Expand Down

12 changes: 6 additions & 6 deletions
azure-pipelines.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -132,15 +132,15 @@ jobs:
 sudo apt-get upgrade -y

 sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
 sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev -y
 sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y
 sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.2', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:
 - bash: |
 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 sleep 60

Expand DownExpand Up@@ -363,7 +363,7 @@ jobs:

 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 workingDirectory: $(Pipeline.Workspace)/dsBaseClient
 displayName: 'Install dsDanger package on Opal server'
Expand Down

7 changes: 3 additions & 4 deletions
docker-compose_armadillo.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@ services:
 hostname: armadillo
 ports:
 - 8080:8080
 image: datashield/armadillo_citest:5.1.4
 image: datashield/armadillo_citest:latest
 environment:
 LOGGING_CONFIG: 'classpath:logback-file.xml'
 AUDIT_LOG_PATH: '/app/logs/audit.log'
Expand All@@ -16,7 +16,6 @@ services:

 default:
 hostname: default
# image: datashield/rock-margin-joule-permissive:latest
 image: datashield/rserver-neutron-gypsum-permissive:latest
 image: datashield/rock-omicron-karma-permissive:latest
 environment:
 DEBUG: "TRUE"
 DEBUG: "FALSE"

6 changes: 4 additions & 2 deletions
docker-compose_opal.yml

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Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
services:
 opal:
 image: obiba/opal:5.1.4
 image: datashield/opal_citest:latest
 ports:
 - "8443:8443"
 - 8443:8443
 links:
 - mongo
 - rock
Expand All@@ -21,3 +21,5 @@ services:
 - MONGO_INITDB_ROOT_PASSWORD=foobar
 rock:
 image: datashield/rock-omicron-karma-permissive:latest
 environment:
 DEBUG: "FALSE"
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10 changes: 5 additions & 5 deletions
opal_azure-pipelines.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -140,7 +140,7 @@ jobs:
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:
 - bash: |
 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 sleep 60

Expand DownExpand Up@@ -363,7 +363,7 @@ jobs:

 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 workingDirectory: $(Pipeline.Workspace)/dsBaseClient
 displayName: 'Install dsDanger package on Opal server'
Expand Down

6 changes: 3 additions & 3 deletions
tests/docker/armadillo/standard/config/application.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -14,10 +14,10 @@ armadillo:
 # oidc-admin-user: user@yourdomain.org
 profiles:
 - name: default
 image: datashield/rserver-neutron-gypsum-permissive:latest
 port: 6311
 image: datashield/rock-omicron-karma:latest
 port: 8080
 host: default
 package-whitelist: # Packages for 'gypsum-permissive'
 package-whitelist: # Packages for 'permissive'
 - dsBase
 - dsMediation
 - dsMTLBase
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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 Merged

StuartWheater
merged 4 commits into

from

Aug 4, 2025
 Merged


V6.3.4 dev
#605
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805a6a2

Switch to 'rock-omicron-karma-permissive:latest'


StuartWheater Aug 4, 2025
e03d3c6

Update profile and server images


StuartWheater Aug 4, 2025
bb5d234

Updated


StuartWheater Aug 4, 2025
52ca585

Update packages


StuartWheater Aug 4, 2025

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10 changes: 5 additions & 5 deletions
armadillo_azure-pipelines.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -139,7 +139,7 @@ jobs:
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:

 curl -u admin:admin -X GET http://localhost:8080/packages

 curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.2-permissive.tar.gz" -X POST http://localhost:8080/install-package
 curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.4-permissive.tar.gz" -X POST http://localhost:8080/install-package
 sleep 60

 docker container restart dsbaseclient_armadillo_1
Expand DownExpand Up@@ -364,7 +364,7 @@ jobs:
 - bash: |
 curl -u admin:admin http://localhost:8080/whitelist

 curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.2.tar.gz" -X POST http://localhost:8080/install-package
 curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.4.tar.gz" -X POST http://localhost:8080/install-package

 docker container restart dsbaseclient_armadillo_1
 sleep 60
Expand Down

12 changes: 6 additions & 6 deletions
azure-pipelines.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -132,15 +132,15 @@ jobs:
 sudo apt-get upgrade -y

 sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
 sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev -y
 sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y
 sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.2', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:
 - bash: |
 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 sleep 60

Expand DownExpand Up@@ -363,7 +363,7 @@ jobs:

 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 workingDirectory: $(Pipeline.Workspace)/dsBaseClient
 displayName: 'Install dsDanger package on Opal server'
Expand Down

7 changes: 3 additions & 4 deletions
docker-compose_armadillo.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@ services:
 hostname: armadillo
 ports:
 - 8080:8080
 image: datashield/armadillo_citest:5.1.4
 image: datashield/armadillo_citest:latest
 environment:
 LOGGING_CONFIG: 'classpath:logback-file.xml'
 AUDIT_LOG_PATH: '/app/logs/audit.log'
Expand All@@ -16,7 +16,6 @@ services:

 default:
 hostname: default
# image: datashield/rock-margin-joule-permissive:latest
 image: datashield/rserver-neutron-gypsum-permissive:latest
 image: datashield/rock-omicron-karma-permissive:latest
 environment:
 DEBUG: "TRUE"
 DEBUG: "FALSE"

6 changes: 4 additions & 2 deletions
docker-compose_opal.yml

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Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
services:
 opal:
 image: obiba/opal:5.1.4
 image: datashield/opal_citest:latest
 ports:
 - "8443:8443"
 - 8443:8443
 links:
 - mongo
 - rock
Expand All@@ -21,3 +21,5 @@ services:
 - MONGO_INITDB_ROOT_PASSWORD=foobar
 rock:
 image: datashield/rock-omicron-karma-permissive:latest
 environment:
 DEBUG: "FALSE"
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10 changes: 5 additions & 5 deletions
opal_azure-pipelines.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -140,7 +140,7 @@ jobs:
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:
 - bash: |
 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 sleep 60

Expand DownExpand Up@@ -363,7 +363,7 @@ jobs:

 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 workingDirectory: $(Pipeline.Workspace)/dsBaseClient
 displayName: 'Install dsDanger package on Opal server'
Expand Down

6 changes: 3 additions & 3 deletions
tests/docker/armadillo/standard/config/application.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -14,10 +14,10 @@ armadillo:
 # oidc-admin-user: user@yourdomain.org
 profiles:
 - name: default
 image: datashield/rserver-neutron-gypsum-permissive:latest
 port: 6311
 image: datashield/rock-omicron-karma:latest
 port: 8080
 host: default
 package-whitelist: # Packages for 'gypsum-permissive'
 package-whitelist: # Packages for 'permissive'
 - dsBase
 - dsMediation
 - dsMTLBase
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
V6.3.4 dev#605

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

StuartWheater
merged 4 commits into

from

Aug 4, 2025
 Merged


V6.3.4 dev
#605
Show file tree
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805a6a2

Switch to 'rock-omicron-karma-permissive:latest'


StuartWheater Aug 4, 2025
e03d3c6

Update profile and server images


StuartWheater Aug 4, 2025
bb5d234

Updated


StuartWheater Aug 4, 2025
52ca585

Update packages


StuartWheater Aug 4, 2025

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10 changes: 5 additions & 5 deletions
armadillo_azure-pipelines.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -139,7 +139,7 @@ jobs:
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:

 curl -u admin:admin -X GET http://localhost:8080/packages

 curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.2-permissive.tar.gz" -X POST http://localhost:8080/install-package
 curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.4-permissive.tar.gz" -X POST http://localhost:8080/install-package
 sleep 60

 docker container restart dsbaseclient_armadillo_1
Expand DownExpand Up@@ -364,7 +364,7 @@ jobs:
 - bash: |
 curl -u admin:admin http://localhost:8080/whitelist

 curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.2.tar.gz" -X POST http://localhost:8080/install-package
 curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.4.tar.gz" -X POST http://localhost:8080/install-package

 docker container restart dsbaseclient_armadillo_1
 sleep 60
Expand Down

12 changes: 6 additions & 6 deletions
azure-pipelines.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -132,15 +132,15 @@ jobs:
 sudo apt-get upgrade -y

 sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
 sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev -y
 sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y
 sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.2', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:
 - bash: |
 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 sleep 60

Expand DownExpand Up@@ -363,7 +363,7 @@ jobs:

 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 workingDirectory: $(Pipeline.Workspace)/dsBaseClient
 displayName: 'Install dsDanger package on Opal server'
Expand Down

7 changes: 3 additions & 4 deletions
docker-compose_armadillo.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@ services:
 hostname: armadillo
 ports:
 - 8080:8080
 image: datashield/armadillo_citest:5.1.4
 image: datashield/armadillo_citest:latest
 environment:
 LOGGING_CONFIG: 'classpath:logback-file.xml'
 AUDIT_LOG_PATH: '/app/logs/audit.log'
Expand All@@ -16,7 +16,6 @@ services:

 default:
 hostname: default
# image: datashield/rock-margin-joule-permissive:latest
 image: datashield/rserver-neutron-gypsum-permissive:latest
 image: datashield/rock-omicron-karma-permissive:latest
 environment:
 DEBUG: "TRUE"
 DEBUG: "FALSE"

6 changes: 4 additions & 2 deletions
docker-compose_opal.yml

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Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
services:
 opal:
 image: obiba/opal:5.1.4
 image: datashield/opal_citest:latest
 ports:
 - "8443:8443"
 - 8443:8443
 links:
 - mongo
 - rock
Expand All@@ -21,3 +21,5 @@ services:
 - MONGO_INITDB_ROOT_PASSWORD=foobar
 rock:
 image: datashield/rock-omicron-karma-permissive:latest
 environment:
 DEBUG: "FALSE"
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10 changes: 5 additions & 5 deletions
opal_azure-pipelines.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -140,7 +140,7 @@ jobs:
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:
 - bash: |
 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 sleep 60

Expand DownExpand Up@@ -363,7 +363,7 @@ jobs:

 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 workingDirectory: $(Pipeline.Workspace)/dsBaseClient
 displayName: 'Install dsDanger package on Opal server'
Expand Down

6 changes: 3 additions & 3 deletions
tests/docker/armadillo/standard/config/application.yml

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Expand Up@@ -14,10 +14,10 @@ armadillo:
 # oidc-admin-user: user@yourdomain.org
 profiles:
 - name: default
 image: datashield/rserver-neutron-gypsum-permissive:latest
 port: 6311
 image: datashield/rock-omicron-karma:latest
 port: 8080
 host: default
 package-whitelist: # Packages for 'gypsum-permissive'
 package-whitelist: # Packages for 'permissive'
 - dsBase
 - dsMediation
 - dsMTLBase
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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 Merged

StuartWheater
merged 4 commits into

from

Aug 4, 2025
 Merged


V6.3.4 dev
#605
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805a6a2

Switch to 'rock-omicron-karma-permissive:latest'


StuartWheater Aug 4, 2025
e03d3c6

Update profile and server images


StuartWheater Aug 4, 2025
bb5d234

Updated


StuartWheater Aug 4, 2025
52ca585

Update packages


StuartWheater Aug 4, 2025

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10 changes: 5 additions & 5 deletions
armadillo_azure-pipelines.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -139,7 +139,7 @@ jobs:
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:

 curl -u admin:admin -X GET http://localhost:8080/packages

 curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.2-permissive.tar.gz" -X POST http://localhost:8080/install-package
 curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.4-permissive.tar.gz" -X POST http://localhost:8080/install-package
 sleep 60

 docker container restart dsbaseclient_armadillo_1
Expand DownExpand Up@@ -364,7 +364,7 @@ jobs:
 - bash: |
 curl -u admin:admin http://localhost:8080/whitelist

 curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.2.tar.gz" -X POST http://localhost:8080/install-package
 curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.4.tar.gz" -X POST http://localhost:8080/install-package

 docker container restart dsbaseclient_armadillo_1
 sleep 60
Expand Down

12 changes: 6 additions & 6 deletions
azure-pipelines.yml

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -132,15 +132,15 @@ jobs:
 sudo apt-get upgrade -y

 sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
 sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev -y
 sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y
 sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.2', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:
 - bash: |
 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 sleep 60

Expand DownExpand Up@@ -363,7 +363,7 @@ jobs:

 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 workingDirectory: $(Pipeline.Workspace)/dsBaseClient
 displayName: 'Install dsDanger package on Opal server'
Expand Down

7 changes: 3 additions & 4 deletions
docker-compose_armadillo.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@ services:
 hostname: armadillo
 ports:
 - 8080:8080
 image: datashield/armadillo_citest:5.1.4
 image: datashield/armadillo_citest:latest
 environment:
 LOGGING_CONFIG: 'classpath:logback-file.xml'
 AUDIT_LOG_PATH: '/app/logs/audit.log'
Expand All@@ -16,7 +16,6 @@ services:

 default:
 hostname: default
# image: datashield/rock-margin-joule-permissive:latest
 image: datashield/rserver-neutron-gypsum-permissive:latest
 image: datashield/rock-omicron-karma-permissive:latest
 environment:
 DEBUG: "TRUE"
 DEBUG: "FALSE"

6 changes: 4 additions & 2 deletions
docker-compose_opal.yml

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Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
services:
 opal:
 image: obiba/opal:5.1.4
 image: datashield/opal_citest:latest
 ports:
 - "8443:8443"
 - 8443:8443
 links:
 - mongo
 - rock
Expand All@@ -21,3 +21,5 @@ services:
 - MONGO_INITDB_ROOT_PASSWORD=foobar
 rock:
 image: datashield/rock-omicron-karma-permissive:latest
 environment:
 DEBUG: "FALSE"
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10 changes: 5 additions & 5 deletions
opal_azure-pipelines.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -140,7 +140,7 @@ jobs:
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:
 - bash: |
 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 sleep 60

Expand DownExpand Up@@ -363,7 +363,7 @@ jobs:

 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 workingDirectory: $(Pipeline.Workspace)/dsBaseClient
 displayName: 'Install dsDanger package on Opal server'
Expand Down

6 changes: 3 additions & 3 deletions
tests/docker/armadillo/standard/config/application.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -14,10 +14,10 @@ armadillo:
 # oidc-admin-user: user@yourdomain.org
 profiles:
 - name: default
 image: datashield/rserver-neutron-gypsum-permissive:latest
 port: 6311
 image: datashield/rock-omicron-karma:latest
 port: 8080
 host: default
 package-whitelist: # Packages for 'gypsum-permissive'
 package-whitelist: # Packages for 'permissive'
 - dsBase
 - dsMediation
 - dsMTLBase
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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 Merged

StuartWheater
merged 4 commits into

from

Aug 4, 2025
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V6.3.4 dev
#605
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805a6a2

Switch to 'rock-omicron-karma-permissive:latest'


StuartWheater Aug 4, 2025
e03d3c6

Update profile and server images


StuartWheater Aug 4, 2025
bb5d234

Updated


StuartWheater Aug 4, 2025
52ca585

Update packages


StuartWheater Aug 4, 2025

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10 changes: 5 additions & 5 deletions
armadillo_azure-pipelines.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -139,7 +139,7 @@ jobs:
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:

 curl -u admin:admin -X GET http://localhost:8080/packages

 curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.2-permissive.tar.gz" -X POST http://localhost:8080/install-package
 curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.4-permissive.tar.gz" -X POST http://localhost:8080/install-package
 sleep 60

 docker container restart dsbaseclient_armadillo_1
Expand DownExpand Up@@ -364,7 +364,7 @@ jobs:
 - bash: |
 curl -u admin:admin http://localhost:8080/whitelist

 curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.2.tar.gz" -X POST http://localhost:8080/install-package
 curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.4.tar.gz" -X POST http://localhost:8080/install-package

 docker container restart dsbaseclient_armadillo_1
 sleep 60
Expand Down

12 changes: 6 additions & 6 deletions
azure-pipelines.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -132,15 +132,15 @@ jobs:
 sudo apt-get upgrade -y

 sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
 sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev -y
 sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y
 sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.2', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:
 - bash: |
 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 sleep 60

Expand DownExpand Up@@ -363,7 +363,7 @@ jobs:

 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 workingDirectory: $(Pipeline.Workspace)/dsBaseClient
 displayName: 'Install dsDanger package on Opal server'
Expand Down

7 changes: 3 additions & 4 deletions
docker-compose_armadillo.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@ services:
 hostname: armadillo
 ports:
 - 8080:8080
 image: datashield/armadillo_citest:5.1.4
 image: datashield/armadillo_citest:latest
 environment:
 LOGGING_CONFIG: 'classpath:logback-file.xml'
 AUDIT_LOG_PATH: '/app/logs/audit.log'
Expand All@@ -16,7 +16,6 @@ services:

 default:
 hostname: default
# image: datashield/rock-margin-joule-permissive:latest
 image: datashield/rserver-neutron-gypsum-permissive:latest
 image: datashield/rock-omicron-karma-permissive:latest
 environment:
 DEBUG: "TRUE"
 DEBUG: "FALSE"

6 changes: 4 additions & 2 deletions
docker-compose_opal.yml

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Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
services:
 opal:
 image: obiba/opal:5.1.4
 image: datashield/opal_citest:latest
 ports:
 - "8443:8443"
 - 8443:8443
 links:
 - mongo
 - rock
Expand All@@ -21,3 +21,5 @@ services:
 - MONGO_INITDB_ROOT_PASSWORD=foobar
 rock:
 image: datashield/rock-omicron-karma-permissive:latest
 environment:
 DEBUG: "FALSE"
Binary file removeddsBase_6.3.2-permissive.tar.gz

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Binary file addeddsBase_6.3.4-permissive.tar.gz

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Binary file addeddsBase_6.3.4.tar.gz

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Binary file removeddsDanger_6.3.1.tar.gz

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Binary file addeddsDanger_6.3.4.tar.gz

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10 changes: 5 additions & 5 deletions
opal_azure-pipelines.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -58,10 +58,10 @@ schedules:
 - master
 always: true
 - cron: "0 2 * * *"
 displayName: Nightly build - v6.3.2-dev
 displayName: Nightly build - v6.3.4-dev
 branches:
 include:
 - v6.3.2-dev
 - v6.3.4-dev
 always: true

#########################################################################################
Expand DownExpand Up@@ -140,7 +140,7 @@ jobs:
 sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"

 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
 sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.4', dependencies = TRUE)"

 # XML grep for coverage report merging
 sudo apt-get install -qq xml-twig-tools -y
Expand DownExpand Up@@ -235,7 +235,7 @@ jobs:
 - bash: |
 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 sleep 60

Expand DownExpand Up@@ -363,7 +363,7 @@ jobs:

 R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"

 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)"
 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); opal.logout(opal)"

 workingDirectory: $(Pipeline.Workspace)/dsBaseClient
 displayName: 'Install dsDanger package on Opal server'
Expand Down

6 changes: 3 additions & 3 deletions
tests/docker/armadillo/standard/config/application.yml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -14,10 +14,10 @@ armadillo:
 # oidc-admin-user: user@yourdomain.org
 profiles:
 - name: default
 image: datashield/rserver-neutron-gypsum-permissive:latest
 port: 6311
 image: datashield/rock-omicron-karma:latest
 port: 8080
 host: default
 package-whitelist: # Packages for 'gypsum-permissive'
 package-whitelist: # Packages for 'permissive'
 - dsBase
 - dsMediation
 - dsMTLBase
Expand Down